Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007883.1 Hibiscus syriacus cultivar Beakdansim tig00110263_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1590433
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 9
Found at i:1365346 original size:103 final size:103
Alignment explanation
Indices: 1365221--1365541 Score: 588
Period size: 103 Copynumber: 3.1 Consensus size: 103
1365211 TAATGTCCAT
*
1365221 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCG
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1365286 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
1365324 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
1365389 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* * *
1365427 AAGGACCATATATCATTCCTTAAGAATCATATACATATGACAAAGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1365492 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1365530 AAGGACCACATA
1 AAGGACCACATA
1365542 GACCCTCTAC
Statistics
Matches: 209, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 209 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1366058 original size:19 final size:20
Alignment explanation
Indices: 1366021--1366058 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1366011 TTTTTTATTA
*
1366021 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
1366041 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
1366059 TCTAGCGTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:1370378 original size:1 final size:1
Alignment explanation
Indices: 1370372--1370480 Score: 65
Period size: 1 Copynumber: 109.0 Consensus size: 1
1370362 AAAAGAATGG
* * * * * * * * * *
1370372 AAAAAAATAAAAAAAATAAAAGAAAAATAAAAGAAAAATAAAAGAAAAAAGAAAAAAATAAAAGA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * *
1370437 AAAAAGAAAAAATAAAAGAAAAAAAGAGAGAAAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1370481 CTGAAAGGAG
Statistics
Matches: 74, Mismatches: 34, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 74 1.00
ACGTcount: A:0.84, C:0.00, G:0.10, T:0.06
Consensus pattern (1 bp):
A
Found at i:1370386 original size:11 final size:11
Alignment explanation
Indices: 1370372--1370475 Score: 81
Period size: 12 Copynumber: 9.5 Consensus size: 11
1370362 AAAAGAATGG
1370372 AAAAAAAT--A
1 AAAAAAATAAA
1370381 AAAAAAATAAA
1 AAAAAAATAAA
*
1370392 AGAAAAATAAA
1 AAAAAAATAAA
*
1370403 AGAAAAAT-AA
1 AAAAAAATAAA
* *
1370413 AAGAAAA-AAG
1 AAAAAAATAAA
1370423 AAAAAAATAAA
1 AAAAAAATAAA
*
1370434 AGAAAAAAGAAA
1 A-AAAAAATAAA
*
1370446 AAATAAAAGAAA
1 AAA-AAAATAAA
* *
1370458 AAAAGAGAGAAA
1 AAAA-AAATAAA
1370470 AAAAAA
1 AAAAAA
1370476 GAAAACTGAA
Statistics
Matches: 79, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
9 8 0.10
10 14 0.18
11 26 0.33
12 31 0.39
ACGTcount: A:0.85, C:0.00, G:0.10, T:0.06
Consensus pattern (11 bp):
AAAAAAATAAA
Found at i:1370397 original size:20 final size:19
Alignment explanation
Indices: 1370374--1370480 Score: 124
Period size: 22 Copynumber: 5.2 Consensus size: 19
1370364 AAGAATGGAA
1370374 AAAAATAAAAAAAATAAAAG
1 AAAAA-AAAAAAAATAAAAG
1370394 AAAAATAAAAGAAAAATAAAAG
1 -AAAA-AAAA-AAAAATAAAAG
1370416 AAAAAAGAAAAAAATAAAAG
1 AAAAAA-AAAAAAATAAAAG
*
1370436 AAAAAAGAAAAAATAAAAG
1 AAAAAAAAAAAAATAAAAG
*
1370455 AAAAAAAGAGAGAAAAAAAAAG
1 AAAAAAA-A-A-AAAATAAAAG
1370477 AAAA
1 AAAA
1370481 CTGAAAGGAG
Statistics
Matches: 77, Mismatches: 3, Indels: 11
0.85 0.03 0.12
Matches are distributed among these distances:
19 18 0.23
20 20 0.26
21 14 0.18
22 25 0.32
ACGTcount: A:0.84, C:0.00, G:0.10, T:0.06
Consensus pattern (19 bp):
AAAAAAAAAAAAATAAAAG
Found at i:1370412 original size:31 final size:31
Alignment explanation
Indices: 1370373--1370480 Score: 125
Period size: 31 Copynumber: 3.5 Consensus size: 31
1370363 AAAGAATGGA
*
1370373 AAAAAATAAAAAAAATAAAAGAAAAATAAAAG
1 AAAAAA-AAAGAAAATAAAAGAAAAATAAAAG
1370405 AAAAATAAAAGAAAA-AAGAA-AAAAATAAAAG
1 AAAAA-AAAAGAAAATAA-AAGAAAAATAAAAG
*
1370436 AAAAAAGAA-AAAATAAAAGAAAAA-AAGAGAG
1 AAAAAAAAAGAAAATAAAAGAAAAATAA-A-AG
1370467 AAAAAAAAAGAAAA
1 AAAAAAAAAGAAAA
1370481 CTGAAAGGAG
Statistics
Matches: 66, Mismatches: 3, Indels: 14
0.80 0.04 0.17
Matches are distributed among these distances:
29 8 0.12
30 11 0.17
31 28 0.42
32 18 0.27
33 1 0.02
ACGTcount: A:0.84, C:0.00, G:0.10, T:0.06
Consensus pattern (31 bp):
AAAAAAAAAGAAAATAAAAGAAAAATAAAAG
Found at i:1372059 original size:64 final size:63
Alignment explanation
Indices: 1371991--1372171 Score: 200
Period size: 64 Copynumber: 2.8 Consensus size: 63
1371981 TTGGAACACT
* *** *
1371991 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTTGATGTTTGAAAAATAGCC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCC
** * * **
1372055 TGATGCATCGATGCATGGCTTGTGCATTGATGCATCAAATGCATTCGATGTTTTGAAAATATTC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCC
* * * *
1372119 AGAGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 TGA-TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTT
1372172 CAATTAATTC
Statistics
Matches: 96, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
64 52 0.54
65 44 0.46
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (63 bp):
TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCC
Found at i:1372143 original size:19 final size:19
Alignment explanation
Indices: 1372119--1372169 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1372109 GAAAATATTC
1372119 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
1372138 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
1372157 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
1372170 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:1372145 original size:65 final size:65
Alignment explanation
Indices: 1372012--1372171 Score: 198
Period size: 65 Copynumber: 2.5 Consensus size: 65
1372002 TGCACCAAGT
* * ***
1372012 GTGCATCGATGCATGAAATGCATTTGATG-TTTGAAAAATAGCCTGATGCATCGATGCATGGCTT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
* * **
1372076 GTGCATTGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATGGAG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGA-TGCATCGATGCATGGAG
1372140 A
65 A
* *
1372141 GTGCATCGGTGCATGGAATGCATTCGATGTT
1 GTGCATCGATGCATGAAATGCATTCGATGTT
1372172 CAATTAATTC
Statistics
Matches: 81, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
64 35 0.43
65 46 0.57
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
Found at i:1373995 original size:12 final size:12
Alignment explanation
Indices: 1373978--1374002 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1373968 AGTCCTAAGT
1373978 TCAAAAATTTAA
1 TCAAAAATTTAA
1373990 TCAAAAATTTAA
1 TCAAAAATTTAA
1374002 T
1 T
1374003 GAAATAGAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (12 bp):
TCAAAAATTTAA
Found at i:1380157 original size:64 final size:63
Alignment explanation
Indices: 1380089--1380269 Score: 200
Period size: 64 Copynumber: 2.8 Consensus size: 63
1380079 TTGGAACACT
* *** *
1380089 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTTGATGTTTGAAAAATAGCC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCC
** * * **
1380153 TGATGCATCGATGCATGGCTTGTGCATTGATGCATCAAATGCATTCGATGTTTTGAAAATATTC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCC
* * * *
1380217 AGAGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 TGA-TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTT
1380270 CAATTAATTC
Statistics
Matches: 96, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
64 52 0.54
65 44 0.46
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (63 bp):
TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCC
Found at i:1380241 original size:19 final size:19
Alignment explanation
Indices: 1380217--1380267 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1380207 GAAAATATTC
1380217 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
1380236 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
1380255 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
1380268 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:1380243 original size:65 final size:65
Alignment explanation
Indices: 1380110--1380269 Score: 198
Period size: 65 Copynumber: 2.5 Consensus size: 65
1380100 TGCACCAAGT
* * ***
1380110 GTGCATCGATGCATGAAATGCATTTGATG-TTTGAAAAATAGCCTGATGCATCGATGCATGGCTT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
* * **
1380174 GTGCATTGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATGGAG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGA-TGCATCGATGCATGGAG
1380238 A
65 A
* *
1380239 GTGCATCGGTGCATGGAATGCATTCGATGTT
1 GTGCATCGATGCATGAAATGCATTCGATGTT
1380270 CAATTAATTC
Statistics
Matches: 81, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
64 35 0.43
65 46 0.57
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
Found at i:1381298 original size:18 final size:18
Alignment explanation
Indices: 1381275--1381317 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1381265 TTGAAAAAAC
*
1381275 ATTGAAGCTAAAAGAGGA
1 ATTGAAGATAAAAGAGGA
* *
1381293 ATTGAA-ATAAATGATGA
1 ATTGAAGATAAAAGAGGA
1381310 ATTGAAGA
1 ATTGAAGA
1381318 AATAAGGAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.51, C:0.02, G:0.23, T:0.23
Consensus pattern (18 bp):
ATTGAAGATAAAAGAGGA
Found at i:1385659 original size:19 final size:19
Alignment explanation
Indices: 1385635--1385692 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
1385625 CGGTAAACAG
1385635 AGATATCAGAAATCAAAAC
1 AGATATCAGAAATCAAAAC
1385654 AGATATCAG-AAT-AAAATCC
1 AGATATCAGAAATCAAAA--C
*
1385673 AG--ATCAGAAATCAGAAC
1 AGATATCAGAAATCAAAAC
1385690 AGA
1 AGA
1385693 ATTCATGTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 11
0.73 0.02 0.24
Matches are distributed among these distances:
17 12 0.36
18 6 0.18
19 15 0.45
ACGTcount: A:0.55, C:0.16, G:0.14, T:0.16
Consensus pattern (19 bp):
AGATATCAGAAATCAAAAC
Found at i:1385733 original size:24 final size:25
Alignment explanation
Indices: 1385679--1385735 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 25
1385669 ATCCAGATCA
* *
1385679 GAAATCAGAACAGAATTCATGTCAT
1 GAAATCAGAACAGAATTCAAGTCAG
*
1385704 G-TATCAGAACAGAATTCAAGTC-G
1 GAAATCAGAACAGAATTCAAGTCAG
1385727 GAAATCAGA
1 GAAATCAGA
1385736 TAAAATATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 1 0.04
24 25 0.93
25 1 0.04
ACGTcount: A:0.44, C:0.16, G:0.19, T:0.21
Consensus pattern (25 bp):
GAAATCAGAACAGAATTCAAGTCAG
Found at i:1387532 original size:36 final size:36
Alignment explanation
Indices: 1387485--1387557 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
1387475 GATAAATTAT
1387485 AATCTACATATCCATGGATGATTCTTTTATCACTTA
1 AATCTACATATCCATGGATGATTCTTTTATCACTTA
* *
1387521 AATCTACATATCGATGGCTGATTCTTTTATCACTTA
1 AATCTACATATCCATGGATGATTCTTTTATCACTTA
1387557 A
1 A
1387558 TTCCAAAACT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.41
Consensus pattern (36 bp):
AATCTACATATCCATGGATGATTCTTTTATCACTTA
Found at i:1390366 original size:24 final size:24
Alignment explanation
Indices: 1390334--1390397 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
1390324 GATATCAGAA
* *
1390334 ATCAAAACAGAATTTAGAACATAT
1 ATCAGAACAGAATTCAGAACATAT
** *
1390358 ATCAGAACAGAATTCAGGTCATGT
1 ATCAGAACAGAATTCAGAACATAT
*
1390382 ATCAGAACATAATTCA
1 ATCAGAACAGAATTCA
1390398 AGTCGGAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.25
Consensus pattern (24 bp):
ATCAGAACAGAATTCAGAACATAT
Found at i:1396624 original size:13 final size:13
Alignment explanation
Indices: 1396606--1396630 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1396596 TGTAATTTGA
1396606 AATAAATAAAAAG
1 AATAAATAAAAAG
1396619 AATAAATAAAAA
1 AATAAATAAAAA
1396631 AACTATATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (13 bp):
AATAAATAAAAAG
Found at i:1397247 original size:26 final size:26
Alignment explanation
Indices: 1397184--1397250 Score: 125
Period size: 26 Copynumber: 2.6 Consensus size: 26
1397174 GGCCACCTAA
*
1397184 ACGACGCCGTTCTGGAACTAAACGGG
1 ACGACGCCGTTTTGGAACTAAACGGG
1397210 ACGACGCCGTTTTGGAACTAAACGGG
1 ACGACGCCGTTTTGGAACTAAACGGG
1397236 ACGACGCCGTTTTGG
1 ACGACGCCGTTTTGG
1397251 CGTACGAGAC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.24, C:0.25, G:0.31, T:0.19
Consensus pattern (26 bp):
ACGACGCCGTTTTGGAACTAAACGGG
Found at i:1398997 original size:55 final size:55
Alignment explanation
Indices: 1398913--1399327 Score: 432
Period size: 55 Copynumber: 7.6 Consensus size: 55
1398903 CTCCATAGTC
*
1398913 CTTCAGAGAGTATAAGACTCGAACAATCTTTAACAATCGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* ** *
1398968 CTTCAGAGAGTATAAGACTCGAATAATCTTCAATGATCACGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * *
1399023 CTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTTCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * * *
1399076 CTTCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGTGTCGGCTCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * * * * * *
1399131 CTGCATAGAGTATAAGACTCGACCAATTTTCAACAATCGTGTCTGCTCTCC-ATTC
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGC-CCCCTATTT
* * * * *
1399186 CTTCGGAGAGTATAAGACTCAAACAATCTTCATCAATCGCGTCTGCTCCCTACTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * * ** * * * *
1399241 CTTCAGGGGGTAT-AGAACTTGAA-AATCTTCTGCAAACGGGTTCT-CTCCCTCTTT
1 CTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAATCGCG-TCTGCCCCCTATTT
*
1399295 CTTCAGGGAGTAT-AGAACTCGAAC-ATCTTCAAC
1 CTTCAGAGAGTATAAG-ACTCGAACAATCTTCAAC
1399328 TGGGTTCGCT
Statistics
Matches: 299, Mismatches: 54, Indels: 15
0.81 0.15 0.04
Matches are distributed among these distances:
53 45 0.15
54 55 0.18
55 197 0.66
56 2 0.01
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (55 bp):
CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
Found at i:1399104 original size:108 final size:109
Alignment explanation
Indices: 1398913--1399246 Score: 413
Period size: 108 Copynumber: 3.1 Consensus size: 109
1398903 CTCCATAGTC
*
1398913 CTTCAGAGAGTATAAGACTCGAACAATCTTTAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAG
1 CTTCAGAGAGTATAAGACTC-AACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAG
* * * *
1398978 TATAAGACTCGAATAATCTTCAATGATCACGTCTGCCCCCTATTT
65 TATAAGACTCGAACAATCTTCAATAATCGCGTCTGCTCCCTATTT
* * *
1399023 CTTCAGAGAGTATAAGAC-CCACAATCTTCATCAATCGCGTCTTCCCCCTATTTCTTCAGAGAGT
1 CTTCAGAGAGTATAAGACTCAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGT
* * * *
1399087 ATAAGACCCGAACAATCTTCAACAATCGTGTCGGCTCCCTATTT
66 ATAAGACTCGAACAATCTTCAATAATCGCGTCTGCTCCCTATTT
* * * * * * * *
1399131 CTGCATAGAGTATAAGACTCGACCAATTTTCAACAATCGTGTCTGCTCTCC-ATTCCTTCGGAGA
1 CTTCAGAGAGTATAAGACTC-AACAATCTTCAACAATCGCGTCTGC-CCCCTATTTCTTCAGAGA
* *
1399195 GTATAAGACTCAAACAATCTTC-ATCAATCGCGTCTGCTCCCTACTT
64 GTATAAGACTCGAACAATCTTCAAT-AATCGCGTCTGCTCCCTATTT
1399241 CTTCAG
1 CTTCAG
1399247 GGGGTATAGA
Statistics
Matches: 189, Mismatches: 31, Indels: 8
0.83 0.14 0.04
Matches are distributed among these distances:
108 93 0.49
109 3 0.02
110 90 0.48
111 3 0.02
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (109 bp):
CTTCAGAGAGTATAAGACTCAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGT
ATAAGACTCGAACAATCTTCAATAATCGCGTCTGCTCCCTATTT
Found at i:1399197 original size:163 final size:165
Alignment explanation
Indices: 1398913--1399246 Score: 449
Period size: 163 Copynumber: 2.0 Consensus size: 165
1398903 CTCCATAGTC
* * * *
1398913 CTTCAGAGAGTATAAGACTCGAACAATCTTTAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAG
1 CTTCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGCGTCGGCCCCCTATTTCTGCAGAGAG
* ** *
1398978 TATAAGACTCGAATAATCTTCAATGATCACGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C
66 TATAAGACTCGAACAATCTTCAACAATCACGTCTGCCCCCTATTCCTTCAGAGAGTATAAGACTC
* * *
1399042 -CACAATCTTCATCAATCGCGTCTTCCCCCTATTT
131 AAACAATCTTCATCAATCGCGTCTGCCCCCTACTT
* * *
1399076 CTTCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGTGTCGGCTCCCTATTTCTGCATAGAG
1 CTTCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGCGTCGGCCCCCTATTTCTGCAGAGAG
* * ** * *
1399141 TATAAGACTCGACCAATTTTCAACAATCGTGTCTGCTCTCC-ATTCCTTCGGAGAGTATAAGACT
66 TATAAGACTCGAACAATCTTCAACAATCACGTCTGC-CCCCTATTCCTTCAGAGAGTATAAGACT
*
1399205 CAAACAATCTTCATCAATCGCGTCTGCTCCCTACTT
130 CAAACAATCTTCATCAATCGCGTCTGCCCCCTACTT
1399241 CTTCAG
1 CTTCAG
1399247 GGGGTATAGA
Statistics
Matches: 147, Mismatches: 21, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
163 107 0.73
164 4 0.03
165 36 0.24
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (165 bp):
CTTCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGCGTCGGCCCCCTATTTCTGCAGAGAG
TATAAGACTCGAACAATCTTCAACAATCACGTCTGCCCCCTATTCCTTCAGAGAGTATAAGACTC
AAACAATCTTCATCAATCGCGTCTGCCCCCTACTT
Found at i:1399356 original size:51 final size:50
Alignment explanation
Indices: 1399230--1399482 Score: 222
Period size: 51 Copynumber: 4.9 Consensus size: 50
1399220 AATCGCGTCT
* * * *
1399230 GCTCCCTAC-TTCTTCAGGGGGTATAGAACTTGAAAATCTTCTGCAAACGGGTTC
1 GCTCCCT-CTTTCTTTAGGGAGTATAGAACTCGAACATC-T-T-C-AACGGGTTC
* *
1399284 TCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAACATCTTCAACTGGGTTC
1 GCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTTCAAC-GGGTTC
* * * * * *
1399335 GCTCCCTTTTTCTTTACGGAGTATGGGACTCGGATATCTTCACACGGGTTC
1 GCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTTCA-ACGGGTTC
* * *
1399386 GCTCCCTCTTTCTCTAGGGAGTATGGAACT-TAGACATCTCTTCAAACGGGTTC
1 GCTCCCTCTTTCTTTAGGGAGTATAGAACTCGA-ACA--TCTTC-AACGGGTTC
* * * *
1399439 GCTCCTTCTTTCTTTAAGGAGAATAGAACTCGAATATCTTCAAC
1 GCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTTCAAC
1399483 AATCGTGTCT
Statistics
Matches: 165, Mismatches: 26, Indels: 20
0.78 0.12 0.09
Matches are distributed among these distances:
50 6 0.04
51 80 0.48
52 3 0.02
53 42 0.25
54 34 0.21
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (50 bp):
GCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTTCAACGGGTTC
Found at i:1399480 original size:104 final size:102
Alignment explanation
Indices: 1399276--1399516 Score: 258
Period size: 104 Copynumber: 2.3 Consensus size: 102
1399266 TCTTCTGCAA
* *
1399276 ACGGGTTCTCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAACATCTTCAACTGGGTTCGCTCCC
1 ACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTAGAACATCTTCAACTGGGTTCGCTCCC
* * * * *
1399341 TTTTTCTTTACGGAGTATGGGACTCGGATATCTTCAC
66 TTTTTCTTTAAGGAGAATAGAACTCGAATATCTTCAC
*
1399378 ACGGGTTCGCTCCCTCTTTC-TCTAGGGAGTATGGAACTTAG-ACATCTCTTCAAAC-GGGTTCG
1 ACGGGTTCGCTCCCTCTTTCTTC-AGGGAGTATAGAAC-TAGAACA--TCTTC-AACTGGGTTCG
1399440 CT-CCTTCTTTCTTTAAGGAGAATAGAACTCGAATATCTTCAAC
61 CTCCCTT-TTTCTTTAAGGAGAATAGAACTCGAATATCTTC-AC
* * *
1399483 AATCGTG-TCTGCTCCCTATTTCTTCAGAGAGTAT
1 -A-CGGGTTC-GCTCCCTCTTTCTTCAGGGAGTAT
1399517 GAGACTCGAA
Statistics
Matches: 117, Mismatches: 11, Indels: 17
0.81 0.08 0.12
Matches are distributed among these distances:
101 2 0.02
102 35 0.30
103 6 0.05
104 42 0.36
105 5 0.04
106 3 0.03
107 22 0.19
108 2 0.02
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.34
Consensus pattern (102 bp):
ACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTAGAACATCTTCAACTGGGTTCGCTCCC
TTTTTCTTTAAGGAGAATAGAACTCGAATATCTTCAC
Found at i:1399614 original size:53 final size:55
Alignment explanation
Indices: 1399534--1399641 Score: 141
Period size: 53 Copynumber: 2.0 Consensus size: 55
1399524 GAACGATCGT
*
1399534 GTCTGCCCCCTACATCTTCAGAGAGTATAAGAC-C-CACAATCTTC-ATCAATTGC
1 GTCTGCCCCCTACATCTTCAGAGAGTATAAGACTCGAACAATCTTCAAT-AATTGC
* ** *
1399587 GTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATTGC
1 GTCTGCCCCCTACATCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAATTGC
1399642 TGGGAAATCT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
53 29 0.62
54 1 0.02
55 15 0.32
56 2 0.04
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (55 bp):
GTCTGCCCCCTACATCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAATTGC
Found at i:1400657 original size:8 final size:8
Alignment explanation
Indices: 1400639--1400691 Score: 56
Period size: 8 Copynumber: 6.5 Consensus size: 8
1400629 GAACCCTTCT
1400639 TTTTTTCCA
1 TTTTTT-CA
1400648 TTTTTTCA
1 TTTTTTCA
1400656 TTTTTAT-A
1 TTTTT-TCA
*
1400664 TTTTTTTTA
1 -TTTTTTCA
1400673 TTTTTTC-
1 TTTTTTCA
1400680 TTTTTTCA
1 TTTTTTCA
1400688 TTTT
1 TTTT
1400692 CACTCATTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
7 7 0.18
8 19 0.49
9 13 0.33
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTTCA
Found at i:1412352 original size:13 final size:13
Alignment explanation
Indices: 1412334--1412358 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1412324 ATGTAATTGA
1412334 AATAAATAAAAAG
1 AATAAATAAAAAG
1412347 AATAAATAAAAA
1 AATAAATAAAAA
1412359 AACTATATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (13 bp):
AATAAATAAAAAG
Found at i:1412967 original size:26 final size:26
Alignment explanation
Indices: 1412904--1412970 Score: 125
Period size: 26 Copynumber: 2.6 Consensus size: 26
1412894 GGCCACCTAA
*
1412904 ACGACGCCGTTCTGGAACTAAACGGG
1 ACGACGCCGTTTTGGAACTAAACGGG
1412930 ACGACGCCGTTTTGGAACTAAACGGG
1 ACGACGCCGTTTTGGAACTAAACGGG
1412956 ACGACGCCGTTTTGG
1 ACGACGCCGTTTTGG
1412971 CGTACGAGAC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.24, C:0.25, G:0.31, T:0.19
Consensus pattern (26 bp):
ACGACGCCGTTTTGGAACTAAACGGG
Found at i:1420769 original size:23 final size:26
Alignment explanation
Indices: 1420717--1420775 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 26
1420707 TTTTACAATA
1420717 CCCAAAC--AAAACCCTAAATCAGGC
1 CCCAAACTAAAAACCCTAAATCAGGC
*
1420741 CCCAAA-TAAAAACCC-AAA-CATGC
1 CCCAAACTAAAAACCCTAAATCAGGC
1420764 CCCAAACTAAAA
1 CCCAAACTAAAA
1420776 CCTAAACCGG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
23 10 0.32
24 14 0.45
25 7 0.23
ACGTcount: A:0.51, C:0.36, G:0.05, T:0.08
Consensus pattern (26 bp):
CCCAAACTAAAAACCCTAAATCAGGC
Found at i:1420776 original size:23 final size:23
Alignment explanation
Indices: 1420717--1420782 Score: 73
Period size: 23 Copynumber: 2.8 Consensus size: 23
1420707 TTTTACAATA
1420717 CCCAAAC-AAAACCCTAAATCAGGC
1 CCCAAACTAAAACCC-AAA-CAGGC
*
1420741 CCCAAA-TAAAAACCCAAACATGC
1 CCCAAACT-AAAACCCAAACAGGC
*
1420764 CCCAAACTAAAACCTAAAC
1 CCCAAACTAAAACCCAAAC
1420783 CGGGACCAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
23 20 0.54
24 10 0.27
25 7 0.19
ACGTcount: A:0.50, C:0.36, G:0.05, T:0.09
Consensus pattern (23 bp):
CCCAAACTAAAACCCAAACAGGC
Found at i:1423728 original size:14 final size:15
Alignment explanation
Indices: 1423709--1423737 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1423699 AATTTTAATA
1423709 ATAAAAATAT-TATT
1 ATAAAAATATATATT
1423723 ATAAAAATATATATT
1 ATAAAAATATATATT
1423738 TACGTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAAAAATATATATT
Found at i:1424308 original size:29 final size:29
Alignment explanation
Indices: 1424274--1424332 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
1424264 CCAAAATTAA
*
1424274 TTTGATTTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
* *
1424303 TTTGATGTCATTGTTTATATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1424332 T
1 T
1424333 AGGTGAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.24, C:0.10, G:0.12, T:0.54
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:1428955 original size:29 final size:29
Alignment explanation
Indices: 1428921--1428979 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
1428911 CCTAAATTAA
*
1428921 TTTGATTTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1428950 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1428979 T
1 T
1428980 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.14, G:0.12, T:0.51
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:1430417 original size:2 final size:2
Alignment explanation
Indices: 1430410--1430458 Score: 89
Period size: 2 Copynumber: 24.0 Consensus size: 2
1430400 TATTTACCTA
1430410 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
1430453 AT AT AT
1 AT AT AT
1430459 GAGTGACCAA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 44 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1431978 original size:35 final size:35
Alignment explanation
Indices: 1431939--1432011 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
1431929 TAAAGGTTGT
1431939 ATTGCATTGCTTCACTACTCTTTTGTGAAGGCTGA
1 ATTGCATTGCTTCACTACTCTTTTGTGAAGGCTGA
* * *
1431974 ATTGCATTTCTTCACTACTCTTTTTTGAAGGTTGA
1 ATTGCATTGCTTCACTACTCTTTTGTGAAGGCTGA
1432009 ATT
1 ATT
1432012 ACACTGAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.21, C:0.18, G:0.16, T:0.45
Consensus pattern (35 bp):
ATTGCATTGCTTCACTACTCTTTTGTGAAGGCTGA
Found at i:1440259 original size:14 final size:14
Alignment explanation
Indices: 1440240--1440276 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1440230 TAAACATAAT
1440240 ACAGATACAACATC
1 ACAGATACAACATC
*
1440254 ACAGATACAACATT
1 ACAGATACAACATC
*
1440268 ACATATACA
1 ACAGATACA
1440277 TCTGAGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.51, C:0.24, G:0.05, T:0.19
Consensus pattern (14 bp):
ACAGATACAACATC
Found at i:1445567 original size:186 final size:188
Alignment explanation
Indices: 1445203--1445596 Score: 618
Period size: 186 Copynumber: 2.1 Consensus size: 188
1445193 ATTAAATTTT
* * *
1445203 AAATTTTAAATATATTATATATAACATATGGGCTCAGCCAAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGAGATCAGCCAAAACCATTTAAAACCCAATTAATAA
*
1445268 TTTAAGATCCAATAAATTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTTATATAAAATG
66 TTTAAGATCCAATAAATTTTAAACATAAATCAATATTAATTAATTAAAAAAATTTATATAAAATG
1445333 TTTATTTTATAATTATATATTATTTAAATTAATTGTAAAC-TATTTTTTT-AATTAAA
131 TTTATTTTATAATTATATATTATTTAAATTAATTGTAAACTTATTTTTTTCAATTAAA
* * **
1445389 AAATATTATATATATTATATATAATATATGAGATCAGCTGAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGAGATCAGCCAAAACCATTTAAAACCCAATTAATAA
* *
1445454 TTTAAGATCCAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAAAA-TTATATAAAATT
66 TTTAAGATCCAATAAATTTTAAACATAAATCAATATTAATTAATTAAAAAAATTTATATAAAATG
*
1445518 TTTATTTTATAATTATATATTATTTAAATTAATTAG-AAACTGTTTTTTTTTCAATTAAA
131 TTTATTTTATAATTATATATTATTTAAATTAATT-GTAAACT-TATTTTTTTCAATTAAA
* *
1445577 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
1445597 AATTAGAAAA
Statistics
Matches: 190, Mismatches: 14, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
185 49 0.26
186 109 0.57
187 16 0.08
188 16 0.08
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.42
Consensus pattern (188 bp):
AAATATTAAATATATTATATATAACATATGAGATCAGCCAAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAAATTTTAAACATAAATCAATATTAATTAATTAAAAAAATTTATATAAAATG
TTTATTTTATAATTATATATTATTTAAATTAATTGTAAACTTATTTTTTTCAATTAAA
Found at i:1448081 original size:25 final size:26
Alignment explanation
Indices: 1448042--1448091 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
1448032 TTCTCAATAT
*
1448042 TAAAAAAAATTATAA-AACATTTATC
1 TAAAAAAAATAATAATAACATTTATC
* *
1448067 TAAAAATAATAATAATAATATTTAT
1 TAAAAAAAATAATAATAACATTTAT
1448092 TTATTTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (26 bp):
TAAAAAAAATAATAATAACATTTATC
Found at i:1448349 original size:2 final size:2
Alignment explanation
Indices: 1448342--1448381 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1448332 AGTTAAACAA
1448342 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1448382 GAATAATATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1449282 original size:26 final size:26
Alignment explanation
Indices: 1449253--1449305 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1449243 TTTCTAGCAG
1449253 CAAGTGGAGGCTATGGTGAGTTGTCT
1 CAAGTGGAGGCTATGGTGAGTTGTCT
1449279 CAAGTGGAGGCTATGGTGAGTTGTCT
1 CAAGTGGAGGCTATGGTGAGTTGTCT
1449305 C
1 C
1449306 TTTTCCTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.19, C:0.13, G:0.38, T:0.30
Consensus pattern (26 bp):
CAAGTGGAGGCTATGGTGAGTTGTCT
Found at i:1449905 original size:4 final size:4
Alignment explanation
Indices: 1449896--1449926 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
1449886 AATGTATTAA
1449896 AATT AATT AATT AATT AATT AATT AATT AAT
1 AATT AATT AATT AATT AATT AATT AATT AAT
1449927 AATAATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:1450080 original size:15 final size:15
Alignment explanation
Indices: 1450057--1450086 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1450047 CATCAGGCAT
*
1450057 TGGTTTGTCGAGAGA
1 TGGTCTGTCGAGAGA
1450072 TGGTCTGTCGAGAGA
1 TGGTCTGTCGAGAGA
1450087 AAGAGTGCGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.10, G:0.40, T:0.30
Consensus pattern (15 bp):
TGGTCTGTCGAGAGA
Found at i:1450275 original size:35 final size:35
Alignment explanation
Indices: 1450236--1450340 Score: 85
Period size: 33 Copynumber: 3.1 Consensus size: 35
1450226 AAAGCAAAAT
1450236 TGTATGTTGAAATACATATATTCATGGAATTTTTC
1 TGTATGTTGAAATACATATATTCATGGAATTTTTC
* * * * * * **
1450271 TGTAT-AT-ATATATATATATACCAAGCAA--AAT-
1 TGTATGTTGAAATACATATAT-TCATGGAATTTTTC
*
1450302 TGTTTGTTGAAATACATATATTCATGGAATTTTTC
1 TGTATGTTGAAATACATATATTCATGGAATTTTTC
1450337 TGTA
1 TGTA
1450341 ATTATGATAC
Statistics
Matches: 46, Mismatches: 18, Indels: 12
0.61 0.24 0.16
Matches are distributed among these distances:
31 4 0.09
32 7 0.15
33 20 0.43
34 7 0.15
35 8 0.17
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (35 bp):
TGTATGTTGAAATACATATATTCATGGAATTTTTC
Found at i:1450319 original size:66 final size:66
Alignment explanation
Indices: 1450217--1450340 Score: 230
Period size: 66 Copynumber: 1.9 Consensus size: 66
1450207 GAAATGACTG
1450217 TATATATACAAAGCAAAATTGTATGTTGAAATACATATATTCATGGAATTTTTCTGTATATATAT
1 TATATATACAAAGCAAAATTGTATGTTGAAATACATATATTCATGGAATTTTTCTGTATATATAT
1450282 A
66 A
* *
1450283 TATATATACCAAGCAAAATTGTTTGTTGAAATACATATATTCATGGAATTTTTCTGTA
1 TATATATACAAAGCAAAATTGTATGTTGAAATACATATATTCATGGAATTTTTCTGTA
1450341 ATTATGATAC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 56 1.00
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (66 bp):
TATATATACAAAGCAAAATTGTATGTTGAAATACATATATTCATGGAATTTTTCTGTATATATAT
A
Found at i:1453614 original size:29 final size:29
Alignment explanation
Indices: 1453580--1453638 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
1453570 CCTAAATTAA
*
1453580 TTTGATGACATTGCTTACATCAATTTAGT
1 TTTGATGACACTGCTTACATCAATTTAGT
*
1453609 TTTGATGTCACTGCTTACATCAATTTAGT
1 TTTGATGACACTGCTTACATCAATTTAGT
1453638 T
1 T
1453639 AAGTGGAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.46
Consensus pattern (29 bp):
TTTGATGACACTGCTTACATCAATTTAGT
Found at i:1457633 original size:14 final size:15
Alignment explanation
Indices: 1457614--1457642 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1457604 AATTTTAATA
1457614 ATAAAAATAT-TATT
1 ATAAAAATATATATT
1457628 ATAAAAATATATATT
1 ATAAAAATATATATT
1457643 TACGTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAAAAATATATATT
Found at i:1458229 original size:29 final size:29
Alignment explanation
Indices: 1458195--1458253 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
1458185 CCAAAATTAA
*
1458195 TTTGATTTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
* *
1458224 TTTGATGTCATTGTTTATATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1458253 T
1 T
1458254 AGGTGAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.24, C:0.10, G:0.12, T:0.54
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:1464273 original size:14 final size:14
Alignment explanation
Indices: 1464254--1464283 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1464244 TTTAAATTTT
*
1464254 TTAAAATTACATTA
1 TTAAAAATACATTA
1464268 TTAAAAATACATTA
1 TTAAAAATACATTA
1464282 TT
1 TT
1464284 GATAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATACATTA
Found at i:1464415 original size:7 final size:7
Alignment explanation
Indices: 1464402--1464501 Score: 74
Period size: 7 Copynumber: 14.3 Consensus size: 7
1464392 GTATAAGGTC
1464402 TAGGGTT
1 TAGGGTT
*
1464409 TATGGTT
1 TAGGGTT
*
1464416 TAGTGTT
1 TAGGGTT
* *
1464423 TATGGTC
1 TAGGGTT
*
1464430 TAGGGTC
1 TAGGGTT
**
1464437 TATAGTT
1 TAGGGTT
*
1464444 TAGGGTC
1 TAGGGTT
1464451 TAGGGTT
1 TAGGGTT
*
1464458 TAAGGTT
1 TAGGGTT
**
1464465 TATAGTT
1 TAGGGTT
1464472 TAGGGTT
1 TAGGGTT
*
1464479 AAGGGTT
1 TAGGGTT
*
1464486 AAGGGTT
1 TAGGGTT
*
1464493 TGGGGTT
1 TAGGGTT
1464500 TA
1 TA
1464502 AGTTATGCAC
Statistics
Matches: 70, Mismatches: 23, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
7 70 1.00
ACGTcount: A:0.19, C:0.03, G:0.35, T:0.43
Consensus pattern (7 bp):
TAGGGTT
Found at i:1464425 original size:14 final size:14
Alignment explanation
Indices: 1464402--1464493 Score: 85
Period size: 14 Copynumber: 6.6 Consensus size: 14
1464392 GTATAAGGTC
1464402 TAGGGTTTATGGTT
1 TAGGGTTTATGGTT
* *
1464416 TAGTGTTTATGGTC
1 TAGGGTTTATGGTT
* *
1464430 TAGGGTCTATAGTT
1 TAGGGTTTATGGTT
* *
1464444 TAGGGTCTAGGGTT
1 TAGGGTTTATGGTT
* *
1464458 TAAGGTTTATAGTT
1 TAGGGTTTATGGTT
* *
1464472 TAGGGTTAAGGGTT
1 TAGGGTTTATGGTT
*
1464486 AAGGGTTT
1 TAGGGTTT
1464494 GGGGTTTAAG
Statistics
Matches: 60, Mismatches: 18, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 60 1.00
ACGTcount: A:0.20, C:0.03, G:0.34, T:0.43
Consensus pattern (14 bp):
TAGGGTTTATGGTT
Found at i:1464429 original size:28 final size:28
Alignment explanation
Indices: 1464398--1464493 Score: 97
Period size: 28 Copynumber: 3.4 Consensus size: 28
1464388 TATGGTATAA
* * * *
1464398 GGTCTAGGGTTTATGGTTTAGTGTTTAT
1 GGTCTAGGGTTTATAGTTTAGGGTCTAG
*
1464426 GGTCTAGGGTCTATAGTTTAGGGTCTAG
1 GGTCTAGGGTTTATAGTTTAGGGTCTAG
* *
1464454 GGTTTAAGGTTTATAGTTTAGGGT-TAAG
1 GGTCTAGGGTTTATAGTTTAGGGTCT-AG
1464482 GGT-TAAGGGTTT
1 GGTCT-AGGGTTT
1464494 GGGGTTTAAG
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
27 2 0.04
28 55 0.96
ACGTcount: A:0.19, C:0.04, G:0.34, T:0.43
Consensus pattern (28 bp):
GGTCTAGGGTTTATAGTTTAGGGTCTAG
Found at i:1472025 original size:20 final size:20
Alignment explanation
Indices: 1471982--1472025 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1471972 GCTGGCAATG
* * * *
1471982 AACCGGCTGAAAACTGGTAG
1 AACCAGCTGAAAACCGGCAA
1472002 AACCAGCTGAAAACCGGCAA
1 AACCAGCTGAAAACCGGCAA
1472022 AACC
1 AACC
1472026 GATTTGAACC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.27, G:0.23, T:0.09
Consensus pattern (20 bp):
AACCAGCTGAAAACCGGCAA
Found at i:1472250 original size:16 final size:16
Alignment explanation
Indices: 1472229--1472265 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
1472219 ATTAAAACTT
*
1472229 GAACTCGAAAATGCTC
1 GAACTCGAAAAGGCTC
1472245 GAACTCGAAAAGGCTC
1 GAACTCGAAAAGGCTC
1472261 GAACT
1 GAACT
1472266 AAGAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (16 bp):
GAACTCGAAAAGGCTC
Found at i:1476534 original size:23 final size:23
Alignment explanation
Indices: 1476500--1476559 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
1476490 TTTAATAAAA
1476500 AAAAT-TAATTATTAAAATATTT
1 AAAATATAATTATTAAAATATTT
* * *
1476522 AAAATATATTTATTAATATTTTT
1 AAAATATAATTATTAAAATATTT
1476545 AATAATATAA-TATTA
1 AA-AATATAATTATTA
1476560 TGTTTTCAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 5 0.16
23 21 0.66
24 6 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
AAAATATAATTATTAAAATATTT
Found at i:1476545 original size:12 final size:12
Alignment explanation
Indices: 1476516--1476553 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1476506 AATTATTAAA
1476516 ATATTTAA-AAT
1 ATATTTAATAAT
*
1476527 ATATTTATTAAT
1 ATATTTAATAAT
*
1476539 ATTTTTAATAAT
1 ATATTTAATAAT
1476551 ATA
1 ATA
1476554 ATATTATGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
ATATTTAATAAT
Found at i:1477970 original size:21 final size:21
Alignment explanation
Indices: 1477946--1477985 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1477936 TAAAATAATC
* *
1477946 TCTTATTTATTAAAAAATAGA
1 TCTTATATAATAAAAAATAGA
1477967 TCTTATATAATAAAAAATA
1 TCTTATATAATAAAAAATA
1477986 ATATTTTGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.40
Consensus pattern (21 bp):
TCTTATATAATAAAAAATAGA
Found at i:1479678 original size:2 final size:2
Alignment explanation
Indices: 1479618--1479659 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
1479608 ATCTTAACCC
* *
1479618 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1479659 A
1 A
1479660 AAAAATGCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1486659 original size:14 final size:14
Alignment explanation
Indices: 1486642--1486674 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1486632 ACCTGGGAGT
1486642 TACGACCGAATCTA
1 TACGACCGAATCTA
1486656 TACGACCGAATCTA
1 TACGACCGAATCTA
*
1486670 GACGA
1 TACGA
1486675 TCACATATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.18
Consensus pattern (14 bp):
TACGACCGAATCTA
Found at i:1488278 original size:27 final size:27
Alignment explanation
Indices: 1488248--1488315 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
1488238 CCCAACCAGC
*
1488248 CCGTTAACTTTGACCCCACCGGTCTGA
1 CCGTTGACTTTGACCCCACCGGTCTGA
*
1488275 CCGTTGACTTTGACCCGACCGGTCTGA
1 CCGTTGACTTTGACCCCACCGGTCTGA
1488302 CCGTTGACTTTGAC
1 CCGTTGACTTTGAC
1488316 TAAAAAAGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.16, C:0.34, G:0.22, T:0.28
Consensus pattern (27 bp):
CCGTTGACTTTGACCCCACCGGTCTGA
Found at i:1491498 original size:19 final size:19
Alignment explanation
Indices: 1491476--1491512 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1491466 TGATTTCTTC
1491476 TCTGAACTTTGATATATGT
1 TCTGAACTTTGATATATGT
* *
1491495 TCTGATCTTTGATCTATG
1 TCTGAACTTTGATATATG
1491513 CTATGATTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.14, G:0.16, T:0.49
Consensus pattern (19 bp):
TCTGAACTTTGATATATGT
Found at i:1498654 original size:31 final size:28
Alignment explanation
Indices: 1498598--1498667 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 28
1498588 AGTAGAATTC
*
1498598 TAATGAAATTAGGACAAAGGAAAAACAAGGG
1 TAATGAAA-TAGGACAAAAGAAAAAC-A-GG
*
1498629 TAATGAAATA-GACTAAAAGACAAAACATG
1 TAATGAAATAGGAC-AAAAGA-AAAACAGG
1498658 TAATGAAATA
1 TAATGAAATA
1498668 ATCTTCCCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 14 0.40
30 8 0.23
31 13 0.37
ACGTcount: A:0.57, C:0.07, G:0.19, T:0.17
Consensus pattern (28 bp):
TAATGAAATAGGACAAAAGAAAAACAGG
Found at i:1503341 original size:20 final size:19
Alignment explanation
Indices: 1503308--1503366 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
1503298 TACTCCTATG
*
1503308 AGTTTCGAAACTTTTATTA-T
1 AGTTTTGAAAC-TTT-TTAGT
*
1503328 AGTTTTGAATCTTTTTAGT
1 AGTTTTGAAACTTTTTAGT
* *
1503347 AGTTTTGATACTTTTGAGT
1 AGTTTTGAAACTTTTTAGT
1503366 A
1 A
1503367 ATCTGTTTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
18 3 0.09
19 21 0.64
20 9 0.27
ACGTcount: A:0.25, C:0.07, G:0.15, T:0.53
Consensus pattern (19 bp):
AGTTTTGAAACTTTTTAGT
Found at i:1522569 original size:34 final size:34
Alignment explanation
Indices: 1522526--1522610 Score: 152
Period size: 34 Copynumber: 2.5 Consensus size: 34
1522516 TATGATTGAT
1522526 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
1 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
*
1522560 CTCTCGGCGTCTTCAGTTGGATTCTTCGTAGGAA
1 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
*
1522594 ATCTCGGCGTCTTCAGT
1 CTCTCGGCGTCTTCAGT
1522611 GCTGTGCATG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.35
Consensus pattern (34 bp):
CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
Found at i:1522736 original size:23 final size:23
Alignment explanation
Indices: 1522687--1522736 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
1522677 TGAGCAGGGT
* *
1522687 TGCACGTCTACATGTGGGGGTCC
1 TGCACGTCTACATGTGGGGGGCA
*
1522710 TGCACGTCTGCATGTGGGGGGCA
1 TGCACGTCTACATGTGGGGGGCA
1522733 TGCA
1 TGCA
1522737 ATTGTTGGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.14, C:0.24, G:0.38, T:0.24
Consensus pattern (23 bp):
TGCACGTCTACATGTGGGGGGCA
Found at i:1522946 original size:41 final size:41
Alignment explanation
Indices: 1522884--1522961 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
1522874 GAGACTGCTC
*
1522884 GGGCTGAGGCAATTCATAATTACAGAAGCAGTGAGAGTTTG
1 GGGCTGAGGCAATTCACAATTACAGAAGCAGTGAGAGTTTG
1522925 GGGCTGAGGCAATTCACAATTACAGAAGCAGTGAGAG
1 GGGCTGAGGCAATTCACAATTACAGAAGCAGTGAGAG
1522962 CCTGAGAGGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.33, C:0.14, G:0.32, T:0.21
Consensus pattern (41 bp):
GGGCTGAGGCAATTCACAATTACAGAAGCAGTGAGAGTTTG
Found at i:1523491 original size:172 final size:173
Alignment explanation
Indices: 1523204--1523562 Score: 587
Period size: 172 Copynumber: 2.1 Consensus size: 173
1523194 TTGTAAAGTT
* *
1523204 TTAGGGACCGTTTTGTAAAATTTAAGGAATTTAAGGAATAAGAGTAAATTATTAAAAGTTGCTAT
1 TTAGGGATCGTTTTGTAAAATTTAAGGAATTTAAGGAATAAGAGTAAATTATAAAAAGTTGCTAT
*
1523269 ACTATGCTGGAATTTAGTATTAGTATGCTTAATTGGTTAAATTAGAAAGAATTTA-AAATTTA-T
66 ACTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTAGT
*
1523332 GGATTAAATTGCTAAGTTTGAAAATGTTGAGAACCAAATAGTAA
131 -GATTAAATTGCAAAGTTTGAAAATGTTGAGAACCAAATAGTAA
* * *
1523376 TTAGGGATCGTTTTGTAAAATTTGAGGAATTTAAGGAATTAGAGTAAATTATAAAAAGTTGGTAT
1 TTAGGGATCGTTTTGTAAAATTTAAGGAATTTAAGGAATAAGAGTAAATTATAAAAAGTTGCTAT
* *
1523441 ACTATGCTTGAATTTAGTATTAATATGCTTAATTGGTTAAATTTGAAAGAATTTATAAATTTAGT
66 ACTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTAGT
*
1523506 GATTAAATTGCAAAGTTTGAAAATGTTGAGAAGCAAATAGTAA
131 GATTAAATTGCAAAGTTTGAAAATGTTGAGAACCAAATAGTAA
* *
1523549 TTAGTGATCATTTT
1 TTAGGGATCGTTTT
1523563 ATATTTGATG
Statistics
Matches: 173, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
172 112 0.65
173 60 0.35
174 1 0.01
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.38
Consensus pattern (173 bp):
TTAGGGATCGTTTTGTAAAATTTAAGGAATTTAAGGAATAAGAGTAAATTATAAAAAGTTGCTAT
ACTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTAGT
GATTAAATTGCAAAGTTTGAAAATGTTGAGAACCAAATAGTAA
Found at i:1524776 original size:30 final size:30
Alignment explanation
Indices: 1524742--1524800 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
1524732 ATAAGTGAAT
* *
1524742 TTATTT-TTTATTATGTTTATATTATAATTG
1 TTATTTATTAATT-TGTTGATATTATAATTG
*
1524772 TTATTTATTAATTTGTTGATTTTATAATT
1 TTATTTATTAATTTGTTGATATTATAATT
1524801 ATTTAATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (30 bp):
TTATTTATTAATTTGTTGATATTATAATTG
Found at i:1525305 original size:6 final size:6
Alignment explanation
Indices: 1525294--1525348 Score: 101
Period size: 6 Copynumber: 9.2 Consensus size: 6
1525284 CAAGAAGGAC
1525294 TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG
1 TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG
*
1525342 TAGGAG T
1 TGGGAG T
1525349 TCTTCTCACC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.18, C:0.00, G:0.64, T:0.18
Consensus pattern (6 bp):
TGGGAG
Found at i:1525859 original size:14 final size:14
Alignment explanation
Indices: 1525850--1526561 Score: 311
Period size: 14 Copynumber: 51.7 Consensus size: 14
1525840 TAATTATTAA
1525850 TAAATCATTAAAAT
1 TAAATCATTAAAAT
1525864 TAAATCATTAAAAT
1 TAAATCATTAAAAT
* * **
1525878 TAAGTAATTATTAT
1 TAAATCATTAAAAT
*
1525892 TAAATTATTAAAAT
1 TAAATCATTAAAAT
*
1525906 TAAATCATT-AAAG
1 TAAATCATTAAAAT
*
1525919 TAATTATTATTAAATCAT
1 TAA--ATCATTAAA--AT
1525937 TAAATCATTAAATCAT
1 TAAATCATTAAA--AT
* **
1525953 TAAAGTAATTATTAT
1 TAAA-TCATTAAAAT
* *
1525968 TAAAGCATTAAAGT
1 TAAATCATTAAAAT
*
1525982 TAAATCATT-AAAG
1 TAAATCATTAAAAT
*
1525995 T-AATTATT---AT
1 TAAATCATTAAAAT
*
1526005 TAAATCACTAAGTAAT
1 TAAATCATTAA--AAT
*
1526021 T--ATTATTAAATCAT
1 TAAATCATTAAA--AT
* **
1526035 TAAAGTAATTATTAT
1 TAAA-TCATTAAAAT
*
1526050 TAAATCATTAAAGT
1 TAAATCATTAAAAT
1526064 TAAATCATTAAATCAT
1 TAAATCATTAAA--AT
1526080 TAAA--ATTAAATCAT
1 TAAATCATTAAA--AT
* **
1526094 TAAAGTAATTATTAT
1 TAAA-TCATTAAAAT
1526109 TAAATCATTAAAAT
1 TAAATCATTAAAAT
1526123 TAAATCATTAAAA-
1 TAAATCATTAAAAT
*
1526136 T-AATTATT---AT
1 TAAATCATTAAAAT
*
1526146 TAAATCATTAAAGT
1 TAAATCATTAAAAT
*
1526160 TAAATCATT-AAAG
1 TAAATCATTAAAAT
*
1526173 T-AATTATT---AT
1 TAAATCATTAAAAT
*
1526183 TAAATCATTAAAGT
1 TAAATCATTAAAAT
* **
1526197 TAAATAATTATTAT
1 TAAATCATTAAAAT
*
1526211 TAAATCATTAAAGT
1 TAAATCATTAAAAT
*
1526225 TAAATCATT-AAAG
1 TAAATCATTAAAAT
*
1526238 T-AATTATT---AT
1 TAAATCATTAAAAT
1526248 TAAATCATTAAATCAT
1 TAAATCATTAAA--AT
* **
1526264 TAAAGTAATTATTAT
1 TAAA-TCATTAAAAT
* *
1526279 TAAAGCATTAAAGT
1 TAAATCATTAAAAT
*
1526293 TAAATCATT-AAAG
1 TAAATCATTAAAAT
*
1526306 T-AATTATT---AT
1 TAAATCATTAAAAT
1526316 TAAATCATTAAATCAT
1 TAAATCATTAAA--AT
1526332 TAAATCATTAAATTAT
1 TAAATCATTAAA--AT
* **
1526348 TAAAGTAATTATTAT
1 TAAA-TCATTAAAAT
*
1526363 TAAATCATTAAAGT
1 TAAATCATTAAAAT
1526377 TAAATCATTAAATCAT
1 TAAATCATTAAA--AT
1526393 T-AAT-ATTAAATCAT
1 TAAATCATTAAA--AT
* **
1526407 TAAAGTAATTATTAT
1 TAAA-TCATTAAAAT
1526422 TAAATCATTAAAAT
1 TAAATCATTAAAAT
*
1526436 TAAATCATT-AAAG
1 TAAATCATTAAAAT
*
1526449 T-AATTATT---AT
1 TAAATCATTAAAAT
*
1526459 TAAATCATTAAAGT
1 TAAATCATTAAAAT
*
1526473 TAAATCATT-AAAG
1 TAAATCATTAAAAT
*
1526486 T-AATTATT---AT
1 TAAATCATTAAAAT
*
1526496 TAAATCATTAAAGT
1 TAAATCATTAAAAT
* **
1526510 TAAATAATTATTAT
1 TAAATCATTAAAAT
*
1526524 TAAATCATTAAAGT
1 TAAATCATTAAAAT
* *
1526538 TAAATAATTAAATT
1 TAAATCATTAAAAT
*
1526552 TAAATAATTA
1 TAAATCATTA
1526562 TTATTAAATA
Statistics
Matches: 526, Mismatches: 114, Indels: 116
0.70 0.15 0.15
Matches are distributed among these distances:
9 1 0.00
10 13 0.02
11 41 0.08
12 43 0.08
13 26 0.05
14 267 0.51
15 46 0.09
16 57 0.11
17 28 0.05
18 4 0.01
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (14 bp):
TAAATCATTAAAAT
Found at i:1525907 original size:9 final size:8
Alignment explanation
Indices: 1525887--1526570 Score: 147
Period size: 8 Copynumber: 90.2 Consensus size: 8
1525877 TTAAGTAATT
1525887 ATTATTAA
1 ATTATTAA
1525895 ATTATTAA
1 ATTATTAA
1525903 A--ATTAA
1 ATTATTAA
*
1525909 ATCATTAA
1 ATTATTAA
*
1525917 AGTAATT--
1 A-TTATTAA
1525924 ATTATTAA
1 ATTATTAA
*
1525932 ATCATTAA
1 ATTATTAA
*
1525940 ATCATTAA
1 ATTATTAA
*
1525948 ATCATTAA
1 ATTATTAA
*
1525956 AGTAATT--
1 A-TTATTAA
1525963 ATTATTAA
1 ATTATTAA
**
1525971 AGCATTAA
1 ATTATTAA
*
1525979 A--GTTAA
1 ATTATTAA
*
1525985 ATCATTAA
1 ATTATTAA
*
1525993 AGTAATT--
1 A-TTATTAA
1526000 ATTATTAA
1 ATTATTAA
* *
1526008 ATCACTAA
1 ATTATTAA
* *
1526016 GTAATT--
1 ATTATTAA
1526022 ATTATTAA
1 ATTATTAA
*
1526030 ATCATTAA
1 ATTATTAA
*
1526038 AGTAATT--
1 A-TTATTAA
1526045 ATTATTAA
1 ATTATTAA
*
1526053 ATCATTAA
1 ATTATTAA
*
1526061 A--GTTAA
1 ATTATTAA
*
1526067 ATCATTAA
1 ATTATTAA
*
1526075 ATCATTAA
1 ATTATTAA
1526083 A--ATTAA
1 ATTATTAA
*
1526089 ATCATTAA
1 ATTATTAA
*
1526097 AGTAATT--
1 A-TTATTAA
1526104 ATTATTAA
1 ATTATTAA
*
1526112 ATCATTAA
1 ATTATTAA
1526120 A--ATTAA
1 ATTATTAA
*
1526126 ATCATTAAA
1 ATTATT-AA
*
1526135 ATAATT--
1 ATTATTAA
1526141 ATTATTAA
1 ATTATTAA
*
1526149 ATCATTAA
1 ATTATTAA
*
1526157 A--GTTAA
1 ATTATTAA
*
1526163 ATCATTAA
1 ATTATTAA
*
1526171 AGTAATT--
1 A-TTATTAA
1526178 ATTATTAA
1 ATTATTAA
*
1526186 ATCATTAA
1 ATTATTAA
*
1526194 AGTTAAATAA
1 A-TT-ATTAA
1526204 TTATTATTAA
1 --ATTATTAA
*
1526214 ATCATTAA
1 ATTATTAA
*
1526222 A--GTTAA
1 ATTATTAA
*
1526228 ATCATTAA
1 ATTATTAA
*
1526236 AGTAATT--
1 A-TTATTAA
1526243 ATTATTAA
1 ATTATTAA
*
1526251 ATCATTAA
1 ATTATTAA
*
1526259 ATCATTAA
1 ATTATTAA
*
1526267 AGTAATT--
1 A-TTATTAA
1526274 ATTATTAA
1 ATTATTAA
**
1526282 AGCATTAA
1 ATTATTAA
*
1526290 A--GTTAA
1 ATTATTAA
*
1526296 ATCATTAA
1 ATTATTAA
*
1526304 AGTAATT--
1 A-TTATTAA
1526311 ATTATTAA
1 ATTATTAA
*
1526319 ATCATTAA
1 ATTATTAA
*
1526327 ATCATTAA
1 ATTATTAA
*
1526335 ATCATTAA
1 ATTATTAA
1526343 ATTATTAA
1 ATTATTAA
*
1526351 AGTAATT--
1 A-TTATTAA
1526358 ATTATTAA
1 ATTATTAA
*
1526366 ATCATTAA
1 ATTATTAA
*
1526374 A--GTTAA
1 ATTATTAA
*
1526380 ATCATTAA
1 ATTATTAA
*
1526388 ATCATT-A
1 ATTATTAA
1526395 A-TATTAA
1 ATTATTAA
*
1526402 ATCATTAA
1 ATTATTAA
*
1526410 AGTAATT--
1 A-TTATTAA
1526417 ATTATTAA
1 ATTATTAA
*
1526425 ATCATTAA
1 ATTATTAA
1526433 A--ATTAA
1 ATTATTAA
*
1526439 ATCATTAA
1 ATTATTAA
*
1526447 AGTAATT--
1 A-TTATTAA
1526454 ATTATTAA
1 ATTATTAA
*
1526462 ATCATTAA
1 ATTATTAA
*
1526470 A--GTTAA
1 ATTATTAA
*
1526476 ATCATTAA
1 ATTATTAA
*
1526484 AGTAATT--
1 A-TTATTAA
1526491 ATTATTAA
1 ATTATTAA
*
1526499 ATCATTAA
1 ATTATTAA
*
1526507 AGTTAAATAA
1 A-TT-ATTAA
1526517 TTATTATTAA
1 --ATTATTAA
*
1526527 ATCATTAA
1 ATTATTAA
*
1526535 A--GTTAA
1 ATTATTAA
*
1526541 ATAATTAA
1 ATTATTAA
1526549 A-T-TTAA
1 ATTATTAA
*
1526555 ATAATT--
1 ATTATTAA
1526561 ATTATTAA
1 ATTATTAA
1526569 AT
1 AT
1526571 ATGTACTCGA
Statistics
Matches: 513, Mismatches: 81, Indels: 164
0.68 0.11 0.22
Matches are distributed among these distances:
6 138 0.27
7 17 0.03
8 275 0.54
9 61 0.12
10 16 0.03
11 4 0.01
12 2 0.00
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (8 bp):
ATTATTAA
Found at i:1525909 original size:76 final size:76
Alignment explanation
Indices: 1525828--1526542 Score: 318
Period size: 82 Copynumber: 9.1 Consensus size: 76
1525818 AATATAAATC
*
1525828 ATTAAAGTC-AAGTAATTATTAATAAATCATTAAAATTAAATCATTAAAATTAAGTAATTATTAT
1 ATTAAA-TCAAAGTAATTATTATTAAATCATTAAAATTAAATCATTAAAATTAAGTAATTATTAT
*
1525892 TAAATTATTAAA
65 TAAATCATTAAA
1525904 ATTAAATCATTAAAGTAATTATTATTAAATCATTAAATCATTAAATCATT---A--AAGTAATTA
1 ATTAAATC---AAAGTAATTATTATTAAATCATTAAA--ATTAAATCATTAAAATTAAGTAATTA
*
1525964 TTATTAAAGCATTAAA
61 TTATTAAATCATTAAA
* * *
1525980 GTTAAATCATTAAAGTAATTATTATTAAATCACTAAGTAATT--ATTATTAAATCATTAAAGTAA
1 ATTAAATC---AAAGTAATTATTATTAAATCATTAA--AATTAAATCATTAAA--ATT-AAGTAA
1526043 TTATTATTAAATCATTAAA
58 TTATTATTAAATCATTAAA
* * * ** * *
1526062 GTTAAATCATTAAATCATTAAAATTAAATCATT-AAAGTAATTATTATTAAATCATTAA--AATT
1 ATTAAATCA--AAGTAATTATTATTAAATCATTAAAATTAA--ATCATTAAA--ATTAAGTAATT
* * **
1526124 AAATCATTAAAATAATTATT
60 --ATTATT-AAATCATTAAA
* * ** * *
1526144 ATTAAATCATTAAAGTTAA--ATCATTAAAGTAATTATTATTAAATCATTAAAGTTAAATAATTA
1 ATTAAATC---AAAG-TAATTATTATTAAA-TCATTAAAATTAAATCATTAAAATTAAGTAATTA
1526207 TTATTAAATCATTAAA
61 TTATTAAATCATTAAA
* * *
1526223 GTTAAATCATTAAAGTAATTATTATTAAATCATTAAATCATTAAAGTAATT---ATT-ATTAA--
1 ATTAAATC---AAAGTAATTATTATTAAATCATTAAA--ATTAAA-TCATTAAAATTAAGTAATT
** *
1526282 AGCATTAAA--GTT-AA
60 ATTATTAAATCATTAAA
* *
1526296 A-T-CATTAAAGTAATTATTATTAAATCATTAAATCATTAAATCATTAAATTATTAAAGTAATTA
1 ATTAAATCAAAGTAATTATTATTAAATCATTAAA--ATTAAATCATTAAA--ATT-AAGTAATTA
1526359 TTATTAAATCATTAAA
61 TTATTAAATCATTAAA
* * * * * *
1526375 GTTAAATCATTAAATCATTAATATTAAATCATT-AAAGTAATTATTATTAAATCATTAA--AATT
1 ATTAAATCA--AAGTAATTATTATTAAATCATTAAAATTAA--ATCATTAAA--ATTAAGTAATT
* * **
1526437 AAATCATTAAAGTAATTATT
60 --ATTATTAAA-TCATTAAA
* * ** * *
1526457 ATTAAATCATTAAAGTTAA--ATCATTAAAGTAATTATTATTAAATCATTAAAGTTAAATAATTA
1 ATTAAATC---AAAG-TAATTATTATTAAA-TCATTAAAATTAAATCATTAAAATTAAGTAATTA
1526520 TTATTAAATCATTAAA
61 TTATTAAATCATTAAA
*
1526536 GTTAAAT
1 ATTAAAT
1526543 AATTAAATTT
Statistics
Matches: 492, Mismatches: 80, Indels: 131
0.70 0.11 0.19
Matches are distributed among these distances:
67 4 0.01
68 34 0.07
71 2 0.00
72 4 0.01
73 2 0.00
74 11 0.02
75 2 0.00
76 80 0.16
78 14 0.03
79 76 0.15
80 35 0.07
81 54 0.11
82 129 0.26
83 31 0.06
84 12 0.02
85 2 0.00
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.41
Consensus pattern (76 bp):
ATTAAATCAAAGTAATTATTATTAAATCATTAAAATTAAATCATTAAAATTAAGTAATTATTATT
AAATCATTAAA
Found at i:1526424 original size:37 final size:36
Alignment explanation
Indices: 1525879--1526519 Score: 543
Period size: 37 Copynumber: 17.0 Consensus size: 36
1525869 CATTAAAATT
*
1525879 AAGTAATTATTATTAAATTATTAAAATTAAATCATTA
1 AAGTAATTATTATTAAATCATT-AAATTAAATCATTA
1525916 AAGTAATTATTATTAAATCATTAAATCATTAAATCATTA
1 AAGTAATTATTATTAAATCATT-AA--ATTAAATCATTA
*
1525955 AAGTAATTATTATTAAAGCATTAAAGTTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAA-TTAAATCATTA
1525992 AAGTAATTATTATTAAATCACTAAGTAATTATTATTAAATCATTA
1 AAGTAATTATTATTAAATCA-T---T-A--A--ATTAAATCATTA
1526037 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAA-TTAAATCATTA
* ** * *
1526074 AA-TCATTAAAATTAAATCATTAAAGTAATTATTATTA
1 AAGTAATTATTATTAAATCATTAAATTAA--ATCATTA
* ** * *
1526111 AA-TCATTAAAATTAAATCATTAAAATAATTATTATTA
1 AAGTAATTATTATTAAATCATTAAATTAA--ATCATTA
* * * *
1526148 AA-TCATTA-AAGTTAAATCATTAAAGTAATTATTATTA
1 AAGTAATTATTA-TTAAATCATTAAATTAA--ATCATTA
* * * *
1526185 AA-TCATTA-AAGTTAAATAATTATTATTAAATCATTA
1 AAGTAATTATTA-TTAAATCATTA-AATTAAATCATTA
* * *
1526221 AAGTTAAATCATTAAAGTAATTATTATTAAATCATTAAATCATTA
1 AAG-T-AATTATT--ATTAA--ATCATT-AA--ATTAAATCATTA
*
1526266 AAGTAATTATTATTAAAGCATTAAAGTTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAA-TTAAATCATTA
1526303 AAGTAATTATTATTAAATCATTAAATCATTAAATCATTA
1 AAGTAATTATTATTAAATCATT-AA--ATTAAATCATTA
* * * *
1526342 AA-TTATTA-AAGT-AATTATT--ATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAATTAAATCATTA
*
1526373 AAGTTAA--ATCATTAAATCATTAATATTAAATCATTA
1 AAG-TAATTATTATTAAATCATTAA-ATTAAATCATTA
1526409 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
1 AAGTAATTATTATTAAATCATT-AAATTAAATCATTA
1526446 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAA-TTAAATCATTA
*
1526483 AAGTAATTATTATTAAATCATTAAAGTTAAATAATTA
1 AAGTAATTATTATTAAATCATTAAA-TTAAATCATTA
1526520 TTATTAAATC
Statistics
Matches: 526, Mismatches: 35, Indels: 86
0.81 0.05 0.13
Matches are distributed among these distances:
31 15 0.03
32 2 0.00
33 8 0.02
35 6 0.01
36 56 0.11
37 291 0.55
38 20 0.04
39 53 0.10
40 2 0.00
41 9 0.02
42 2 0.00
43 11 0.02
44 4 0.01
45 46 0.09
46 1 0.00
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.41
Consensus pattern (36 bp):
AAGTAATTATTATTAAATCATTAAATTAAATCATTA
Found at i:1526436 original size:313 final size:311
Alignment explanation
Indices: 1525935--1526549 Score: 1140
Period size: 313 Copynumber: 2.0 Consensus size: 311
1525925 TTATTAAATC
1525935 ATTAAATCATTAAATCATTAAAGTAATTATTATTAAAGCATTAAAGTTAAATCATTAAAGTAATT
1 ATTAAATCATTAAATCATTAAAGTAATTATTATTAAAGCATTAAAGTTAAATCATTAAAGTAATT
* *
1526000 ATTATTAAATCACTAAGTAATTATTATTAAATCATTAAAGTAATTATTATTAAATCATTAAAGTT
66 ATTATTAAATCACTAAATAATTATCATTAAATCATTAAAGTAATTATTATTAAATCATTAAAGTT
1526065 AAATCATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAAATCATTAAAATTAAATCA
131 AAATCATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAAATCATTAAAATTAAATCA
1526130 TTAAAATAATTATTATTAAATCATTAAAGTTAAATCATTAAAGTAATTATTATTAAATCATTAAA
196 TTAAAATAATTATTATTAAATCATTAAAGTTAAATCATTAAAGTAATTATTATTAAATCATTAAA
*
1526195 GTTAAATAATTATTATTAAATCATTAAAGTTAAATCATTAAAGTAATTATT
261 GTTAAATAATTATTATTAAATCATTAAAGTTAAATAATTAAAGTAATTATT
1526246 ATTAAATCATTAAATCATTAAAGTAATTATTATTAAAGCATTAAAGTTAAATCATTAAAGTAATT
1 ATTAAATCATTAAATCATTAAAGTAATTATTATTAAAGCATTAAAGTTAAATCATTAAAGTAATT
* * *
1526311 ATTATTAAATCATTAAATCATTAAATCATTAAATTATTAAAGTAATTATTATTAAATCATTAAAG
66 ATTATTAAATCACTAAATAATT--ATCATTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
*
1526376 TTAAATCATTAAATCATTAATATTAAATCATTAAAGTAATTATTATTAAATCATTAAAATTAAAT
129 TTAAATCATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAAATCATTAAAATTAAAT
*
1526441 CATTAAAGTAATTATTATTAAATCATTAAAGTTAAATCATTAAAGTAATTATTATTAAATCATTA
194 CATTAAAATAATTATTATTAAATCATTAAAGTTAAATCATTAAAGTAATTATTATTAAATCATTA
1526506 AAGTTAAATAATTATTATTAAATCATTAAAGTTAAATAATTAAA
259 AAGTTAAATAATTATTATTAAATCATTAAAGTTAAATAATTAAA
1526550 TTTAAATAAT
Statistics
Matches: 294, Mismatches: 8, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
311 84 0.29
313 210 0.71
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (311 bp):
ATTAAATCATTAAATCATTAAAGTAATTATTATTAAAGCATTAAAGTTAAATCATTAAAGTAATT
ATTATTAAATCACTAAATAATTATCATTAAATCATTAAAGTAATTATTATTAAATCATTAAAGTT
AAATCATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAAATCATTAAAATTAAATCA
TTAAAATAATTATTATTAAATCATTAAAGTTAAATCATTAAAGTAATTATTATTAAATCATTAAA
GTTAAATAATTATTATTAAATCATTAAAGTTAAATAATTAAAGTAATTATT
Found at i:1526554 original size:28 final size:27
Alignment explanation
Indices: 1526071--1526561 Score: 151
Period size: 23 Copynumber: 18.9 Consensus size: 27
1526061 AGTTAAATCA
* *
1526071 TTAAATCATTAAAATTAAATCATTAAAG
1 TTAAATAATT-AATTTAAATCATTAAAG
* *
1526099 -T-AATTATT-A-TTAAATCATTAAAA
1 TTAAATAATTAATTTAAATCATTAAAG
* ** *
1526122 TTAAATCATTAAAAT-AATTATT--A-
1 TTAAATAATTAATTTAAATCATTAAAG
* *
1526145 TTAAATCATTAAAGTTAAATCATTAAAG
1 TTAAATAATT-AATTTAAATCATTAAAG
*
1526173 -T-AATTATT-A-TTAAATCATTAAAG
1 TTAAATAATTAATTTAAATCATTAAAG
*
1526196 TTAAATAATTATTATTAAATCATTAAAG
1 TTAAATAATTAAT-TTAAATCATTAAAG
* ** *
1526224 TTAAATCATTAAAGT-AATTATT--A-
1 TTAAATAATTAATTTAAATCATTAAAG
* * *
1526247 TTAAATCATTAAATCATTAAAGTAATTATTA-
1 TTAAATAATT-AAT--TTAAA-TCATTA-AAG
** *
1526278 TTAAAGCATTAAAGTTAAATCATTAAAG
1 TTAAATAATT-AATTTAAATCATTAAAG
* *
1526306 -T-AATTATT-A-TTAAATCATTAAATCA
1 TTAAATAATTAATTTAAATCATTAAA--G
* * *
1526331 TTAAATCATTAAATTATTAAAGTAATTATTA-
1 TTAAATAATT-AA-T-TTAAA-TCATTA-AAG
* *
1526362 TTAAATCATTAAAGTTAAATCATTAAA-
1 TTAAATAATT-AATTTAAATCATTAAAG
* *
1526389 -TCATTAA-T-A-TTAAATCATTAAAG
1 TTAAATAATTAATTTAAATCATTAAAG
* *
1526412 -T-AATTATT-A-TTAAATCATTAAAA
1 TTAAATAATTAATTTAAATCATTAAAG
* ** *
1526435 TTAAATCATTAAAGT-AATTATT--A-
1 TTAAATAATTAATTTAAATCATTAAAG
* *
1526458 TTAAATCATTAAAGTTAAATCATTAAAG
1 TTAAATAATT-AATTTAAATCATTAAAG
*
1526486 -T-AATTATT-A-TTAAATCATTAAAG
1 TTAAATAATTAATTTAAATCATTAAAG
*
1526509 TTAAATAATTATTATTAAATCATTAAAG
1 TTAAATAATTAAT-TTAAATCATTAAAG
*
1526537 TTAAATAATTAAATTTAAATAATTA
1 TTAAATAATT-AATTTAAATCATTA
1526562 TTATTAAATA
Statistics
Matches: 363, Mismatches: 49, Indels: 102
0.71 0.10 0.20
Matches are distributed among these distances:
22 16 0.04
23 101 0.28
24 19 0.05
25 37 0.10
26 49 0.13
27 19 0.05
28 72 0.20
29 13 0.04
31 26 0.07
32 5 0.01
33 5 0.01
34 1 0.00
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (27 bp):
TTAAATAATTAATTTAAATCATTAAAG
Found at i:1530043 original size:42 final size:42
Alignment explanation
Indices: 1529984--1530087 Score: 129
Period size: 42 Copynumber: 2.4 Consensus size: 42
1529974 AACAAATCTC
** *
1529984 ACGCTTCAGGCGAATCTCACGCTTCGACC-CTAAAGCATACAG
1 ACGCTTCAGATGAATCTCACGCTTCGACCAC-AAAGAATACAG
*
1530026 ACGCTTCAGATGAATCTCACGCTTCGGCCACAAAGAATACAG
1 ACGCTTCAGATGAATCTCACGCTTCGACCACAAAGAATACAG
*
1530068 ACGCATGCAGAATGAATCTC
1 ACGC-TTCAG-ATGAATCTC
1530088 GGAGGAAGAA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
42 40 0.74
43 5 0.09
44 9 0.17
ACGTcount: A:0.32, C:0.30, G:0.19, T:0.19
Consensus pattern (42 bp):
ACGCTTCAGATGAATCTCACGCTTCGACCACAAAGAATACAG
Found at i:1531115 original size:23 final size:23
Alignment explanation
Indices: 1531085--1531128 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
1531075 TTGAGCAGGG
1531085 CTGCACGTCTGCATGTGGGGGTC
1 CTGCACGTCTGCATGTGGGGGTC
1531108 CTGCACGTCTGCATGTGGGGG
1 CTGCACGTCTGCATGTGGGGG
1531129 GCATGCAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.09, C:0.25, G:0.41, T:0.25
Consensus pattern (23 bp):
CTGCACGTCTGCATGTGGGGGTC
Found at i:1531135 original size:23 final size:22
Alignment explanation
Indices: 1531082--1531135 Score: 81
Period size: 23 Copynumber: 2.4 Consensus size: 22
1531072 GGGTTGAGCA
1531082 GGGCTGCACGTCTGCATGTGGG
1 GGGCTGCACGTCTGCATGTGGG
*
1531104 GGTCCTGCACGTCTGCATGTGGG
1 GG-GCTGCACGTCTGCATGTGGG
1531127 GGGCATGCA
1 GGGC-TGCA
1531136 ATTGTTGGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 3 0.11
23 25 0.89
ACGTcount: A:0.11, C:0.24, G:0.43, T:0.22
Consensus pattern (22 bp):
GGGCTGCACGTCTGCATGTGGG
Found at i:1531345 original size:41 final size:41
Alignment explanation
Indices: 1531283--1531360 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
1531273 GAGACTGCTC
*
1531283 GGGCTGAGGCAATTCATAATTACAGAAGCAGTGAGAGTTTG
1 GGGCTGAGGCAATTCACAATTACAGAAGCAGTGAGAGTTTG
1531324 GGGCTGAGGCAATTCACAATTACAGAAGCAGTGAGAG
1 GGGCTGAGGCAATTCACAATTACAGAAGCAGTGAGAG
1531361 CCTGAGAGGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.33, C:0.14, G:0.32, T:0.21
Consensus pattern (41 bp):
GGGCTGAGGCAATTCACAATTACAGAAGCAGTGAGAGTTTG
Found at i:1531889 original size:172 final size:172
Alignment explanation
Indices: 1531603--1531955 Score: 575
Period size: 172 Copynumber: 2.1 Consensus size: 172
1531593 TTGTAAAGTT
* *
1531603 TTAGGGACCGTTTTGTAAAATTTAAGGAATTAAGGAATAAGAGTAAATTATTAAAAGTTGCTATA
1 TTAGGGATCGTTTTGTAAAATTTAAGGAATTAAGGAATAAGAGTAAATTATAAAAAGTTGCTATA
*
1531668 CTATGCTGGAATTTAGTATTAGTATGCTTAATTGGTTAAATTAGAAAGAATTTA-AAATTTA-TG
66 CTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTAGT-
*
1531731 GATTAAATTGCTAAGTTTGAAAATGTTGAGAACCAAATAGTAA
130 GATTAAATTGCAAAGTTTGAAAATGTTGAGAACCAAATAGTAA
* * *
1531774 TTAGGGATCGTTTTGTAAAATTTGAGGAATTTAAGGAATTAGAGTAAATTATAAAAAGTTGGTAT
1 TTAGGGATCGTTTTGTAAAATTTAAGGAA-TTAAGGAATAAGAGTAAATTATAAAAAGTTGCTAT
* *
1531839 ACTATGCTTGAATTTAGTATTAATATGCTTAATTGGTTAAATTTGAAAGAATTTATAAATTTAGT
65 ACTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTAGT
*
1531904 GATTAAATTGCAAAGTTTGAAAATGTTGAGAAGCAAATAGTAA
130 GATTAAATTGCAAAGTTTGAAAATGTTGAGAACCAAATAGTAA
*
1531947 TTAGTGATC
1 TTAGGGATC
1531956 ATTTATATTT
Statistics
Matches: 168, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
171 27 0.16
172 84 0.50
173 56 0.33
174 1 0.01
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.37
Consensus pattern (172 bp):
TTAGGGATCGTTTTGTAAAATTTAAGGAATTAAGGAATAAGAGTAAATTATAAAAAGTTGCTATA
CTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTAGTG
ATTAAATTGCAAAGTTTGAAAATGTTGAGAACCAAATAGTAA
Found at i:1533687 original size:6 final size:6
Alignment explanation
Indices: 1533676--1533718 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
1533666 CAAGAAGGAC
* *
1533676 TGGGAG TGGGAG TGGGAG TGGGAG TGAGAG TGGGAG TAGGAG T
1 TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG T
1533719 TCTTCTCACC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.21, C:0.00, G:0.60, T:0.19
Consensus pattern (6 bp):
TGGGAG
Found at i:1534242 original size:14 final size:14
Alignment explanation
Indices: 1534219--1534894 Score: 130
Period size: 14 Copynumber: 46.4 Consensus size: 14
1534209 TAATTATTAA
*
1534219 TAAATCATTAAAAT
1 TAAATAATTAAAAT
* **
1534233 TAAGTAATTATTAT
1 TAAATAATTAAAAT
*
1534247 TAAATTATTAAAAT
1 TAAATAATTAAAAT
* *
1534261 TAAATCATT-AAAG
1 TAAATAATTAAAAT
*
1534274 TAATTATTATTAAATCAT
1 TAA--ATAATTAAA--AT
*
1534292 TAAATCA-TAAATCAT
1 TAAATAATTAAA--AT
* **
1534307 TAAGTAATTATTAT
1 TAAATAATTAAAAT
** *
1534321 TAAAGCATT-AAGT
1 TAAATAATTAAAAT
* *
1534334 TAAATCATT-AAAG
1 TAAATAATTAAAAT
*
1534347 TAATTATTATTAAATCAT
1 TAA--ATAATTAAA--AT
**
1534365 TAAAGTAATTATTAT
1 TAAA-TAATTAAAAT
* *
1534380 TAAATCATTAAAGT
1 TAAATAATTAAAAT
* *
1534394 T-AATCATTAATCAT
1 TAAATAATTAA-AAT
1534408 T-AA-AATTAAATCAT
1 TAAATAATTAAA--AT
* **
1534422 TAAGTAATTATTAT
1 TAAATAATTAAAAT
*
1534436 TAAATCATTAAAAT
1 TAAATAATTAAAAT
*
1534450 TAAATCATTAAAA-
1 TAAATAATTAAAAT
* *
1534463 TAATTATTATTAATCAT
1 TAA--ATAATTAA-AAT
*
1534480 T-AA-AGTTAAATCAT
1 TAAATAATTAAA--AT
**
1534494 TAAAGTAATTATTAT
1 TAAA-TAATTAAAAT
* *
1534509 TAAATCATT-AAGT
1 TAAATAATTAAAAT
*
1534522 TAAATAATT-ATAT
1 TAAATAATTAAAAT
* *
1534535 TAAATCATTAAAGT
1 TAAATAATTAAAAT
* *
1534549 TAAATCATT-AAAG
1 TAAATAATTAAAAT
*
1534562 TAATTATTATTAAATCAT
1 TAA--ATAATTAAA--AT
*
1534580 TAAATCATTAAATCAT
1 TAAATAATTAAA--AT
**
1534596 TAAAGTAATTATTAT
1 TAAA-TAATTAAAAT
** *
1534611 TAAAGCATTAAAGT
1 TAAATAATTAAAAT
* *
1534625 TAAATCATT-AAAG
1 TAAATAATTAAAAT
*
1534638 TAATTATTATTAAATCAT
1 TAA--ATAATTAAA--AT
*
1534656 TAAATCATTAAATTAT
1 TAAATAATTAAA--AT
**
1534672 TAAAGTAATTATTAT
1 TAAA-TAATTAAAAT
* *
1534687 TAAATCATTAAAGT
1 TAAATAATTAAAAT
*
1534701 TAAATCATTAAATCAT
1 TAAATAATTAAA--AT
1534717 T-AA-AATTAAATCAT
1 TAAATAATTAAA--AT
**
1534731 TAAAGTAATTATTAT
1 TAAA-TAATTAAAAT
*
1534746 TAAATCATTAAAAT
1 TAAATAATTAAAAT
* *
1534760 TAAATCATT-AAAG
1 TAAATAATTAAAAT
*
1534773 TAATTATTATTAAATCAT
1 TAA--ATAATTAAA--AT
* *
1534791 T-AA-AGTTAATCAT
1 TAAATAATTAA-AAT
**
1534804 TAAAGTAATTATTAT
1 TAAA-TAATTAAAAT
* *
1534819 TAAATCATTAAAGT
1 TAAATAATTAAAAT
**
1534833 TAAATAATTATTAT
1 TAAATAATTAAAAT
* *
1534847 TAAATCATTAAAGT
1 TAAATAATTAAAAT
*
1534861 TAAATAATTAAATT
1 TAAATAATTAAAAT
**
1534875 TAAATAATTATTAT
1 TAAATAATTAAAAT
1534889 TAAATA
1 TAAATA
1534895 TGTACTCGAG
Statistics
Matches: 485, Mismatches: 124, Indels: 106
0.68 0.17 0.15
Matches are distributed among these distances:
13 79 0.16
14 213 0.44
15 89 0.18
16 60 0.12
17 26 0.05
18 18 0.04
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (14 bp):
TAAATAATTAAAAT
Found at i:1534253 original size:8 final size:8
Alignment explanation
Indices: 1534245--1534858 Score: 230
Period size: 8 Copynumber: 83.8 Consensus size: 8
1534235 AGTAATTATT
*
1534245 ATTAAATT
1 ATTAAATC
1534253 ATTAAA--
1 ATTAAATC
1534259 ATTAAATC
1 ATTAAATC
*
1534267 ATTAAAGTA
1 ATTAAA-TC
*
1534276 ATT--ATT
1 ATTAAATC
1534282 ATTAAATC
1 ATTAAATC
1534290 ATTAAATC
1 ATTAAATC
1534298 A-TAAATC
1 ATTAAATC
* *
1534305 ATTAAGTA
1 ATTAAATC
*
1534313 ATT--ATT
1 ATTAAATC
*
1534319 ATTAAAGC
1 ATTAAATC
1534327 ATT-AA--
1 ATTAAATC
*
1534332 GTTAAATC
1 ATTAAATC
*
1534340 ATTAAAGTA
1 ATTAAA-TC
*
1534349 ATT--ATT
1 ATTAAATC
1534355 ATTAAATC
1 ATTAAATC
*
1534363 ATTAAAGTA
1 ATTAAA-TC
*
1534372 ATT--ATT
1 ATTAAATC
1534378 ATTAAATC
1 ATTAAATC
1534386 ATTAAA--
1 ATTAAATC
*
1534392 GTT-AATC
1 ATTAAATC
1534399 ATT-AATC
1 ATTAAATC
1534406 ATTAAA--
1 ATTAAATC
1534412 ATTAAATC
1 ATTAAATC
* *
1534420 ATTAAGTA
1 ATTAAATC
*
1534428 ATT--ATT
1 ATTAAATC
1534434 ATTAAATC
1 ATTAAATC
1534442 ATTAAA--
1 ATTAAATC
1534448 ATTAAATC
1 ATTAAATC
*
1534456 ATTAAAATA
1 ATT-AAATC
*
1534465 ATT--ATT
1 ATTAAATC
1534471 ATT-AATC
1 ATTAAATC
1534478 ATTAAA--
1 ATTAAATC
*
1534484 GTTAAATC
1 ATTAAATC
*
1534492 ATTAAAGTA
1 ATTAAA-TC
*
1534501 ATT--ATT
1 ATTAAATC
1534507 ATTAAATC
1 ATTAAATC
1534515 ATT-AA--
1 ATTAAATC
* *
1534520 GTTAAATA
1 ATTAAATC
1534528 ATT--AT-
1 ATTAAATC
1534533 ATTAAATC
1 ATTAAATC
1534541 ATTAAA--
1 ATTAAATC
*
1534547 GTTAAATC
1 ATTAAATC
*
1534555 ATTAAAGTA
1 ATTAAA-TC
*
1534564 ATT--ATT
1 ATTAAATC
1534570 ATTAAATC
1 ATTAAATC
1534578 ATTAAATC
1 ATTAAATC
1534586 ATTAAATC
1 ATTAAATC
*
1534594 ATTAAAGTA
1 ATTAAA-TC
*
1534603 ATT--ATT
1 ATTAAATC
*
1534609 ATTAAAGC
1 ATTAAATC
1534617 ATTAAA--
1 ATTAAATC
*
1534623 GTTAAATC
1 ATTAAATC
*
1534631 ATTAAAGTA
1 ATTAAA-TC
*
1534640 ATT--ATT
1 ATTAAATC
1534646 ATTAAATC
1 ATTAAATC
1534654 ATTAAATC
1 ATTAAATC
*
1534662 ATTAAATT
1 ATTAAATC
*
1534670 ATTAAAGTA
1 ATTAAA-TC
*
1534679 ATT--ATT
1 ATTAAATC
1534685 ATTAAATC
1 ATTAAATC
1534693 ATTAAA--
1 ATTAAATC
*
1534699 GTTAAATC
1 ATTAAATC
1534707 ATTAAATC
1 ATTAAATC
1534715 ATTAAA--
1 ATTAAATC
1534721 ATTAAATC
1 ATTAAATC
*
1534729 ATTAAAGTA
1 ATTAAA-TC
*
1534738 ATT--ATT
1 ATTAAATC
1534744 ATTAAATC
1 ATTAAATC
1534752 ATTAAA--
1 ATTAAATC
1534758 ATTAAATC
1 ATTAAATC
*
1534766 ATTAAAGTA
1 ATTAAA-TC
*
1534775 ATT--ATT
1 ATTAAATC
1534781 ATTAAATC
1 ATTAAATC
1534789 ATTAAA--
1 ATTAAATC
*
1534795 GTT-AATC
1 ATTAAATC
*
1534802 ATTAAAGTA
1 ATTAAA-TC
*
1534811 ATT--ATT
1 ATTAAATC
1534817 ATTAAATC
1 ATTAAATC
1534825 ATTAAA--
1 ATTAAATC
* *
1534831 GTTAAATA
1 ATTAAATC
*
1534839 ATT--ATT
1 ATTAAATC
1534845 ATTAAATC
1 ATTAAATC
1534853 ATTAAA
1 ATTAAA
1534859 GTTAAATAAT
Statistics
Matches: 459, Mismatches: 69, Indels: 156
0.67 0.10 0.23
Matches are distributed among these distances:
5 11 0.02
6 127 0.28
7 40 0.09
8 230 0.50
9 51 0.11
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.41
Consensus pattern (8 bp):
ATTAAATC
Found at i:1534261 original size:28 final size:28
Alignment explanation
Indices: 1534190--1534263 Score: 112
Period size: 28 Copynumber: 2.6 Consensus size: 28
1534180 ATCAGTAAAT
* *
1534190 ATAAATCATTAAAGTCAAGTAATTATTA
1 ATAAATCATTAAAATTAAGTAATTATTA
1534218 ATAAATCATTAAAATTAAGTAATTATTA
1 ATAAATCATTAAAATTAAGTAATTATTA
* *
1534246 TTAAATTATTAAAATTAA
1 ATAAATCATTAAAATTAA
1534264 ATCATTAAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (28 bp):
ATAAATCATTAAAATTAAGTAATTATTA
Found at i:1534279 original size:37 final size:37
Alignment explanation
Indices: 1534234--1534842 Score: 500
Period size: 37 Copynumber: 16.0 Consensus size: 37
1534224 CATTAAAATT
*
1534234 AAGTAATTATTATTAAATTATTAAAATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
1534271 AAGTAATTATTATTAAATCATT-AAATCATAAATCATT-
1 AAGTAATTATTATTAAATCATTAAAAT--TAAATCATTA
* *
1534308 AAGTAATTATTATTAAAGCATT-AAGTTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
1534344 AAGTAATTATTATTAAATCATTAAAGTAATTATTATTAAATCATTA
1 AAGTAATTATTATTAAATCA-T----TAA--A--ATTAAATCATTA
* *
1534390 AAGT--TAATCATT-AATCATTAAAATTAAATCATT-
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
1534423 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
* *
1534460 AAATAATTATTATT-AATCATTAAAGTTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
* *
1534496 AAGTAATTATTATTAAATCATT-AAGTTAAATAATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
* * * * *
1534532 TATTAAATCATTAAAGTTAAATCATT-AAAGTAATTATTATTA
1 AAGT-AATTATT--A-TTAAATCATTAAAATTAA--ATCATTA
* * * *
1534574 AA-TCATTAAATCATTAAATCATT-AAAGTAATTATTATTA
1 AAGTAATT--ATTATTAAATCATTAAAATTAA--ATCATTA
* * * *
1534613 AAG-CATTA-AAGTTAAATCATT-AAAGTAATTATTATTA
1 AAGTAATTATTA-TTAAATCATTAAAATTAA--ATCATTA
* * *
1534650 AA-TCATTAAATCATTAAATTATTAAAGTAATTATTATTAAATCATTA
1 AAGTAATT--ATTATTAAATCA-T----TAA--A--ATTAAATCATTA
*
1534697 AAGTTAA--ATCATTAAATCATTAAAATTAAATCATTA
1 AAG-TAATTATTATTAAATCATTAAAATTAAATCATTA
1534733 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
*
1534770 AAGTAATTATTATTAAATCATTAAAGTT-AATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
* *
1534806 AAGTAATTATTATTAAATCATTAAAGTTAAATAATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
1534843 TTATTAAATC
Statistics
Matches: 492, Mismatches: 33, Indels: 94
0.79 0.05 0.15
Matches are distributed among these distances:
33 4 0.01
34 11 0.02
35 18 0.04
36 146 0.30
37 167 0.34
38 13 0.03
39 41 0.08
40 23 0.05
41 2 0.00
42 11 0.02
43 5 0.01
44 9 0.02
45 12 0.02
46 15 0.03
47 9 0.02
49 6 0.01
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (37 bp):
AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
Found at i:1534285 original size:23 final size:23
Alignment explanation
Indices: 1534259--1534893 Score: 250
Period size: 23 Copynumber: 26.3 Consensus size: 23
1534249 AATTATTAAA
1534259 ATTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAAGTAATTATT
* *
1534282 ATTAAATCATTAAATCATAAATCATT
1 ATTAAATCATTAAA--GT-AATTATT
* * *
1534308 AAGTAATTATTATTAAAG-CATTA--
1 -ATTAA--ATCATTAAAGTAATTATT
1534331 AGTTAAATCATTAAAGTAATTATT
1 A-TTAAATCATTAAAGTAATTATT
1534355 ATTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAAGTAATTATT
* *
1534378 ATTAAATCATTAAAGT--TAATC
1 ATTAAATCATTAAAGTAATTATT
* *
1534399 ATT-AATCATTAAAATTAAATCATT
1 ATTAAATCATT-AAAGT-AATTATT
* * * **
1534423 AAGTAATTATTATTAAA-TCATTAAA
1 -ATTAA--ATCATTAAAGTAATTATT
*
1534448 ATTAAATCATTAAAATAATTATT
1 ATTAAATCATTAAAGTAATTATT
*
1534471 ATT-AATCATTAAAGTTAA--ATC
1 ATTAAATCATTAAAG-TAATTATT
* * * *
1534492 ATTAAAGTAATTATTATTAAATCATT
1 ATTAAA-TCATTA-AAGT-AATTATT
* * * *
1534518 AAGTTAAATAATTATATTAAATCATT
1 -A-TTAAATCATTAAAGT-AATTATT
1534544 AAAGTTAAATCATTAAAGTAATTATT
1 --A-TTAAATCATTAAAGTAATTATT
* *
1534570 ATTAAATCATTAAA-TCATTAAATC
1 ATTAAATCATTAAAGTAATT--ATT
* * * **
1534594 ATTAAAGTAATTATTATTAAAGCATT
1 ATTAAA-TCATTA-AAGT-AATTATT
1534620 AAAGTTAAATCATTAAAGTAATTATT
1 --A-TTAAATCATTAAAGTAATTATT
*
1534646 ATTAAATCATTAAA-TCATTAAATT
1 ATTAAATCATTAAAGTAATT--ATT
* * * *
1534670 ATTAAAGTAATTATTATTAAATCATT
1 ATTAAA-TCATTA-AAGT-AATTATT
* **
1534696 AAAGTTAAATCATTAAA-TCATTAAA
1 --A-TTAAATCATTAAAGTAATTATT
1534721 ATTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAAGTAATTATT
* *
1534744 ATTAAATCATTAAAATTAAATCATT
1 ATTAAATCATT-AAAGT-AATTATT
* * * *
1534769 AAAGTAATTATTATTAAA-TCATTA-A
1 --ATTAA--ATCATTAAAGTAATTATT
1534794 AGTT-AATCATTAAAGTAATTATT
1 A-TTAAATCATTAAAGTAATTATT
1534817 ATTAAATCATTAAAGTTAAATAATTATT
1 ATTAAATCATTAAAG-----TAATTATT
*
1534845 ATTAAATCATTAAAGTTAA--ATA
1 ATTAAATCATTAAAG-TAATTATT
1534867 ATTAAAT--TTAAA-TAATTATT
1 ATTAAATCATTAAAGTAATTATT
1534887 ATTAAAT
1 ATTAAAT
1534894 ATGTACTCGA
Statistics
Matches: 470, Mismatches: 77, Indels: 133
0.69 0.11 0.20
Matches are distributed among these distances:
18 3 0.01
20 21 0.04
21 32 0.07
22 62 0.13
23 129 0.27
24 38 0.08
25 28 0.06
26 44 0.09
27 39 0.08
28 51 0.11
29 23 0.05
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (23 bp):
ATTAAATCATTAAAGTAATTATT
Found at i:1534355 original size:36 final size:37
Alignment explanation
Indices: 1534234--1534773 Score: 609
Period size: 37 Copynumber: 14.7 Consensus size: 37
1534224 CATTAAAATT
* *
1534234 AAGTAATTATTATTAAATTATTAAAATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
1534271 AAGTAATTATTATTAAATCATTAAA-TCATAAATCATT-
1 AAGTAATTATTATTAAATCATTAAAGT--TAAATCATTA
*
1534308 AAGTAATTATTATTAAAGCATT-AAGTTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
*
1534344 AAGTAATTATTATTAAATCATTAAAG-TAATTATTATTA
1 AAGTAATTATTATTAAATCATTAAAGTTAA--ATCATTA
* * *
1534382 AA-TCATTAAAGTTAATCATTAATCATTAAAATTAAATCATT-
1 AAGTAATT--A-TT-AT--TAAATCATTAAAGTTAAATCATTA
*
1534423 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
*
1534460 AAATAATTATTATT-AATCATTAAAGTTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
1534496 AAGTAATTATTATTAAATCATT-AAG--------TTA
1 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
1534524 AA-TAATTA-TATTAAATCATTAAAGTTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
*
1534559 AAGTAATTATTATTAAATCATTAAATCATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAA--GTTAAATCATTA
*
1534598 AAGTAATTATTATTAAAGCATTAAAGTTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
* *
1534635 AAGTAATTATTATTAAATCATTAAATCATTAAATTATTA
1 AAGTAATTATTATTAAATCATTAAA--GTTAAATCATTA
1534674 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
* ** *
1534711 AA-TCATTAAAATTAAATCATTAAAG-TAATTATTATTA
1 AAGTAATTATTATTAAATCATTAAAGTTAA--ATCATTA
* **
1534748 AA-TCATTAAAATTAAATCATTAAAGT
1 AAGTAATTATTATTAAATCATTAAAGT
1534774 AATTATTATT
Statistics
Matches: 443, Mismatches: 25, Indels: 69
0.82 0.05 0.13
Matches are distributed among these distances:
26 12 0.03
27 9 0.02
28 5 0.01
35 17 0.04
36 112 0.25
37 166 0.37
38 19 0.04
39 73 0.16
40 3 0.01
41 4 0.01
42 9 0.02
43 11 0.02
44 3 0.01
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (37 bp):
AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
Found at i:1534541 original size:63 final size:66
Alignment explanation
Indices: 1534356--1534842 Score: 386
Period size: 76 Copynumber: 7.2 Consensus size: 66
1534346 GTAATTATTA
* *
1534356 TTAAATCATTAAAGTAATTATTATTAAATCATTAA-AGTTAATCATTAATCATTAAAATTAAATC
1 TTAAATCATTAAAGTAATTATTATTAAATCATTAACA-TTAA--AATAATTATT---ATTAAATC
1534420 ATT-AAG
60 ATTAAAG
* * *
1534426 -T-AATTATT--ATTAA--ATCATTAAA--ATTAAATCATTAAAATAATTATTATT-AATCATTA
1 TTAAATCATTAAAGTAATTATTATTAAATCATT-AA-CATTAAAATAATTATTATTAAATCATTA
1534482 AAG
64 AAG
*
1534485 TTAAATCATTAAAGTAATTATTATTAAATCATTAA-GTT-AAATAATTA-TATTAAATCATTAAA
1 TTAAATCATTAAAGTAATTATTATTAAATCATTAACATTAAAATAATTATTATTAAATCATTAAA
1534547 G
66 G
1534548 TTAAATCATTAAAGTAATTATTATTAAATCATTAAATCATTAAATCATTAAAGTAATTATTATTA
1 TTAAATCATTAAAGTAATTATTATTAAATCATT-AA-CA-T---T-A--AAA-TAATTATTATTA
*
1534613 AAGCATTAAAG
56 AATCATTAAAG
1534624 TTAAATCATTAAAGTAATTATTATTAAATCATTAAATCATTAAATTATTAAAGTAATTATTATTA
1 TTAAATCATTAAAGTAATTATTATTAAATCATT-AA-C-----ATTA--AAA-TAATTATTATTA
1534689 AATCATTAAAG
56 AATCATTAAAG
* ** *
1534700 TTAAATCATTAAA-TCATTAAAATT-AA--A-T--CATTAAAGTAATTATTATTAAATCATTAAA
1 TTAAATCATTAAAGTAATTATTATTAAATCATTAACATTAAAATAATTATTATTAAATCATTAAA
*
1534758 A
66 G
*
1534759 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAGTTAATCATTAAAGTAATTATTATTAAAT
1 TTAAATCATTAAAGTAATTATTATTAAATC-----A-TTAA-CATTAAAATAATTATTATTAAAT
1534824 CATTAAAG
59 CATTAAAG
*
1534832 TTAAATAATTA
1 TTAAATCATTA
1534843 TTATTAAATC
Statistics
Matches: 350, Mismatches: 22, Indels: 87
0.76 0.05 0.19
Matches are distributed among these distances:
58 7 0.02
59 41 0.12
60 11 0.03
61 8 0.02
62 19 0.05
63 59 0.17
64 16 0.05
65 9 0.03
66 6 0.02
67 5 0.01
68 7 0.02
69 1 0.00
70 2 0.01
71 1 0.00
72 1 0.00
73 40 0.11
74 5 0.01
75 14 0.04
76 95 0.27
77 1 0.00
80 1 0.00
81 1 0.00
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (66 bp):
TTAAATCATTAAAGTAATTATTATTAAATCATTAACATTAAAATAATTATTATTAAATCATTAAA
G
Found at i:1534804 original size:36 final size:37
Alignment explanation
Indices: 1534356--1534842 Score: 274
Period size: 36 Copynumber: 13.3 Consensus size: 37
1534346 GTAATTATTA
1534356 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
* **
1534393 TT-AATCATT-AA-TCATTAAAATTAAATCATT-AAG
1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
* * **
1534426 -TAATTATTATTAAA-TCATTAAAATTAAATCATTAAA-
1 TTAA--ATCATTAAAGTAATTATTATTAAATCATTAAAG
* * * *
1534462 AT-AATTATTATTAA-TCATTA-AAGTTAAATCATTAAAG
1 TTAAATCATTA--AAGTAATTATTA-TTAAATCATTAAAG
* * * *
1534499 -TAATTATTATTAAA-TCATTA--AGTTAAATAATTATA-
1 TTAA--ATCATTAAAGTAATTATTA-TTAAATCATTAAAG
* * *
1534534 TTAAATCATTAAAGTTAA--ATCATTAAAGTAATTATTA-
1 TTAAATCATTAAAG-TAATTATTATTAAA-TCATTA-AAG
* * * *
1534571 TTAAATCATTAAA-TCATTAAATCATTAAAGTAATTATTA-
1 TTAAATCATTAAAGTAATT--ATTATTAAA-TCATTA-AAG
* * * *
1534610 TTAAAGCATTAAAGTTAA--ATCATTAAAGTAATTATTA-
1 TTAAATCATTAAAG-TAATTATTATTAAA-TCATTA-AAG
* * *
1534647 TTAAATCATTAAA-TCATTAAATTATTAAAGTAATTATTA-
1 TTAAATCATTAAAGTAATT--ATTATTAAA-TCATTA-AAG
* *
1534686 TTAAATCATTAAAGTTAA--ATCATTAAATCATTAAAA
1 TTAAATCATTAAAG-TAATTATTATTAAATCATTAAAG
*
1534722 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAA
1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
1534759 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
1534796 TT-AATCATTAAAGTAATTATTATTAAATCATTAAAG
1 TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
*
1534832 TTAAATAATTA
1 TTAAATCATTA
1534843 TTATTAAATC
Statistics
Matches: 393, Mismatches: 21, Indels: 72
0.81 0.04 0.15
Matches are distributed among these distances:
32 1 0.00
33 4 0.01
34 32 0.08
35 22 0.06
36 131 0.33
37 130 0.33
39 69 0.18
41 4 0.01
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (37 bp):
TTAAATCATTAAAGTAATTATTATTAAATCATTAAAG
Found at i:1534836 original size:73 final size:73
Alignment explanation
Indices: 1534245--1534893 Score: 409
Period size: 73 Copynumber: 8.9 Consensus size: 73
1534235 AGTAATTATT
* * * ** * * *
1534245 ATTAAATTATTAAAATTAAATCATTAAAGTAATTATTATTAAATCATTAAA-TCATAAATCATTA
1 ATTAAATCATTAAAGTTAAATCATTAAA-TCATTAAAATTAAATCATTAAAGTAAT-TATTATTA
* * **
1534309 AGTAATTATT
64 AATCATTAAA
* * **
1534319 ATTAAAGCATT-AAGTTAAATCATTAAAGTAATTATTATTAAATCATTAAAGTAATTATTATTAA
1 ATTAAATCATTAAAGTTAAATCATTAAA-TCATTAAAATTAAATCATTAAAGTAATTATTATTAA
1534383 ATCATTAAA
65 ATCATTAAA
* * * **
1534392 GTT-AATCATTAATCA-TTAAA--ATTAAATCATTAAGTAATT--ATTATTAAA-TCATTAAAAT
1 ATTAAATCATTAA--AGTTAAATCATTAAATCATTAA--AATTAAATCATTAAAGTAATTATTAT
1534450 TAAATCATTAAA
62 TAAATCATTAAA
* * * * *
1534462 A-TAATTATTATTAATCA-TTAAA--GTTAAATCATT-AAAGTAATTATTATTAAA-TCATTA--
1 ATTAA--ATCATTAA--AGTTAAATCATTAAATCATTAAAATTAA--ATCATTAAAGTAATTATT
* *
1534519 AGTTAAATAATT-AT
60 A-TTAAATCATTAAA
* ** * *
1534533 ATTAAATCATTAAAGTTAAATCATTAAAGTAATTATTATTAAATCATTAAA-TCATTAAATCATT
1 ATTAAATCATTAAAGTTAAATCATTAAA-TCATTAAAATTAAATCATTAAAGTAATT--ATTATT
* **
1534597 AAAGTAATTATT
63 AAA-TCATTAAA
* * ** *
1534609 ATTAAAGCATTAAAGTTAAATCATTAAAGTAATTATTATTAAATCATTAAA-TCATTAAATTATT
1 ATTAAATCATTAAAGTTAAATCATTAAA-TCATTAAAATTAAATCATTAAAGTAATT--ATTATT
* **
1534673 AAAGTAATTATT
63 AAA-TCATTAAA
1534685 ATTAAATCATTAAAGTTAAATCATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAAA
1 ATTAAATCATTAAAGTTAAATCATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAAA
1534750 TCATTAAA
66 TCATTAAA
* *
1534758 ATTAAATCATTAAAG-TAATTATTATTAAATCATTAAAGTT-AATCATTAAAGTAATTATTATTA
1 ATTAAATCATTAAAGTTAA--ATCATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTA
1534821 AATCATTAAA
64 AATCATTAAA
* * * *
1534831 GTTAAATAATTATTA-TTAAATCATTAAAGT--TAAATAATTAAAT--TTAAA-TAATTATTATT
1 ATTAAATCATTA-AAGTTAAATCATTAAA-TCATTAA-AATTAAATCATTAAAGTAATTATTATT
1534890 AAAT
63 AAAT
1534894 ATGTACTCGA
Statistics
Matches: 490, Mismatches: 51, Indels: 72
0.80 0.08 0.12
Matches are distributed among these distances:
68 1 0.00
69 9 0.02
70 42 0.09
71 43 0.09
72 67 0.14
73 143 0.29
74 53 0.11
75 26 0.05
76 106 0.22
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (73 bp):
ATTAAATCATTAAAGTTAAATCATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAAA
TCATTAAA
Found at i:1538358 original size:42 final size:42
Alignment explanation
Indices: 1538299--1538402 Score: 129
Period size: 42 Copynumber: 2.4 Consensus size: 42
1538289 AACAAATTTC
** *
1538299 ACGCTTCAGGCGAATCTCACGCTTCGACC-CTAAAGCATACAG
1 ACGCTTCAGATGAATCTCACGCTTCGACCAC-AAAGAATACAG
*
1538341 ACGCTTCAGATGAATCTCACGCTTCGGCCACAAAGAATACAG
1 ACGCTTCAGATGAATCTCACGCTTCGACCACAAAGAATACAG
*
1538383 ACGCATGCAGAATGAATCTC
1 ACGC-TTCAG-ATGAATCTC
1538403 GGAGGAAGAA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
42 40 0.74
43 5 0.09
44 9 0.17
ACGTcount: A:0.32, C:0.30, G:0.19, T:0.19
Consensus pattern (42 bp):
ACGCTTCAGATGAATCTCACGCTTCGACCACAAAGAATACAG
Found at i:1539449 original size:23 final size:23
Alignment explanation
Indices: 1539402--1539449 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
1539392 AGCAGGGCTA
* *
1539402 CACGTCTGCATGTGGGGGTCCTG
1 CACGTCTGCATGTGGGGGGCATG
1539425 CACGTCTGCATGTGGGGGGCATG
1 CACGTCTGCATGTGGGGGGCATG
1539448 CA
1 CA
1539450 ATTGTTGGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.12, C:0.25, G:0.40, T:0.23
Consensus pattern (23 bp):
CACGTCTGCATGTGGGGGGCATG
Found at i:1539680 original size:35 final size:38
Alignment explanation
Indices: 1539600--1539680 Score: 87
Period size: 41 Copynumber: 2.1 Consensus size: 38
1539590 ACTACTCGGG
* * *
1539600 CTGAGGCAATTCATAATTACAGAAGCAATGAGAGTTTGGGG
1 CTGAGGCAATTCACAATTACAGAAGCAATGAGA---TGAGC
1539641 CTGAGGCAATTCACAATTACAGAAGC-A-GAGA-GAGC
1 CTGAGGCAATTCACAATTACAGAAGCAATGAGATGAGC
1539676 CTGAG
1 CTGAG
1539681 AGGGAGATCA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
35 7 0.19
39 4 0.11
40 1 0.03
41 25 0.68
ACGTcount: A:0.36, C:0.16, G:0.28, T:0.20
Consensus pattern (38 bp):
CTGAGGCAATTCACAATTACAGAAGCAATGAGATGAGC
Found at i:1542011 original size:6 final size:6
Alignment explanation
Indices: 1542000--1542042 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
1541990 CAAGAAGGAC
*
1542000 TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG TAGGAG T
1 TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG T
1542043 TCTTCTCACC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.19, C:0.00, G:0.63, T:0.19
Consensus pattern (6 bp):
TGGGAG
Found at i:1542550 original size:14 final size:14
Alignment explanation
Indices: 1542541--1543241 Score: 330
Period size: 14 Copynumber: 49.7 Consensus size: 14
1542531 TAATTATTAA
1542541 TAAATCATTAAAAT
1 TAAATCATTAAAAT
1542555 TAAATCATTAAAAT
1 TAAATCATTAAAAT
* * **
1542569 TAAGTAATTATTAT
1 TAAATCATTAAAAT
*
1542583 TAAATTATTAAAAT
1 TAAATCATTAAAAT
*
1542597 T-AATCATT-AAAG
1 TAAATCATTAAAAT
1542609 TAATAT-ATTAAATCAT
1 TAA-ATCATTAAA--AT
*
1542625 TAAATCATTAATCAT
1 TAAATCATTAA-AAT
* **
1542640 TAAAGTAATTATTAT
1 TAAA-TCATTAAAAT
* *
1542655 TAAAGCATTAAAGT
1 TAAATCATTAAAAT
*
1542669 TAAATCATT-AAAG
1 TAAATCATTAAAAT
*
1542682 TAATTATTATTAAATCAT
1 TAA--ATCATTAAA--AT
* **
1542700 TAAAGTAATTATTAT
1 TAAA-TCATTAAAAT
*
1542715 TAAATCATTAAAGT
1 TAAATCATTAAAAT
1542729 TAAATCATTAAATCAT
1 TAAATCATTAAA--AT
1542745 TAAA--ATTAAATCAT
1 TAAATCATTAAA--AT
* **
1542759 TAAAGTAATTATTAT
1 TAAA-TCATTAAAAT
1542774 TAAATCATTAAAAT
1 TAAATCATTAAAAT
1542788 TAAATCATT-AAA-
1 TAAATCATTAAAAT
*
1542800 -AAATTATT---AT
1 TAAATCATTAAAAT
*
1542810 TAAATCATTAAAGT
1 TAAATCATTAAAAT
*
1542824 TAAATCATT-AAAG
1 TAAATCATTAAAAT
*
1542837 T-AATTATT---AT
1 TAAATCATTAAAAT
*
1542847 TAAATCATTAAAGT
1 TAAATCATTAAAAT
* **
1542861 TAAATAATTATTAT
1 TAAATCATTAAAAT
*
1542875 TAAATCATTAAAGT
1 TAAATCATTAAAAT
*
1542889 TAAATCATT-AAAG
1 TAAATCATTAAAAT
*
1542902 TAATTATTATTAAATCAT
1 TAA--ATCATTAAA--AT
1542920 TAAATCATTAAATCAT
1 TAAATCATTAAA--AT
* **
1542936 TAAAGTAATTATTAT
1 TAAA-TCATTAAAAT
* *
1542951 TAAAGCATTAAAGT
1 TAAATCATTAAAAT
*
1542965 TAAATCATT-AAAG
1 TAAATCATTAAAAT
*
1542978 TAATTATTATTAAATCAT
1 TAA--ATCATTAAA--AT
1542996 TAAATCATTAAATCAT
1 TAAATCATTAAA--AT
1543012 TAAATCATTAAATTAT
1 TAAATCATTAAA--AT
* **
1543028 TAAAGTAATTATTAT
1 TAAA-TCATTAAAAT
*
1543043 TAAATCATTAAAGT
1 TAAATCATTAAAAT
1543057 TAAATCATTAAATCAT
1 TAAATCATTAAA--AT
1543073 TAAA--ATTAAATCAT
1 TAAATCATTAAA--AT
* **
1543087 TAAAGTAATTATTAT
1 TAAA-TCATTAAAAT
1543102 TAAATCATTAAAAT
1 TAAATCATTAAAAT
*
1543116 TAAATCATT-AAAG
1 TAAATCATTAAAAT
*
1543129 T-AATTATT---AT
1 TAAATCATTAAAAT
*
1543139 TAAATCATTAAAGT
1 TAAATCATTAAAAT
*
1543153 TAAATCATT-AAAG
1 TAAATCATTAAAAT
*
1543166 T-AATTATT---AT
1 TAAATCATTAAAAT
*
1543176 TAAATCATTAAAGT
1 TAAATCATTAAAAT
* **
1543190 TAAATAATTATTAT
1 TAAATCATTAAAAT
*
1543204 TAAATCATTAAAGT
1 TAAATCATTAAAAT
* *
1543218 TAAATAATTAAATT
1 TAAATCATTAAAAT
*
1543232 TAAATAATTA
1 TAAATCATTA
1543242 TTATTAAATA
Statistics
Matches: 525, Mismatches: 109, Indels: 106
0.71 0.15 0.14
Matches are distributed among these distances:
9 1 0.00
10 6 0.01
11 32 0.06
12 22 0.04
13 38 0.07
14 254 0.48
15 59 0.11
16 78 0.15
17 23 0.04
18 12 0.02
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (14 bp):
TAAATCATTAAAAT
Found at i:1542564 original size:8 final size:8
Alignment explanation
Indices: 1542541--1543215 Score: 311
Period size: 8 Copynumber: 91.5 Consensus size: 8
1542531 TAATTATTAA
1542541 TAAATCAT
1 TAAATCAT
1542549 TAAA--AT
1 TAAATCAT
1542555 TAAATCAT
1 TAAATCAT
1542563 TAAA--AT
1 TAAATCAT
* *
1542569 TAAGTAAT
1 TAAATCAT
*
1542577 T--ATTAT
1 TAAATCAT
*
1542583 TAAATTAT
1 TAAATCAT
1542591 TAAA--AT
1 TAAATCAT
1542597 T-AATCAT
1 TAAATCAT
1542604 TAAAGT-A-
1 TAAA-TCAT
*
1542611 -ATAT-AT
1 TAAATCAT
1542617 TAAATCAT
1 TAAATCAT
1542625 TAAATCAT
1 TAAATCAT
1542633 T-AATCAT
1 TAAATCAT
*
1542640 TAAAGTAAT
1 TAAA-TCAT
*
1542649 T--ATTAT
1 TAAATCAT
*
1542655 TAAAGCAT
1 TAAATCAT
*
1542663 TAAA--GT
1 TAAATCAT
1542669 TAAATCAT
1 TAAATCAT
*
1542677 TAAAGTAAT
1 TAAA-TCAT
*
1542686 T--ATTAT
1 TAAATCAT
1542692 TAAATCAT
1 TAAATCAT
*
1542700 TAAAGTAAT
1 TAAA-TCAT
*
1542709 T--ATTAT
1 TAAATCAT
1542715 TAAATCAT
1 TAAATCAT
*
1542723 TAAA--GT
1 TAAATCAT
1542729 TAAATCAT
1 TAAATCAT
1542737 TAAATCAT
1 TAAATCAT
1542745 TAAA--AT
1 TAAATCAT
1542751 TAAATCAT
1 TAAATCAT
*
1542759 TAAAGTAAT
1 TAAA-TCAT
*
1542768 T--ATTAT
1 TAAATCAT
1542774 TAAATCAT
1 TAAATCAT
1542782 TAAA--AT
1 TAAATCAT
1542788 TAAATCAT
1 TAAATCAT
**
1542796 TAAAAAAT
1 TAAATCAT
*
1542804 T--ATTAT
1 TAAATCAT
1542810 TAAATCAT
1 TAAATCAT
*
1542818 TAAA--GT
1 TAAATCAT
1542824 TAAATCAT
1 TAAATCAT
*
1542832 TAAAGTAAT
1 TAAA-TCAT
*
1542841 T--ATTAT
1 TAAATCAT
1542847 TAAATCAT
1 TAAATCAT
*
1542855 TAAA--GT
1 TAAATCAT
*
1542861 TAAATAAT
1 TAAATCAT
*
1542869 T--ATTAT
1 TAAATCAT
1542875 TAAATCAT
1 TAAATCAT
*
1542883 TAAA--GT
1 TAAATCAT
1542889 TAAATCAT
1 TAAATCAT
*
1542897 TAAAGTAAT
1 TAAA-TCAT
*
1542906 T--ATTAT
1 TAAATCAT
1542912 TAAATCAT
1 TAAATCAT
1542920 TAAATCAT
1 TAAATCAT
1542928 TAAATCAT
1 TAAATCAT
*
1542936 TAAAGTAAT
1 TAAA-TCAT
*
1542945 T--ATTAT
1 TAAATCAT
*
1542951 TAAAGCAT
1 TAAATCAT
*
1542959 TAAA--GT
1 TAAATCAT
1542965 TAAATCAT
1 TAAATCAT
*
1542973 TAAAGTAAT
1 TAAA-TCAT
*
1542982 T--ATTAT
1 TAAATCAT
1542988 TAAATCAT
1 TAAATCAT
1542996 TAAATCAT
1 TAAATCAT
1543004 TAAATCAT
1 TAAATCAT
1543012 TAAATCAT
1 TAAATCAT
*
1543020 TAAATTAT
1 TAAATCAT
*
1543028 TAAAGTAAT
1 TAAA-TCAT
*
1543037 T--ATTAT
1 TAAATCAT
1543043 TAAATCAT
1 TAAATCAT
*
1543051 TAAA--GT
1 TAAATCAT
1543057 TAAATCAT
1 TAAATCAT
1543065 TAAATCAT
1 TAAATCAT
1543073 TAAA--AT
1 TAAATCAT
1543079 TAAATCAT
1 TAAATCAT
*
1543087 TAAAGTAAT
1 TAAA-TCAT
*
1543096 T--ATTAT
1 TAAATCAT
1543102 TAAATCAT
1 TAAATCAT
1543110 TAAA--AT
1 TAAATCAT
1543116 TAAATCAT
1 TAAATCAT
*
1543124 TAAAGTAAT
1 TAAA-TCAT
*
1543133 T--ATTAT
1 TAAATCAT
1543139 TAAATCAT
1 TAAATCAT
*
1543147 TAAA--GT
1 TAAATCAT
1543153 TAAATCAT
1 TAAATCAT
*
1543161 TAAAGTAAT
1 TAAA-TCAT
*
1543170 T--ATTAT
1 TAAATCAT
1543176 TAAATCAT
1 TAAATCAT
*
1543184 TAAA--GT
1 TAAATCAT
*
1543190 TAAATAAT
1 TAAATCAT
*
1543198 T--ATTAT
1 TAAATCAT
1543204 TAAATCAT
1 TAAATCAT
1543212 TAAA
1 TAAA
1543216 GTTAAATAAT
Statistics
Matches: 514, Mismatches: 71, Indels: 164
0.69 0.09 0.22
Matches are distributed among these distances:
5 4 0.01
6 151 0.29
7 25 0.05
8 285 0.55
9 49 0.10
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (8 bp):
TAAATCAT
Found at i:1542684 original size:37 final size:37
Alignment explanation
Indices: 1542570--1543199 Score: 769
Period size: 37 Copynumber: 17.0 Consensus size: 37
1542560 CATTAAAATT
* *
1542570 AAGTAATTATTATTAAATTATTAAAATT-AATCATTA
1 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
*
1542606 AAGTAA-TA-TATTAAATCATTAAA-TCATTAATCATTA
1 AAGTAATTATTATTAAATCATTAAAGT--TAAATCATTA
*
1542642 AAGTAATTATTATTAAAGCATTAAAGTTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
1542679 AAGTAATTATTATTAAATCATTAAAGTAATTATTATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAG---------TTAAATCATTA
* *
1542725 AAGTTAA--ATCATTAAATCATTAAAATTAAATCATTA
1 AAG-TAATTATTATTAAATCATTAAAGTTAAATCATTA
*
1542761 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
*
1542798 AA-AAATTATTATTAAATCATTAAAGTTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
1542834 AAGTAATTATTATTAAATCATTAAAG--------TTA
1 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
1542863 AA-TAATTATTATTAAATCATTAAAGTTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
*
1542899 AAGTAATTATTATTAAATCATTAAATCATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAA--GTTAAATCATTA
*
1542938 AAGTAATTATTATTAAAGCATTAAAGTTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
*
1542975 AAGTAATTATTATTAAATCATTAAATCATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAA--GTTAAATCATTA
* * *
1543014 AA-TCATTAAATTATTAAAGTAATTATTA-TTAAATCATTA
1 AAGTAATT--ATTATTAAA-TCATTA-AAGTTAAATCATTA
* *
1543053 AAGTTAA--ATCATTAAATCATTAAAATTAAATCATTA
1 AAG-TAATTATTATTAAATCATTAAAGTTAAATCATTA
*
1543089 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
1543126 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
*
1543163 AAGTAATTATTATTAAATCATTAAAGTTAAATAATTA
1 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
1543200 TTATTAAATC
Statistics
Matches: 528, Mismatches: 25, Indels: 81
0.83 0.04 0.13
Matches are distributed among these distances:
28 23 0.04
29 5 0.01
33 1 0.00
34 14 0.03
35 10 0.02
36 92 0.17
37 253 0.48
38 18 0.03
39 62 0.12
40 9 0.02
41 7 0.01
42 1 0.00
45 16 0.03
46 14 0.03
47 3 0.01
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (37 bp):
AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
Found at i:1542694 original size:23 final size:23
Alignment explanation
Indices: 1542668--1543250 Score: 195
Period size: 23 Copynumber: 25.3 Consensus size: 23
1542658 AGCATTAAAG
1542668 TTAAATCATTAAAGTAATTATTA
1 TTAAATCATTAAAGTAATTATTA
1542691 TTAAATCATTAAAGTAATTATTA
1 TTAAATCATTAAAGTAATTATTA
*
1542714 TTAAATCATTAAAGTTAA--ATCA
1 TTAAATCATTAAAG-TAATTATTA
* *
1542736 TTAAATCATTAAAATTAAATCATTAAA
1 TTAAATCATT-AAAGT-AATTATT--A
* * * **
1542763 GTAATTATTATTAAA-TCATTAAAA
1 TTAA--ATCATTAAAGTAATTATTA
*** * **
1542787 TTAAA-TCATTAAAAAATTATTA
1 TTAAATCATTAAAGTAATTATTA
*
1542809 TTAAATCATTAAAGTTAA--ATCA
1 TTAAATCATTAAAG-TAATTATTA
* * * *
1542831 TTAAAGTAATTATTATTAA--ATCA
1 TTAAA-TCATTA-AAGTAATTATTA
*
1542854 TTAAA--GTTAAA-TAATTATTA
1 TTAAATCATTAAAGTAATTATTA
*
1542874 TTAAATCATTAAAGTTAA--ATCA
1 TTAAATCATTAAAG-TAATTATTA
* * * *
1542896 TTAAAGTAATTATTATTAA--ATCA
1 TTAAA-TCATTA-AAGTAATTATTA
* *
1542919 TTAAATCATTAAA-TCATTA-AA
1 TTAAATCATTAAAGTAATTATTA
* * * *
1542940 GTAATTATTATTAAAG-CATTA-AA
1 TTAA--ATCATTAAAGTAATTATTA
1542963 GTTAAATCATTAAAGTAATTATTA
1 -TTAAATCATTAAAGTAATTATTA
* *
1542987 TTAAATCATTAAA-TCATTAAATCA
1 TTAAATCATTAAAGTAATT--ATTA
* *
1543011 TTAAATCATTAAA-TTATTA-AA
1 TTAAATCATTAAAGTAATTATTA
* * * *
1543032 GTAATTATTATTAAA-TCATTA-AA
1 TTAA--ATCATTAAAGTAATTATTA
* **
1543055 GTTAAATCATTAAA-TCATTAAAA
1 -TTAAATCATTAAAGTAATTATTA
1543078 TTAAATCATTAAAGTAATTATTA
1 TTAAATCATTAAAGTAATTATTA
* *
1543101 TTAAATCATTAAAATTAAATCATTAAA
1 TTAAATCATT-AAAGT-AATTATT--A
* * * *
1543128 GTAATTATTATTAAA-TCATTA-AA
1 TTAA--ATCATTAAAGTAATTATTA
1543151 GTTAAATCATTAAAGTAATTATTA
1 -TTAAATCATTAAAGTAATTATTA
1543175 TTAAATCATTAAAGTTAAATAATTATTA
1 TTAAATCATTAAAG-----TAATTATTA
*
1543203 TTAAATCATTAAAGTTAA--ATAA
1 TTAAATCATTAAAG-TAATTATTA
1543225 TTAAAT--TTAAA-TAATTATTA
1 TTAAATCATTAAAGTAATTATTA
1543245 TTAAAT
1 TTAAAT
1543251 ATGTACTCGA
Statistics
Matches: 436, Mismatches: 71, Indels: 109
0.71 0.12 0.18
Matches are distributed among these distances:
18 6 0.01
19 1 0.00
20 27 0.06
21 13 0.03
22 110 0.25
23 164 0.38
24 52 0.12
25 8 0.02
26 6 0.01
27 10 0.02
28 29 0.07
29 10 0.02
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (23 bp):
TTAAATCATTAAAGTAATTATTA
Found at i:1547761 original size:19 final size:21
Alignment explanation
Indices: 1547724--1547762 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
1547714 CTGAAAATTA
1547724 AATAACAAAATTAACATTTTT
1 AATAACAAAATTAACATTTTT
*
1547745 AATAA-AAAA-TAATATTTT
1 AATAACAAAATTAACATTTT
1547763 ATATAACGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 4 0.24
21 5 0.29
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (21 bp):
AATAACAAAATTAACATTTTT
Found at i:1553423 original size:2 final size:2
Alignment explanation
Indices: 1553418--1553464 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1553408 AATGATTACT
1553418 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1553460 TA TA T
1 TA TA T
1553465 TTGAAATATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1554016 original size:13 final size:13
Alignment explanation
Indices: 1553998--1554025 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1553988 TAAGTATCGT
1553998 TTAATGAGTGTAG
1 TTAATGAGTGTAG
1554011 TTAATGAGTGTAG
1 TTAATGAGTGTAG
1554024 TT
1 TT
1554026 TACCCTTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.43
Consensus pattern (13 bp):
TTAATGAGTGTAG
Found at i:1554287 original size:20 final size:20
Alignment explanation
Indices: 1554188--1554541 Score: 188
Period size: 20 Copynumber: 17.6 Consensus size: 20
1554178 AAATAACCAA
* *
1554188 CAAATTCGCAACGC-AATCT
1 CAAATTCGCAACACGAATTT
* *
1554207 CAAATTCGCAACACGAACTC
1 CAAATTCGCAACACGAATTT
* *
1554227 CAATTTCGCAACGCGAATTT
1 CAAATTCGCAACACGAATTT
** * *
1554247 GGAATTCACAATACGGAATTT
1 CAAATTCGCAACAC-GAATTT
* *
1554268 CGAATTCGCAACTCGAATTT
1 CAAATTCGCAACACGAATTT
** *
1554288 C-TTTTACGCAATAC-AATTTT
1 CAAATT-CGCAACACGAA-TTT
** *
1554308 C-TGTTACGCAACGC-AATTTT
1 CAAATT-CGCAACACGAA-TTT
*
1554328 CAAATTCGCAACACGAA-CT
1 CAAATTCGCAACACGAATTT
*
1554347 CTAATTTCGC-A-ACGTAATTT
1 C-AAATTCGCAACACG-AATTT
1554367 CTAAATTCGCAACACGAAATTT
1 C-AAATTCGCAACACG-AATTT
*
1554389 CAAATTCGCAACTCG-ATTT
1 CAAATTCGCAACACGAATTT
* * *
1554408 CTGAATTCGCAACGCGATTTT
1 C-AAATTCGCAACACGAATTT
*
1554429 TAAATTCGCAACAC-AAGTTT
1 CAAATTCGCAACACGAA-TTT
** * *
1554449 CATTTTCGCAACAAGATTTT
1 CAAATTCGCAACACGAATTT
* *
1554469 CTAATTCGCAACGCGAATTT
1 CAAATTCGCAACACGAATTT
* ** * *
1554489 TATTTTCGCAACTCGATTTT
1 CAAATTCGCAACACGAATTT
*
1554509 CGAATTCGCAACACGAATTT
1 CAAATTCGCAACACGAATTT
* *
1554529 TAATTTCGCAACA
1 CAAATTCGCAACA
1554542 GCTTTTATTT
Statistics
Matches: 253, Mismatches: 67, Indels: 29
0.72 0.19 0.08
Matches are distributed among these distances:
18 3 0.01
19 28 0.11
20 175 0.69
21 38 0.15
22 9 0.04
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.31
Consensus pattern (20 bp):
CAAATTCGCAACACGAATTT
Found at i:1554419 original size:121 final size:120
Alignment explanation
Indices: 1554194--1554409 Score: 310
Period size: 121 Copynumber: 1.8 Consensus size: 120
1554184 CCAACAAATT
* *
1554194 CGCAACGCAATCTCAAATTCGCAACACGAACTCCAATTTCGCAACGCGAATTTGGAATTCACAAT
1 CGCAACGCAATCTCAAATTCGCAACACGAACTCCAATTTCGCAACGCGAATTTGAAATTCACAAC
* * *
1554259 ACGGAATTTCGAATTCGCAACTCGAATTTCTTTTACGCAATACAATTTTCTGTTA
66 ACGAAATTTCAAATTCGCAACTCGAATTTCTATTACGCAATACAATTTTCTGTTA
* * * * *
1554314 CGCAACGCAATTTTCAAATTCGCAACACGAACTCTAATTTCGCAACG-TAATTTCTAAATTCGCA
1 CGCAACGCAA-TCTCAAATTCGCAACACGAACTCCAATTTCGCAACGCGAATTT-GAAATTCACA
1554378 ACACGAAATTTCAAATTCGCAACTCG-ATTTCT
64 ACACGAAATTTCAAATTCGCAACTCGAATTTCT
1554410 GAATTCGCAA
Statistics
Matches: 85, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
120 21 0.25
121 64 0.75
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.29
Consensus pattern (120 bp):
CGCAACGCAATCTCAAATTCGCAACACGAACTCCAATTTCGCAACGCGAATTTGAAATTCACAAC
ACGAAATTTCAAATTCGCAACTCGAATTTCTATTACGCAATACAATTTTCTGTTA
Found at i:1554439 original size:121 final size:121
Alignment explanation
Indices: 1554189--1554541 Score: 301
Period size: 121 Copynumber: 2.9 Consensus size: 121
1554179 AATAACCAAC
* *
1554189 AAATTCGCAACGCAATCTCAAATTCGCAACACGAACTCCAATTTCGCAACGCGAATTTGGAATTC
1 AAATTCGCAACGCAATTTCAAATTCGCAACACGAACTCCAATTTCGCAACGCGAATTTGAAATTC
* * * * *
1554254 ACAATACGGAATTTCGAATTCGCAACTCGAATTTCTTTTACGCAATACAATTTTCT
66 ACAACACGAAATTTCAAATTCGCAACTCGAATTTCTATTACGCAACACAATTTTCT
* * * *
1554310 --GTTACGCAACGCAATTTTCAAATTCGCAACACGAACTCTAATTTCGCAACG-TAATTTCTAAA
1 AAATT-CGCAACGCAA-TTTCAAATTCGCAACACGAACTCCAATTTCGCAACGCGAATTT-GAAA
* * *
1554372 TTCGCAACACGAAATTTCAAATTCGCAACTCG-ATTTCTGAATT-CGCAACGCGATTTT-T
63 TTCACAACACGAAATTTCAAATTCGCAACTCGAATTTCT--ATTACGCAACACAATTTTCT
* ** * ** * * **
1554430 AAATTCGCAACACAAGTTTCATTTTCGCAACAAGATTTTCTAA-TTCGCAACGCGAATTTTATTT
1 AAATTCGCAACGCAA-TTTCAAATTCGCAACACGA-ACTCCAATTTCGCAACGCGAATTTGAAAT
* * * * * *
1554494 TCGCAACTCG-ATTTTCGAATTCGCAACACGAATTT-TAATTTCGCAACA
64 TCACAACACGAAATTTCAAATTCGCAACTCGAATTTCT-ATTACGCAACA
1554542 GCTTTTATTT
Statistics
Matches: 191, Mismatches: 30, Indels: 23
0.78 0.12 0.09
Matches are distributed among these distances:
119 6 0.03
120 46 0.24
121 125 0.65
122 14 0.07
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.31
Consensus pattern (121 bp):
AAATTCGCAACGCAATTTCAAATTCGCAACACGAACTCCAATTTCGCAACGCGAATTTGAAATTC
ACAACACGAAATTTCAAATTCGCAACTCGAATTTCTATTACGCAACACAATTTTCT
Found at i:1555347 original size:12 final size:12
Alignment explanation
Indices: 1555326--1555359 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1555316 ACCACATTTC
*
1555326 CAATACCAAACA
1 CAATATCAAACA
1555338 CAATATCAAACA
1 CAATATCAAACA
*
1555350 CAATCTCAAA
1 CAATATCAAA
1555360 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1555515 original size:24 final size:24
Alignment explanation
Indices: 1555483--1555536 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
1555473 GTATTCGAAA
1555483 TTTGATCTTGGA-CAATACCCGGAC
1 TTTGATCTT-GATCAATACCCGGAC
* *
1555507 TTTGATCTTGATCAATACTCGGAT
1 TTTGATCTTGATCAATACCCGGAC
1555531 TTTGAT
1 TTTGAT
1555537 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 2 0.07
24 25 0.93
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.39
Consensus pattern (24 bp):
TTTGATCTTGATCAATACCCGGAC
Found at i:1558105 original size:20 final size:20
Alignment explanation
Indices: 1558076--1558166 Score: 83
Period size: 20 Copynumber: 4.5 Consensus size: 20
1558066 TTCACAACTC
* *
1558076 AAATTTGCAATGCGAAAATA
1 AAATTCGCAACGCGAAAATA
** * * *
1558096 AAATTCGCAACTTGATACTC
1 AAATTCGCAACGCGAAAATA
* *
1558116 AAATTCGCAACACGAAAATC
1 AAATTCGCAACGCGAAAATA
*
1558136 GAATTCGCAACGCGAAAATA
1 AAATTCGCAACGCGAAAATA
*
1558156 AAATTTGCAAC
1 AAATTCGCAAC
1558167 ATGAAAATTG
Statistics
Matches: 55, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.45, C:0.20, G:0.13, T:0.22
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAATA
Found at i:1558172 original size:20 final size:20
Alignment explanation
Indices: 1558088--1558174 Score: 84
Period size: 20 Copynumber: 4.3 Consensus size: 20
1558078 ATTTGCAATG
*
1558088 CGAAAATAAAATTCGCAACT
1 CGAAAATAAAATTCGCAACA
* * * *
1558108 TGATACTCAAATTCGCAACA
1 CGAAAATAAAATTCGCAACA
** *
1558128 CGAAAATCGAATTCGCAACG
1 CGAAAATAAAATTCGCAACA
*
1558148 CGAAAATAAAATTTGCAACA
1 CGAAAATAAAATTCGCAACA
*
1558168 TGAAAAT
1 CGAAAAT
1558175 TGCAACACGA
Statistics
Matches: 52, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.47, C:0.20, G:0.13, T:0.21
Consensus pattern (20 bp):
CGAAAATAAAATTCGCAACA
Found at i:1558298 original size:20 final size:20
Alignment explanation
Indices: 1558191--1558290 Score: 119
Period size: 20 Copynumber: 5.0 Consensus size: 20
1558181 ACGAAGATGG
* **
1558191 TTATTTTCGTGTTGTAAATT
1 TTATTTTCGCGTTGCGAATT
*
1558211 TTATTTTTGCGTTGCGAATT
1 TTATTTTCGCGTTGCGAATT
* *
1558231 TTATTTTCGCATTGCAAATT
1 TTATTTTCGCGTTGCGAATT
*
1558251 TTATTTTCGCATTGCGAATT
1 TTATTTTCGCGTTGCGAATT
* *
1558271 TGATTTTCGTGTTGCGAATT
1 TTATTTTCGCGTTGCGAATT
1558291 CGATTTTCTT
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 69 1.00
ACGTcount: A:0.19, C:0.11, G:0.17, T:0.53
Consensus pattern (20 bp):
TTATTTTCGCGTTGCGAATT
Found at i:1558298 original size:40 final size:40
Alignment explanation
Indices: 1558193--1558290 Score: 133
Period size: 40 Copynumber: 2.5 Consensus size: 40
1558183 GAAGATGGTT
* * * *
1558193 ATTTTCGTGTTGTAAATTTTATTTTTGCGTTGCGAATTTT
1 ATTTTCGTGTTGCAAATTTTATTTTCGCATTGCGAATTTG
**
1558233 ATTTTCGCATTGCAAATTTTATTTTCGCATTGCGAATTTG
1 ATTTTCGTGTTGCAAATTTTATTTTCGCATTGCGAATTTG
*
1558273 ATTTTCGTGTTGCGAATT
1 ATTTTCGTGTTGCAAATT
1558291 CGATTTTCTT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.19, C:0.11, G:0.17, T:0.52
Consensus pattern (40 bp):
ATTTTCGTGTTGCAAATTTTATTTTCGCATTGCGAATTTG
Found at i:1559814 original size:21 final size:21
Alignment explanation
Indices: 1559788--1559829 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1559778 GAATGTCATA
*
1559788 TGGATCCTAAACGGTGGGAGG
1 TGGATCCTAAACGATGGGAGG
*
1559809 TGGATCCTGAACGATGGGAGG
1 TGGATCCTAAACGATGGGAGG
1559830 GGCCTCTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.14, G:0.43, T:0.19
Consensus pattern (21 bp):
TGGATCCTAAACGATGGGAGG
Found at i:1559840 original size:21 final size:21
Alignment explanation
Indices: 1559816--1559866 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
1559806 AGGTGGATCC
1559816 TGAACGATGGGAGGGGCCTCT
1 TGAACGATGGGAGGGGCCTCT
* * *
1559837 TGAACGACGGGATGGGCCTTT
1 TGAACGATGGGAGGGGCCTCT
1559858 TGAACGATG
1 TGAACGATG
1559867 ACAGGTAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.22, C:0.18, G:0.39, T:0.22
Consensus pattern (21 bp):
TGAACGATGGGAGGGGCCTCT
Found at i:1559899 original size:21 final size:21
Alignment explanation
Indices: 1559875--1559919 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 21
1559865 TGACAGGTAA
1559875 ATCCTAAACAATAGG-AGGTGG
1 ATCCTAAACAAT-GGTAGGTGG
1559896 ATCCTAAACAATGGTAGGTGG
1 ATCCTAAACAATGGTAGGTGG
1559917 ATC
1 ATC
1559920 AGGCTTCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.36, C:0.16, G:0.27, T:0.22
Consensus pattern (21 bp):
ATCCTAAACAATGGTAGGTGG
Found at i:1560074 original size:4 final size:4
Alignment explanation
Indices: 1560053--1560086 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
1560043 GGGCCGCTAA
* *
1560053 AAAT AAAT TAAT ATAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1560087 TACCGAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (4 bp):
AAAT
Found at i:1560345 original size:21 final size:21
Alignment explanation
Indices: 1560321--1560364 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1560311 ACCATTGTCG
1560321 TCACGTAAAGCACTGACCTCA
1 TCACGTAAAGCACTGACCTCA
1560342 TCACGTAAAGCACTGACCTCA
1 TCACGTAAAGCACTGACCTCA
1560363 TC
1 TC
1560365 CCGTGGAGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.34, G:0.14, T:0.20
Consensus pattern (21 bp):
TCACGTAAAGCACTGACCTCA
Found at i:1560530 original size:21 final size:21
Alignment explanation
Indices: 1560464--1560531 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
1560454 GTGATGGAAT
*
1560464 AGGTGATGGCTCTCGGTGTCA
1 AGGTGATGGATCTCGGTGTCA
*
1560485 AGGTG-TAGAAT-T-GGCTCGATC-
1 AGGTGAT-GGATCTCGG-T-G-TCA
1560506 AGGTGATGGATCTCGGTGTCA
1 AGGTGATGGATCTCGGTGTCA
1560527 AGGTG
1 AGGTG
1560532 TAGAATCGAC
Statistics
Matches: 36, Mismatches: 3, Indels: 16
0.65 0.05 0.29
Matches are distributed among these distances:
19 2 0.06
20 5 0.14
21 22 0.61
22 5 0.14
23 2 0.06
ACGTcount: A:0.19, C:0.15, G:0.38, T:0.28
Consensus pattern (21 bp):
AGGTGATGGATCTCGGTGTCA
Found at i:1560615 original size:42 final size:42
Alignment explanation
Indices: 1560464--1560606 Score: 207
Period size: 42 Copynumber: 3.4 Consensus size: 42
1560454 GTGATGGAAT
* *
1560464 AGGTGATGGCTCTCGGTGTCAAGGTGTAGAATTGGCTCGATC
1 AGGTGATGGATCTCGGTGTCAAGGTGTAGAATAGGCTCGATC
* *
1560506 AGGTGATGGATCTCGGTGTCAAGGTGTAGAATCGACTCGATC
1 AGGTGATGGATCTCGGTGTCAAGGTGTAGAATAGGCTCGATC
* * *
1560548 AGGTGATGGATCTCGGTGTCGAA-GTGGAGAAGAGGCTCGATG
1 AGGTGATGGATCTCGGTGTC-AAGGTGTAGAATAGGCTCGATC
1560590 AGGTGATGGATCTCGGT
1 AGGTGATGGATCTCGGT
1560607 ATCGAAGTGA
Statistics
Matches: 92, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
42 90 0.98
43 2 0.02
ACGTcount: A:0.22, C:0.15, G:0.38, T:0.26
Consensus pattern (42 bp):
AGGTGATGGATCTCGGTGTCAAGGTGTAGAATAGGCTCGATC
Found at i:1562035 original size:20 final size:20
Alignment explanation
Indices: 1562012--1562049 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1562002 TCACAACTCG
1562012 AAAATGAAATTCGAAACGCA
1 AAAATGAAATTCGAAACGCA
* *
1562032 AAAATGATATTCGCAACG
1 AAAATGAAATTCGAAACG
1562050 TGAAAACTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAATGAAATTCGAAACGCA
Found at i:1562055 original size:20 final size:20
Alignment explanation
Indices: 1562010--1562055 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1562000 AATCACAACT
1562010 CGAAAATGAAATTCGAAACG
1 CGAAAATGAAATTCGAAACG
* * *
1562030 CAAAAATGATATTCGCAACG
1 CGAAAATGAAATTCGAAACG
*
1562050 TGAAAA
1 CGAAAA
1562056 CTAAAATCGC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.50, C:0.15, G:0.17, T:0.17
Consensus pattern (20 bp):
CGAAAATGAAATTCGAAACG
Found at i:1562103 original size:20 final size:20
Alignment explanation
Indices: 1562066--1562104 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1562056 CTAAAATCGC
* *
1562066 GTTGCGAATTTCATTTTCAT
1 GTTGCGAATTTAAGTTTCAT
1562086 GTTGCGAATTTAAGTTTCA
1 GTTGCGAATTTAAGTTTCA
1562105 AAAACTACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (20 bp):
GTTGCGAATTTAAGTTTCAT
Done.