Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009266.1 Hibiscus syriacus cultivar Beakdansim tig00112921_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: 1543912
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 7
Found at i:1194542 original size:65 final size:63
Alignment explanation
Indices: 1194492--1194647 Score: 199
Period size: 65 Copynumber: 2.4 Consensus size: 63
1194482 TACACTAAGG
* * *
1194492 GTGCATCGATGCATAAAATGCATTCGATGTTTTAA-ACAAGA-CTGGAGTGCATTGATGCATGGT
1 GTGCATCGATGCATAAAATGCATTCGATGATTCAATA-AA-ATCTGGAGTGCATCGATGCATGG-
1194555 CT
63 -T
* * *
1194557 GTGCATCGATGCATAAAATGCATTCAATGATTCAATAAAATTTTGAGTGCATCGATGCATGGTT
1 GTGCATCGATGCATAAAATGCATTCGATGATTCAATAAAATCTGGAGTGCATCGATGCATGG-T
1194621 GTGCATCGATGCATAAAATGCATTCGA
1 GTGCATCGATGCATAAAATGCATTCGA
1194648 AATGGGGTGT
Statistics
Matches: 81, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 28 0.35
65 52 0.64
66 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCATAAAATGCATTCGATGATTCAATAAAATCTGGAGTGCATCGATGCATGGT
Found at i:1197210 original size:20 final size:22
Alignment explanation
Indices: 1197185--1197257 Score: 64
Period size: 23 Copynumber: 3.4 Consensus size: 22
1197175 CAACGGGTGT
*
1197185 ATCGATGCA-ATGC-TGAGTGC
1 ATCGATGCACATGCAGGAGTGC
*
1197205 ATCGATGCACATTCAAGGAGTGC
1 ATCGATGCACATGC-AGGAGTGC
* *
1197228 ATCGATGCATC-TTCATGA-TGC
1 ATCGATGCA-CATGCAGGAGTGC
1197249 ATCGATGCA
1 ATCGATGCA
1197258 TATTCAAAGG
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
20 9 0.20
21 15 0.33
22 3 0.07
23 18 0.39
24 1 0.02
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.26
Consensus pattern (22 bp):
ATCGATGCACATGCAGGAGTGC
Found at i:1197251 original size:21 final size:22
Alignment explanation
Indices: 1197202--1197278 Score: 95
Period size: 23 Copynumber: 3.5 Consensus size: 22
1197192 CAATGCTGAG
1197202 TGCATCGATGCA-CATTCAAGGA
1 TGCATCGATGCATC-TTCAAGGA
*
1197224 GTGCATCGATGCATCTTC-ATGA
1 -TGCATCGATGCATCTTCAAGGA
*
1197246 TGCATCGATGCATATTCAAAGGA
1 TGCATCGATGCATCTTC-AAGGA
1197269 TGCATCGATG
1 TGCATCGATG
1197279 TATTAGATAG
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
21 16 0.33
22 3 0.06
23 28 0.58
24 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (22 bp):
TGCATCGATGCATCTTCAAGGA
Found at i:1198892 original size:25 final size:23
Alignment explanation
Indices: 1198847--1198893 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
1198837 AGTTTCTAAA
*
1198847 AAATGTAAAAAATGTTAGATAAC
1 AAATGTAAAAAATATTAGATAAC
*
1198870 AAATAGTAAACAAATATTGGATAA
1 AAAT-GTAAA-AAATATTAGATAA
1198894 ATTAAAGGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 5 0.25
25 11 0.55
ACGTcount: A:0.57, C:0.04, G:0.13, T:0.26
Consensus pattern (23 bp):
AAATGTAAAAAATATTAGATAAC
Found at i:1200260 original size:4 final size:4
Alignment explanation
Indices: 1200247--1200300 Score: 72
Period size: 4 Copynumber: 13.0 Consensus size: 4
1200237 AAAAAGAAGA
* *
1200247 AAAT AGAT AAAT AAAT AAAT GAAAT AAAAT AAAT AAAT AAAT AGAT AAAT
1 AAAT AAAT AAAT AAAT AAAT -AAAT -AAAT AAAT AAAT AAAT AAAT AAAT
1200297 AAAT
1 AAAT
1200301 TAAAAACATT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
4 36 0.82
5 8 0.18
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:1200287 original size:30 final size:30
Alignment explanation
Indices: 1200247--1200305 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
1200237 AAAAAGAAGA
*
1200247 AAATAGATAAATAAATAAATGAAA-TAAAAT
1 AAATAAATAAATAAATAAAT-AAATTAAAAT
*
1200277 AAATAAATAAATAGATAAATAAATTAAAA
1 AAATAAATAAATAAATAAATAAATTAAAA
1200306 ACATTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (30 bp):
AAATAAATAAATAAATAAATAAATTAAAAT
Found at i:1200371 original size:45 final size:46
Alignment explanation
Indices: 1200316--1200408 Score: 143
Period size: 46 Copynumber: 2.0 Consensus size: 46
1200306 ACATTTTTTA
* *
1200316 AAACTATATAATATATGT-TTTAAAAAATAATTTTCAAAACCATAT
1 AAACCATATAATATATATATTTAAAAAATAATTTTCAAAACCATAT
* *
1200361 AAACCATATAATATATATATTTAAAAACTAATTTTCAAAACTATAT
1 AAACCATATAATATATATATTTAAAAAATAATTTTCAAAACCATAT
1200407 AA
1 AA
1200409 TATATATGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
45 16 0.37
46 27 0.63
ACGTcount: A:0.53, C:0.10, G:0.01, T:0.37
Consensus pattern (46 bp):
AAACCATATAATATATATATTTAAAAAATAATTTTCAAAACCATAT
Found at i:1200442 original size:38 final size:37
Alignment explanation
Indices: 1200361--1200616 Score: 175
Period size: 38 Copynumber: 6.6 Consensus size: 37
1200351 AAAACCATAT
* * *
1200361 AAACCATATAATATATA-TATTT-AAAAACTAATTTTCA
1 AAACTATATAATATATATTTTTTCAAAAA-T-GTTTTCA
1200398 AAACTATATAATATATATGTTTTTCAAAAATGTTTTCA
1 AAACTATATAATATATAT-TTTTTCAAAAATGTTTTCA
* *
1200436 AAACTATATAATATATA-TTTTT-AAAAACTAATTCTCA
1 AAACTATATAATATATATTTTTTCAAAAA-T-GTTTTCA
* *
1200473 AAACTATATAATATATATATTTTCAAAAATGTTTTTAA
1 AAACTATATAATATATATTTTTTCAAAAATG-TTTTCA
* * *
1200511 AAATTATATTATATATATATATATATATATATATATAAAAAAGTTTTCA
1 AAACTATA-TA-ATATATAT-T-T-T-T-T-CA-A-AAAT--GTTTTCA
* *
1200560 AAACGATATAATATATA--TTTTGAAAAATGTTTTCAA
1 AAACTATATAATATATATTTTTTCAAAAATGTTTTC-A
1200596 AAACTATAT-ATCATATATTTT
1 AAACTATATAAT-ATATATTTT
1200617 CAAAACATTC
Statistics
Matches: 176, Mismatches: 19, Indels: 47
0.73 0.08 0.19
Matches are distributed among these distances:
35 13 0.07
36 20 0.11
37 41 0.23
38 42 0.24
39 13 0.07
40 14 0.08
41 1 0.01
42 2 0.01
43 2 0.01
44 1 0.01
45 1 0.01
46 1 0.01
47 8 0.05
48 5 0.03
49 11 0.06
50 1 0.01
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.43
Consensus pattern (37 bp):
AAACTATATAATATATATTTTTTCAAAAATGTTTTCA
Found at i:1200445 original size:75 final size:75
Alignment explanation
Indices: 1200361--1200530 Score: 261
Period size: 75 Copynumber: 2.3 Consensus size: 75
1200351 AAAACCATAT
* * *
1200361 AAACCATATAATATATATATTTAAAAACTAATTTTCAAAACTATATAATATATATGTTTTTCAAA
1 AAACTATATAATATATATATTTAAAAACTAATTCTCAAAACTATATAATATATAT-ATTTTCAAA
*
1200426 AATG-TTTTCA
65 AATGTTTTTAA
*
1200436 AAACTATATAATATATATTTTTAAAAACTAATTCTCAAAACTATATAATATATATATTTTCAAAA
1 AAACTATATAATATATATATTTAAAAACTAATTCTCAAAACTATATAATATATATATTTTCAAAA
1200501 ATGTTTTTAA
66 ATGTTTTTAA
* *
1200511 AAATTATATTATATATATAT
1 AAACTATATAATATATATAT
1200531 ATATATATAT
Statistics
Matches: 86, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
74 12 0.14
75 74 0.86
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.43
Consensus pattern (75 bp):
AAACTATATAATATATATATTTAAAAACTAATTCTCAAAACTATATAATATATATATTTTCAAAA
ATGTTTTTAA
Found at i:1200527 original size:2 final size:2
Alignment explanation
Indices: 1200515--1200547 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1200505 TTTTAAAAAT
1200515 TA TA T- 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
1200548 AAAAAGTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1200574 original size:35 final size:36
Alignment explanation
Indices: 1200529--1200613 Score: 102
Period size: 35 Copynumber: 2.3 Consensus size: 36
1200519 TTATATATAT
1200529 ATATATATATATATATAT-AAAAAAGTTTTCAAAACG
1 ATATATATATATAT-TATGAAAAAAGTTTTCAAAACG
* * *
1200565 ATATA-ATATATATTTTGAAAAATGTTTTCAAAAACT
1 ATATATATATATATTATGAAAAAAGTTTTC-AAAACG
1200601 ATATATCATATAT
1 ATATAT-ATATAT
1200614 TTTCAAAACA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
34 2 0.05
35 19 0.45
36 15 0.36
38 6 0.14
ACGTcount: A:0.49, C:0.06, G:0.05, T:0.40
Consensus pattern (36 bp):
ATATATATATATATTATGAAAAAAGTTTTCAAAACG
Found at i:1203215 original size:22 final size:21
Alignment explanation
Indices: 1203173--1203212 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1203163 GAGATTATTT
*
1203173 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
1203194 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1203213 ATAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:1205221 original size:46 final size:46
Alignment explanation
Indices: 1205153--1205261 Score: 175
Period size: 46 Copynumber: 2.4 Consensus size: 46
1205143 AGGGTTCATT
*
1205153 GATGCATAAAATGCATTAAATGTTTTAA-ACAAGCCTGGAGTGCATC
1 GATGCATAAAATGCATTAAATGTTTTAATAAAAGCCT-GAGTGCATC
* *
1205199 GATGCATAAAATGCATTTAATGTTTTAATAAAATCCTGAGTGCATC
1 GATGCATAAAATGCATTAAATGTTTTAATAAAAGCCTGAGTGCATC
1205245 GATGCATAAAATGCATT
1 GATGCATAAAATGCATT
1205262 CGAAATGGGG
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
46 53 0.90
47 6 0.10
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (46 bp):
GATGCATAAAATGCATTAAATGTTTTAATAAAAGCCTGAGTGCATC
Found at i:1212905 original size:18 final size:18
Alignment explanation
Indices: 1212879--1212914 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1212869 TCGAAAGGAC
*
1212879 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1212897 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
1212915 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1214381 original size:2 final size:2
Alignment explanation
Indices: 1214374--1214398 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1214364 CGGATGGGGG
1214374 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1214399 GTTTTAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1218573 original size:35 final size:35
Alignment explanation
Indices: 1218522--1218590 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
1218512 TAAATAATTG
1218522 AACAATCTTAATAGCATTTATTTTGATACTTTTTC
1 AACAATCTTAATAGCATTTATTTTGATACTTTTTC
* *
1218557 AACATTCTTAATAGCATTTATTTTGATGCTTTTT
1 AACAATCTTAATAGCATTTATTTTGATACTTTTT
1218591 TCATAATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.29, C:0.13, G:0.07, T:0.51
Consensus pattern (35 bp):
AACAATCTTAATAGCATTTATTTTGATACTTTTTC
Found at i:1218654 original size:2 final size:2
Alignment explanation
Indices: 1218647--1218674 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1218637 GATCTAAATA
1218647 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
1218675 TTTCTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1226410 original size:23 final size:23
Alignment explanation
Indices: 1226345--1226413 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
1226335 CACCACAGCT
* *
1226345 CGTATAATTGCACCGAAGTACCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
1226368 CGTAGAATTGCACCGGAGTGTCG
1 CGTAGAATTGCACCGAAGTGCCA
*
1226391 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
1226414 TATAATAATG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:1226600 original size:103 final size:103
Alignment explanation
Indices: 1226429--1226749 Score: 588
Period size: 103 Copynumber: 3.1 Consensus size: 103
1226419 TAATGTCCAT
* * * *
1226429 AAGGACTACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1226494 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1226532 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
* *
1226597 GACTTCATATATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1226635 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1226700 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1226738 AAGGACCACATA
1 AAGGACCACATA
1226750 GACCCTCAAC
Statistics
Matches: 210, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 210 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1237406 original size:15 final size:15
Alignment explanation
Indices: 1237386--1237414 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1237376 TAGAACAGAC
1237386 GCAGTGAGCAGTTTT
1 GCAGTGAGCAGTTTT
1237401 GCAGTGAGCAGTTT
1 GCAGTGAGCAGTTT
1237415 CAGCAAGAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.34, T:0.31
Consensus pattern (15 bp):
GCAGTGAGCAGTTTT
Found at i:1244020 original size:114 final size:114
Alignment explanation
Indices: 1243820--1244051 Score: 329
Period size: 114 Copynumber: 2.0 Consensus size: 114
1243810 ATGTTTCCTG
* * *
1243820 AATTTTTGTTATGAGAAATGATGAATGAAACATTTGGTATTCTCTAATGATAAAGTTGCAGTATG
1 AATTTTTGTTATAAGAAACGATGAATGAAACATTTGGTATTCTCTAATGATAAAGTTGCAATATG
** * * * * *
1243885 CTCATGGTTTTCATGTCAAAACATGCACATCTCCGTCCTCCTTCCCCTA
66 AACATGGCTTTCATGTCAAAACATGCAAATATCCATCCTCCTTCCCCCA
* * *
1243934 AATTTTTGTTATAAGAAACGGTGAATGAAACATTTTGTATTCTCTAATGATAAGGTTGCAATATG
1 AATTTTTGTTATAAGAAACGATGAATGAAACATTTGGTATTCTCTAATGATAAAGTTGCAATATG
* *
1243999 AACGTGGCTTTCATGTCAAAACATGCAAATATCCATCCTTCTTCCCCCA
66 AACATGGCTTTCATGTCAAAACATGCAAATATCCATCCTCCTTCCCCCA
1244048 AATT
1 AATT
1244052 CTTCTGTTGC
Statistics
Matches: 103, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
114 103 1.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (114 bp):
AATTTTTGTTATAAGAAACGATGAATGAAACATTTGGTATTCTCTAATGATAAAGTTGCAATATG
AACATGGCTTTCATGTCAAAACATGCAAATATCCATCCTCCTTCCCCCA
Found at i:1262400 original size:47 final size:47
Alignment explanation
Indices: 1262346--1262535 Score: 308
Period size: 47 Copynumber: 4.0 Consensus size: 47
1262336 AACAAATGGA
*
1262346 AAATGAAGTAACCCAAGTGAAATAAACACTGGCCTTGTGCCTTTAGT
1 AAATGAAGTAACCCAAGTGAAATAAACACTGACCTTGTGCCTTTAGT
1262393 AAATGAAGTAACCCAAGTGAAATAAACACTGACCTTGTGCCTTTAGT
1 AAATGAAGTAACCCAAGTGAAATAAACACTGACCTTGTGCCTTTAGT
* *
1262440 AAATGAATTAACCTAAGTGAAATAAACACTGACCTTGTGCCTTTAGT
1 AAATGAAGTAACCCAAGTGAAATAAACACTGACCTTGTGCCTTTAGT
* * * * *
1262487 AAATGAATTAACCTAAATGAAATAAACACTGGCCTTGTTCCTTTAGT
1 AAATGAAGTAACCCAAGTGAAATAAACACTGACCTTGTGCCTTTAGT
1262534 AA
1 AA
1262536 GCTAGCTCAT
Statistics
Matches: 137, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 137 1.00
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (47 bp):
AAATGAAGTAACCCAAGTGAAATAAACACTGACCTTGTGCCTTTAGT
Found at i:1266423 original size:83 final size:82
Alignment explanation
Indices: 1266285--1266460 Score: 282
Period size: 83 Copynumber: 2.1 Consensus size: 82
1266275 AGAAAACCCC
* * *
1266285 AGAAAAGGAAGAGGTAAACCATGATCTTAGTTGTTTTCCCATGGCAATAGCAATTTTCCCATCCA
1 AGAAAAGGAAAAGGTAAACCATGATCTTAGCTGTTTTCCCATGGCAATAGCAATTTTCCCACCCA
1266350 TGTAAACCATAAACAAA
66 TGTAAACCATAAACAAA
*
1266367 AGAAAAGGAAAATGGTAAACCATGATCTTAGCTGTTTTCCCATGGCATTAGCAATTTTCCCACCC
1 AGAAAAGGAAAA-GGTAAACCATGATCTTAGCTGTTTTCCCATGGCAATAGCAATTTTCCCACCC
*
1266432 ATGTAAATCATAAACAAA
65 ATGTAAACCATAAACAAA
*
1266450 AG-GAAGGAAAA
1 AGAAAAGGAAAA
1266461 AAGGGAGAGT
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
82 19 0.22
83 68 0.78
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.24
Consensus pattern (82 bp):
AGAAAAGGAAAAGGTAAACCATGATCTTAGCTGTTTTCCCATGGCAATAGCAATTTTCCCACCCA
TGTAAACCATAAACAAA
Found at i:1267280 original size:37 final size:37
Alignment explanation
Indices: 1267224--1267319 Score: 120
Period size: 37 Copynumber: 2.6 Consensus size: 37
1267214 CTTTTCGTCC
* *
1267224 TACTAGGATTCAAACTCCTAAAAATAAGATAGAATTT
1 TACTATGATTCAAACTCCTAAAAATAAGATAGAATTA
* * * *
1267261 TGCTATGATTCAAACTCCTAATAATAGGATAGAGTTA
1 TACTATGATTCAAACTCCTAAAAATAAGATAGAATTA
* *
1267298 TACTATTATTTAAACTCCTAAA
1 TACTATGATTCAAACTCCTAAA
1267320 GATAGGATCC
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (37 bp):
TACTATGATTCAAACTCCTAAAAATAAGATAGAATTA
Found at i:1267772 original size:23 final size:23
Alignment explanation
Indices: 1267744--1267790 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
1267734 TATATGAATA
1267744 TATTTAATTAT-ATTTTATTT-ATT
1 TATTT-ATTATAATTTT-TTTCATT
1267767 TATTTATTATAATTTTTTTCATT
1 TATTTATTATAATTTTTTTCATT
1267790 T
1 T
1267791 TTCTTTGCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (23 bp):
TATTTATTATAATTTTTTTCATT
Found at i:1268061 original size:23 final size:23
Alignment explanation
Indices: 1268035--1268089 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 23
1268025 CTATTTAGTA
1268035 TTTTATTATATTATACATACAT-T
1 TTTTATTAT-TTATACATACATAT
* * *
1268058 TTTTA-TATTTTTATATATATAT
1 TTTTATTATTTATACATACATAT
1268080 TTTTATTATT
1 TTTTATTATT
1268090 ATTTTATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 9 0.33
22 9 0.33
23 9 0.33
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTTATTATTTATACATACATAT
Found at i:1268088 original size:25 final size:25
Alignment explanation
Indices: 1268035--1268112 Score: 74
Period size: 23 Copynumber: 3.2 Consensus size: 25
1268025 CTATTTAGTA
* *
1268035 TTTTATTATATTATACATAC-A-TT
1 TTTTATTATTTTATATATACTATTT
1268058 TTTTA-TATTTTTATATATA-TATTT
1 TTTTATTA-TTTTATATATACTATTT
*
1268082 TTATTATTATTTTATTTATACTATTT
1 TT-TTATTATTTTATATATACTATTT
1268108 ATTTT
1 -TTTT
1268113 TTTCATTATA
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
22 2 0.04
23 15 0.33
24 4 0.09
25 13 0.29
26 9 0.20
27 2 0.04
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (25 bp):
TTTTATTATTTTATATATACTATTT
Found at i:1268092 original size:12 final size:14
Alignment explanation
Indices: 1268061--1268128 Score: 59
Period size: 14 Copynumber: 4.7 Consensus size: 14
1268051 ATACATTTTT
1268061 TATATTTTTATATA
1 TATATTTTTATATA
1268075 TATATTTTTAT-TA
1 TATATTTTTATATA
*
1268088 TTATTTTATTTATACTA
1 -TATATT-TTTATA-TA
* *
1268105 TTTATTTTTTTCAT-
1 TATATTTTTAT-ATA
1268119 TATATTTTTA
1 TATATTTTTA
1268129 GTTTTTTTGC
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
13 2 0.05
14 24 0.56
15 10 0.23
16 5 0.12
17 2 0.05
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (14 bp):
TATATTTTTATATA
Found at i:1268101 original size:23 final size:22
Alignment explanation
Indices: 1267995--1268136 Score: 71
Period size: 23 Copynumber: 6.4 Consensus size: 22
1267985 ATATGTATAT
* *
1267995 TTATTTTTCATTTAT-TTATTA
1 TTATTTTTTATTTATATTTTTA
*
1268016 TTATTATTACTATTTAGTA-TTTTA
1 TTATT-TT-TTATTTA-TATTTTTA
* * ** *
1268040 TTATATTATACATACATTTTT-
1 TTATTTTTTATTTATATTTTTA
*
1268061 TATATTTTTATATATATATTTTTA
1 T-TATTTTT-TATTTATATTTTTA
*
1268085 TTATTATTTTATTTATACTATTTA
1 TTATT-TTTTATTTATA-TTTTTA
*
1268109 TT-TTTTTCA-TTATATTTTTA
1 TTATTTTTTATTTATATTTTTA
*
1268129 GT-TTTTTT
1 TTATTTTTT
1268137 GCTTTTATTA
Statistics
Matches: 93, Mismatches: 18, Indels: 21
0.70 0.14 0.16
Matches are distributed among these distances:
20 11 0.12
21 12 0.13
22 19 0.20
23 31 0.33
24 20 0.22
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68
Consensus pattern (22 bp):
TTATTTTTTATTTATATTTTTA
Found at i:1268115 original size:21 final size:20
Alignment explanation
Indices: 1268097--1268136 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1268087 ATTATTTTAT
1268097 TTATACTATTTATTTTTTTCA
1 TTATA-TATTTATTTTTTTCA
*
1268118 TTATATTTTTAGTTTTTTT
1 TTATATATTTA-TTTTTTT
1268137 GCTTTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.20, C:0.05, G:0.03, T:0.72
Consensus pattern (20 bp):
TTATATATTTATTTTTTTCA
Found at i:1268142 original size:27 final size:26
Alignment explanation
Indices: 1268112--1268162 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
1268102 CTATTTATTT
*
1268112 TTTTCATTA-TATTTTTAGTTTTTTTGC
1 TTTT-ATTATTATTTTT-CTTTTTTTGC
1268139 TTTTATTATTATTTTTCTTTTTTT
1 TTTTATTATTATTTTTCTTTTTTT
1268163 AAAAAAACAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.14, C:0.06, G:0.04, T:0.76
Consensus pattern (26 bp):
TTTTATTATTATTTTTCTTTTTTTGC
Found at i:1272555 original size:16 final size:15
Alignment explanation
Indices: 1272531--1272581 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
1272521 ATTCAATCAG
*
1272531 AACAAAAAGGGAA-AA
1 AACAAAAA-AGAAGAA
1272546 AACAAAAAAGAAGAA
1 AACAAAAAAGAAGAA
1272561 AACAAAAAA-AA-AA
1 AACAAAAAAGAAGAA
1272574 GAACAAAA
1 -AACAAAA
1272582 GTCAAAAAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
13 2 0.06
14 12 0.36
15 19 0.58
ACGTcount: A:0.80, C:0.08, G:0.12, T:0.00
Consensus pattern (15 bp):
AACAAAAAAGAAGAA
Found at i:1272604 original size:23 final size:21
Alignment explanation
Indices: 1272544--1272596 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 21
1272534 AAAAAGGGAA
*
1272544 AAAACAAAAAAGAAGAAAA--C
1 AAAA-AAAAAAGAACAAAAGTC
1272564 AAAAAAAAAAGAACAAAAGTC
1 AAAAAAAAAAGAACAAAAGTC
1272585 AAAAAGAAAAAG
1 AAAAA-AAAAAG
1272597 GGACAAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 13 0.45
20 4 0.14
21 6 0.21
22 6 0.21
ACGTcount: A:0.79, C:0.08, G:0.11, T:0.02
Consensus pattern (21 bp):
AAAAAAAAAAGAACAAAAGTC
Found at i:1273434 original size:23 final size:21
Alignment explanation
Indices: 1273407--1273469 Score: 63
Period size: 24 Copynumber: 2.8 Consensus size: 21
1273397 TGAAAGAGAC
1273407 AATATTTTCAAAACTTTTGATT
1 AATATTTTCAAAACTTTT-ATT
*
1273429 AAATATTTTTCGAAACTCTTTATT
1 -AATA-TTTTCAAAACT-TTTATT
* *
1273453 GATATTTTCAGAACTTT
1 AATATTTTCAAAACTTT
1273470 GAAAATAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 2 0.06
22 9 0.26
23 7 0.21
24 13 0.38
25 3 0.09
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.49
Consensus pattern (21 bp):
AATATTTTCAAAACTTTTATT
Found at i:1274314 original size:106 final size:106
Alignment explanation
Indices: 1274199--1275445 Score: 1971
Period size: 106 Copynumber: 11.9 Consensus size: 106
1274189 ACAACAAAAA
* * *
1274199 TTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCCAAATTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
* *
1274264 CAACTTCACAGCGAAGGATATTGGACTTCAGACAACACAAG
66 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
*
1274305 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
*
1274370 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
66 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
* *
1274411 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
*
1274476 CAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAG
66 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
* * *
1274517 TTCAACTTCATGACGAAGAGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
*
1274582 CAACTTCACAGTGAAGGATATTGGACTCCAGACAACGCAAG
66 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
* *
1274623 TTCAACTTCACGACGAAGGGACTGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
*
1274688 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
66 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
* *
1274729 TTCAACTTCACGACAAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCATAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
* *
1274794 CAACTTCACAGCGAAGGATATTAGACTCAAGACAACGCAAG
66 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
1274835 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC--A-AA-----CAATTTC----CCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
* *
1274888 TAACTTCACAGCGAAAGATATTGGACTCCAGACAACGCAAG
66 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
* *
1274929 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCTGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
*
1274994 CAACTTCACAGCGAAGGATATTGGACTCCATACAACGCAAG
66 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
*
1275035 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
* *
1275100 CAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAG
66 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
* * *
1275141 TTTAACTTCACGACGAAGGGATCGCTGGTTGTCAACAAATAACTTCCCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
*
1275206 CAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAG
66 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
* * *
1275247 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTTCGGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
* * * * *
1275312 CAACTTCACAACAAAGGATATTGGACTCGAGACAGCACAAG
66 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
* * * * *
1275353 TTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGATTCCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
*
1275418 CAACTTCAC-GACGGAGGATATTGGACTC
66 CAACTTCACAG-CGAAGGATATTGGACTC
1275446 GGAACAATAC
Statistics
Matches: 1059, Mismatches: 69, Indels: 26
0.92 0.06 0.02
Matches are distributed among these distances:
94 80 0.08
96 1 0.00
97 2 0.00
98 7 0.01
102 7 0.01
103 2 0.00
104 1 0.00
106 959 0.91
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:1276023 original size:8 final size:8
Alignment explanation
Indices: 1276012--1276073 Score: 61
Period size: 8 Copynumber: 7.5 Consensus size: 8
1276002 TTATACATAC
*
1276012 ATTTTTAT
1 ATTTATAT
1276020 ATTTATAT
1 ATTTATAT
*
1276028 ATATATAT
1 ATTTATAT
*
1276036 ATATATAT
1 ATTTATAT
*
1276044 ATTTATTTT
1 ATTTA-TAT
1276053 ATTTATACT
1 ATTTATA-T
*
1276062 ATTTATTT
1 ATTTATAT
1276070 ATTT
1 ATTT
1276074 TCATTATATT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
8 32 0.70
9 14 0.30
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (8 bp):
ATTTATAT
Found at i:1277062 original size:3 final size:3
Alignment explanation
Indices: 1277054--1277135 Score: 71
Period size: 3 Copynumber: 27.0 Consensus size: 3
1277044 TTTTCTTTAT
* *
1277054 TTA TTA TTA TTA TTC TGT- TTA TTTA TTA TTA TTA TTC TGT- TTA TTTA
1 TTA TTA TTA TTA TTA T-TA TTA -TTA TTA TTA TTA TTA T-TA TTA -TTA
* *
1277101 TTA TTA -TA TTA TTA TTA ATA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1277136 CAGGCCCAAA
Statistics
Matches: 68, Mismatches: 4, Indels: 14
0.79 0.05 0.16
Matches are distributed among these distances:
2 4 0.06
3 56 0.82
4 8 0.12
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1277074 original size:22 final size:22
Alignment explanation
Indices: 1277049--1277107 Score: 118
Period size: 22 Copynumber: 2.7 Consensus size: 22
1277039 TGGTTTTTTC
1277049 TTTATTTATTATTATTATTCTG
1 TTTATTTATTATTATTATTCTG
1277071 TTTATTTATTATTATTATTCTG
1 TTTATTTATTATTATTATTCTG
1277093 TTTATTTATTATTAT
1 TTTATTTATTATTAT
1277108 ATTATTATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.69
Consensus pattern (22 bp):
TTTATTTATTATTATTATTCTG
Found at i:1280388 original size:18 final size:19
Alignment explanation
Indices: 1280353--1280389 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
1280343 TGAAAGACTG
1280353 TTCATCAAATTGGAAAAAA
1 TTCATCAAATTGGAAAAAA
1280372 TTCAT-AAA-TGGACAAAAA
1 TTCATCAAATTGGA-AAAAA
1280390 AATTTATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.24
18 8 0.47
19 5 0.29
ACGTcount: A:0.54, C:0.11, G:0.11, T:0.24
Consensus pattern (19 bp):
TTCATCAAATTGGAAAAAA
Found at i:1281643 original size:43 final size:44
Alignment explanation
Indices: 1281576--1281659 Score: 125
Period size: 43 Copynumber: 1.9 Consensus size: 44
1281566 CTAACTTAGA
* *
1281576 GAAGTTAGGAGGGACAGTTATCCCCTATATGT-AAAGTTTTATT
1 GAAGTTAGGACGGAAAGTTATCCCCTATATGTAAAAGTTTTATT
* *
1281619 GAAGTTAGGACTGAAAGTTGTCCCCTATATGTAAAAGTTTT
1 GAAGTTAGGACGGAAAGTTATCCCCTATATGTAAAAGTTTT
1281660 GTTTGATGCA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 28 0.78
44 8 0.22
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.35
Consensus pattern (44 bp):
GAAGTTAGGACGGAAAGTTATCCCCTATATGTAAAAGTTTTATT
Found at i:1281846 original size:20 final size:20
Alignment explanation
Indices: 1281823--1281872 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
1281813 CATATTTAAA
*
1281823 TTTGCATTTGCATTTTTATG
1 TTTGCATTTGCATTTTCATG
* ** *
1281843 TTTGTATTTATATTTTCATT
1 TTTGCATTTGCATTTTCATG
1281863 TTTGCATTTG
1 TTTGCATTTG
1281873 TATCTTTGCA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.16, C:0.08, G:0.12, T:0.64
Consensus pattern (20 bp):
TTTGCATTTGCATTTTCATG
Found at i:1285131 original size:32 final size:32
Alignment explanation
Indices: 1285095--1285157 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
1285085 TCTGGAAATA
1285095 AGAAGTATCTCTACG-AGATGAGCATAACAACG
1 AGAAGTATCTCTA-GAAGATGAGCATAACAACG
*
1285127 AGAAGTATTTCTAGAAGATGAGCATAACAAC
1 AGAAGTATCTCTAGAAGATGAGCATAACAAC
1285158 CATTTCTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 1 0.03
32 28 0.97
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.21
Consensus pattern (32 bp):
AGAAGTATCTCTAGAAGATGAGCATAACAACG
Found at i:1287717 original size:70 final size:72
Alignment explanation
Indices: 1287557--1287728 Score: 188
Period size: 70 Copynumber: 2.4 Consensus size: 72
1287547 CAACAAGAAG
* * * * *
1287557 CAAATATTGGGGTATGCTGAAAACCCATTTCAATCATAATCAGGAATATTGACGCATTTTGAATG
1 CAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATAAGGAATA-T-AC-CATTTTGAATG
*
1287622 TTCACGTCAA
63 TTCACATCAA
*
1287632 CAAATGTTGGAGCATGCTGAAAGCCCATTTCAATCAGAA-AATGGAATA-A-CATTTTGAATGTT
1 CAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATAA-GGAATATACCATTTTGAATGTT
* *
1287694 CATATCAG
65 CACATCAA
* *
1287702 TAAATGTTGGGGCATGCTGAAGGCCCA
1 CAAATGTTGGGGCATGCTGAAAGCCCA
1287729 CATCATTATG
Statistics
Matches: 84, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
70 42 0.50
72 1 0.01
74 1 0.01
75 40 0.48
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.28
Consensus pattern (72 bp):
CAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATAAGGAATATACCATTTTGAATGTTC
ACATCAA
Found at i:1288676 original size:54 final size:54
Alignment explanation
Indices: 1288601--1288754 Score: 168
Period size: 54 Copynumber: 2.9 Consensus size: 54
1288591 AAATCTGGGA
*
1288601 AGAAACCACATGAAATGATGAATGTATTGTCAAATATTTTACGAACATCTG-AGC
1 AGAAACCACAAGAAATGATGAATGTATTGTCAAATATTTTACGAACATCTGTA-C
* * * * *
1288655 AGAAGCCATAGGAAATGATGAATGTATTATTAAATA-TTTACGAAACATCTGTAC
1 AGAAACCACAAGAAATGATGAATGTATTGTCAAATATTTTACG-AACATCTGTAC
* * * * * *
1288709 ATAAATCACAAGAAAAGATGAATGTGTTGTCAAATGTTTTATGAAC
1 AGAAACCACAAGAAATGATGAATGTATTGTCAAATATTTTACGAAC
1288755 CAATTATTCT
Statistics
Matches: 81, Mismatches: 16, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
53 6 0.07
54 69 0.85
55 6 0.07
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (54 bp):
AGAAACCACAAGAAATGATGAATGTATTGTCAAATATTTTACGAACATCTGTAC
Found at i:1289146 original size:22 final size:22
Alignment explanation
Indices: 1289118--1289174 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
1289108 ACATCTACAT
1289118 TCTTCAAAGATGATAGATT-TAC
1 TCTTCAAAGATGATAGATTCT-C
*
1289140 TCTTCAAAGATGATGGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
1289162 TTTTCAAAGATGA
1 TCTTCAAAGATGA
1289175 AAGTTTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 31 0.97
23 1 0.03
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:1290393 original size:113 final size:113
Alignment explanation
Indices: 1290027--1290663 Score: 825
Period size: 113 Copynumber: 5.6 Consensus size: 113
1290017 TCCAGAAGAT
*
1290027 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAGTTCATAATGAGAAGAACTTGTTCAA
1 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
* *
1290092 CCTTTTGCTCAAATCCATCAC-CAGATGGATCAACATTGCCAGGTAGAG
66 CCTTTTGCTCGAATTCATCACTC-GATGGATCAACATTGCCAGGTAGAG
*
1290140 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAGTTCATAATGAGAAGAACTTGTTCAA
1 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
*
1290205 CCTTTTGCTCGAATTC-TCACTCAATGGATCAACATTGCCAGGTAGAG
66 CCTTTTGCTCGAATTCATCACTCGATGGATCAACATTGCCAGGTAGAG
* **
1290252 TTCATAATGAGAAGAACTCATCTGAAGAAGAAAGGGGAAGTTCATAATGAGAAGAACTTGTTCAA
1 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
1290317 CCTTTTGCTCGAATTCATCACTCGATGGATCAACATTGCCAGGTAGAG
66 CCTTTTGCTCGAATTCATCACTCGATGGATCAACATTGCCAGGTAGAG
* *
1290365 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATCATGAGAAGAACTTGTTTAA
1 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
* * * *
1290430 CCTTTTGCTCG-ATTC-T-A-TC-A-GCACCAACATTTCCAGAGGA-AG
66 CCTTTTGCTCGAATTCATCACTCGATGGATCAACATTGCCAG-GTAGAG
*
1290472 TTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
1 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
* * * * * *
1290536 -CTTCTTACTCG-ATTCTATCACAGAAGAAGATAGATCAGCATCAACGTTTCCAGATAGAG
66 CCTT-TTGCTCGAATTC-ATCAC---------TCGAT--GGATCAACATTGCCAGGTAGAG
*
1290595 TTCATAATGAGAAGAACTCATCTGAAG--GGAAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
1 TTCATAATGAGAAGAACTCATCTGAAGAAGG-AAGAAGAAGTTCATAATGAGAAGAACTTGTTC-
1290658 AACCTT
64 AACCTT
1290664 GCCTTAATTC
Statistics
Matches: 471, Mismatches: 28, Indels: 38
0.88 0.05 0.07
Matches are distributed among these distances:
105 3 0.01
106 45 0.10
107 41 0.09
108 4 0.01
109 3 0.01
110 1 0.00
111 1 0.00
112 111 0.24
113 179 0.38
119 1 0.00
120 1 0.00
122 3 0.01
123 73 0.15
124 2 0.00
125 3 0.01
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (113 bp):
TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
CCTTTTGCTCGAATTCATCACTCGATGGATCAACATTGCCAGGTAGAG
Found at i:1290418 original size:225 final size:220
Alignment explanation
Indices: 1290027--1290663 Score: 838
Period size: 225 Copynumber: 2.8 Consensus size: 220
1290017 TCCAGAAGAT
*
1290027 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAGTTCATAATGAGAAGAACTTGTTCAA
1 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
* *
1290092 CCTTTTGCTCAAATCCATCAC-CAGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAA
66 CCTTTTGCTCGAATTCATCACTC-GATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAA
*
1290156 CTCATCTGAAGAAGGAAGAGGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTC
130 CTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCG-ATTC
* * *
1290221 TCACTCAATGGATCAACATTGCCAG-GTAGAG
194 T-A-TC-A-GCACCAACATTGCCAGAGGA-AG
* **
1290252 TTCATAATGAGAAGAACTCATCTGAAGAAGAAAGGGGAAGTTCATAATGAGAAGAACTTGTTCAA
1 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
1290317 CCTTTTGCTCGAATTCATCACTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAAC
66 CCTTTTGCTCGAATTCATCACTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAAC
* *
1290382 TCATCTGAAGAAGGAAGAAGAAGTTCATCATGAGAAGAACTTGTTTAACCTTTTGCTCGATTCTA
131 TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGATTCTA
*
1290447 TCAGCACCAACATTTCCAGAGGAAG
196 TCAGCACCAACATTGCCAGAGGAAG
*
1290472 TTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
1 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
* * * * * *
1290536 -CTTCTTACTCG-ATTCTATCACAGAAGAAGATAGATCAGCATCAACGTTTCCAGATAGAGTTCA
66 CCTT-TTGCTCGAATTC-ATCAC---------TCGAT--GGATCAACATTGCCAGGTAGAGTTCA
*
1290599 TAATGAGAAGAACTCATCTGAAG--GGAAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAAACC
118 TAATGAGAAGAACTCATCTGAAGAAGG-AAGAAGAAGTTCATAATGAGAAGAACTTGTTC-AACC
1290662 TT
181 TT
1290664 GCCTTAATTC
Statistics
Matches: 369, Mismatches: 26, Indels: 29
0.87 0.06 0.07
Matches are distributed among these distances:
218 7 0.02
219 45 0.12
220 41 0.11
221 3 0.01
222 2 0.01
223 1 0.00
224 5 0.01
225 178 0.48
226 1 0.00
228 6 0.02
229 29 0.08
230 51 0.14
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (220 bp):
TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
CCTTTTGCTCGAATTCATCACTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAAC
TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGATTCTA
TCAGCACCAACATTGCCAGAGGAAG
Found at i:1290533 original size:20 final size:20
Alignment explanation
Indices: 1290471--1290534 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
1290461 TCCAGAGGAA
1290471 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* ***
1290491 -ATC-TGAA-GAGGAAGAAGAA
1 GTTCAT-AATGA-GAAGAACTT
1290510 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
1290530 GTTCA
1 GTTCA
1290535 ACTTCTTACT
Statistics
Matches: 31, Mismatches: 8, Indels: 10
0.63 0.16 0.20
Matches are distributed among these distances:
18 3 0.10
19 10 0.32
20 15 0.48
21 3 0.10
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.25
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:1290985 original size:16 final size:16
Alignment explanation
Indices: 1290952--1291013 Score: 58
Period size: 16 Copynumber: 4.0 Consensus size: 16
1290942 AAGACACTAG
**
1290952 TTTTT-TTTATTTGGT
1 TTTTTCTTTATTTATT
1290967 TTTTTCTTTATTTATT
1 TTTTTCTTTATTTATT
1290983 TTTATTC-TTA-TTATT
1 TTT-TTCTTTATTTATT
* *
1290998 ATTTTATTTATTTATT
1 TTTTTCTTTATTTATT
1291014 ATTATATTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
14 2 0.05
15 15 0.38
16 19 0.49
17 3 0.08
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTTTCTTTATTTATT
Found at i:1290998 original size:3 final size:3
Alignment explanation
Indices: 1290978--1291057 Score: 92
Period size: 3 Copynumber: 26.3 Consensus size: 3
1290968 TTTTCTTTAT
* *
1290978 TTA TTT TTA TTC TTA TTA TTA TT- TTA TTTA TTTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA -TTA TTA TTA TTA TTA
*
1291023 TTTA TTA TTA TTA GTA TTA TTA TTA TTA TTA TTA T
1 -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1291058 AGGCCCAAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
2 4 0.06
3 53 0.79
4 10 0.15
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1291011 original size:31 final size:34
Alignment explanation
Indices: 1290968--1291056 Score: 98
Period size: 34 Copynumber: 2.7 Consensus size: 34
1290958 TTATTTGGTT
*
1290968 TTTTCTTTATTTATT-TT-TATT-CTTATTATTA
1 TTTTATTTATTTATTATTATATTACTTATTATTA
*
1290999 TTTTATTTATTTATTATTATATTATTTATTATTA
1 TTTTATTTATTTATTATTATATTACTTATTATTA
*
1291033 TTAGTA-TTA-TTATTATTATTATTA
1 TT-TTATTTATTTATTATTA-TATTA
1291057 TAGGCCCAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
31 14 0.28
32 2 0.04
33 13 0.26
34 19 0.38
35 2 0.04
ACGTcount: A:0.27, C:0.02, G:0.01, T:0.70
Consensus pattern (34 bp):
TTTTATTTATTTATTATTATATTACTTATTATTA
Found at i:1292973 original size:23 final size:24
Alignment explanation
Indices: 1292934--1292978 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
1292924 TTTTTTCTGA
*
1292934 TATTTCTAAATAAATAA-ATATCT
1 TATTTATAAATAAATAATATATCT
1292957 TATTTATAAA-AATATAATATAT
1 TATTTATAAATAA-ATAATATAT
1292979 ATATATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 2 0.11
23 13 0.68
24 4 0.21
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (24 bp):
TATTTATAAATAAATAATATATCT
Found at i:1293026 original size:2 final size:2
Alignment explanation
Indices: 1292968--1293015 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
1292958 ATTTATAAAA
1292968 AT AT A- 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 AT
1293009 AT AT AT A
1 AT AT AT A
1293016 AGTTAATATA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1293028 original size:150 final size:149
Alignment explanation
Indices: 1292716--1293028 Score: 375
Period size: 150 Copynumber: 2.1 Consensus size: 149
1292706 TTTAGGAATT
*
1292716 TTAATATTTATTTACTTTTTAATATTAAGAAAATGATTGTCTTAAAGCAACTAGAAGTCTTTTTC
1 TTAATA-TTATTTACTTTTTAATATTAAGAAAATGATTGTCTTAAAACAACTAGAAGTCTTTTTC
* * * *
1292781 TGATATTTCTAAATAACTAAATATCCTACTTTTACAAATTATATATATATTAATTTATTTTAATT
65 TGATATTTCTAAATAAATAAATATCCTACTTTTAAAAATTATATATATATTAATATATTATAATT
* * * * *
1292846 ATTTTTAGAGAAATGTTTTA
130 ATATATAGAGAAATATATAA
* *
1292866 TTAATATTTATTTATTTTTTAATATTAAGAAAATGATTGTCTTAAAACAACTAGAAGTTTTTTTC
1 TTAATA-TTATTTACTTTTTAATATTAAGAAAATGATTGTCTTAAAACAACTAGAAGTCTTTTTC
*
1292931 TGATATTTCTAAATAAATAAATATCTTA-TTTATAAAAA-TATA-ATATA-TATATATATATATA
65 TGATATTTCTAAATAAATAAATATCCTACTTT-TAAAAATTATATATATATTA-ATATAT-TATA
* * *
1292992 TATATATATATATATATATATATAA
127 -AT-TATATATAGAGAAATATATAA
1293017 GTTAATA-TATTT
1 -TTAATATTATTT
1293029 TTCTTAAAAT
Statistics
Matches: 141, Mismatches: 16, Indels: 12
0.83 0.09 0.07
Matches are distributed among these distances:
147 2 0.01
148 10 0.07
149 10 0.07
150 100 0.71
151 13 0.09
152 6 0.04
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.48
Consensus pattern (149 bp):
TTAATATTATTTACTTTTTAATATTAAGAAAATGATTGTCTTAAAACAACTAGAAGTCTTTTTCT
GATATTTCTAAATAAATAAATATCCTACTTTTAAAAATTATATATATATTAATATATTATAATTA
TATATAGAGAAATATATAA
Found at i:1297660 original size:18 final size:16
Alignment explanation
Indices: 1297637--1297670 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
1297627 ACTTGAGTTG
1297637 CAAATCCAGAATTGTTAA
1 CAAATCCA-AATT-TTAA
1297655 CAAATCCAAATTTTAA
1 CAAATCCAAATTTTAA
1297671 TTGAATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 4 0.25
18 8 0.50
ACGTcount: A:0.47, C:0.18, G:0.06, T:0.29
Consensus pattern (16 bp):
CAAATCCAAATTTTAA
Found at i:1301471 original size:31 final size:31
Alignment explanation
Indices: 1301403--1301471 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
1301393 TTCTAATCTT
* * **
1301403 ATATGATATTAAAATAGTAATAAAATATATC
1 ATATCATATGAAAATAACAATAAAATATATC
*
1301434 ACATCATATGAAAATAACAATAAAATA-ATTC
1 ATATCATATGAAAATAACAATAAAATATA-TC
1301465 ATATCAT
1 ATATCAT
1301472 CGTAGAATGA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
30 1 0.03
31 30 0.97
ACGTcount: A:0.55, C:0.09, G:0.04, T:0.32
Consensus pattern (31 bp):
ATATCATATGAAAATAACAATAAAATATATC
Found at i:1304160 original size:20 final size:21
Alignment explanation
Indices: 1304121--1304161 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1304111 TTACTTAAAT
* *
1304121 ATTTAATATATAAATTATTAA
1 ATTTAATATACAAATAATTAA
1304142 ATTTAA-ATACAAATAATTAA
1 ATTTAATATACAAATAATTAA
1304162 TCACTCTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTTAATATACAAATAATTAA
Found at i:1307552 original size:31 final size:30
Alignment explanation
Indices: 1307517--1307575 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
1307507 ATGGTTCAAA
* *
1307517 CCGATTTTGCCGGTTTTCAGCCGGGTTCACC
1 CCGATTTTACCGGTTATCAGCC-GGTTCACC
1307548 CCGATTTTACCGGTTATCAGCCGGTTCA
1 CCGATTTTACCGGTTATCAGCCGGTTCA
1307576 TTGCCAGCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 6 0.23
31 20 0.77
ACGTcount: A:0.14, C:0.31, G:0.24, T:0.32
Consensus pattern (30 bp):
CCGATTTTACCGGTTATCAGCCGGTTCACC
Found at i:1307717 original size:14 final size:13
Alignment explanation
Indices: 1307689--1307776 Score: 54
Period size: 14 Copynumber: 6.2 Consensus size: 13
1307679 CAAGATACAA
*
1307689 TTTTTTTATCCATT
1 TTTTTTTAT-TATT
1307703 TGTTTTTTATTATT
1 T-TTTTTTATTATT
1307717 TTTATTATTA-TATT
1 TTT-TT-TTATTATT
1307731 ATTTTTATTATTATAT
1 -TTTTT-TTATTAT-T
*
1307747 TATTTTACTATTATT
1 T-TTTT-TTATTATT
*
1307762 TTTATTT-TTATT
1 TTTTTTTATTATT
1307774 TTT
1 TTT
1307777 ATATTAATAT
Statistics
Matches: 63, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
12 8 0.13
13 3 0.05
14 20 0.32
15 20 0.32
16 12 0.19
ACGTcount: A:0.22, C:0.03, G:0.01, T:0.74
Consensus pattern (13 bp):
TTTTTTTATTATT
Found at i:1307724 original size:3 final size:3
Alignment explanation
Indices: 1307709--1307802 Score: 97
Period size: 3 Copynumber: 32.7 Consensus size: 3
1307699 CATTTGTTTT
* *
1307709 TTA TTA TTT TTA TTA TTA -TA TTA TTT TTA TTA TTA -TA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
1307754 CTA TTA TTT TTA TTT TTA TTT TTA -TA TTA ATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1307801 TT
1 TT
1307803 TACATTACAG
Statistics
Matches: 73, Mismatches: 14, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
2 8 0.11
3 65 0.89
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:1307732 original size:17 final size:17
Alignment explanation
Indices: 1307710--1307803 Score: 120
Period size: 17 Copynumber: 5.5 Consensus size: 17
1307700 ATTTGTTTTT
1307710 TATTATTTTTATTATTA
1 TATTATTTTTATTATTA
1307727 TATTATTTTTATTATTA
1 TATTATTTTTATTATTA
1307744 TATTATTTTACTATTATT-
1 TATTATTTT--TATTATTA
*
1307762 T-TTATTTTTATTTTTA
1 TATTATTTTTATTATTA
* *
1307778 TATTAATATTATTATTA
1 TATTATTTTTATTATTA
1307795 TTATTATTT
1 -TATTATTT
1307804 ACATTACAGG
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
15 6 0.09
16 1 0.02
17 45 0.68
18 7 0.11
19 7 0.11
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (17 bp):
TATTATTTTTATTATTA
Found at i:1307805 original size:51 final size:50
Alignment explanation
Indices: 1307712--1307809 Score: 144
Period size: 51 Copynumber: 1.9 Consensus size: 50
1307702 TTGTTTTTTA
* *
1307712 TTATTTTTATTATTATATTATTTTTATTATTATATTATTTTACTATTATTT
1 TTATTTTTATTATTATATTAATATTATTATTATATTATTTTAC-ATTATTT
*
1307763 TTATTTTTATTTTTATATTAATATTATTATTATTATTA-TTTACATTA
1 TTATTTTTATTATTATATTAATATTATTATTA-TATTATTTTACATTA
1307810 CAGGCCCAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
50 4 0.09
51 34 0.79
52 5 0.12
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (50 bp):
TTATTTTTATTATTATATTAATATTATTATTATATTATTTTACATTATTT
Found at i:1308344 original size:19 final size:19
Alignment explanation
Indices: 1308320--1308366 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
1308310 GTCTCGATCA
1308320 TCGCCGGAAGCACCAAACG
1 TCGCCGGAAGCACCAAACG
1308339 TCGCCGGAAGCACCAAACG
1 TCGCCGGAAGCACCAAACG
1308358 TCGCCGGAA
1 TCGCCGGAA
1308367 AACAAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.30, C:0.36, G:0.28, T:0.06
Consensus pattern (19 bp):
TCGCCGGAAGCACCAAACG
Found at i:1313377 original size:15 final size:15
Alignment explanation
Indices: 1313357--1313388 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1313347 GATCAATACC
1313357 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
1313372 TTTTGCATACATTCA
1 TTTTGCATACATGCA
1313387 TT
1 TT
1313389 ATTCATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:1320230 original size:23 final size:23
Alignment explanation
Indices: 1320204--1320250 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1320194 AGATCCCGTC
1320204 ACTTCGAATCTTGAGAGAGGTAA
1 ACTTCGAATCTTGAGAGAGGTAA
*
1320227 ACTTTGAATCTTGAGAGAGGTAA
1 ACTTCGAATCTTGAGAGAGGTAA
1320250 A
1 A
1320251 ATTGGATGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.28
Consensus pattern (23 bp):
ACTTCGAATCTTGAGAGAGGTAA
Found at i:1320612 original size:11 final size:11
Alignment explanation
Indices: 1320596--1320653 Score: 86
Period size: 11 Copynumber: 5.5 Consensus size: 11
1320586 CTTGAAGAAG
1320596 AAAAAAAATGA
1 AAAAAAAATGA
1320607 AAAAAAAATG-
1 AAAAAAAATGA
1320617 -AAAAAAATGA
1 AAAAAAAATGA
1320627 AAAAAAAA-GA
1 AAAAAAAATGA
1320637 AAAAAAAATAGA
1 AAAAAAAAT-GA
1320649 AAAAA
1 AAAAA
1320654 TGGTCAAGCT
Statistics
Matches: 43, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
9 9 0.21
10 10 0.23
11 17 0.40
12 7 0.16
ACGTcount: A:0.84, C:0.00, G:0.09, T:0.07
Consensus pattern (11 bp):
AAAAAAAATGA
Found at i:1320631 original size:30 final size:31
Alignment explanation
Indices: 1320595--1320653 Score: 102
Period size: 30 Copynumber: 1.9 Consensus size: 31
1320585 GCTTGAAGAA
*
1320595 GAAAAAAAATGAAAAAAAAAT-GAAAAAAAT
1 GAAAAAAAAAGAAAAAAAAATAGAAAAAAAT
1320625 GAAAAAAAAAGAAAAAAAAATAGAAAAAA
1 GAAAAAAAAAGAAAAAAAAATAGAAAAAA
1320654 TGGTCAAGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 20 0.74
31 7 0.26
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (31 bp):
GAAAAAAAAAGAAAAAAAAATAGAAAAAAAT
Found at i:1320643 original size:20 final size:20
Alignment explanation
Indices: 1320593--1320653 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 20
1320583 ATGCTTGAAG
1320593 AAGAAAAAAAATGAAAAAAA
1 AAGAAAAAAAATGAAAAAAA
1320613 AATG-AAAAAAATGAAAAAAA
1 AA-GAAAAAAAATGAAAAAAA
1320633 AAGAAAAAAAAATAGAAAAAA
1 AAG-AAAAAAAAT-GAAAAAA
1320654 TGGTCAAGCT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.03
20 20 0.54
21 9 0.24
22 7 0.19
ACGTcount: A:0.84, C:0.00, G:0.10, T:0.07
Consensus pattern (20 bp):
AAGAAAAAAAATGAAAAAAA
Found at i:1321031 original size:22 final size:22
Alignment explanation
Indices: 1321000--1321042 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1320990 CAAGTTTATT
*
1321000 TTTTCTAAATTCAATTTATTCA
1 TTTTCGAAATTCAATTTATTCA
1321022 TTTTCGAAATTCAATTTATTC
1 TTTTCGAAATTCAATTTATTC
1321043 TTTCATATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTTCGAAATTCAATTTATTCA
Found at i:1321713 original size:20 final size:22
Alignment explanation
Indices: 1321668--1321730 Score: 99
Period size: 22 Copynumber: 2.9 Consensus size: 22
1321658 ACATCTACAT
1321668 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
1321690 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
* * *
1321712 TTTTCAAAGAAGAAAGATT
1 TCTTCAAAGATGATAGATT
1321731 TATTGGATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:1322106 original size:118 final size:118
Alignment explanation
Indices: 1321922--1322448 Score: 722
Period size: 118 Copynumber: 4.5 Consensus size: 118
1321912 CATTTAATGG
1321922 ATCAGCATTTCCAGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
1 ATCAGCATTTCCAGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
*
1321987 ATGAGAAGAACTTGTTCAACTTTTTGCTCGAATTCATCACTCGATGGATCAGC
66 ATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAGC
1322040 ATCAGCATTTCCAGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
1 ATCAGCATTTCCAGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
*
1322105 ATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAAC
66 ATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAGC
* * *
1322158 ATCAACATTTCCAGTAGAGTTCACAATGAGAAGAACTCATTTGAAGAAGGAAGAAGAAGTTCATA
1 ATCAGCATTTCCAGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
*
1322223 ATGAGAAGAGCTTGTTCAACCTTTTGCTCGAATTCATCACTC----GAT--GC
66 ATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAGC
* * *
1322270 ATCAACTTTTCCAG-AGAAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCA
1 ATCAGCATTTCCAGTAG--AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* * * *
1322333 TAATGAGAAGAGCTTGTTCAACC-TTTGCAT-G-ACTCTATCAC-AGAAGGAGATAAATCAGC
64 TAATGAGAAGAACTTGTTCAACCTTTTGC-TCGAATTC-ATCACTCG-ATG-G----ATCAGC
* *
1322392 ATC-GACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAA
1 ATCAG-CATTTCCAGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
1322449 CTTGTTCAAC
Statistics
Matches: 373, Mismatches: 17, Indels: 35
0.88 0.04 0.08
Matches are distributed among these distances:
110 3 0.01
111 13 0.03
112 54 0.14
113 26 0.07
114 3 0.01
116 1 0.00
118 219 0.59
120 2 0.01
121 34 0.09
122 16 0.04
123 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (118 bp):
ATCAGCATTTCCAGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAGC
Found at i:1322811 original size:3 final size:3
Alignment explanation
Indices: 1322796--1322889 Score: 106
Period size: 3 Copynumber: 32.7 Consensus size: 3
1322786 CATTTGTTTT
*
1322796 TTA TTA TTT TTA TTA TTA -TA TTA TTA TTA TTA TTA TT- TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
1322841 CTA TTA TTT TTA TTT TTA -TA TTA TTA ATA TTA TTA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1322888 TT
1 TT
1322890 TACATTACAG
Statistics
Matches: 75, Mismatches: 12, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
2 8 0.11
3 67 0.89
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1323903 original size:5 final size:5
Alignment explanation
Indices: 1323893--1323918 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1323883 TGATCTCATA
1323893 ATTTT ATTTT ATTTT ATTTT ATTTT A
1 ATTTT ATTTT ATTTT ATTTT ATTTT A
1323919 GTCCTTTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:1324222 original size:20 final size:20
Alignment explanation
Indices: 1324181--1324237 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
1324171 ATAATATAGT
* *
1324181 TTTAATTATATTTATTTTTG
1 TTTATTTATATTTATTTATG
1324201 TTTATTTATATTT-TTATATG
1 TTTATTTATATTTATT-TATG
*
1324221 TTTA--TATATTTAATTAT
1 TTTATTTATATTTATTTAT
1324238 TATTTTTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
18 10 0.31
19 3 0.09
20 19 0.59
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (20 bp):
TTTATTTATATTTATTTATG
Found at i:1329872 original size:29 final size:30
Alignment explanation
Indices: 1329802--1329860 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
1329792 CAATTTAAGG
1329802 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
1329833 CAAAATGTTTTTGGACTT-AATTGAATTT
1 CAAAATGTTTTTGGACTTGAATTGAATTT
1329861 GATCAAAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 10 0.36
30 12 0.43
31 6 0.21
ACGTcount: A:0.32, C:0.07, G:0.17, T:0.44
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:1330004 original size:22 final size:23
Alignment explanation
Indices: 1329970--1330012 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1329960 GCATCCCTGC
1329970 AGTGAATCCATGCACC-TGCACT
1 AGTGAATCCATGCACCATGCACT
* *
1329992 AGTGCATCGATGCACCATGCA
1 AGTGAATCCATGCACCATGCA
1330013 GTGCATCCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (23 bp):
AGTGAATCCATGCACCATGCACT
Found at i:1330072 original size:20 final size:20
Alignment explanation
Indices: 1330047--1330120 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
1330037 AATGCAATTA
*
1330047 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTGCT
* **
1330067 GTGCATCGATGTATCAAGGCT
1 GTGCATCGATGCATC-CTGCT
*
1330088 ATGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
*
1330108 GTGCATCCATGCA
1 GTGCATCGATGCA
1330121 CGAAGGTTGC
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 28 0.65
21 15 0.35
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.30
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGCT
Found at i:1330516 original size:34 final size:32
Alignment explanation
Indices: 1330477--1330546 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
1330467 TTTTGTAAAG
*
1330477 GGGAAAGGTTCTAGTTAATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGTTAATCCCG-G-AAAAACTA
*
1330511 GGGAAAGGTTCTAGTTTATCCCGGAAAAACTA
1 GGGAAAGGTTCTAGTTAATCCCGGAAAAACTA
1330543 GGGA
1 GGGA
1330547 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTCTAGTTAATCCCGGAAAAACTA
Found at i:1348067 original size:23 final size:23
Alignment explanation
Indices: 1348041--1348104 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
1348031 CAGCTCATAT
1348041 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCTAAGTGCCACGTAG
* *
1348064 AATTGCACCGAAGTGCCGCGTAG
1 AATTGCACCTAAGTGCCACGTAG
1348087 AATTGCACCGT-AGTGCCA
1 AATTGCACC-TAAGTGCCA
1348105 TATAATATTG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.28, C:0.27, G:0.25, T:0.20
Consensus pattern (23 bp):
AATTGCACCTAAGTGCCACGTAG
Found at i:1348246 original size:103 final size:103
Alignment explanation
Indices: 1348120--1348337 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
1348110 TATTGTCCAT
* *
1348120 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACAA
*
1348185 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
1348223 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACAA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACAA
1348288 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
1348326 AAGGACCACATA
1 AAGGACCACATA
1348338 GACCCTCTAC
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACAA
GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1348911 original size:21 final size:21
Alignment explanation
Indices: 1348887--1348929 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1348877 TCATATTCGT
*
1348887 TTGAGGGGGTATCAATTCCCC
1 TTGAAGGGGTATCAATTCCCC
* *
1348908 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCAATTCCCC
1348929 T
1 T
1348930 AGCCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCAATTCCCC
Found at i:1350271 original size:15 final size:15
Alignment explanation
Indices: 1350251--1350281 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1350241 CAACAAATAG
1350251 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
1350266 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
1350281 A
1 A
1350282 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:1352456 original size:41 final size:41
Alignment explanation
Indices: 1352399--1352482 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
1352389 AAGGTATGTA
1352399 TCAACATAATCGGCAGTAACAAGATAGTTTGGTTGCTTTGC
1 TCAACATAATCGGCAGTAACAAGATAGTTTGGTTGCTTTGC
*
1352440 TCAACATCATCGGCAGTAACAAGATAGTTTGGTTGCTTTGC
1 TCAACATAATCGGCAGTAACAAGATAGTTTGGTTGCTTTGC
1352481 TC
1 TC
1352483 CTGTTATTCA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.32
Consensus pattern (41 bp):
TCAACATAATCGGCAGTAACAAGATAGTTTGGTTGCTTTGC
Found at i:1354409 original size:12 final size:12
Alignment explanation
Indices: 1354392--1354416 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1354382 CTAATCACCA
1354392 TAATACTGTGAT
1 TAATACTGTGAT
1354404 TAATACTGTGAT
1 TAATACTGTGAT
1354416 T
1 T
1354417 CCTTTAGCTT
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:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (12 bp):
TAATACTGTGAT
Found at i:1355950 original size:26 final size:26
Alignment explanation
Indices: 1355905--1355958 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
1355895 TATAAACAGT
* *
1355905 TAATCAAATCAATTTCTCAAATCAGC
1 TAATCAAATCAATTGCTCAAACCAGC
* *
1355931 TAATCAAATCAGTTGGTCAAACCAGC
1 TAATCAAATCAATTGCTCAAACCAGC
1355957 TA
1 TA
1355959 CTGGAATCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (26 bp):
TAATCAAATCAATTGCTCAAACCAGC
Found at i:1357661 original size:21 final size:20
Alignment explanation
Indices: 1357633--1357671 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1357623 CACTACAGGA
*
1357633 ATTTATGGCATCGACAAAAG
1 ATTTATGGCATCAACAAAAG
*
1357653 ATTTCATGGCTTCAACAAA
1 ATTT-ATGGCATCAACAAA
1357672 GACCTTGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (20 bp):
ATTTATGGCATCAACAAAAG
Found at i:1360306 original size:23 final size:23
Alignment explanation
Indices: 1360247--1360307 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 23
1360237 AAATATCCCA
* *
1360247 AAGGACCGTGTAGAAATGTCCTG
1 AAGGACAGCGTAGAAATGTCCTG
* * * *
1360270 AAGAACAACATAGAATTGTCCTG
1 AAGGACAGCGTAGAAATGTCCTG
*
1360293 AAGGACTGCGTAGAA
1 AAGGACAGCGTAGAA
1360308 CCCTTGACTC
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.38, C:0.16, G:0.26, T:0.20
Consensus pattern (23 bp):
AAGGACAGCGTAGAAATGTCCTG
Found at i:1367250 original size:24 final size:23
Alignment explanation
Indices: 1367202--1367253 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 23
1367192 AACTGCCACC
*
1367202 TAGAATTGCACCGAAGTGTCGCG
1 TAGAATTGCACCGAAGTGTCACG
1367225 TAGAATATGCACCGAAGTG-CAACG
1 TAGAAT-TGCACCGAAGTGTC-ACG
1367249 TAGAA
1 TAGAA
1367254 ATTGTCCCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 7 0.27
24 19 0.73
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.19
Consensus pattern (23 bp):
TAGAATTGCACCGAAGTGTCACG
Found at i:1367263 original size:24 final size:23
Alignment explanation
Indices: 1367236--1367359 Score: 81
Period size: 23 Copynumber: 5.3 Consensus size: 23
1367226 AGAATATGCA
*
1367236 CCGAAGTG-CAACGTAGAAATTGTC
1 CCGAAG-GACAACATAGAAA-TGTC
*
1367260 CCGAAGGACCACATAGAAATGTC
1 CCGAAGGACAACATAGAAATGTC
***
1367283 CCGAAGGATC-GTGTAGAAATGTC
1 CCGAAGGA-CAACATAGAAATGTC
* * * **
1367306 CTGAATGACCACATAGAGTTGTC
1 CCGAAGGACAACATAGAAATGTC
* * * *
1367329 CCGAATGACCACATAGAATTATC
1 CCGAAGGACAACATAGAAATGTC
1367352 CCGAAGGA
1 CCGAAGGA
1367360 TCGTGTATAA
Statistics
Matches: 81, Mismatches: 16, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
22 1 0.01
23 64 0.79
24 16 0.20
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19
Consensus pattern (23 bp):
CCGAAGGACAACATAGAAATGTC
Found at i:1367286 original size:23 final size:23
Alignment explanation
Indices: 1367249--1367359 Score: 114
Period size: 23 Copynumber: 4.8 Consensus size: 23
1367239 AAGTGCAACG
1367249 TAGAAATTGTCCCGAAGGACCACA
1 TAGAAA-TGTCCCGAAGGACCACA
* ***
1367273 TAGAAATGTCCCGAAGGATCGTG
1 TAGAAATGTCCCGAAGGACCACA
* *
1367296 TAGAAATGTCCTGAATGACCACA
1 TAGAAATGTCCCGAAGGACCACA
** *
1367319 TAGAGTTGTCCCGAATGACCACA
1 TAGAAATGTCCCGAAGGACCACA
* *
1367342 TAGAATTATCCCGAAGGA
1 TAGAAATGTCCCGAAGGA
1367360 TCGTGTATAA
Statistics
Matches: 71, Mismatches: 16, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
23 65 0.92
24 6 0.08
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.21
Consensus pattern (23 bp):
TAGAAATGTCCCGAAGGACCACA
Found at i:1367656 original size:3 final size:3
Alignment explanation
Indices: 1367650--1367685 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1367640 TTCTTTTCAT
1367650 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1367686 TATTCTAGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1373881 original size:18 final size:18
Alignment explanation
Indices: 1373853--1373917 Score: 112
Period size: 18 Copynumber: 3.6 Consensus size: 18
1373843 TTTATATCTA
*
1373853 GAATAGGCACAAGTCTTG
1 GAATAGTCACAAGTCTTG
*
1373871 GAATACTCACAAGTCTTG
1 GAATAGTCACAAGTCTTG
1373889 GAATAGTCACAAGTCTTG
1 GAATAGTCACAAGTCTTG
1373907 GAATAGTCACA
1 GAATAGTCACA
1373918 CTTGTATAGC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (18 bp):
GAATAGTCACAAGTCTTG
Found at i:1392357 original size:27 final size:27
Alignment explanation
Indices: 1392300--1392357 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
1392290 CTATCACCCA
* *
1392300 TTTCTCTCTCACTTTTATCTTTATCTT
1 TTTCTCTCTCACTTTTATATCTATCTT
* *
1392327 TTTCTCTCTCATTTTTTTATCT-TCTT
1 TTTCTCTCTCACTTTTATATCTATCTT
1392353 CTTTC
1 -TTTC
1392358 ATTTTCCCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 4 0.15
27 22 0.85
ACGTcount: A:0.09, C:0.26, G:0.00, T:0.66
Consensus pattern (27 bp):
TTTCTCTCTCACTTTTATATCTATCTT
Found at i:1392361 original size:21 final size:23
Alignment explanation
Indices: 1392301--1392362 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 23
1392291 TATCACCCAT
*
1392301 TTCTCTCTCACTTTTATCTTTATCTTT
1 TTCTCTCTCA--TTT-T-TTTATCTTC
1392328 TTCTCTCTCATTTTTTTATCTTC
1 TTCTCTCTCATTTTTTTATCTTC
1392351 TTCT-T-TCATTTT
1 TTCTCTCTCATTTT
1392363 CCCCATAGCC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
21 7 0.21
22 1 0.03
23 12 0.35
24 1 0.03
25 3 0.09
27 10 0.29
ACGTcount: A:0.10, C:0.24, G:0.00, T:0.66
Consensus pattern (23 bp):
TTCTCTCTCATTTTTTTATCTTC
Found at i:1413420 original size:911 final size:910
Alignment explanation
Indices: 1411661--1413463 Score: 2585
Period size: 911 Copynumber: 2.0 Consensus size: 910
1411651 CGCAAGCAAG
* * * *
1411661 ATATATAAGTCTCTAAAATAAATAGGAATGGTCCCATGAAATCAATACCCCAAACATCAAAGAGC
1 ATATATAAGTATCCAAAAGAAATAGGAATGGTCCCACGAAATCAATACCCCAAACATCAAAGAGC
* * *
1411726 TCGATCTCCAGAATGTTTCACAAAGGCATTTCGTGTCATCTAGAAATCTTCCCAGTGCGCTGGCA
66 TCGATATCCAAAATGTTTCACAAAGGCATTTCGTGTCATCTAGAAATCTTCCCAGTGCACTGGCA
* * * *
1411791 TCTATCACACGCTTTGTAAAACTCGTGAGCATCCTTGAACAGTGAAGGCCAATAAAAGCCAGATT
131 TCTATCACACACTTTGCAAAACTCATGAGCATCCTTGAACAATGAAGGCCAATAAAAGCCAGATT
* * * * * * *
1411856 GAAGGACCTTGGTAGCGGTCCTCATACCTCCAAAATGGCCTCCATAGGGGCTGTGTGACAATGGT
196 GAAGAACCCTGGCAGCGGTCCTCACACCTCCAAAATGGCCTCCATAGAGGCTGTGTGAAAATGAT
* * * *
1411921 GTAGAATGTTCCTTTGCTCATCCTCAGAGACACAACATAGAATCATTTGGTATGCGCATTGTTCG
261 GTAGAATGTTCCTTTACTCATCATCAGAGACACAACATAGAATCATTTGGTATGCACATTATTCG
* * *
1411986 AATAAATATGGTTGGTACCAGAAATAGAACTTGGCACTGTGCTGGAACTTCCTCATACCCTAGTT
326 AATAAATATGGATGGTACCAGAAATAGAACTTGGAAATGTGCTGGAACTTCCTCATACCCTAGTT
*
1412051 GTTCAATTTATAAGGTAAAATACCACTAACAAGAAAATTGATACATGAAATTACCTTGGAAAAAG
391 GTTCAATTCATAAGGTAAAATACCACTAACAAGAAAATTGATACATGAAATTACCTTGGAAAAAG
* * * * *
1412116 CATTCGTTCATGCCATTTTTGGTTTTTTTTCTTATAAAGCTTGGCATTTTCATATGCTTGTGCTC
456 CATTAGTTCATGCCATTCTTGGTTATTATCCTTATAAAGCTTGGCATTTTCATATGCTTGTGCTC
* * * *
1412181 TAAACTCTTTTATTTCATTCATATCGAGTAATCTTCGCTCCTCAGCTAGTTGTGCGTCAAAATTT
521 TAAACTCTTCTATTTCATTCATATCGAGTAATCTTCACTCCCCAGCTAGTTGTGCATCAAAATTT
* *
1412246 AGCTTTTTGATGGCCCAATATGCCTTATGCTTTAAATCTACGGGTAAGTGGCATGCTTTCACATA
586 AGCTTTTTGATAGCCCAATATGCCTTATGCTCTAAATCTACGGGTAAGTGGCATGCTTTCACATA
* * * * * *
1412311 CACAATCTTGAAAGATGACATTTCCAAAGGTGTTTTGAATGTCGTTTAATAAGTCCAAAATGCTT
651 CACAATCTTGAAAGATGACATTCCCAAAGCTGTTTTAAATATCGTTCAATAAGCCCAAAATGCTT
* * ** * *
1412376 CATCAAGCTTTGGGGACCAATCTTTCTCCCTCGGATTCACCACCTTCTTTATAATTTGCTTAATC
716 CATCAAGCTTTGGGGACCAATCTTTCTCCATCAGATTCACCACCTTCTCCAGAATTTACTTAATC
* * * * *
1412441 TCACGGTTGGATACTTCAACTTGCCCATTGGTTTGTGGGTGATATGCCATGGCAATTTTATGTCG
781 TCACGGTTGGATACTTCAACTTGCCCACTAGTTTATGGGTAATATGCCATGGCAATGTTATGTCG
** * *
1412506 CACTCCATATTGCTGCAATGCCTTGGCAATTAGCTTGTTATCAAAATGACTCCTCTAAAAGAAAT
846 CACTCCATATCACTGCAATACCTTGGCAATTAGCTCGTTATCAAAATGACTCCTCTAAAAGAAAT
* * ** *
1412571 ATATATAAGTATCCAAAAGAAATGGGAATGGTCCGACGAAATCAATGGCCCACACATCAAAGAGC
1 ATATATAAGTATCCAAAAGAAATAGGAATGGTCCCACGAAATCAATACCCCAAACATCAAAGAGC
* * * * * *
1412636 TTGATATCCAAAATGATTTGA-AATGGTATTTCGTGTCGTCTAGAAATGTTCCCAGTGCACTGGC
66 TCGATATCCAAAATG-TTTCACAAAGGCATTTCGTGTCATCTAGAAATCTTCCCAGTGCACTGGC
*
1412700 CTCTATCACACACTTTGCAAAACTCATGAGCATCCTTGAACAATGAAGGCCAATAAAAGCCAGAT
130 ATCTATCACACACTTTGCAAAACTCATGAGCATCCTTGAACAATGAAGGCCAATAAAAGCCAGAT
* * * *
1412765 TGAAGAACCCTGGCAGTGGTCTTCGCACCTCCAAAATGGCCTCCATAGCAGGTTGTGTGAAAATG
195 TGAAGAACCCTGGCAGCGGTCCTCACACCTCCAAAATGGCCTCCATAG-AGGCTGTGTGAAAATG
* * * * * *
1412830 ATGTAGAATG-TCCATTTACTCTTTATCAGGGACACAACGTCGAATCATTTGGTTTGCACATTAT
259 ATGTAGAATGTTCC-TTTACTCATCATCAGAGACACAACATAGAATCATTTGGTATGCACATTAT
* *
1412894 TTGAATAAATATGGATGGT-CCTAGAAATAGAACTTGGAAATGTGCTGGAACTTCCTCCTACCCT
323 TCGAATAAATATGGATGGTACC-AGAAATAGAACTTGGAAATGTGCTGGAACTTCCTCATACCCT
* * *
1412958 GGTTGTTCAATTCATAAGGTAAAATACCATTAACAAGAAAATTGATACATGAAATTGCCTTGGAA
387 AGTTGTTCAATTCATAAGGTAAAATACCACTAACAAGAAAATTGATACATGAAATTACCTTGGAA
* *
1413023 AAAGCATTAGATT-ATGCCACTTCTTGG-TATTATCCTTGTAAATCTTGGCATTTTCATATGCTT
452 AAAGCATTAG-TTCATGCCA-TTCTTGGTTATTATCCTTATAAAGCTTGGCATTTTCATATGCTT
* *
1413086 GTGCTCTGAACTCTTCTATTTCATTCA-AGTCGAGTAATCTTTACTCCCCAGCTAGTTGTGCATC
515 GTGCTCTAAACTCTTCTATTTCATTCATA-TCGAGTAATCTTCACTCCCCAGCTAGTTGTGCATC
* *
1413150 AAAATTTAGCTTTTTGATATCCCAATATGCCTTATGCTCTAACTCTACGGGTAAGTGGCATGCTT
579 AAAATTTAGCTTTTTGATAGCCCAATATGCCTTATGCTCTAAATCTACGGGTAAGTGGCATGCTT
* * * *
1413215 TCCCATACACCATCTTGAAAGGTGACATTCCCAAAGCTGTTTTAAATATCGTTCGATAAGCCCAA
644 TCACATACACAATCTTGAAAGATGACATTCCCAAAGCTGTTTTAAATATCGTTCAATAAGCCCAA
* *
1413280 AATGCTTCATCAAGCTTTGGGGACCAATCTTTC-CTCATCAGTTTCACTACCTTCTCCAGAATTT
709 AATGCTTCATCAAGCTTTGGGGACCAATCTTTCTC-CATCAGATTCACCACCTTCTCCAGAATTT
*
1413344 ACTTAATCTCACGGTTGGATACTTCAGCTTGCCCACTAGTTTATGGGTAATATGCCATGGCAATG
773 ACTTAATCTCACGGTTGGATACTTCAACTTGCCCACTAGTTTATGGGTAATATGCCATGGCAATG
* *
1413409 TTGTTTCGCACTCCATATCACTGCAATACCTTGGCAATTAGCTCGTTATCAAAAT
838 TTATGTCGCACTCCATATCACTGCAATACCTTGGCAATTAGCTCGTTATCAAAAT
1413464 AAGTGCCTTC
Statistics
Matches: 785, Mismatches: 100, Indels: 15
0.87 0.11 0.02
Matches are distributed among these distances:
910 214 0.27
911 563 0.72
912 8 0.01
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (910 bp):
ATATATAAGTATCCAAAAGAAATAGGAATGGTCCCACGAAATCAATACCCCAAACATCAAAGAGC
TCGATATCCAAAATGTTTCACAAAGGCATTTCGTGTCATCTAGAAATCTTCCCAGTGCACTGGCA
TCTATCACACACTTTGCAAAACTCATGAGCATCCTTGAACAATGAAGGCCAATAAAAGCCAGATT
GAAGAACCCTGGCAGCGGTCCTCACACCTCCAAAATGGCCTCCATAGAGGCTGTGTGAAAATGAT
GTAGAATGTTCCTTTACTCATCATCAGAGACACAACATAGAATCATTTGGTATGCACATTATTCG
AATAAATATGGATGGTACCAGAAATAGAACTTGGAAATGTGCTGGAACTTCCTCATACCCTAGTT
GTTCAATTCATAAGGTAAAATACCACTAACAAGAAAATTGATACATGAAATTACCTTGGAAAAAG
CATTAGTTCATGCCATTCTTGGTTATTATCCTTATAAAGCTTGGCATTTTCATATGCTTGTGCTC
TAAACTCTTCTATTTCATTCATATCGAGTAATCTTCACTCCCCAGCTAGTTGTGCATCAAAATTT
AGCTTTTTGATAGCCCAATATGCCTTATGCTCTAAATCTACGGGTAAGTGGCATGCTTTCACATA
CACAATCTTGAAAGATGACATTCCCAAAGCTGTTTTAAATATCGTTCAATAAGCCCAAAATGCTT
CATCAAGCTTTGGGGACCAATCTTTCTCCATCAGATTCACCACCTTCTCCAGAATTTACTTAATC
TCACGGTTGGATACTTCAACTTGCCCACTAGTTTATGGGTAATATGCCATGGCAATGTTATGTCG
CACTCCATATCACTGCAATACCTTGGCAATTAGCTCGTTATCAAAATGACTCCTCTAAAAGAAAT
Found at i:1424108 original size:6 final size:6
Alignment explanation
Indices: 1424094--1424136 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
1424084 GGAAAATGAA
* * *
1424094 GATGAT GATGCT GATGCT GATGCT GATGCT GACGCT AATGCT G
1 GATGCT GATGCT GATGCT GATGCT GATGCT GATGCT GATGCT G
1424137 GTTCTGGTGA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.21, C:0.16, G:0.33, T:0.30
Consensus pattern (6 bp):
GATGCT
Found at i:1435343 original size:32 final size:30
Alignment explanation
Indices: 1435274--1435344 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 30
1435264 AAGTTTATTT
* * *
1435274 TTTAATTTAATTACTTAATTTTCAAATTAC
1 TTTAATTTAATCACTTAACTTTCAAATTAA
*
1435304 TCATAATTTAATCACTCTAACTTTCAAATTTAA
1 T-TTAATTTAATCACT-TAACTTTCAAA-TTAA
1435337 TTTAATTT
1 TTTAATTT
1435345 TAATTATATA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
30 1 0.03
31 12 0.36
32 16 0.48
33 4 0.12
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.51
Consensus pattern (30 bp):
TTTAATTTAATCACTTAACTTTCAAATTAA
Found at i:1435945 original size:29 final size:29
Alignment explanation
Indices: 1435911--1436002 Score: 87
Period size: 29 Copynumber: 3.1 Consensus size: 29
1435901 TTTGGATGAA
*
1435911 TTTGGGGATAAAATTAGAATATTCAAAAG
1 TTTGGGGATGAAATTAGAATATTCAAAAG
* * *
1435940 TTTGGGGATGAATTTAGAAAGATAGTC-ATAG
1 TTTGGGGATGAAATTAG--A-ATATTCAAAAG
* * *
1435971 TTTAGTGATGAAATTAGAATGTTCAAAAG
1 TTTGGGGATGAAATTAGAATATTCAAAAG
1436000 TTT
1 TTT
1436003 AAGGTGTAAC
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
28 4 0.08
29 22 0.45
31 18 0.37
32 5 0.10
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.35
Consensus pattern (29 bp):
TTTGGGGATGAAATTAGAATATTCAAAAG
Found at i:1436660 original size:23 final size:23
Alignment explanation
Indices: 1436630--1436699 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
1436620 TTCCATATAG
1436630 AATGTCCCGAAGGACCGCGTAGA
1 AATGTCCCGAAGGACCGCGTAGA
* * *
1436653 AATGTCCCGAAGGATCACGCAGA
1 AATGTCCCGAAGGACCGCGTAGA
* *
1436676 ATTGTCCCGAAGGACCGCATAGA
1 AATGTCCCGAAGGACCGCGTAGA
1436699 A
1 A
1436700 CCCTCGACTC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.33, C:0.26, G:0.27, T:0.14
Consensus pattern (23 bp):
AATGTCCCGAAGGACCGCGTAGA
Found at i:1439050 original size:19 final size:19
Alignment explanation
Indices: 1439014--1439050 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1439004 TAAAATTGAT
*
1439014 TTGATTTTGAAAGCCAAAG
1 TTGATTTTGAAAACCAAAG
*
1439033 TTGATTTTGAAAATCAAA
1 TTGATTTTGAAAACCAAA
1439051 ATGAAATTTC
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:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (19 bp):
TTGATTTTGAAAACCAAAG
Found at i:1443465 original size:24 final size:23
Alignment explanation
Indices: 1443410--1443467 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 23
1443400 CAATCTTATA
*
1443410 TGGCACTTCGGTACATTTCTACG
1 TGGCACTTCGGGACATTTCTACG
*
1443433 CGGTC-CTTCGGGACAATTTCTACG
1 TGG-CACTTCGGGAC-ATTTCTACG
1443457 TGGCACTTCGG
1 TGGCACTTCGG
1443468 TGTAATTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 11 0.38
24 18 0.62
ACGTcount: A:0.16, C:0.28, G:0.26, T:0.31
Consensus pattern (23 bp):
TGGCACTTCGGGACATTTCTACG
Found at i:1443474 original size:24 final size:23
Alignment explanation
Indices: 1443410--1443480 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 23
1443400 CAATCTTATA
1443410 TGGCACTTC-GGTACATTTCTACG
1 TGGCACTTCGGGTA-ATTTCTACG
* *
1443433 CGGTC-CTTCGGGACAATTTCTACG
1 TGG-CACTTCGGG-TAATTTCTACG
*
1443457 TGGCACTTCGGTGTAATTTATACG
1 TGGCACTTCGG-GTAATTTCTACG
1443481 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
23 7 0.18
24 29 0.76
25 2 0.05
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.34
Consensus pattern (23 bp):
TGGCACTTCGGGTAATTTCTACG
Found at i:1444800 original size:18 final size:18
Alignment explanation
Indices: 1444777--1444818 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1444767 AGAGAAGGTT
*
1444777 TTATGATGTTAAATGGTA
1 TTATGATGTTAAATGATA
*
1444795 TTATGATGTTAAATTATA
1 TTATGATGTTAAATGATA
1444813 TTATGA
1 TTATGA
1444819 CGTGTTTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.48
Consensus pattern (18 bp):
TTATGATGTTAAATGATA
Found at i:1445985 original size:2 final size:2
Alignment explanation
Indices: 1445978--1446017 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1445968 ATTGGAAAGA
1445978 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
1446018 GGATAGTTTG
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:1447911 original size:21 final size:21
Alignment explanation
Indices: 1447885--1447925 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1447875 AGATTGTGCA
*
1447885 GGGGGTA-CAGATTCCTCCCTG
1 GGGGGTATC-GATTCCCCCCTG
1447906 GGGGGTATCGATTCCCCCCT
1 GGGGGTATCGATTCCCCCCT
1447926 AAATGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.12, C:0.32, G:0.32, T:0.24
Consensus pattern (21 bp):
GGGGGTATCGATTCCCCCCTG
Found at i:1449022 original size:24 final size:24
Alignment explanation
Indices: 1448958--1449023 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
1448948 CAATCTTATA
*
1448958 TGGCACTTCGGTGC-ATTTCTACG
1 TGGCACTTCGGTGCAATTTCGACG
* * *
1448981 CGGTC-CTTCGGGGAAATTTCGACG
1 TGG-CACTTCGGTGCAATTTCGACG
1449005 TGGCACTTCGGTGCAATTT
1 TGGCACTTCGGTGCAATTT
1449024 ATACGAGCTG
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
23 10 0.30
24 23 0.70
ACGTcount: A:0.15, C:0.24, G:0.29, T:0.32
Consensus pattern (24 bp):
TGGCACTTCGGTGCAATTTCGACG
Found at i:1450197 original size:19 final size:19
Alignment explanation
Indices: 1450173--1450216 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
1450163 AGTATAGTAC
1450173 CGATACTATACTTCAATAT
1 CGATACTATACTTCAATAT
1450192 CGATACTATACTTCAATAT
1 CGATACTATACTTCAATAT
1450211 CGATAC
1 CGATAC
1450217 CCTTACTGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.34
Consensus pattern (19 bp):
CGATACTATACTTCAATAT
Found at i:1456056 original size:6 final size:6
Alignment explanation
Indices: 1456013--1456043 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1456003 AAAATAAAAA
*
1456013 TCCTTC TCCTTC TCCTTC TCCTTC TGCTTC T
1 TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC T
1456044 AGGTCTCCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.45, G:0.03, T:0.52
Consensus pattern (6 bp):
TCCTTC
Found at i:1456514 original size:19 final size:18
Alignment explanation
Indices: 1456470--1456514 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
1456460 AAAATGAAAA
*
1456470 TATTTTTTTTACTATTTT
1 TATTTTTTTTAATATTTT
* *
1456488 TCTATTTTTTAAATATTTT
1 TAT-TTTTTTTAATATTTT
1456507 TATTTTTT
1 TATTTTTT
1456515 AAAAATTCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (18 bp):
TATTTTTTTTAATATTTT
Found at i:1458700 original size:86 final size:90
Alignment explanation
Indices: 1458546--1458725 Score: 289
Period size: 86 Copynumber: 2.0 Consensus size: 90
1458536 TAAAATTGTG
1458546 TCGTTTAATTGTCATAGTTCAAGTAGACTATATGTGATTTTGCAATTCCATTCAAAGCTGTGAGT
1 TCGTTTAATTGTCATAGTTCAAGTA-ACTATATGTGATTTTGCAATTCCATTCAAAGCTGTGAGT
1458611 GCTAGAATAA-AAGTCTTAAACCAGAC
65 GCTAGAATAATAAGTCTTAAACC-GAC
1458637 TCGTTTAATTGTCATAGTTCAAGT-ACTATAT-TGA-TTTGC-ATTCCATTCAAAGCTGTGAGTG
1 TCGTTTAATTGTCATAGTTCAAGTAACTATATGTGATTTTGCAATTCCATTCAAAGCTGTGAGTG
1458698 CTAGAATAACTTAAGTCTTAAACCGAC
66 CTAGAATAA--TAAGTCTTAAACCGAC
1458725 T
1 T
1458726 TGACTCTTTT
Statistics
Matches: 86, Mismatches: 0, Indels: 9
0.91 0.00 0.09
Matches are distributed among these distances:
86 31 0.36
87 5 0.06
88 7 0.08
89 19 0.22
91 24 0.28
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.36
Consensus pattern (90 bp):
TCGTTTAATTGTCATAGTTCAAGTAACTATATGTGATTTTGCAATTCCATTCAAAGCTGTGAGTG
CTAGAATAATAAGTCTTAAACCGAC
Found at i:1463817 original size:2 final size:2
Alignment explanation
Indices: 1463810--1463834 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1463800 TACCAGTGCT
1463810 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1463835 TTTTTACTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1468162 original size:31 final size:31
Alignment explanation
Indices: 1468126--1468185 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
1468116 AACTTAAAAG
*
1468126 AGTTTTGCAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
1468157 AGTTTTATAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
1468186 CATACAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:1468207 original size:31 final size:31
Alignment explanation
Indices: 1468133--1468208 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
1468123 AAGAGTTTTG
* ***
1468133 CAATACTGAAATTTAAATAATTTTAGTTTTA
1 CAATACTGAAATTTAAATAATTATACAATTA
*
1468164 TAATACTGAAATTTAAATAATTCATACAATTA
1 CAATACTGAAATTTAAATAATT-ATACAATTA
1468196 CAATACT-AAATTT
1 CAATACTGAAATTT
1468209 TTTAAAATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 27 0.71
32 11 0.29
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (31 bp):
CAATACTGAAATTTAAATAATTATACAATTA
Found at i:1468233 original size:22 final size:22
Alignment explanation
Indices: 1468208--1468785 Score: 840
Period size: 22 Copynumber: 26.6 Consensus size: 22
1468198 ATACTAAATT
*
1468208 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
1468230 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
1468252 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
1468274 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
1468296 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
1468318 TTTTAAAATAAAGCAATCCATA
1 TTTTAAAATAAATCAATCCATA
1468340 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
1468362 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
1468384 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
*
1468406 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
***
1468428 TTTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
*
1468450 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
1468472 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
1468494 TTTTAAAATAAATCAATACATA
1 TTTTAAAATAAATCAATCCATA
*
1468516 TTTTAAAATAAATCTATCCATA
1 TTTTAAAATAAATCAATCCATA
1468538 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
* **
1468560 TTTTAAATAGTTTTAAGT-TTTCCATA
1 TTTTAAA-A----TAAATCAATCCATA
*
1468586 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
1468608 TTTTAAAAT-AAT---T---TA
1 TTTTAAAATAAATCAATCCATA
1468623 TTTTAAAATAAATCAAT--ATA
1 TTTTAAAATAAATCAATCCATA
1468643 -TTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
1468664 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
1468686 TTTTAAAATAAAT-TTTCCATA
1 TTTTAAAATAAATCAATCCATA
1468707 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
1468729 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
*
1468751 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
1468773 TTTTAAAATAAAT
1 TTTTAAAATAAAT
1468786 TTTAAAATAA
Statistics
Matches: 506, Mismatches: 33, Indels: 34
0.88 0.06 0.06
Matches are distributed among these distances:
15 11 0.02
16 3 0.01
18 1 0.00
19 17 0.03
20 2 0.00
21 33 0.07
22 416 0.82
23 5 0.01
25 1 0.00
26 13 0.03
27 4 0.01
ACGTcount: A:0.49, C:0.11, G:0.01, T:0.40
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:1468789 original size:12 final size:12
Alignment explanation
Indices: 1468772--1468798 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1468762 ATCAATCTAT
1468772 ATTTTAAAATAA
1 ATTTTAAAATAA
1468784 ATTTTAAAATAA
1 ATTTTAAAATAA
1468796 ATT
1 ATT
1468799 AATTTTCGCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
ATTTTAAAATAA
Found at i:1469526 original size:21 final size:21
Alignment explanation
Indices: 1469500--1469548 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
1469490 AAAGTTTCCA
1469500 CAATTCTGCTCTGTGAGTGTT
1 CAATTCTGCTCTGTGAGTGTT
1469521 CAATTCTGCTCTGTGAGTGTT
1 CAATTCTGCTCTGTGAGTGTT
1469542 CAATTCT
1 CAATTCT
1469549 ACTAGTACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.16, C:0.20, G:0.20, T:0.43
Consensus pattern (21 bp):
CAATTCTGCTCTGTGAGTGTT
Found at i:1475867 original size:24 final size:24
Alignment explanation
Indices: 1475835--1475898 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
1475825 AGAGTCCATG
* *
1475835 TCAAGTATCATATAAAAATTCAGA
1 TCAAATATCATATAAAAATCCAGA
* * *
1475859 TCAAATATCATATCAGAATCCAGG
1 TCAAATATCATATAAAAATCCAGA
* *
1475883 TCAAAAATCAGATAAA
1 TCAAATATCATATAAA
1475899 CTATTTATGA
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.50, C:0.16, G:0.09, T:0.25
Consensus pattern (24 bp):
TCAAATATCATATAAAAATCCAGA
Found at i:1476660 original size:29 final size:29
Alignment explanation
Indices: 1476593--1476660 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
1476583 CATTTTACAC
1476593 AAATAGCACCCTTTTTAAAATAATTACCA
1 AAATAGCACCCTTTTTAAAATAATTACCA
* * * *
1476622 ACACAGCACCC-TTTTAGAATTAATTCCCA
1 AAATAGCACCCTTTTTA-AAATAATTACCA
*
1476651 AAATAACACC
1 AAATAGCACC
1476661 AAAACCGAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
28 5 0.16
29 26 0.84
ACGTcount: A:0.43, C:0.26, G:0.04, T:0.26
Consensus pattern (29 bp):
AAATAGCACCCTTTTTAAAATAATTACCA
Found at i:1476734 original size:17 final size:18
Alignment explanation
Indices: 1476696--1476772 Score: 122
Period size: 17 Copynumber: 4.4 Consensus size: 18
1476686 CACTGGTCAA
*
1476696 CGGGTCGGGTCAACATGT
1 CGGGTCGGGTCAACAGGT
1476714 CGGGTCGGGTCAAC-GGT
1 CGGGTCGGGTCAACAGGT
1476731 CGGGTCGGGTCAACA-GT
1 CGGGTCGGGTCAACAGGT
*
1476748 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACAGGT
1476766 CGGGTCG
1 CGGGTCG
1476773 TGACCGGTCA
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
17 32 0.58
18 23 0.42
ACGTcount: A:0.13, C:0.23, G:0.45, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTCAACAGGT
Found at i:1476739 original size:35 final size:35
Alignment explanation
Indices: 1476696--1476772 Score: 138
Period size: 35 Copynumber: 2.2 Consensus size: 35
1476686 CACTGGTCAA
1476696 CGGGTCGGGTCAACATGTCGGGTCGGGTCAAC-GGT
1 CGGGTCGGGTCAACA-GTCGGGTCGGGTCAACGGGT
1476731 CGGGTCGGGTCAACAGTCGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACAGTCGGGTCGGGTCAACGGGT
1476766 CGGGTCG
1 CGGGTCG
1476773 TGACCGGTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
34 16 0.39
35 25 0.61
ACGTcount: A:0.13, C:0.23, G:0.45, T:0.18
Consensus pattern (35 bp):
CGGGTCGGGTCAACAGTCGGGTCGGGTCAACGGGT
Done.