Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008796.1 Hibiscus syriacus cultivar Beakdansim tig00111941_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: 1607457
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 6 of 7
Found at i:1171917 original size:2 final size:2
Alignment explanation
Indices: 1171872--1171900 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1171862 GACAAAAATG
1171872 TA TA 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 TA TA T
1171901 TTATGTCGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1173459 original size:61 final size:62
Alignment explanation
Indices: 1173355--1173497 Score: 189
Period size: 61 Copynumber: 2.3 Consensus size: 62
1173345 TCTCATCGCC
* * * *
1173355 TGCTTTATGAAATAGAAATAATTAAATATATAATTATGGATTTTGAGCCATGTACGACTACT
1 TGCTTTCTGAAATAGAAATAATTAAATATATAATCATGCATTTTGAACCATGTACGACTACT
* * **
1173417 TGCTTTCTGAAA-CGAAATAATTAAATATATAATCATGCATTTTGAACTATGTACGACTTGT
1 TGCTTTCTGAAATAGAAATAATTAAATATATAATCATGCATTTTGAACCATGTACGACTACT
* *
1173478 TGCTTTCTGATATGGAAATA
1 TGCTTTCTGAAATAGAAATA
1173498 TATAATATTT
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
61 53 0.76
62 17 0.24
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (62 bp):
TGCTTTCTGAAATAGAAATAATTAAATATATAATCATGCATTTTGAACCATGTACGACTACT
Found at i:1173851 original size:2 final size:2
Alignment explanation
Indices: 1173844--1173871 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1173834 AGAAAGATTG
1173844 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
1173872 GAAAAATGGG
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):
TA
Found at i:1186712 original size:21 final size:22
Alignment explanation
Indices: 1186688--1186735 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
1186678 ATAGTTGAGT
1186688 CAAATAAAATTA-AATTAAAAA
1 CAAATAAAATTATAATTAAAAA
* *
1186709 CAAAT-TAATTATAATTAAGAA
1 CAAATAAAATTATAATTAAAAA
*
1186730 TAAATA
1 CAAATA
1186736 TTAGTAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (22 bp):
CAAATAAAATTATAATTAAAAA
Found at i:1187452 original size:29 final size:30
Alignment explanation
Indices: 1187415--1187477 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
1187405 TTACTTTTTA
* *
1187415 TTTTGAATAA-AATTCATATTTTTTTTAGT
1 TTTTAAATAATAATTCATATTTCTTTTAGT
* * *
1187444 TTTTAAATAATTATTCTTATTTCTTTTATT
1 TTTTAAATAATAATTCATATTTCTTTTAGT
1187474 TTTT
1 TTTT
1187478 TTATCTCGAG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 9 0.32
30 19 0.68
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.65
Consensus pattern (30 bp):
TTTTAAATAATAATTCATATTTCTTTTAGT
Found at i:1200855 original size:3 final size:3
Alignment explanation
Indices: 1200847--1200880 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1200837 TCCGAGTAGT
*
1200847 TTA TTA TTA TTA GTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1200881 ATATATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1200920 original size:16 final size:16
Alignment explanation
Indices: 1200896--1200926 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1200886 TATATATATA
1200896 ATATAATGGATTATTT
1 ATATAATGGATTATTT
*
1200912 ATATTATGGATTATT
1 ATATAATGGATTATT
1200927 AGATTTTGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (16 bp):
ATATAATGGATTATTT
Found at i:1202292 original size:60 final size:59
Alignment explanation
Indices: 1202227--1202377 Score: 194
Period size: 60 Copynumber: 2.5 Consensus size: 59
1202217 AATGATCCCA
* * * * *
1202227 AAACTTTTAAATATTCTAATTGCATCCCTAAACTATGACTCTGATTCTAAATTAGTCCTT
1 AAACTTTTGAATATTCTAATTTCATCCCTAAACTATGACCCTCATTCTAAATTAGT-CAT
* * *
1202287 AAACTTTTGAACATTCTAATTTCATCCCTAAACTATGACCCTCTTTCTAAATTGGTCAT
1 AAACTTTTGAATATTCTAATTTCATCCCTAAACTATGACCCTCATTCTAAATTAGTCAT
* * *
1202346 CAACTTTTGAATGTTCAAATTTCATCCCTAAA
1 AAACTTTTGAATATTCTAATTTCATCCCTAAA
1202378 TCCACCCAAA
Statistics
Matches: 79, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
59 30 0.38
60 49 0.62
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (59 bp):
AAACTTTTGAATATTCTAATTTCATCCCTAAACTATGACCCTCATTCTAAATTAGTCAT
Found at i:1202318 original size:29 final size:29
Alignment explanation
Indices: 1202221--1202320 Score: 78
Period size: 29 Copynumber: 3.4 Consensus size: 29
1202211 TTTTAAAATG
* * * *
1202221 ATCCCAAAACTTTTAAATATTCTAATTGC
1 ATCCCTAAACTTTTGAACATTCTAATTTC
* * *
1202250 ATCCCTAAAC-TATGACTCTGATTCTAAATT-
1 ATCCCTAAACTTTTGA-AC--ATTCTAATTTC
*
1202280 AGTCCTTAAACTTTTGAACATTCTAATTTC
1 A-TCCCTAAACTTTTGAACATTCTAATTTC
1202310 ATCCCTAAACT
1 ATCCCTAAACT
1202321 ATGACCCTCT
Statistics
Matches: 53, Mismatches: 12, Indels: 12
0.69 0.16 0.16
Matches are distributed among these distances:
28 3 0.06
29 27 0.51
30 2 0.04
31 17 0.32
32 4 0.08
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (29 bp):
ATCCCTAAACTTTTGAACATTCTAATTTC
Found at i:1202631 original size:60 final size:60
Alignment explanation
Indices: 1202553--1202669 Score: 139
Period size: 60 Copynumber: 1.9 Consensus size: 60
1202543 TGGAGACCAA
* * **
1202553 TTTAGAATGAGTGTCATAGTTTCGG-GATGAAAATAAAATGTTTAAAAGTTTAAGGACTTG
1 TTTAGAATGAATGTCATAGTTTAGGAG-TGAAAATAAAACATTTAAAAGTTTAAGGACTTG
* * *
1202613 TTTAGAATGATATG-CATAGTTTAGGAGTGAAATTAGAACATTTAAAAGTTTAGGGAC
1 TTTAGAATGA-ATGTCATAGTTTAGGAGTGAAAATAAAACATTTAAAAGTTTAAGGAC
1202670 CAATTTAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
60 45 0.94
61 3 0.06
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.34
Consensus pattern (60 bp):
TTTAGAATGAATGTCATAGTTTAGGAGTGAAAATAAAACATTTAAAAGTTTAAGGACTTG
Found at i:1203113 original size:2 final size:2
Alignment explanation
Indices: 1203106--1203131 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1203096 TGAATGGACG
1203106 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
1203132 TGTTTTCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1205363 original size:45 final size:45
Alignment explanation
Indices: 1205312--1205405 Score: 188
Period size: 45 Copynumber: 2.1 Consensus size: 45
1205302 ATAAATTTTT
1205312 TAAATGGATCGAGTATAAATAAAGTTTTAGAGTAAATATCGTCTG
1 TAAATGGATCGAGTATAAATAAAGTTTTAGAGTAAATATCGTCTG
1205357 TAAATGGATCGAGTATAAATAAAGTTTTAGAGTAAATATCGTCTG
1 TAAATGGATCGAGTATAAATAAAGTTTTAGAGTAAATATCGTCTG
1205402 TAAA
1 TAAA
1205406 ATAAATAACT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.33
Consensus pattern (45 bp):
TAAATGGATCGAGTATAAATAAAGTTTTAGAGTAAATATCGTCTG
Found at i:1205809 original size:51 final size:51
Alignment explanation
Indices: 1205706--1205817 Score: 120
Period size: 51 Copynumber: 2.2 Consensus size: 51
1205696 TGTGATAAAT
* * * *
1205706 TTTAAT-AAAAAATTATATTTTATTAGAATTCAACACCTCAAAGTGACTAA
1 TTTAATAAAAAAAATATATTTTATTAGAACTCAACACCTCAAAGTAACAAA
* * * *
1205756 TTTAAATAAAAAAAATAT-TTTTATTAGAACTCATCATCTCGACGTAACAAA
1 TTT-AATAAAAAAAATATATTTTATTAGAACTCAACACCTCAAAGTAACAAA
*
1205807 TTTTATAAAAA
1 TTTAATAAAAA
1205818 CTATAAAAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
50 10 0.20
51 32 0.63
52 9 0.18
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.36
Consensus pattern (51 bp):
TTTAATAAAAAAAATATATTTTATTAGAACTCAACACCTCAAAGTAACAAA
Found at i:1209190 original size:4 final size:4
Alignment explanation
Indices: 1209181--1209210 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
1209171 GATCAACAAA
1209181 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1209211 CAGTGAAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1216188 original size:24 final size:24
Alignment explanation
Indices: 1216161--1216233 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
1216151 TTCAGGCTCC
** *
1216161 TTCTCCTCGACTTCATTTGCAGCA
1 TTCTCCTCGACGGCATCTGCAGCA
* *
1216185 TTCTCCTTGCCGGCATCTGCAGCA
1 TTCTCCTCGACGGCATCTGCAGCA
* *
1216209 TTCTCCTTGCCGGCATCTGCAGCA
1 TTCTCCTCGACGGCATCTGCAGCA
1216233 T
1 T
1216234 CTTCCTCACC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.14, C:0.36, G:0.18, T:0.33
Consensus pattern (24 bp):
TTCTCCTCGACGGCATCTGCAGCA
Found at i:1216239 original size:24 final size:24
Alignment explanation
Indices: 1216178--1216233 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
1216168 CGACTTCATT
1216178 TGCAGCATTCTCCTTGCCGGCATC
1 TGCAGCATTCTCCTTGCCGGCATC
1216202 TGCAGCATTCTCCTTGCCGGCATC
1 TGCAGCATTCTCCTTGCCGGCATC
1216226 TGCAGCAT
1 TGCAGCAT
1216234 CTTCCTCACC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.14, C:0.36, G:0.21, T:0.29
Consensus pattern (24 bp):
TGCAGCATTCTCCTTGCCGGCATC
Found at i:1218617 original size:23 final size:23
Alignment explanation
Indices: 1218581--1218627 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1218571 TAATAATAAT
* * *
1218581 TATGTCTTTGTGACATGTTTATC
1 TATGTCATTATGACATATTTATC
1218604 TATGTCATTATGACATATTTATC
1 TATGTCATTATGACATATTTATC
1218627 T
1 T
1218628 CAAACTTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.51
Consensus pattern (23 bp):
TATGTCATTATGACATATTTATC
Found at i:1229666 original size:33 final size:34
Alignment explanation
Indices: 1229620--1229705 Score: 120
Period size: 35 Copynumber: 2.5 Consensus size: 34
1229610 TGAGAGTCGG
*
1229620 TATCTAGCAGGCTTGGAATT-AGTTAAGAGCCGA
1 TATCTAGCAGGCTTAGAATTCAGTTAAGAGCCGA
*
1229653 TATCTAGCCGGCTTAGAATTCCAGTTAAGAGCCGA
1 TATCTAGCAGGCTTAGAATT-CAGTTAAGAGCCGA
* *
1229688 TACCTAGCAGGTTTAGAA
1 TATCTAGCAGGCTTAGAA
1229706 CTACAGTTCT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
33 18 0.39
35 28 0.61
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (34 bp):
TATCTAGCAGGCTTAGAATTCAGTTAAGAGCCGA
Found at i:1234197 original size:20 final size:20
Alignment explanation
Indices: 1234152--1234197 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1234142 CACGCTTTTG
*
1234152 AATAAATATAAGTTTATTAT
1 AATAAATATAAGATTATTAT
*
1234172 ATTAAAT-TAAGATTATTAAT
1 AATAAATATAAGATTATT-AT
1234192 AATAAA
1 AATAAA
1234198 ATGCAATGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (20 bp):
AATAAATATAAGATTATTAT
Found at i:1235979 original size:12 final size:12
Alignment explanation
Indices: 1235958--1236007 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
1235948 AAATATTTGA
1235958 AATATATTTATT
1 AATATATTTATT
*
1235970 AATATGTTTATT
1 AATATATTTATT
*
1235982 AATATA-ATATT
1 AATATATTTATT
*
1235993 -ATAT-TTTTTT
1 AATATATTTATT
1236003 AATAT
1 AATAT
1236008 TACAATAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
10 7 0.23
11 8 0.26
12 16 0.52
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (12 bp):
AATATATTTATT
Found at i:1236006 original size:21 final size:23
Alignment explanation
Indices: 1235966--1236007 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
1235956 GAAATATATT
1235966 TATTAATATGTTTATTAATATAA
1 TATTAATATGTTTATTAATATAA
*
1235989 TATT-ATAT-TTTTTTAATAT
1 TATTAATATGTTTATTAATAT
1236008 TACAATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 4 0.22
23 4 0.22
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
TATTAATATGTTTATTAATATAA
Found at i:1236201 original size:32 final size:35
Alignment explanation
Indices: 1236130--1236202 Score: 89
Period size: 32 Copynumber: 2.2 Consensus size: 35
1236120 GAAATAATAT
* * **
1236130 TATTAAATTATTAATAATGAATAATATTATTTATG
1 TATTAAATTATTAATAATGAATAAAAATATTTAAA
1236165 TATTAAA-TATTAAT-AT-AATAAAAATATTTAAA
1 TATTAAATTATTAATAATGAATAAAAATATTTAAA
1236197 TATTAA
1 TATTAA
1236203 TTAATATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 18 0.53
33 2 0.06
34 7 0.21
35 7 0.21
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (35 bp):
TATTAAATTATTAATAATGAATAAAAATATTTAAA
Found at i:1236512 original size:14 final size:14
Alignment explanation
Indices: 1236493--1236525 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1236483 CAAAAATTGT
1236493 AAAATGTTTT-TCAG
1 AAAATGTTTTAT-AG
1236507 AAAATGTTTTATAG
1 AAAATGTTTTATAG
1236521 AAAAT
1 AAAAT
1236526 ATAATTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 17 0.94
15 1 0.06
ACGTcount: A:0.45, C:0.03, G:0.12, T:0.39
Consensus pattern (14 bp):
AAAATGTTTTATAG
Found at i:1236922 original size:27 final size:26
Alignment explanation
Indices: 1236892--1236949 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
1236882 TTAGAAACCC
*
1236892 TTAATCAAA-TAATTTTAAAAAATATAT
1 TTAATAAAATTAATTTT-AAAAAT-TAT
1236919 TTAATAAAATTTAATTTTAAAAATTAT
1 TTAATAAAA-TTAATTTTAAAAATTAT
1236946 TTAA
1 TTAA
1236950 AATAAACATG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 15 0.54
28 6 0.21
29 7 0.25
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (26 bp):
TTAATAAAATTAATTTTAAAAATTAT
Found at i:1236937 original size:16 final size:15
Alignment explanation
Indices: 1236900--1236941 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
1236890 CCTTAATCAA
1236900 ATAATTTTAAAAAAT
1 ATAATTTTAAAAAAT
1236915 AT-A-TTTAATAAAAT
1 ATAATTTTAA-AAAAT
*
1236929 TTAATTTTAAAAA
1 ATAATTTTAAAAA
1236942 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
13 5 0.22
14 7 0.30
15 6 0.26
16 5 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATAATTTTAAAAAAT
Found at i:1237671 original size:45 final size:46
Alignment explanation
Indices: 1237575--1237681 Score: 155
Period size: 45 Copynumber: 2.3 Consensus size: 46
1237565 ATGCACATAC
* *
1237575 CATGCATCGATGCACTCAGGTTTTTATGAAAACATCGAATGCATTT
1 CATGCATCGATGCACTCAGGTTGTTATGAAAACATCGAATGCACTT
* *
1237621 GATGCATCGATGCACTCGGGCTTGTT-TG-AAACATCGAATGCACTT
1 CATGCATCGATGCACTCAGG-TTGTTATGAAAACATCGAATGCACTT
1237666 CATGCATCGATGCACT
1 CATGCATCGATGCACT
1237682 AAGGGTCCAA
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
45 31 0.56
46 20 0.36
47 4 0.07
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (46 bp):
CATGCATCGATGCACTCAGGTTGTTATGAAAACATCGAATGCACTT
Found at i:1243395 original size:23 final size:22
Alignment explanation
Indices: 1243345--1243404 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 22
1243335 ATCCCTTTGT
*
1243345 ATGTGCATCGATACA-TCATGA
1 ATGTGCATCGATGCACTCATGA
1243366 A-GATGCATCGATGCACTCATTGA
1 ATG-TGCATCGATGCACTCA-TGA
1243389 ATGTGCATCGATGCAC
1 ATGTGCATCGATGCAC
1243405 AAAGCCATGC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
20 1 0.03
21 12 0.35
22 3 0.09
23 17 0.50
24 1 0.03
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (22 bp):
ATGTGCATCGATGCACTCATGA
Found at i:1245448 original size:2 final size:2
Alignment explanation
Indices: 1245441--1245468 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1245431 TTAAATCTTA
1245441 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
1245469 GTTTGGTTTG
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:1246199 original size:84 final size:83
Alignment explanation
Indices: 1246111--1246272 Score: 220
Period size: 84 Copynumber: 1.9 Consensus size: 83
1246101 AATGCATTAT
* * *
1246111 ATGCATCAATGCACATA-TCATGCATCGATGCACTC-AGATTTTTATGAAAACATCGAATGCATT
1 ATGCATCAATGCACA-AGCCATGCATCGATGCACTCGAGATTGTT-TG-AAACATCGAATGCACT
*
1246174 TGATGCATCGATGCACAAGCC
63 TCATGCATCGATGCACAAGCC
* * *
1246195 ATGCATCGATGCACAAGCCATGCATCGATGCACTCGGGCTTGTTTGAAACATCGAATGCACTTCA
1 ATGCATCAATGCACAAGCCATGCATCGATGCACTCGAGATTGTTTGAAACATCGAATGCACTTCA
1246260 TGCATCGATGCAC
66 TGCATCGATGCAC
1246273 TCTTAGTGCA
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
83 31 0.45
84 33 0.48
85 5 0.07
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (83 bp):
ATGCATCAATGCACAAGCCATGCATCGATGCACTCGAGATTGTTTGAAACATCGAATGCACTTCA
TGCATCGATGCACAAGCC
Found at i:1246200 original size:19 final size:19
Alignment explanation
Indices: 1246176--1246227 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
1246166 AATGCATTTG
1246176 ATGCATCGATGCACAAGCC
1 ATGCATCGATGCACAAGCC
1246195 ATGCATCGATGCACAAGCC
1 ATGCATCGATGCACAAGCC
1246214 ATGCATCGATGCAC
1 ATGCATCGATGCAC
1246228 TCGGGCTTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.31, C:0.31, G:0.21, T:0.17
Consensus pattern (19 bp):
ATGCATCGATGCACAAGCC
Found at i:1248546 original size:20 final size:20
Alignment explanation
Indices: 1248510--1248591 Score: 119
Period size: 20 Copynumber: 4.1 Consensus size: 20
1248500 CCGTTAGACA
*
1248510 GGGGGAATCGGTACCCCCTG
1 GGGGGAATCTGTACCCCCTG
* *
1248530 GGGGGGATCTGTTCCCCCTG
1 GGGGGAATCTGTACCCCCTG
*
1248550 GGGGGAATCTGTACCCCATG
1 GGGGGAATCTGTACCCCCTG
*
1248570 GGGGGAATCTGTACCCACTG
1 GGGGGAATCTGTACCCCCTG
1248590 GG
1 GG
1248592 TAATCTGATT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.15, C:0.27, G:0.39, T:0.20
Consensus pattern (20 bp):
GGGGGAATCTGTACCCCCTG
Found at i:1250031 original size:19 final size:20
Alignment explanation
Indices: 1249988--1250034 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
1249978 TCTAAATCAT
*
1249988 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
1250008 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
1250027 TTTTCAAA
1 TTTTCAAA
1250035 TGAAAATCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.28, C:0.13, G:0.06, T:0.53
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:1250058 original size:23 final size:24
Alignment explanation
Indices: 1250013--1250058 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
1250003 TTTGGCTTTC
*
1250013 AAAATCTATTTTTGTTTTCAAATG
1 AAAATCTATTTTCGTTTTCAAATG
1250037 AAAATC-ATTTTCGATTTT-AAAT
1 AAAATCTATTTTCG-TTTTCAAAT
1250059 TTTGAAATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.48
Consensus pattern (24 bp):
AAAATCTATTTTCGTTTTCAAATG
Found at i:1251337 original size:20 final size:21
Alignment explanation
Indices: 1251312--1251361 Score: 84
Period size: 20 Copynumber: 2.4 Consensus size: 21
1251302 CCGTTAGACA
1251312 GGGGGAATCGGTACCCCCT-G
1 GGGGGAATCGGTACCCCCTGG
*
1251332 GGGGGAATCTGTACCCCCTGG
1 GGGGGAATCGGTACCCCCTGG
1251353 GGGGGAATC
1 GGGGGAATC
1251362 TATACCCTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 18 0.64
21 10 0.36
ACGTcount: A:0.16, C:0.26, G:0.42, T:0.16
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCCTGG
Found at i:1251349 original size:21 final size:21
Alignment explanation
Indices: 1251312--1251374 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
1251302 CCGTTAGACA
*
1251312 GGGGGAATCGGTACCCCCT-G
1 GGGGGAATCTGTACCCCCTGG
1251332 GGGGGAATCTGTACCCCCTGG
1 GGGGGAATCTGTACCCCCTGG
* *
1251353 GGGGGAATCTATACCCTCTGG
1 GGGGGAATCTGTACCCCCTGG
1251374 G
1 G
1251375 CAATCTGATT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 18 0.46
21 21 0.54
ACGTcount: A:0.16, C:0.27, G:0.38, T:0.19
Consensus pattern (21 bp):
GGGGGAATCTGTACCCCCTGG
Found at i:1259076 original size:12 final size:12
Alignment explanation
Indices: 1259061--1259110 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
1259051 CCTGAAAAAG
*
1259061 ACAAGGAAAATA
1 ACAAGTAAAATA
1259073 ACAAGTAAAACTA
1 ACAAGTAAAA-TA
1259086 TACAA--AAAATAA
1 -ACAAGTAAAAT-A
1259098 ACAAGTAAAATA
1 ACAAGTAAAATA
1259110 A
1 A
1259111 AAATGTTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
11 5 0.16
12 16 0.50
13 7 0.22
14 4 0.12
ACGTcount: A:0.68, C:0.10, G:0.08, T:0.14
Consensus pattern (12 bp):
ACAAGTAAAATA
Found at i:1268213 original size:18 final size:19
Alignment explanation
Indices: 1268190--1268226 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1268180 TCTGTTCAAA
1268190 GTTGGTTAT-GTTGTTAAG
1 GTTGGTTATGGTTGTTAAG
*
1268208 GTTGGTTTTGGTTGTTAAG
1 GTTGGTTATGGTTGTTAAG
1268227 CCCGGTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.14, C:0.00, G:0.35, T:0.51
Consensus pattern (19 bp):
GTTGGTTATGGTTGTTAAG
Found at i:1270562 original size:100 final size:98
Alignment explanation
Indices: 1270347--1270616 Score: 461
Period size: 100 Copynumber: 2.7 Consensus size: 98
1270337 CCCTCTCTCT
* * *
1270347 CTCCTCCAGGAACCTCTCTCTACATTTCTACGTATATATTTTGTATATATATCGATGACTTATGT
1 CTCCTCCAGTAATCTCTCTCTAAATTTCTACGTATATATTTTGTATATATATCGATGACTTATGT
1270412 ACATA-TTTTTTTCTCTCACTTCAACTCCCTCC
66 ACATATTTTTTTTCTCTCACTTCAACTCCCTCC
*
1270444 CTCCTCCGGTAATCTCTCTCTAAATTTCTACGTATATATTTTGTATATATATATCGATGACTTAT
1 CTCCTCCAGTAATCTCTCTCTAAATTTCTACGTATATATTTTG--TATATATATCGATGACTTAT
1270509 GTACATATTTTTTTTCTCTCACTTCAACTCCCTCC
64 GTACATATTTTTTTTCTCTCACTTCAACTCCCTCC
* *
1270544 CTCCTCCAGTAATCTCTCTCTAAGTTTCTACGTATATATTTTGTATATATATCGATGACTTATAT
1 CTCCTCCAGTAATCTCTCTCTAAATTTCTACGTATATATTTTGTATATATATCGATGACTTATGT
1270609 ACATATTT
66 ACATATTT
1270617 GAATGTATTC
Statistics
Matches: 163, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
97 39 0.24
98 29 0.18
99 27 0.17
100 68 0.42
ACGTcount: A:0.24, C:0.24, G:0.07, T:0.44
Consensus pattern (98 bp):
CTCCTCCAGTAATCTCTCTCTAAATTTCTACGTATATATTTTGTATATATATCGATGACTTATGT
ACATATTTTTTTTCTCTCACTTCAACTCCCTCC
Found at i:1274455 original size:39 final size:38
Alignment explanation
Indices: 1274412--1274493 Score: 121
Period size: 39 Copynumber: 2.1 Consensus size: 38
1274402 ATACATATAA
1274412 ATAACAATT-AATTATTATATTTAATAAGAAAATATTATC
1 ATAAC-ATTCAATTATTATATTTAATAA-AAAATATTATC
* *
1274451 ATAACATTCGATTATTTTATTTAATAAAAAATATTATC
1 ATAACATTCAATTATTATATTTAATAAAAAATATTATC
1274489 ATAAC
1 ATAAC
1274494 TTTTTTCTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
38 19 0.47
39 21 0.52
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (38 bp):
ATAACATTCAATTATTATATTTAATAAAAAATATTATC
Found at i:1276923 original size:25 final size:25
Alignment explanation
Indices: 1276890--1276949 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
1276880 AATACATATT
*
1276890 AACAAGAACATTAAAGAAAATAATA
1 AACATGAACATTAAAGAAAATAATA
* * *
1276915 AACATGAACATTAAATATAATAATT
1 AACATGAACATTAAAGAAAATAATA
*
1276940 AATATGAACA
1 AACATGAACA
1276950 CAAATAATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.62, C:0.08, G:0.07, T:0.23
Consensus pattern (25 bp):
AACATGAACATTAAAGAAAATAATA
Found at i:1279956 original size:13 final size:13
Alignment explanation
Indices: 1279938--1279968 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1279928 AATGATTAAA
1279938 TTAAAAAAATAGG
1 TTAAAAAAATAGG
1279951 TTAAAAAAATAGG
1 TTAAAAAAATAGG
*
1279964 GTAAA
1 TTAAA
1279969 CTATATCAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (13 bp):
TTAAAAAAATAGG
Found at i:1281566 original size:16 final size:17
Alignment explanation
Indices: 1281545--1281577 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1281535 TTTTATCTTA
1281545 AATTT-AAATATATTTT
1 AATTTAAAATATATTTT
1281561 AATTTAAAATATATTTT
1 AATTTAAAATATATTTT
1281578 TTATCTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AATTTAAAATATATTTT
Found at i:1281610 original size:82 final size:82
Alignment explanation
Indices: 1281405--1281610 Score: 209
Period size: 82 Copynumber: 2.4 Consensus size: 82
1281395 AAATATTTTA
* * ** *
1281405 TTTTTATCTTAATTTTTAAATTATTATAAGAATCATTATATTTTATTTTATCTTAAATTTTAAAA
1 TTTTTATCTTAA-TTTTAAAATATTATAAG-ATTAAAATATATTATTTTATCTTAAATTTTAAAA
* * * *
1281470 TATTTTGATTTTAATTTTT
64 TATTTTAATTTAAATATAT
* * * *
1281489 TTGACTTTGATTTTTATTTTAAAATATTATAAGAATAAAATCTATT-TTTTATCTTAAA-TTTAA
1 TT---TTT-ATCTTAATTTTAAAATATTATAAGATTAAAATATATTATTTTATCTTAAATTTTAA
1281552 ATATATTTTAATTTAAAATATAT
62 A-ATATTTTAATTT-AAATATAT
1281575 TTTTTATCTTAATTTTAAAATATTATAAGATTAAAA
1 TTTTTATCTTAATTTTAAAATATTATAAGATTAAAA
1281611 ATAAATATTT
Statistics
Matches: 100, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
82 28 0.28
83 3 0.03
84 8 0.08
85 23 0.23
86 14 0.14
87 19 0.19
88 5 0.05
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.55
Consensus pattern (82 bp):
TTTTTATCTTAATTTTAAAATATTATAAGATTAAAATATATTATTTTATCTTAAATTTTAAAATA
TTTTAATTTAAATATAT
Found at i:1281613 original size:42 final size:41
Alignment explanation
Indices: 1281405--1281610 Score: 157
Period size: 41 Copynumber: 4.9 Consensus size: 41
1281395 AAATATTTTA
* * ** *
1281405 TTTTTATCTTAATTTTTAAATTATTATAAGAATCATTATATTT
1 TTTTTATCTTAA-TTTTAAAATATTATAAG-ATTAAAATATAT
* ** * *
1281448 TATTTTATCTTAAATTTTAAAATATT-T-TGATTTTAATTTTT
1 T-TTTTATCTT-AATTTTAAAATATTATAAGATTAAAATATAT
* * * *
1281489 TTGACTTTGATTTTTATTTTAAAATATTATAAGAATAAAATCTAT
1 TT---TTT-ATCTTAATTTTAAAATATTATAAGATTAAAATATAT
* * *
1281534 TTTTTATCTTAAATTTAAATATATTTTAA-TTTAAAATATAT
1 TTTTTATCTTAATTTTAAA-ATATTATAAGATTAAAATATAT
1281575 TTTTTATCTTAATTTTAAAATATTATAAGATTAAAA
1 TTTTTATCTTAATTTTAAAATATTATAAGATTAAAA
1281611 ATAAATATTT
Statistics
Matches: 129, Mismatches: 24, Indels: 22
0.74 0.14 0.13
Matches are distributed among these distances:
40 9 0.07
41 53 0.41
42 12 0.09
43 18 0.14
44 25 0.19
45 12 0.09
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.55
Consensus pattern (41 bp):
TTTTTATCTTAATTTTAAAATATTATAAGATTAAAATATAT
Found at i:1281679 original size:40 final size:40
Alignment explanation
Indices: 1281634--1281769 Score: 154
Period size: 40 Copynumber: 3.4 Consensus size: 40
1281624 TTAAAGTAAG
*
1281634 AATAAATTATATTTTTAAGTTAAATTAAAATTAAGATAAA
1 AATAAATTATATTTTTAAGTTAAATCAAAATTAAGATAAA
* *
1281674 AATAAAATATATTTTATTTAATTTAAATCAAAATTAAGATACAAA
1 AAT-AAAT-TATATT-TTTAAGTTAAATCAAAATTAAGAT--AAA
* *
1281719 AATATATT-T-TATTTAAGTTAAATCAAAATTAAGATAAA
1 AATAAATTATATTTTTAAGTTAAATCAAAATTAAGATAAA
1281757 AATAAA--ATATTTT
1 AATAAATTATATTTT
1281770 AAAATTTAAG
Statistics
Matches: 81, Mismatches: 8, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
37 1 0.01
38 11 0.14
40 26 0.32
41 5 0.06
42 6 0.07
43 23 0.28
44 3 0.04
45 6 0.07
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (40 bp):
AATAAATTATATTTTTAAGTTAAATCAAAATTAAGATAAA
Found at i:1285501 original size:3 final size:3
Alignment explanation
Indices: 1285493--1286438 Score: 813
Period size: 3 Copynumber: 313.7 Consensus size: 3
1285483 CCCCGGTCTT
1285493 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
1285541 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
*
1285589 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTTC TTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC C-TC CTC
* * * * * * * *
1285635 CTC TTC CTC TTC CTC TTC CTC TTC CTC TTC CTC TTC CTC TTC CT- CTT
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
* * * * * * * *
1285682 CTT CTC CTC CTTC CT- CTT CTT CTC C-C TTT CTT CTC CTC CTT CTT
1 CTC CTC CTC C-TC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
* *
1285726 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTT CTC CTC CTC CTC CTT CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
* * *
1285774 CTC CTC CTC CTT CTC CTC CTC CTC CTT CTC CTC CTC CTC CTC CTT CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
* * * * * * *
1285822 CTC CTT CTT CTC CTC CTT CTT CTC CTC CTTT CTT CTC CTC CTT CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC C-TC CTC CTC CTC CTC CTC
* * *
1285868 CTC CTC CTT CTC CTC CTC CTC CTT CTC CTC CTC CTC CTT CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
* * * * *
1285916 CTT CTC CTC CTTT CTT CTC CTC CTT CTC CTC CTC CTT CTC CTC CTC
1 CTC CTC CTC C-TC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
* * * * *
1285962 CTC CTT CTC CTC CTC CTC CTT CTC CTC CTT CTT CTC CTC CTC CTT CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
* *
1286010 CTC CTC CTT CTC CTC CTC CTC CTT CTC CTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
* * * *
1286058 CTC CTC CTC CTT CTC CTC CTC CT- CTC CTC CTT CT- CTT CTC CTT CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
* * * * * * * * * * * *
1286104 TTC TCTT CTC TTC TTC CTT CTT CTC CTT CTT CTT CTC CTT CTT CTT
1 CTC -CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
* * * * * * * * *
1286150 CTC CTT CTT CTC CTT CTT CTC CTT CTT CTC CTT CTT CTCC CTC TCTT
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CT-C CTC -CTC
1286197 CTC CTC CTC CTCC CTC CTC CTC CTTC CTC CTC CTC CTC CTC CTC TCTC
1 CTC CTC CTC CT-C CTC CTC CTC C-TC CTC CTC CTC CTC CTC CTC -CTC
* * * * * * *
1286245 ATT CTC CTC CTT CTC CTC CTT CTC CTC CTT CTC CTC CTT CTC CTC CTT
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
* * * * * * * * * * *
1286293 CTT CTC CTT CTT CTC CTT CTC CTT CTT CTC TTT CTT CTC CTC ATT CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
* * * * * * * * * *
1286341 CTC CTT CTC CTC CTT CTT CTC CTT CTT CTC ATT CTT CTC CTT CTT CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
* * * * * * * * *
1286389 CTT CTT CTC CTT CTT CTC CTT CTT CTC CTT CTC CTT CTC CTC CTT CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
1286437 CT
1 CT
1286439 TCTTCTTCTC
Statistics
Matches: 780, Mismatches: 148, Indels: 30
0.81 0.15 0.03
Matches are distributed among these distances:
2 9 0.01
3 748 0.96
4 23 0.03
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (3 bp):
CTC
Found at i:1286439 original size:6 final size:6
Alignment explanation
Indices: 1285490--1286737 Score: 729
Period size: 6 Copynumber: 208.8 Consensus size: 6
1285480 ACCCCCCGGT
* * * * * * *
1285490 CTTCTC CTCCTC CTCCTC CTCCTC CTCCTC CTCCTC CTCCTC CTCCTC
1 CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC
* * * * * * * *
1285538 CTCCTC CTCCTC CTCCTC CTCCTC CTCCTC CTCCTC CTCCTC CTCCTC
1 CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC
* * * * * * *
1285586 CTCCTC CTCCTC CTCCTC CTCCTC CTCCTC CTCCTC CTCCTC CTTCTTC
1 CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTC-TC
1285635 C-TCTTC C-TCTTC C-TCTTC C-TCTTC C-TCTTC C-TCTTC C-TCTTC
1 CTTC-TC CTTC-TC CTTC-TC CTTC-TC CTTC-TC CTTC-TC CTTC-TC
* * * * *
1285677 C-TCTT CTTCTC CTCCTTC C-TCTT CTTCTCC CTT-T- CTTCTC CTCCTT
1 CTTCTC CTTCTC CTTC-TC CTTCTC CTTCT-C CTTCTC CTTCTC CTTCTC
* * * *
1285723 CTTCTC CTCCTC CTCCTC CTCCTC CTCCTC CTTCTC CTCCTCCTC CTTCTC
1 CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CT--T-CTC CTTCTC
* * * * * * *
1285774 CTCCTC CTCCTT CTCCTC CTCCTC CTTCTC CTCCTC CTCCTC CTTCTC
1 CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC
* * * * * * *
1285822 CTCCTT CTTCTC CTCCTT CTTCTC C-TC-C TTTCTT CTCCTC CTTCTC
1 CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC
* * * * * * *
1285868 CTCCTC CTTCTC CTCCTC CTCCTT CTCCTC CTCCTC CTTCTC CTCCTC
1 CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC
* * * * *
1285916 CTTCTC C-TC-C TTTCTT CTCCTC CTTCTC CTCCTC CTTCTC CTCCTC
1 CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC
* * * * * * *
1285962 CTCCTT CTCCTC CTCCTC CTTCTC CTCCTT CTTCTC CTCCTC CTTCTC
1 CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC
* * * * *
1286010 CTCCTC CTTCTC CTCCTCCTC CTTCTC CTCCTC CTCCTC CTCCTC CTCCTC
1 CTTCTC CTTCTC CT--T-CTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC
* *
1286061 CTCCTC CTTCTC CTCCTC CTCTCCTC CTTCT- CTTCTC CTTCT- CTTCT-
1 CTTCTC CTTCTC CTTCTC CT-T-CTC CTTCTC CTTCTC CTTCTC CTTCTC
* * * *
1286108 CTTCTC TTCTTCCTT CTTCTC CTTCTT CTTCTC CTTCTT CTTCTC CTTCTT
1 CTTCTC --CTT-CTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC
* * * * * * *
1286159 CTCCTT CTTCTC CTTCTT CTCCTT CTTCTC CCTCT- CTTCTC CTCCTC
1 CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC
* * * * * * *
1286206 CTCCCTC CTCCTC CTTCCTC CTCCTC CTCCTC CTCTCTC ATTCTC CTCCTT
1 CT-TCTC CTTCTC CTT-CTC CTTCTC CTTCTC CT-TCTC CTTCTC CTTCTC
* * * * * *
1286257 CTCCTC CTTCTC CTCCTT CTCCTC CTTCTC CTCCTT CTTCTC C-T-T-
1 CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC
* *
1286302 CTTCTC CTTCTC CTTCTTC TCTT-T- CTTCTC C-TCATT CTCCTC CTTCTC
1 CTTCTC CTTCTC CTTC-TC -CTTCTC CTTCTC CTTC-TC CTTCTC CTTCTC
* * * * * * *
1286350 CTCCTT CTTCTC CTTCTT C-TCATT CTTCTC CTTCTT CTCCTT CTTCTC
1 CTTCTC CTTCTC CTTCTC CTTC-TC CTTCTC CTTCTC CTTCTC CTTCTC
* * * *
1286398 CTTCTT CTCCTT CTTCTC CTTCTC CTTCT- C--CTC CTTCTC CTTCTT
1 CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC
* * * * *
1286443 CTTCTC CTTCTT CTCCTT CTTCT- CTTCTT CTTCTT C-TCTC CTTCTC
1 CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC
* * * * *
1286489 CTCCTT CTTCTT CTTCTT CTTCTC TTCTTCTC CTTCCTC CTTCTTT CTTCTC
1 CTTCTC CTTCTC CTTCTC CTTCTC --CTTCTC CTT-CTC CTTC-TC CTTCTC
*
1286541 CTTCTC CTTCT- C--CTC CTTCTC CTTCTC C-T-T- CTTCTC CTTCTT
1 CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC
* * *
1286583 CTCCTT CTTCTC CTTCTT CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC
1 CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC
*
1286631 CTTCTC CTTCT- CTTCTC TTCTTCTC CTTCT- TTTCTC CTTCTC CTTCTC
1 CTTCTC CTTCTC CTTCTC --CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC
* * * * * * * *
1286679 CTTCTC CTTCTT CTTCTT CTTCTT CTTCTT CTTTTT CTTCTT CTTCTT
1 CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC CTTCTC
*
1286727 CTTCTT CTTCT
1 CTTCTC CTTCT
1286738 TTCTTCTTCT
Statistics
Matches: 1043, Mismatches: 141, Indels: 116
0.80 0.11 0.09
Matches are distributed among these distances:
3 6 0.01
4 14 0.01
5 61 0.06
6 879 0.84
7 46 0.04
8 25 0.02
9 12 0.01
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (6 bp):
CTTCTC
Found at i:1286443 original size:3 final size:3
Alignment explanation
Indices: 1286087--1286751 Score: 440
Period size: 3 Copynumber: 223.0 Consensus size: 3
1286077 TCCTCTCCTC
* *
1286087 CTT C-T CTT CTC CTT C-T CTT C-T CTT C-T CTT CTT CCTT CTT CTC
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT -CTT CTT CTT
* * * *
1286129 CTT CTT CTT CTC CTT CTT CTT CTC CTT CTT CTC CTT CTT CTC CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* * * * * * * * * *
1286177 CTC CTT CTT CTC CCT C-T CTT CTC CTC CTC CTCC CTC CTC CTC CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT-T CTT CTT CTT CTT
* * * * * * * * * * *
1286222 CCT CCT CCT CCT CCT CCT CTCT CATT CTC CTC CTT CTC CTC CTT CTC
1 CTT CTT CTT CTT CTT CTT CT-T C-TT CTT CTT CTT CTT CTT CTT CTT
* * * * * * * *
1286269 CTC CTT CTC CTC CTT CTC CTC CTT CTT CTC CTT CTT CTC CTT CTC CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* * * * * *
1286317 CTT C-T CTTT CTT C-T CCT CATT CTC CTC CTT CTC CTC CTT CTT CTC
1 CTT CTT C-TT CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT
* * * *
1286362 CTT CTT C-T CATT CTT CTC CTT CTT CTC CTT CTT CTC CTT CTT CTC
1 CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* * * * * *
1286407 CTT CTT CTC CTT CTC CTT CTC CTC CTT CTC CTT CTT CTT CTC CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* * * *
1286455 CTC CTT CTT C-T CTT CTT CTT CTT C-T CTC CTT CTC CTC CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* * * *
1286501 CTT CTT CTT C-T CTT CTT CTC CTT CCTC CTT CTTT CTT CTC CTT CTC
1 CTT CTT CTT CTT CTT CTT CTT CTT -CTT CTT C-TT CTT CTT CTT CTT
* * * * * * *
1286547 CTT CTC CTC CTT CTC CTT CTC CTT CTT CTC CTT CTT CTC CTT CTT CTC
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* * * * * *
1286595 CTT CTT CTT CTC CTT CTC CTT CTC CTT CTC CTT CTC CTT CTC CTT C-T
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
* * * * *
1286642 CTT C-T CTT CTT CTC CTT CTT -TT CTC CTT CTC CTT CTC CTT CTC CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
*
1286688 CTT CTT CTT CTT CTT CTT CTT CTT TTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1286736 CTTT CTT CTT CTT CTT
1 C-TT CTT CTT CTT CTT
1286752 AGCTCGTAAA
Statistics
Matches: 526, Mismatches: 112, Indels: 48
0.77 0.16 0.07
Matches are distributed among these distances:
2 28 0.05
3 473 0.90
4 24 0.05
5 1 0.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.54
Consensus pattern (3 bp):
CTT
Found at i:1286443 original size:9 final size:9
Alignment explanation
Indices: 1285679--1286751 Score: 778
Period size: 9 Copynumber: 120.7 Consensus size: 9
1285669 TCCTCTTCCT
1285679 CTTCTTCTC
1 CTTCTTCTC
*
1285688 CTCCTTC-C
1 CTTCTTCTC
1285696 TCTTCTTCTCC
1 -CTTCTTCT-C
1285707 CTTTCTTCTC
1 C-TTCTTCTC
* *
1285717 CTCCTTCTT
1 CTTCTTCTC
* *
1285726 CTCCTCCTC
1 CTTCTTCTC
* *
1285735 CTCCTCCTC
1 CTTCTTCTC
* *
1285744 CTCCTCCTC
1 CTTCTTCTC
*
1285753 CTTCTCCTC
1 CTTCTTCTC
* * *
1285762 CTCCTCCTT
1 CTTCTTCTC
* *
1285771 CTCCTCCTC
1 CTTCTTCTC
*
1285780 CTCCTTCTC
1 CTTCTTCTC
* *
1285789 CTCCTCCTC
1 CTTCTTCTC
*
1285798 CTTCTCCTC
1 CTTCTTCTC
* *
1285807 CTCCTCCTC
1 CTTCTTCTC
*
1285816 CTTCTCCTC
1 CTTCTTCTC
1285825 CTTCTTCTCCTC
1 CTTC-T-T-CTC
1285837 CTTCTTCTC
1 CTTCTTCTC
*
1285846 CTCCTT-T-
1 CTTCTTCTC
*
1285853 CTTCTCCTC
1 CTTCTTCTC
*
1285862 CTTCTCCTC
1 CTTCTTCTC
*
1285871 CTCCTTCTC
1 CTTCTTCTC
1285880 C-TC--CTC
1 CTTCTTCTC
*
1285886 CTCCTTCTC
1 CTTCTTCTC
* *
1285895 CTCCTCCTC
1 CTTCTTCTC
*
1285904 CTTCTCCTC
1 CTTCTTCTC
*
1285913 CTCCTTCTC
1 CTTCTTCTC
*
1285922 CTCCTT-T-
1 CTTCTTCTC
*
1285929 CTTCTCCTC
1 CTTCTTCTC
*
1285938 CTTCTCCTC
1 CTTCTTCTC
*
1285947 CTCCTTCTC
1 CTTCTTCTC
1285956 C-TC--CTC
1 CTTCTTCTC
*
1285962 CTCCTTCTC
1 CTTCTTCTC
* *
1285971 CTCCTCCTC
1 CTTCTTCTC
*
1285980 CTTCTCCTC
1 CTTCTTCTC
1285989 CTTCTTCTC
1 CTTCTTCTC
1285998 C-TC--CTC
1 CTTCTTCTC
*
1286004 CTTCTCCTC
1 CTTCTTCTC
*
1286013 CTCCTTCTC
1 CTTCTTCTC
* *
1286022 CTCCTCCTC
1 CTTCTTCTC
*
1286031 CTTCTCCTC
1 CTTCTTCTC
* *
1286040 CTCCTCCTC
1 CTTCTTCTC
* *
1286049 CTCCTCCTC
1 CTTCTTCTC
* *
1286058 CTCCTCCTC
1 CTTCTTCTC
*
1286067 CTTCTCCTC
1 CTTCTTCTC
*
1286076 C-TCCTCTC
1 CTTCTTCTC
*
1286084 CTCCTTCT-
1 CTTCTTCTC
* *
1286092 CTTCTCCTT
1 CTTCTTCTC
1286101 C-TCTTCTC
1 CTTCTTCTC
*
1286109 TTCTCTTCTTC
1 CT-TCTTC-TC
1286120 CTTCTTCTC
1 CTTCTTCTC
1286129 CTTC-T-T-
1 CTTCTTCTC
* *
1286135 CTTCTCCTT
1 CTTCTTCTC
1286144 CTTCTTCTC
1 CTTCTTCTC
1286153 CTTCTTCTC
1 CTTCTTCTC
1286162 CTTCTTCTC
1 CTTCTTCTC
1286171 CTTCTTCTC
1 CTTCTTCTC
1286180 CTTCTTCTCC
1 CTTCTTCT-C
1286190 CTCTCTTCTC
1 CT-TCTTCTC
* *
1286200 CTCCTCCTC
1 CTTCTTCTC
*
1286209 C--CTCCTC
1 CTTCTTCTC
*
1286216 CTCCTTCCTC
1 CTTCTT-CTC
* *
1286226 CTCCTCCTC
1 CTTCTTCTC
*
1286235 CTCCTCTCTC
1 CTTCT-TCTC
* *
1286245 ATTCTCCTC
1 CTTCTTCTC
*
1286254 CTTCTCCTC
1 CTTCTTCTC
*
1286263 CTTCTCCTC
1 CTTCTTCTC
*
1286272 CTTCTCCTC
1 CTTCTTCTC
*
1286281 CTTCTCCTC
1 CTTCTTCTC
1286290 CTTCTTCTC
1 CTTCTTCTC
1286299 CTTCTTCT-
1 CTTCTTCTC
1286307 C--CTTCTC
1 CTTCTTCTC
1286314 CTTCTTCTC
1 CTTCTTCTC
*
1286323 TTTCTTCTCC
1 CTTCTTCT-C
*
1286333 TCATTCTCCTC
1 -C-TTCTTCTC
*
1286344 CTTCTCCTC
1 CTTCTTCTC
1286353 CTTCTTCTC
1 CTTCTTCTC
1286362 CTTCTTCTC
1 CTTCTTCTC
*
1286371 ATTCTTCTC
1 CTTCTTCTC
1286380 CTTCTTCTC
1 CTTCTTCTC
1286389 CTTCTTCTC
1 CTTCTTCTC
1286398 CTTCTTCTC
1 CTTCTTCTC
1286407 CTTCTTCT-
1 CTTCTTCTC
1286415 C--CTTCTC
1 CTTCTTCTC
*
1286422 CTTCTCCTC
1 CTTCTTCTC
* *
1286431 CTTCTCCTT
1 CTTCTTCTC
1286440 CTTCTTCTC
1 CTTCTTCTC
1286449 CTTCTTCTC
1 CTTCTTCTC
1286458 CTTCTTCT-
1 CTTCTTCTC
*
1286466 CTTCTTCTT
1 CTTCTTCTC
1286475 CTTC-TCTC
1 CTTCTTCTC
*
1286483 CTTCTCCTC
1 CTTCTTCTC
*
1286492 CTTCTTCTT
1 CTTCTTCTC
1286501 CTTCTTCTTC
1 CTTCTTC-TC
1286511 TCTTCTTCTC
1 -CTTCTTCTC
1286521 CTTC--CTC
1 CTTCTTCTC
*
1286528 CTTCTTTCTT
1 CTTC-TTCTC
*
1286538 CTCCTTCTC
1 CTTCTTCTC
*
1286547 CTTCTCCTC
1 CTTCTTCTC
1286556 CTTCTCCTTCTC
1 C-T-T-CTTCTC
1286568 CTTCTTCTC
1 CTTCTTCTC
1286577 CTTCTTCTC
1 CTTCTTCTC
1286586 CTTCTTCTC
1 CTTCTTCTC
*
1286595 CTTCTTCTT
1 CTTCTTCTC
*
1286604 CTCCTTCTC
1 CTTCTTCTC
* *
1286613 CTTCTCCTT
1 CTTCTTCTC
*
1286622 CTCCTTCTC
1 CTTCTTCTC
* *
1286631 CTTCTCCTT
1 CTTCTTCTC
1286640 C-TCTTCT-
1 CTTCTTCTC
1286647 CTTCTTCTC
1 CTTCTTCTC
1286656 CTTCTTTTCTC
1 CTTC--TTCTC
* *
1286667 CTTCTCCTT
1 CTTCTTCTC
*
1286676 CTCCTTCTC
1 CTTCTTCTC
*
1286685 CTTCTTCTT
1 CTTCTTCTC
*
1286694 CTTCTTCTT
1 CTTCTTCTC
*
1286703 CTTCTTCTT
1 CTTCTTCTC
* *
1286712 TTTCTTCTT
1 CTTCTTCTC
*
1286721 CTTCTTCTT
1 CTTCTTCTC
1286730 CTTCTTCT-
1 CTTCTTCTC
*
1286738 -TTCTTCTT
1 CTTCTTCTC
1286746 CTTCTT
1 CTTCTT
1286752 AGCTCGTAAA
Statistics
Matches: 897, Mismatches: 108, Indels: 118
0.80 0.10 0.11
Matches are distributed among these distances:
6 26 0.03
7 37 0.04
8 56 0.06
9 675 0.75
10 47 0.05
11 37 0.04
12 19 0.02
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (9 bp):
CTTCTTCTC
Found at i:1286872 original size:74 final size:74
Alignment explanation
Indices: 1286751--1286895 Score: 272
Period size: 74 Copynumber: 2.0 Consensus size: 74
1286741 TTCTTCTTCT
* *
1286751 TAGCTCGTAAACTGACATTAAGAGTTAGTGTACGAGCATGTTTAAAGAATCCGGACCTACCTGCT
1 TAGCTCGTAAACTGACATTAAAAGGTAGTGTACGAGCATGTTTAAAGAATCCGGACCTACCTGCT
1286816 TTCCGGCGA
66 TTCCGGCGA
1286825 TAGCTCGTAAACTGACATTAAAAGGTAGTGTACGAGCATGTTTAAAGAATCCGGACCTACCTGCT
1 TAGCTCGTAAACTGACATTAAAAGGTAGTGTACGAGCATGTTTAAAGAATCCGGACCTACCTGCT
1286890 TTCCGG
66 TTCCGG
1286896 ACTTAATGCT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 69 1.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (74 bp):
TAGCTCGTAAACTGACATTAAAAGGTAGTGTACGAGCATGTTTAAAGAATCCGGACCTACCTGCT
TTCCGGCGA
Found at i:1287696 original size:3 final size:3
Alignment explanation
Indices: 1287688--1287783 Score: 111
Period size: 3 Copynumber: 29.3 Consensus size: 3
1287678 GGGCTAACGA
*
1287688 AAG AAG AAG AAG AAG AGG AAG AAGG AAG AAGG AAG AAGG AAG AAGG AAG
1 AAG AAG AAG AAG AAG AAG AAG AA-G AAG AA-G AAG AA-G AAG AA-G AAG
1287737 AAGG AAG AAG AAG AAG AAG AAGG AAG AAGG AAGG AAG AAG AAG AAG A
1 AA-G AAG AAG AAG AAG AAG AA-G AAG AA-G AA-G AAG AAG AAG AAG A
1287784 CCTGGGGTGT
Statistics
Matches: 84, Mismatches: 2, Indels: 14
0.84 0.02 0.14
Matches are distributed among these distances:
3 59 0.70
4 25 0.30
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1287715 original size:7 final size:7
Alignment explanation
Indices: 1287688--1287783 Score: 134
Period size: 7 Copynumber: 14.6 Consensus size: 7
1287678 GGGCTAACGA
1287688 AAGAA-G
1 AAGAAGG
1287694 AAGAA-G
1 AAGAAGG
1287700 AAG-AGG
1 AAGAAGG
1287706 AAGAAGG
1 AAGAAGG
1287713 AAGAAGG
1 AAGAAGG
1287720 AAGAAGG
1 AAGAAGG
1287727 AAGAAGG
1 AAGAAGG
1287734 AAGAAGG
1 AAGAAGG
1287741 AAGAA-G
1 AAGAAGG
1287747 AAGAA-G
1 AAGAAGG
1287753 AAGAAGG
1 AAGAAGG
1287760 AAGAAGG
1 AAGAAGG
1287767 AAGGAA-G
1 AA-GAAGG
1287774 AAGAA-G
1 AAGAAGG
1287780 AAGA
1 AAGA
1287784 CCTGGGGTGT
Statistics
Matches: 86, Mismatches: 0, Indels: 8
0.91 0.00 0.09
Matches are distributed among these distances:
5 1 0.01
6 33 0.38
7 49 0.57
8 3 0.03
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (7 bp):
AAGAAGG
Found at i:1287744 original size:47 final size:45
Alignment explanation
Indices: 1287688--1287783 Score: 149
Period size: 47 Copynumber: 2.1 Consensus size: 45
1287678 GGGCTAACGA
*
1287688 AAGAAGAAGAAGAAGAGGAAGAAGGAAGAAGGAA-GAAGGAAGAAGG
1 AAGAAGAAGAAGAAGAAGAAGAAGGAAGAAGGAAGGAA-GAAGAA-G
1287734 AAGAAGGAAGAAGAAGAAGAAGAAGGAAGAAGGAAGGAAGAAGAAG
1 AAGAA-GAAGAAGAAGAAGAAGAAGGAAGAAGGAAGGAAGAAGAAG
1287780 AAGA
1 AAGA
1287784 CCTGGGGTGT
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
46 10 0.21
47 34 0.72
48 3 0.06
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (45 bp):
AAGAAGAAGAAGAAGAAGAAGAAGGAAGAAGGAAGGAAGAAGAAG
Found at i:1290057 original size:23 final size:24
Alignment explanation
Indices: 1290010--1290073 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 24
1290000 CATAATATCT
**
1290010 TATATTATTATAATA-TAACTGAA
1 TATATTATTATAATATTAACAAAA
1290033 TATATTATTATAATATTAA-AAAA
1 TATATTATTATAATATTAACAAAA
* * *
1290056 TATAATAGTATATTATTA
1 TATATTATTATAATATTA
1290074 GAAATATTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 32 0.91
24 3 0.09
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (24 bp):
TATATTATTATAATATTAACAAAA
Found at i:1290173 original size:19 final size:19
Alignment explanation
Indices: 1290132--1290173 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1290122 TTAAAATGAT
* *
1290132 ATTAAAATATTATATTAAC
1 ATTAAAATATAAAATTAAC
1290151 ATTAAAATCATAAAATTAA-
1 ATTAAAAT-ATAAAATTAAC
1290170 ATTA
1 ATTA
1290174 TTTTGAGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
ATTAAAATATAAAATTAAC
Found at i:1291443 original size:27 final size:27
Alignment explanation
Indices: 1291399--1291466 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 27
1291389 TTATTAAATT
*
1291399 ATATT-TATTGATAATTTTAATAA-TATA
1 ATATTATATT-AT-ATTTTTATAACTATA
1291426 ATATTATATTATATTTTTATAACTATA
1 ATATTATATTATATTTTTATAACTATA
* * *
1291453 TTTTTATAATATAT
1 ATATTATATTATAT
1291467 AATATTATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
26 9 0.26
27 22 0.63
28 4 0.11
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (27 bp):
ATATTATATTATATTTTTATAACTATA
Found at i:1291445 original size:13 final size:13
Alignment explanation
Indices: 1291412--1291495 Score: 69
Period size: 13 Copynumber: 6.2 Consensus size: 13
1291402 TTTATTGATA
*
1291412 ATTTTAATAATAT
1 ATTTTTATAATAT
* * *
1291425 AATATTATATTAT
1 ATTTTTATAATAT
1291438 ATTTTTATAACTAT
1 ATTTTTATAA-TAT
1291452 ATTTTTATAATAT
1 ATTTTTATAATAT
* *
1291465 ATAATATTATAATTGT
1 AT--TTTTATAA-TAT
*
1291481 ATTTTAATAATAT
1 ATTTTTATAATAT
1291494 AT
1 AT
1291496 AATAAATTAT
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
13 25 0.45
14 19 0.35
15 7 0.13
16 4 0.07
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (13 bp):
ATTTTTATAATAT
Found at i:1291456 original size:40 final size:42
Alignment explanation
Indices: 1291380--1291495 Score: 118
Period size: 42 Copynumber: 2.9 Consensus size: 42
1291370 ATATTAATAA
* * *
1291380 AATATTTAATTATTA-AATTATA-TTTATTGATA-ATTTTAAT
1 AATATATAA-TATTATAATTATATTTTAATAATATATTTTAAT
* *
1291420 -A-ATATAATATTAT-ATTATATTTTTATAACTATATTTTTAT
1 AATATATAATATTATAATTATATTTTAATAA-TATATTTTAAT
*
1291460 AATATATAATATTATAATTGTATTTTAATAATATAT
1 AATATATAATATTATAATTATATTTTAATAATATAT
1291496 AATAAATTAT
Statistics
Matches: 62, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
37 11 0.18
38 10 0.16
39 3 0.05
40 7 0.11
41 1 0.02
42 17 0.27
43 13 0.21
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (42 bp):
AATATATAATATTATAATTATATTTTAATAATATATTTTAAT
Found at i:1291505 original size:31 final size:29
Alignment explanation
Indices: 1291442--1291499 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
1291432 TATTATATTT
*
1291442 TTATAACTATATTTTTATAATATATAATA
1 TTATAACTATATTTTAATAATATATAATA
* *
1291471 TTATAATTGTATTTTAATAATATATAATA
1 TTATAACTATATTTTAATAATATATAATA
1291500 AATTATTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (29 bp):
TTATAACTATATTTTAATAATATATAATA
Found at i:1291671 original size:37 final size:37
Alignment explanation
Indices: 1291630--1291733 Score: 122
Period size: 42 Copynumber: 2.7 Consensus size: 37
1291620 TTTTAATTTT
1291630 TTAATAATATTATTATTTTAATAAATAATTAATATAA
1 TTAATAATATTATTATTTTAATAAATAATTAATATAA
1291667 TTAATAATATATGATTCTTATTTT-ATCAAATAATTAATATAA
1 TTAATAATAT-T-A---TTATTTTAAT-AAATAATTAATATAA
*
1291709 TTTATAATTATT-TTATTTTAATAAA
1 TTAATAA-TATTATTATTTTAATAAA
1291734 ATATAATAAT
Statistics
Matches: 58, Mismatches: 1, Indels: 16
0.77 0.01 0.21
Matches are distributed among these distances:
37 20 0.34
38 3 0.05
39 1 0.02
41 2 0.03
42 29 0.50
43 3 0.05
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (37 bp):
TTAATAATATTATTATTTTAATAAATAATTAATATAA
Found at i:1291790 original size:14 final size:14
Alignment explanation
Indices: 1291700--1291796 Score: 58
Period size: 14 Copynumber: 7.1 Consensus size: 14
1291690 TATCAAATAA
1291700 TTAA-TATAAT-TT
1 TTAATTATAATATT
* **
1291712 ATAATTATTTTATT
1 TTAATTATAATATT
* *
1291726 TTAA-TAAAATATA
1 TTAATTATAATATT
*
1291739 ATAATCT-TAATATTT
1 TTAAT-TATAATA-TT
* *
1291754 TTATTTATAAAATT
1 TTAATTATAATATT
* *
1291768 GTAAATATAATATT
1 TTAATTATAATATT
1291782 TTAATTATAATATT
1 TTAATTATAATATT
1291796 T
1 T
1291797 ACATATTAAA
Statistics
Matches: 59, Mismatches: 20, Indels: 10
0.66 0.22 0.11
Matches are distributed among these distances:
12 3 0.05
13 12 0.20
14 35 0.59
15 9 0.15
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (14 bp):
TTAATTATAATATT
Found at i:1294199 original size:21 final size:20
Alignment explanation
Indices: 1294153--1294200 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
1294143 CAACCTAAAT
*
1294153 TTTTTTTATTTTTTATTATA
1 TTTTTTTATATTTTATTATA
*
1294173 TGTTTTTAGTATTTTATT-TA
1 TTTTTTTA-TATTTTATTATA
*
1294193 ATTTTTTA
1 TTTTTTTA
1294201 AATAATTATG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (20 bp):
TTTTTTTATATTTTATTATA
Found at i:1296940 original size:203 final size:203
Alignment explanation
Indices: 1296591--1296999 Score: 671
Period size: 203 Copynumber: 2.0 Consensus size: 203
1296581 TAATTTACCC
* * *
1296591 TAAATAATTTTAGTGACTAAAATAGGAATGAGGAAAAAATTCAATGATAAATTTTTAATTTTCCT
1 TAAATAATTTTAGTGACTAAAATAGGAATGAGGAAAAAATTCAATGATAAAGTTTTAATTTACCC
* * * *
1296656 TTATTTAATTTATTGATTGAAAAAAGTTTGATGATAAAATTTTAAATTATCCAAGTTTTAATTTA
66 ATATTTAATTAATTGATTGAAAAAAGTTTAATCATAAAATTTTAAATTATCCAAG-TTTAATTTA
* *
1296721 TCATTCTCTATTATTTTATTTAAAAATTATAAG-AAAACACTATTTTAATAATATTGTAATATTA
130 TCATTCTCAATTATTTTATTTAAAAATTATAAGAAAAACACTATTTTAATAACATTGTAATATTA
1296785 CATAAGAGT
195 CATAAGAGT
1296794 TAAATAATTTTAGTGACTAAAATAGGAATGA-GAAAAAAGTTCAATGATAAAGTTTTAATTTACC
1 TAAATAATTTTAGTGACTAAAATAGGAATGAGGAAAAAA-TTCAATGATAAAGTTTTAATTTACC
1296858 CATATTTAATTAATTGATTGAAAAAAGTTTAATCATAAAATTTTAAATTATCCATA-TTTAATTT
65 CATATTTAATTAATTGATTGAAAAAAGTTTAATCATAAAATTTTAAATTATCCA-AGTTTAATTT
1296922 ATCGATTCTCAATTATTTTATTTAAAAATTATAAGAAAAACACTATTTTAATAACATTGTAATAT
129 ATC-ATTCTCAATTATTTTATTTAAAAATTATAAGAAAAACACTATTTTAATAACATTGTAATAT
*
1296987 TATATAAGAGT
193 TACATAAGAGT
1296998 TA
1 TA
1297000 TATTCTTCTC
Statistics
Matches: 192, Mismatches: 10, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
202 18 0.09
203 133 0.69
204 41 0.21
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (203 bp):
TAAATAATTTTAGTGACTAAAATAGGAATGAGGAAAAAATTCAATGATAAAGTTTTAATTTACCC
ATATTTAATTAATTGATTGAAAAAAGTTTAATCATAAAATTTTAAATTATCCAAGTTTAATTTAT
CATTCTCAATTATTTTATTTAAAAATTATAAGAAAAACACTATTTTAATAACATTGTAATATTAC
ATAAGAGT
Found at i:1298932 original size:24 final size:25
Alignment explanation
Indices: 1298886--1298932 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
1298876 AAGTTATTTA
*
1298886 TTTTCTTTTCAAGTTTTCATTTTTC
1 TTTTATTTTCAAGTTTTCATTTTTC
1298911 TTTTATTTT-AAGTTTT-ATTTTT
1 TTTTATTTTCAAGTTTTCATTTTT
1298933 AAACATACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 7 0.33
25 8 0.38
ACGTcount: A:0.15, C:0.09, G:0.04, T:0.72
Consensus pattern (25 bp):
TTTTATTTTCAAGTTTTCATTTTTC
Found at i:1310372 original size:8 final size:8
Alignment explanation
Indices: 1310359--1310388 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
1310349 TCAATATATT
1310359 TAATTTAA
1 TAATTTAA
1310367 TAATTTAA
1 TAATTTAA
1310375 TAATTTAA
1 TAATTTAA
1310383 TAATTT
1 TAATTT
1310389 TTATTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
TAATTTAA
Found at i:1310570 original size:11 final size:11
Alignment explanation
Indices: 1310554--1310579 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1310544 TTTTATTTTG
1310554 TTTAAATTATT
1 TTTAAATTATT
1310565 TTTAAATTATT
1 TTTAAATTATT
1310576 TTTA
1 TTTA
1310580 GGAAAATGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TTTAAATTATT
Found at i:1310737 original size:2 final size:2
Alignment explanation
Indices: 1310698--1310722 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1310688 TATAAAAATC
1310698 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
1310723 TAAAAATTAA
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:1311307 original size:22 final size:23
Alignment explanation
Indices: 1311282--1311326 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
1311272 ATATATCCTG
1311282 ATATACTAA-TATTTTTTATTTC
1 ATATACTAATTATTTTTTATTTC
*
1311304 ATATATTAACTTTATTTTTTATT
1 ATATACTAA--TTATTTTTTATT
1311327 GGTTATTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 8 0.42
25 11 0.58
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (23 bp):
ATATACTAATTATTTTTTATTTC
Found at i:1313572 original size:64 final size:64
Alignment explanation
Indices: 1313434--1313595 Score: 202
Period size: 64 Copynumber: 2.5 Consensus size: 64
1313424 TCTTTCAATG
* *
1313434 AAAGTATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTA
1 AAAGTATGCATCGATGCACTACTAATGCATCGATGCATAAAATGCATTCGATGTTGTATTATTA
*** * * * *
1313498 CTGGTATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTTTTATT-TTA
1 AAAGTATGCATCGATGCACTACTAATGCATCGATGCATAAAATGCATTCGATG-TTGTATTATTA
*
1313562 AAAG-AGTGCATCGATGCACTACCAATGCATCGAT
1 AAAGTA-TGCATCGATGCACTACTAATGCATCGAT
1313596 ACACCTTCAA
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
63 1 0.01
64 76 0.92
65 6 0.07
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (64 bp):
AAAGTATGCATCGATGCACTACTAATGCATCGATGCATAAAATGCATTCGATGTTGTATTATTA
Found at i:1317132 original size:31 final size:31
Alignment explanation
Indices: 1317094--1317156 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
1317084 CCCGAAGGAC
* *
1317094 CAGTCCATA-GATCCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATACGTAAA
1317125 CAGTCCATATGTCCCGAAGAACATACGTAAA
1 CAGTCCATATGTCCCGAAGAACATACGTAAA
1317156 C
1 C
1317157 CCTCGACCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 28 0.97
32 1 0.03
ACGTcount: A:0.38, C:0.27, G:0.17, T:0.17
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATACGTAAA
Found at i:1317947 original size:64 final size:64
Alignment explanation
Indices: 1317808--1317970 Score: 193
Period size: 64 Copynumber: 2.5 Consensus size: 64
1317798 TCTTTAAATA
* *
1317808 AAAAGTATGCATCGATGCACTACTGATGCATCGGTGCATAAAATACATTCGATGTTGTATTATT
1 AAAAGTATGCATCGATGCACTACTAATGCATCGATGCATAAAATACATTCGATGTTGTATTATT
*** * * * * * *
1317872 ACCGGTATGCATCGACGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTTTTATT-TT
1 AAAAGTATGCATCGATGCACTACTAATGCATCGATGCATAAAATACATTCGATG-TTGTATTATT
* *
1317936 AAAAGTGTGCATCGATGCACTACCAATGCATCGAT
1 AAAAGTATGCATCGATGCACTACTAATGCATCGAT
1317971 ACACCTTCAA
Statistics
Matches: 81, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
64 75 0.93
65 6 0.07
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (64 bp):
AAAAGTATGCATCGATGCACTACTAATGCATCGATGCATAAAATACATTCGATGTTGTATTATT
Found at i:1328622 original size:14 final size:14
Alignment explanation
Indices: 1328603--1328641 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
1328593 ATTATGCTTG
1328603 AAGAAAAAAAGAAA
1 AAGAAAAAAAGAAA
1328617 AAGAAAATAAA-AAA
1 AAGAAAA-AAAGAAA
*
1328631 AATAAAAAAAG
1 AAGAAAAAAAG
1328642 GAGGGTCAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 3 0.14
14 16 0.73
15 3 0.14
ACGTcount: A:0.85, C:0.00, G:0.10, T:0.05
Consensus pattern (14 bp):
AAGAAAAAAAGAAA
Found at i:1330583 original size:257 final size:257
Alignment explanation
Indices: 1330127--1330643 Score: 917
Period size: 257 Copynumber: 2.0 Consensus size: 257
1330117 ATGCTAGCTT
1330127 GAAATGATTTTGACTAAGTAAAGGAAGACCGAGTTTGCCATATTGAAGTCAAATAAATATGAACT
1 GAAATGATTTTGACTAAGTAAAGGAAGACCGAGTTTGCCATATTGAAGTCAAATAAATATGAACT
1330192 TAACATTCATGCATCATATTTAGACATTTAAAAAAATAGGGGCATTTCCATTCATTTTATCAATG
66 TAACATTCATGCATCATATTTAGACATTTAAAAAAATAGGGGCATTTCCATTCATTTTATCAATG
* *
1330257 TTGATTATTTAACAAGAACCTAAAAGATTAGAAAAGATTTGAATCTATCACTTGATGATTCAACA
131 TTGATTATTTAACAAGAACCCAAAAGATTAGAAAAGATTTGAATATATCACTTGATGATTCAACA
* *
1330322 TTGCCAAAAAGAGTTCATAATTAGAAGAACTCATCTGAAAAGGAAGAAGAAGTTCATAATGA
196 TTGCCAAAAAGAGTTCATAATGAGAAGAACTCATCTGAAAAGGAAGAAGAAATTCATAATGA
* * *
1330384 GAAATGATTTTGACTAAGTAAAGGAAGATCGTGTTTGTCATATTGAAGTCAAATAAATATGAACT
1 GAAATGATTTTGACTAAGTAAAGGAAGACCGAGTTTGCCATATTGAAGTCAAATAAATATGAACT
* *
1330449 TAACATTCATGCATCATATTTAGACATTTACAAAAATAGGGGCATTTTCATTCATTTTATCAATG
66 TAACATTCATGCATCATATTTAGACATTTAAAAAAATAGGGGCATTTCCATTCATTTTATCAATG
* * *
1330514 TTGATTATTTAACAAGAACCCCAAAGATTAGCAAAGATTTGAATATATTACTTGATGATTCAACA
131 TTGATTATTTAACAAGAACCCAAAAGATTAGAAAAGATTTGAATATATCACTTGATGATTCAACA
*
1330579 TTGCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAAAGGAAGAAGAAATTCATAATGA
196 TTGCCAAAAAGAGTTCATAATGAGAAGAACTCATCTGAAAAGGAAGAAGAAATTCATAATGA
1330641 GAA
1 GAA
1330644 GAACTTGTTC
Statistics
Matches: 247, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
257 247 1.00
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (257 bp):
GAAATGATTTTGACTAAGTAAAGGAAGACCGAGTTTGCCATATTGAAGTCAAATAAATATGAACT
TAACATTCATGCATCATATTTAGACATTTAAAAAAATAGGGGCATTTCCATTCATTTTATCAATG
TTGATTATTTAACAAGAACCCAAAAGATTAGAAAAGATTTGAATATATCACTTGATGATTCAACA
TTGCCAAAAAGAGTTCATAATGAGAAGAACTCATCTGAAAAGGAAGAAGAAATTCATAATGA
Found at i:1330798 original size:123 final size:123
Alignment explanation
Indices: 1330582--1330899 Score: 455
Period size: 123 Copynumber: 2.6 Consensus size: 123
1330572 TTCAACATTG
*
1330582 CCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAAAGGAAGAAGAAA-TTCATAATGAGAAGA
1 CCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAA-AAAGTTCATAATGAGAAGA
* *
1330646 ACTTGTTCAACCTTTTGCTCGATTCTATCATACAAGGAGATAGATC-AGCACCAACATCA
65 ACTTATTCAACCTTTTGCTCGATTCTATCATACAAAGAGATAGATCGA-CACCAACATCA
1330705 CCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAAAAGCTT-ATAATGAGAAGA
1 CCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAAAAG-TTCATAATGAGAAGA
* * * * **
1330769 ATTTATTCAACCTTTTGCTCGATTTTATCATAGAAAGAGATAGATCGACACCAATATTT
65 ACTTATTCAACCTTTTGCTCGATTCTATCATACAAAGAGATAGATCGACACCAACATCA
* * * *
1330828 CCA-AAAGGAGTTCATAATGAGAAGAACCCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAATA
1 CCAGAAA-GAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATAATGAGAAGA
1330892 ACTTATTC
65 ACTTATTC
1330900 TACTTTAACT
Statistics
Matches: 176, Mismatches: 14, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
122 8 0.05
123 165 0.94
124 3 0.02
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.24
Consensus pattern (123 bp):
CCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATAATGAGAAGAA
CTTATTCAACCTTTTGCTCGATTCTATCATACAAAGAGATAGATCGACACCAACATCA
Found at i:1331147 original size:137 final size:138
Alignment explanation
Indices: 1330820--1331181 Score: 403
Period size: 139 Copynumber: 2.6 Consensus size: 138
1330810 AGATCGACAC
* *
1330820 CAATATTTCCAAAAGGAGTTCATAATGAGAAGAACCCATCTGAAGAAGAAGAAGAAGTTCATAAT
1 CAATATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAAT
* * * * * *
1330885 GAGAATAACTTATTCTACTTTAACTTGATTTAGCTCTTATAAAGATGAATGAAAGAAGAACCTCA
66 GAGAATAACTTGTTCAACCTTAACTTAATTCA-CTCTTATAAAGATGAATGAAAGAACAACCTCA
1330950 TTTAGAGAT
130 TTTAGAGAT
* * * *
1330959 CAACATTTTCAG-AGAAAGTTCATAATGAGAAGAATTCATCTGAA-AATGAAGAAGAAGTTCATA
1 CAATATTTCCAGAAG-GAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAGTTCATA
* ** * * * * *
1331022 ATGAGAAGAACTTGTTCAACCTTGCCTTAATTCA-TCATATATGAAGTTGAAT-CAA-CACCACC
64 ATGAGAATAACTTGTTCAACCTTAACTTAATTCACTC-T-TATAAAGATGAATGAAAGAACAACC
*
1331084 TC-TTTTGAGGAT
127 TCATTTAGA-GAT
* * * *
1331096 CAGTATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATTTGAAGAGGAAGAAAAAGTTCATAAT
1 CAATATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAAT
1331161 GAGAATAACTTGTTCAACCTT
66 GAGAATAACTTGTTCAACCTT
1331182 TTGCTAGATT
Statistics
Matches: 186, Mismatches: 30, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
136 5 0.03
137 83 0.45
138 10 0.05
139 88 0.47
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (138 bp):
CAATATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAAT
GAGAATAACTTGTTCAACCTTAACTTAATTCACTCTTATAAAGATGAATGAAAGAACAACCTCAT
TTAGAGAT
Found at i:1332891 original size:11 final size:11
Alignment explanation
Indices: 1332875--1332900 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1332865 TTTTGTTTTG
1332875 TTTAAATTATT
1 TTTAAATTATT
1332886 TTTAAATTATT
1 TTTAAATTATT
1332897 TTTA
1 TTTA
1332901 GGAAAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TTTAAATTATT
Found at i:1333029 original size:2 final size:2
Alignment explanation
Indices: 1333022--1333057 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1333012 AAAAATCTAA
1333022 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1333058 AATAATTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1335108 original size:11 final size:9
Alignment explanation
Indices: 1335102--1335141 Score: 55
Period size: 9 Copynumber: 4.3 Consensus size: 9
1335092 TAATAATACT
1335102 TATATAATA
1 TATATAATA
1335111 TATATATATAA
1 TATATA-AT-A
1335122 TATATAATA
1 TATATAATA
1335131 TATA-AATA
1 TATATAATA
1335139 TAT
1 TAT
1335142 GTTTTTTCGG
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
8 7 0.24
9 11 0.38
10 4 0.14
11 7 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
TATATAATA
Found at i:1335113 original size:2 final size:2
Alignment explanation
Indices: 1335102--1335141 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
1335092 TAATAATACT
*
1335102 TA TA TA -A TA TA TA TA TA TA -A TA TA TA -A TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1335141 T
1 T
1335142 GTTTTTTCGG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
1 3 0.09
2 30 0.91
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1335114 original size:7 final size:7
Alignment explanation
Indices: 1335102--1335140 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
1335092 TAATAATACT
1335102 TATATAA
1 TATATAA
1335109 TATAT-A
1 TATATAA
1335115 TATATAA
1 TATATAA
1335122 TATATAA
1 TATATAA
1335129 TATATAA
1 TATATAA
1335136 -ATATA
1 TATATA
1335141 TGTTTTTTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 11 0.35
7 20 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TATATAA
Found at i:1335127 original size:20 final size:20
Alignment explanation
Indices: 1335102--1335140 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1335092 TAATAATACT
*
1335102 TATATAATATATATATATAA
1 TATATAATATATAAATATAA
1335122 TATATAATATATAAATATA
1 TATATAATATATAAATATA
1335141 TGTTTTTTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TATATAATATATAAATATAA
Found at i:1336087 original size:43 final size:43
Alignment explanation
Indices: 1336026--1336276 Score: 151
Period size: 43 Copynumber: 5.4 Consensus size: 43
1336016 ACCAGCGGTC
1336026 CCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATGT
1 CCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATGT
* * * * ** **
1336069 CCTTCGTTGTGAAATTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGT
1 CCTTCGTTGTGAAGTTGAACTTGCG---TTGTCTG--GA-GTCCA-ATGT
* *
1336119 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 -CCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATGT
* * * * ** **
1336163 CCTTCGCTGTGAAGTTGAAATTGGGAAATTGTTTGTTTGACAACCAGCGGT
1 CCTTCGTTGTGAAGTTGAACTTGCG---TTGTCTG---GA-GTCCA-ATGT
* * *
1336214 CCCTTCGTCGTGAAGTTGAACTTGAGTTGTCTGGAGTCCAATAT
1 -CCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATGT
*
1336258 CCTTCGCTGTGAAGTTGAA
1 CCTTCGTTGTGAAGTTGAA
1336277 ATTGGCTCTG
Statistics
Matches: 151, Mismatches: 40, Indels: 34
0.67 0.18 0.15
Matches are distributed among these distances:
43 60 0.40
44 2 0.01
45 6 0.04
46 16 0.11
48 8 0.05
49 11 0.07
50 5 0.03
51 22 0.15
52 21 0.14
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.34
Consensus pattern (43 bp):
CCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATGT
Found at i:1336321 original size:106 final size:106
Alignment explanation
Indices: 1336178--1336815 Score: 1114
Period size: 106 Copynumber: 6.0 Consensus size: 106
1336168 GCTGTGAAGT
* * * *
1336178 TGAAATTGGGAAATTGTTTGTTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGAGTTG
1 TGAAATTGAGAAGTTGTTTG-TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTG
*
1336243 TCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
65 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* *
1336285 TGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGT
*
1336350 CTGGAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* *
1336391 TGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGT
1336456 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
*
1336497 TAAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGT
*
1336562 CTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* *
1336603 TGAAATTGAGAAGTTGTTTGTTGACGACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTCGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGT
1336668 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* *
1336709 TGAAATTGAGAAGTTGTTTGTTGACGACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTCGT
1 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGT
*
1336774 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTC
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
1336815 T
1 T
1336816 CGAGCAAATT
Statistics
Matches: 515, Mismatches: 16, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
106 498 0.97
107 17 0.03
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (106 bp):
TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGT
CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
Found at i:1336650 original size:318 final size:311
Alignment explanation
Indices: 1335953--1336815 Score: 1323
Period size: 318 Copynumber: 2.8 Consensus size: 311
1335943 AATTGTTCCA
* * * *
1335953 AGTCCAATAT-CTTCCGCCGTGAAGTTGAAATTGGCTCTAGAACTGGA-AAATTGTTTATTGACA
1 AGTCCAATATCCTT-CGCTGTGAAGTTGAAATTGGCTCT-GAAATTGAGAAGTTGTTTATTGACA
* *
1336016 ACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATGTCCTTCGTTGTGA
64 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
*
1336081 AATTGAAATT-G----G-----GA-AA-TTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
129 AGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
*
1336134 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG----GAAATTGT
194 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGT
*
1336195 TTGTTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGAGTTGTCTGG
259 TTGTTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGAGTTGTCTGG
1336248 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAAC
*
1336313 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCATTGTGAAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
*
1336378 TTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
131 TTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
1336443 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGA
196 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC------TGA-A
*
1336508 AGTTGTTTG-TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
254 A-TTGTTTGTTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGAGTTGTCTGG
* *
1336566 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACGAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAAC
* *
1336631 CAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTCGTCTGGAGTCCAATATCCTTCGTTGTGAAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
*
1336696 TTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACGACCAGCGGTCCCTTCGTCGTGAAGTT
131 TTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
* * *
1336761 GAACATGCGTCGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCT
196 GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
1336816 CGAGCAAATT
Statistics
Matches: 520, Mismatches: 22, Indels: 35
0.90 0.04 0.06
Matches are distributed among these distances:
294 6 0.01
295 119 0.23
296 4 0.01
300 1 0.00
305 2 0.00
306 2 0.00
307 88 0.17
312 1 0.00
317 2 0.00
318 288 0.55
319 7 0.01
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.33
Consensus pattern (311 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
TTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
GAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGTTT
GTTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGAGTTGTCTGG
Found at i:1337017 original size:35 final size:35
Alignment explanation
Indices: 1336968--1337143 Score: 154
Period size: 35 Copynumber: 5.1 Consensus size: 35
1336958 TCAATGTTTA
*
1336968 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAATTT
* * *
1337003 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGAC-AATTT
** *
1337039 CATTTCAAGGGAAA-TGTTTTC----GATG----TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGGGA-GACAATTT
* *
1337067 ATATTTCAAGAGAAACTGTCTCAAGGGAGACAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGGGAGACAATTT
*
1337103 TGTTTCAAGGGAAACTGTCTCAAGGGAGACGAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGAC-AATTT
1337139 TGTTT
1 TGTTT
1337144 TAAGAAAAAC
Statistics
Matches: 112, Mismatches: 15, Indels: 27
0.73 0.10 0.18
Matches are distributed among these distances:
28 2 0.02
29 15 0.13
30 2 0.02
32 3 0.03
33 3 0.03
35 56 0.50
36 31 0.28
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31
Consensus pattern (35 bp):
TGTTTCAAGGGAAACTGTCTCAAGGGAGACAATTT
Found at i:1337020 original size:100 final size:100
Alignment explanation
Indices: 1336876--1337138 Score: 454
Period size: 100 Copynumber: 2.6 Consensus size: 100
1336866 TAGTTCAAAA
* *
1336876 AGAAATTGTCTCAAGGGAGACGAACTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
1 AGAAACTGTCTCAAGGGAGAC-AATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
*
1336941 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAG
65 TTTCAAGGGAAATGTTTTCAATGTTTATATTTCAAG
1336977 AGAAACTGTCTCAAGGGAGACAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCAT
1 AGAAACTGTCTCAAGGGAGACAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCAT
*
1337042 TTCAAGGGAAATGTTTTCGATGTTTATATTTCAAG
66 TTCAAGGGAAATGTTTTCAATGTTTATATTTCAAG
* * *
1337077 AGAAACTGTCTCAAGGGAGACAATTTTGTTTCAAGGGAAACTGTCTCAAGGGAGACGAAATT
1 AGAAACTGTCTCAAGGGAGACAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1337139 TGTTTTAAGA
Statistics
Matches: 155, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
100 135 0.87
101 20 0.13
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (100 bp):
AGAAACTGTCTCAAGGGAGACAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCAT
TTCAAGGGAAATGTTTTCAATGTTTATATTTCAAG
Found at i:1337359 original size:84 final size:84
Alignment explanation
Indices: 1337157--1337543 Score: 355
Period size: 84 Copynumber: 4.7 Consensus size: 84
1337147 GAAAAACAAT
* * * * *
1337157 CTCAAAGGT-TTTTGTTGACAGATAACTCC-TCTAGCCTTGAGTTATGCTGTAAATGATGTGCCC
1 CTCAAAGGTATTTTGTTGGCAGATAAC-CCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCC
* * *
1337220 TCGGAGCTGAGTGGAATCGAA
65 T-TGAGCTGAGCGTAATCGAA
* * * * * *
1337241 CTC--GGGGA-TCT-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGT
1 CTCAAAGGTATTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCT
*
1337302 TGAGCTGAGCGTAGTCGAA
66 TGAGCTGAGCGTAATCGAA
* * * * **
1337321 CTCAAAGGTATTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGTTGCAAATGACATG-CCT
1 CTCAAAGGTATTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCT
*
1337385 TGGAGCTGAGCGTAGTCGAA
66 T-GAGCTGAGCGTAATCGAA
* * *
1337405 CTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGATGCAAATGATGTGCCCT
1 CTCAAAGGTATTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCT
* *
1337470 CGAAGCTGAGTGTAATCGAA
66 TG-AGCTGAGCGTAATCGAA
*** * * * *
1337490 CTC---GGGGGTCT-TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGAT
1 CTCAAAGGTATTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAT
1337544 TTGTTTTAAA
Statistics
Matches: 247, Mismatches: 47, Indels: 21
0.78 0.15 0.07
Matches are distributed among these distances:
80 20 0.08
81 78 0.32
82 10 0.04
83 5 0.02
84 113 0.46
85 21 0.09
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (84 bp):
CTCAAAGGTATTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCT
TGAGCTGAGCGTAATCGAA
Found at i:1342039 original size:2 final size:2
Alignment explanation
Indices: 1342028--1342061 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1342018 TAATAATACT
*
1342028 TA TA TA -A TA TA TA TA TA TA TA TA TA TA AA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1342062 GTTTTTTCGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1349499 original size:14 final size:14
Alignment explanation
Indices: 1349480--1349510 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1349470 CTTAATAATT
1349480 TTTTATATTTTTAA
1 TTTTATATTTTTAA
1349494 TTTTATATTTTTAA
1 TTTTATATTTTTAA
1349508 TTT
1 TTT
1349511 AAATAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTATATTTTTAA
Found at i:1349666 original size:20 final size:20
Alignment explanation
Indices: 1349641--1349680 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1349631 CACACCAATA
*
1349641 TTGTAAATTGTCATGTAAGT
1 TTGTAAACTGTCATGTAAGT
1349661 TTGTAAACTGTCATGTAAGT
1 TTGTAAACTGTCATGTAAGT
1349681 GTCGTGAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.42
Consensus pattern (20 bp):
TTGTAAACTGTCATGTAAGT
Found at i:1350184 original size:34 final size:34
Alignment explanation
Indices: 1350147--1350211 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 34
1350137 AAATTTCAAA
* *
1350147 AAAAAAT-GAAAATGAAAACTA-TTTTCTAGAAT
1 AAAAAATAAAAAATAAAAACTATTTTTCTAGAAT
1350179 AAAAAATAAAAAATAAAAACTATTTTTCTAGAA
1 AAAAAATAAAAAATAAAAACTATTTTTCTAGAA
1350212 CCAAACGAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 7 0.24
33 12 0.41
34 10 0.34
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.28
Consensus pattern (34 bp):
AAAAAATAAAAAATAAAAACTATTTTTCTAGAAT
Found at i:1352110 original size:37 final size:37
Alignment explanation
Indices: 1352034--1352110 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
1352024 TTTTTATATT
*
1352034 TTTAATTTTATAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTATAAAAAAAATTATATAAATATTATCAA
* * *
1352071 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTATAAAAAAAATTATATAAATATTAT-CAA
1352108 TTT
1 TTT
1352111 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (37 bp):
TTTAATTTTATAAAAAAAATTATATAAATATTATCAA
Found at i:1353688 original size:35 final size:35
Alignment explanation
Indices: 1353649--1353743 Score: 122
Period size: 35 Copynumber: 2.7 Consensus size: 35
1353639 ACACAATCAT
1353649 CAATTACATTCTAAACC-CAAAAGTT-CAAAATACTA
1 CAATTACATTCTAAACCTC-AAA-TTCCAAAATACTA
*
1353684 CAATTACATTCTAAACCTCAAATTCCAAAATACTT
1 CAATTACATTCTAAACCTCAAATTCCAAAATACTA
* **
1353719 CAATTACATGCCCAACCTCAAATTC
1 CAATTACATTCTAAACCTCAAATTC
1353744 ATAATCCATT
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
34 2 0.04
35 51 0.94
36 1 0.02
ACGTcount: A:0.43, C:0.27, G:0.02, T:0.27
Consensus pattern (35 bp):
CAATTACATTCTAAACCTCAAATTCCAAAATACTA
Found at i:1354420 original size:148 final size:140
Alignment explanation
Indices: 1354225--1354509 Score: 426
Period size: 148 Copynumber: 2.0 Consensus size: 140
1354215 AAACTATTTA
* *
1354225 AATTAGAATCAAATAATTATAGTATTATAAATATTTATAATTAAATTTAAACAGAAACTCGAAAA
1 AATTAGAATCAAATAATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCGAAAA
* * * *
1354290 TTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTCGAGTCAATTAT
66 TTCAATTC-A----ACTTGATTTAAATTTTATAAACTCAAAT-AAAAAAAATTAGAGTCAACTAT
1354355 TTTATAAACTGAACTG
125 TTTATAAACTGAACTG
*
1354371 AATTGGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCGAA
1 AATTAGAATCAAAT-A-ATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCGAA
*
1354436 AATTCAATTCAACTTTATTTAAATTTTATAAACTCAAATAAAAAAAATTAGAGTCAACTATTTTA
64 AATTCAATTCAACTTGATTTAAATTTTATAAACTCAAATAAAAAAAATTAGAGTCAACTATTTTA
1354501 TAAACTGAA
129 TAAACTGAA
1354510 TTGAGTATTT
Statistics
Matches: 129, Mismatches: 8, Indels: 8
0.89 0.06 0.06
Matches are distributed among these distances:
142 31 0.24
143 27 0.21
146 13 0.10
147 2 0.02
148 56 0.43
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.36
Consensus pattern (140 bp):
AATTAGAATCAAATAATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCGAAAA
TTCAATTCAACTTGATTTAAATTTTATAAACTCAAATAAAAAAAATTAGAGTCAACTATTTTATA
AACTGAACTG
Found at i:1354719 original size:35 final size:35
Alignment explanation
Indices: 1354680--1354759 Score: 126
Period size: 35 Copynumber: 2.3 Consensus size: 35
1354670 GGGGTTGGGC
1354680 ATGTAATTGAAACATTTTGGAA-TTTGAGGTTTAGA
1 ATGTAATTGAAACATTTT-GAATTTTGAGGTTTAGA
**
1354715 ATGTAATTGAAGTATTTTGAATTTTGAGGTTTAGA
1 ATGTAATTGAAACATTTTGAATTTTGAGGTTTAGA
1354750 ATGTAATTGA
1 ATGTAATTGA
1354760 TGATTGTGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
34 3 0.07
35 39 0.93
ACGTcount: A:0.34, C:0.01, G:0.23, T:0.42
Consensus pattern (35 bp):
ATGTAATTGAAACATTTTGAATTTTGAGGTTTAGA
Found at i:1364185 original size:2 final size:2
Alignment explanation
Indices: 1364178--1364211 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1364168 AGTCAGATTA
1364178 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
1364212 TTAAAAAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1367532 original size:21 final size:21
Alignment explanation
Indices: 1367498--1367610 Score: 72
Period size: 20 Copynumber: 5.5 Consensus size: 21
1367488 ATACTGACTA
*
1367498 TCGCAATGCAATTTTTC-TAAT
1 TCGCAATGCGA-TTTTCATAAT
* * *
1367519 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
**
1367539 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
* * *
1367560 TCGCAATGCGA-ATACATAAA
1 TCGCAATGCGATTTTCATAAT
* ** *
1367580 TCGCAACGCGA-TTAAATAAA
1 TCGCAATGCGATTTTCATAAT
1367600 TCGCAATGCGA
1 TCGCAATGCGA
1367611 ATTAGGAAAA
Statistics
Matches: 75, Mismatches: 15, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
20 54 0.72
21 21 0.28
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:1367583 original size:20 final size:20
Alignment explanation
Indices: 1367554--1367653 Score: 112
Period size: 20 Copynumber: 5.0 Consensus size: 20
1367544 TTGCGATTTT
*
1367554 CATAATTCGCAATGCGAATA
1 CATAAATCGCAATGCGAATA
* *
1367574 CATAAATCGCAACGCGATTA
1 CATAAATCGCAATGCGAATA
*
1367594 AATAAATCGCAATGCGAATTA
1 CATAAATCGCAATGCGAA-TA
* *
1367615 GGA-AAATCGCAATGCAAATA
1 -CATAAATCGCAATGCGAATA
*
1367635 CGTAAATCGCAATGCGAAT
1 CATAAATCGCAATGCGAAT
1367654 CTTACTATCG
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
20 49 0.74
21 16 0.24
22 1 0.02
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (20 bp):
CATAAATCGCAATGCGAATA
Found at i:1367622 original size:41 final size:41
Alignment explanation
Indices: 1367555--1367653 Score: 112
Period size: 41 Copynumber: 2.4 Consensus size: 41
1367545 TGCGATTTTC
* * *
1367555 ATAATTCGCAATGCGAA-TACATAAATCGCAACGCGATTAA
1 ATAAATCGCAATGCGAATTACATAAATCGCAACGCAAATAA
* * *
1367595 ATAAATCGCAATGCGAATTAGGA-AAATCGCAATGCAAATAC
1 ATAAATCGCAATGCGAATTA-CATAAATCGCAACGCAAATAA
*
1367636 GTAAATCGCAATGCGAAT
1 ATAAATCGCAATGCGAAT
1367654 CTTACTATCG
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
40 16 0.32
41 33 0.66
42 1 0.02
ACGTcount: A:0.43, C:0.18, G:0.17, T:0.21
Consensus pattern (41 bp):
ATAAATCGCAATGCGAATTACATAAATCGCAACGCAAATAA
Found at i:1367664 original size:61 final size:59
Alignment explanation
Indices: 1367560--1367673 Score: 140
Period size: 61 Copynumber: 1.9 Consensus size: 59
1367550 TTTTCATAAT
*
1367560 TCGCAATGCGAATACATAAATCGCAACGCGATTAAATAAATCGCAATGCGAATTAGGAAAA
1 TCGCAATGCAAATACATAAATCGCAACGCGATTAAAT-AATCGCAATGC-AATTAGGAAAA
* * * *
1367621 TCGCAATGCAAATACGTAAATCGCAATGCGAATCTTACT-ATCGCAATGCAATT
1 TCGCAATGCAAATACATAAATCGCAACGCG-AT-TAAATAATCGCAATGCAATT
1367674 TACATAGCGC
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
60 4 0.09
61 37 0.80
62 2 0.04
63 3 0.07
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (59 bp):
TCGCAATGCAAATACATAAATCGCAACGCGATTAAATAATCGCAATGCAATTAGGAAAA
Found at i:1368230 original size:19 final size:19
Alignment explanation
Indices: 1368206--1368250 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1368196 GCAACGAGAG
**
1368206 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAACCAA
1368225 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
1368244 AATCGCA
1 AATCGCA
1368251 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:1368268 original size:19 final size:19
Alignment explanation
Indices: 1368246--1368371 Score: 92
Period size: 19 Copynumber: 7.1 Consensus size: 19
1368236 GAAACCAAAA
*
1368246 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1368265 TCGCGTTGTGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1368279 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1368298 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1368312 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1368331 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1368350 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1368370 TC
1 TC
1368372 AACCAAAAGA
Statistics
Matches: 83, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
14 19 0.23
16 4 0.05
17 5 0.06
19 37 0.45
20 18 0.22
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1368297 original size:33 final size:33
Alignment explanation
Indices: 1368251--1368343 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
1368241 CAAAATCGCA
** *
1368251 TTGCGATTTTCATTTCGCGTTGTGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
1368284 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
1368317 TTGCGATAGTCATTTCGCGTTGCGATT
1 TTGCGATAGTCATTTCGCGTTGCGATT
1368344 TTCATTATCT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.12, C:0.22, G:0.24, T:0.43
Consensus pattern (33 bp):
TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
Found at i:1370166 original size:91 final size:87
Alignment explanation
Indices: 1370014--1370192 Score: 261
Period size: 86 Copynumber: 2.0 Consensus size: 87
1370004 TAGATTGCTT
*
1370014 AGTAAATTTATTCGGTTGCTGTCAATACGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTGT
1 AGTAAATTTATTCGGTTGCTGCCAATACGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTGT
*
1370079 -TTTGTTTTGTCTTTTGGTTGA
66 CTTTGTTTTATCTTTTGGTTGA
* * *
1370100 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAATTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATAC-GCTAAA--CTGT-TT-ATTAACACTGTGAAGTTAGT
1370165 ATTGTCTTTGTTTTATCTTTTGGTTGA
61 ATTGTCTTTGTTTTATCTTTTGGTTGA
1370192 A
1 A
1370193 AGTTTGAATA
Statistics
Matches: 82, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
86 26 0.32
87 6 0.07
89 3 0.04
90 2 0.02
91 24 0.29
92 21 0.26
ACGTcount: A:0.23, C:0.11, G:0.19, T:0.47
Consensus pattern (87 bp):
AGTAAATTTATTCGGTTGCTGCCAATACGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTGT
CTTTGTTTTATCTTTTGGTTGA
Found at i:1370487 original size:21 final size:21
Alignment explanation
Indices: 1370463--1370529 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1370453 TCATTCCTCG
1370463 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1370484 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1370505 AGATGTCCCC-CCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1370526 AGAG
1 AGAG
1370530 CCCGATCACA
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 27 0.84
22 4 0.12
ACGTcount: A:0.24, C:0.37, G:0.19, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1370487 original size:42 final size:42
Alignment explanation
Indices: 1370436--1370529 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 42
1370426 CCACTCATAT
* *
1370436 CGTTGAAGAGGCCTCTATCATTCCTCG-AGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCACTATCA-TCCTCGAAGATGTCCCC-CCCAC
* * *
1370478 CGTTCAAGAGGCCACTGTCATCGTTGAAGATGTCCCCCCCAC
1 CGTTCAAGAGGCCACTATCATCCTCGAAGATGTCCCCCCCAC
*
1370520 CATTCAAGAG
1 CGTTCAAGAG
1370530 CCCGATCACA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
41 4 0.09
42 34 0.77
43 6 0.14
ACGTcount: A:0.22, C:0.35, G:0.20, T:0.22
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCTCGAAGATGTCCCCCCCAC
Found at i:1371879 original size:14 final size:14
Alignment explanation
Indices: 1371860--1371895 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1371850 ATTGCTTAAT
1371860 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1371874 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1371888 TGATTTGT
1 TGATTTGT
1371896 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1372022 original size:19 final size:19
Alignment explanation
Indices: 1372000--1372058 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
1371990 AAAAATTACT
1372000 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1372019 ATCGCAA--CG--AT-ATA
1 ATCGCAATGCGAAATGAAA
1372033 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1372052 ATCGCAA
1 ATCGCAA
1372059 CGAGAAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 9 0.27
15 2 0.06
16 2 0.06
17 2 0.06
18 2 0.06
19 16 0.48
ACGTcount: A:0.46, C:0.19, G:0.19, T:0.17
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1372042 original size:33 final size:33
Alignment explanation
Indices: 1372000--1372073 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 33
1371990 AAAAATTACT
* *
1372000 ATCGCAATGCGAAATGAAAATCGCAACGATATA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1372033 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1372066 ATCGCAAT
1 ATCGCAAT
1372074 ACAGGTCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.46, C:0.19, G:0.19, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:1372065 original size:19 final size:19
Alignment explanation
Indices: 1372000--1372065 Score: 61
Period size: 19 Copynumber: 3.7 Consensus size: 19
1371990 AAAAATTACT
*
1372000 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
1372019 ATCGCAA--CG--AT-ATA
1 ATCGCAACGCGAAATGAAA
*
1372033 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
1372052 ATCGCAACGAGAAA
1 ATCGCAACGCGAAA
1372066 ATCGCAATAC
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.24
15 2 0.05
16 2 0.05
17 2 0.05
18 2 0.05
19 21 0.55
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:1372067 original size:14 final size:14
Alignment explanation
Indices: 1372015--1372072 Score: 53
Period size: 14 Copynumber: 3.8 Consensus size: 14
1372005 AATGCGAAAT
1372015 GAAAATCGCAACGA
1 GAAAATCGCAACGA
* *
1372029 TATAATCGCAATGCGAAA
1 GAAAATCGCAA--CG--A
1372047 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
1372062 GAAAATCGCAA
1 GAAAATCGCAA
1372073 TACAGGTCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
14 20 0.57
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.26
ACGTcount: A:0.48, C:0.19, G:0.19, T:0.14
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:1372090 original size:32 final size:33
Alignment explanation
Indices: 1372000--1372097 Score: 108
Period size: 33 Copynumber: 3.0 Consensus size: 33
1371990 AAAAATTACT
* * * *
1372000 ATCGCAATGCGAAATGAAAATCGCAACGATATA
1 ATCGCAATACGAAATCAAAATCGCAACGAGAAA
* *
1372033 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATACGAAATCAAAATCGCAACGAGAAA
** *
1372066 ATCGCAATAC-AGGTCAAAATCGCAACGCGAAA
1 ATCGCAATACGAAATCAAAATCGCAACGAGAAA
1372098 CTAAATTCGC
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
32 18 0.31
33 40 0.69
ACGTcount: A:0.46, C:0.20, G:0.19, T:0.14
Consensus pattern (33 bp):
ATCGCAATACGAAATCAAAATCGCAACGAGAAA
Found at i:1372125 original size:19 final size:19
Alignment explanation
Indices: 1372103--1372201 Score: 74
Period size: 19 Copynumber: 5.7 Consensus size: 19
1372093 CGAAACTAAA
1372103 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1372122 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1372137 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1372155 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1372170 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1372188 TTCGCATTGCGATT
1 TTCGCGTTGCGATT
1372202 ATCTCGTTGC
Statistics
Matches: 59, Mismatches: 11, Indels: 20
0.66 0.12 0.22
Matches are distributed among these distances:
14 17 0.29
16 6 0.10
17 6 0.10
19 30 0.51
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.45
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1372149 original size:33 final size:33
Alignment explanation
Indices: 1372107--1372233 Score: 209
Period size: 33 Copynumber: 3.8 Consensus size: 33
1372097 ACTAAATTCG
* *
1372107 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1372140 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
1372173 CGTTGCGATTTTCATTTCGCATTGCGATTATCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* *
1372206 CGTTGCGATTTTTATTTTGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1372234 AGTAATTTTC
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 89 1.00
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:1372180 original size:14 final size:14
Alignment explanation
Indices: 1372128--1372215 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 14
1372118 TCATTTCGCT
*
1372128 TTGCGATTCCCTCG
1 TTGCGATTCTCTCG
*
1372142 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
1372159 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
*
1372175 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
*
1372192 CATTGCGATTATCTCG
1 --TTGCGATTCTCTCG
1372208 TTGCGATT
1 TTGCGATT
1372216 TTTATTTTGC
Statistics
Matches: 58, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 20 0.34
16 14 0.24
17 12 0.21
19 12 0.21
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:1375507 original size:20 final size:21
Alignment explanation
Indices: 1375482--1375533 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1375472 TTTTCCCAAT
*
1375482 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
1375502 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1375523 TCGCAATGCGA
1 TCGCAATGCGA
1375534 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1375607 original size:20 final size:20
Alignment explanation
Indices: 1375518--1375609 Score: 67
Period size: 20 Copynumber: 4.5 Consensus size: 20
1375508 TGCGAATTTG
* *
1375518 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATACT
** *
1375538 GACTATCGCAACGAGATAAT
1 GAAAATCGCAACGAGATACT
* * *
1375558 ACAAAATCACAACGAGATTCT
1 -GAAAATCGCAACGAGATACT
*** *
1375579 GACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATACT
1375599 GAAAATCGCAA
1 GAAAATCGCAA
1375610 TCATCTTCAA
Statistics
Matches: 52, Mismatches: 19, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
20 38 0.73
21 14 0.27
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.21
Consensus pattern (20 bp):
GAAAATCGCAACGAGATACT
Found at i:1375878 original size:20 final size:20
Alignment explanation
Indices: 1375823--1375870 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
1375813 CAACAGGGAA
1375823 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
1375843 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
1375863 ATCGCAAC
1 ATCGCAAC
1375871 TAGAAAATCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.35, C:0.27, G:0.23, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:1375921 original size:14 final size:14
Alignment explanation
Indices: 1375902--1375955 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
1375892 GAAAATCGCA
1375902 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
1375916 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
*
1375933 CATTTCGATTTTCTCG
1 --TTGCGATTTTCTCG
1375949 TTGCGAT
1 TTGCGAT
1375956 AGTCAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
16 3 0.09
17 3 0.09
19 10 0.30
ACGTcount: A:0.11, C:0.20, G:0.19, T:0.50
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:1375921 original size:33 final size:33
Alignment explanation
Indices: 1375884--1375954 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
1375874 AAAATCGCAA
1375884 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** ** *
1375917 TGCGATTTTCATTTCGCATTTCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1375950 TGCGA
1 TGCGA
1375955 TAGTCAGTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Done.