Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold337
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: 2178121
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.32
Warning! 137747 characters in sequence are not A, C, G, or T
File 5 of 7
Found at i:1207101 original size:180 final size:180
Alignment explanation
Indices: 1206799--1207161 Score: 717
Period size: 180 Copynumber: 2.0 Consensus size: 180
1206789 TTAAACAAAT
1206799 TTTACTTTATCCTTGATTCATTACGACTATCATTTTTTTATTAAACATCATATTAATTAAATCAT
1 TTTACTTTATCCTTGATTCATTACGACTATCATTTTTTTATTAAACATCATATTAATTAAATCAT
*
1206864 TATCGTCATTATTATTATTATCATTGTCAATTTATTATTAAAGCTGTTTCATCACCATTTGATAA
66 TATCGTCATTATTATTATTATCATCGTCAATTTATTATTAAAGCTGTTTCATCACCATTTGATAA
1206929 TGGTATACCTACTATTATTTTGTTCTTATATTATTATTTTACGATAGTCA
131 TGGTATACCTACTATTATTTTGTTCTTATATTATTATTTTACGATAGTCA
1206979 TTTACTTTATCCTTGATTCATTACGACTATCATTTTTTTATTAAACATCATATTAATTAAATCAT
1 TTTACTTTATCCTTGATTCATTACGACTATCATTTTTTTATTAAACATCATATTAATTAAATCAT
1207044 TATCGTCATTATTATTATTATCATCGTCAATTTATTATTAAAGCTGTTTCATCACCATTTGATAA
66 TATCGTCATTATTATTATTATCATCGTCAATTTATTATTAAAGCTGTTTCATCACCATTTGATAA
1207109 TGGTATACCTACTATTATTTTGTTCTTATATTATTATTTTACGATAGTCA
131 TGGTATACCTACTATTATTTTGTTCTTATATTATTATTTTACGATAGTCA
1207159 TTT
1 TTT
1207162 CAAATTTTAT
Statistics
Matches: 182, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
180 182 1.00
ACGTcount: A:0.30, C:0.14, G:0.07, T:0.50
Consensus pattern (180 bp):
TTTACTTTATCCTTGATTCATTACGACTATCATTTTTTTATTAAACATCATATTAATTAAATCAT
TATCGTCATTATTATTATTATCATCGTCAATTTATTATTAAAGCTGTTTCATCACCATTTGATAA
TGGTATACCTACTATTATTTTGTTCTTATATTATTATTTTACGATAGTCA
Found at i:1216678 original size:14 final size:14
Alignment explanation
Indices: 1216637--1216684 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
1216627 ATGTGCAAAC
1216637 CCCCTGTATGCGAA
1 CCCCTGTATGCGAA
* *
1216651 TCCCCTATAGGCGAA
1 -CCCCTGTATGCGAA
1216666 CCCCTGTATGCGAA
1 CCCCTGTATGCGAA
1216680 CCCCT
1 CCCCT
1216685 ATAGATGAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 17 0.59
15 12 0.41
ACGTcount: A:0.21, C:0.40, G:0.19, T:0.21
Consensus pattern (14 bp):
CCCCTGTATGCGAA
Found at i:1216694 original size:28 final size:29
Alignment explanation
Indices: 1216637--1216695 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 29
1216627 ATGTGCAAAC
*
1216637 CCCCTGTATGCGAATCCCCTATAGGCGAA
1 CCCCTGTATGCGAATCCCCTATAGACGAA
*
1216666 CCCCTGTATGCGAA-CCCCTATAGATGAA
1 CCCCTGTATGCGAATCCCCTATAGACGAA
1216694 CC
1 CC
1216696 TTTTATATGC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 14 0.50
29 14 0.50
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.20
Consensus pattern (29 bp):
CCCCTGTATGCGAATCCCCTATAGACGAA
Found at i:1216942 original size:23 final size:22
Alignment explanation
Indices: 1216911--1216969 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
1216901 TCTGTTTAAC
1216911 ATGCGAACCCTACATG-TACTATT
1 ATGCGAACCCTACATGTTA-T-TT
* * *
1216934 ATGCAAACCTTATATGTTATTT
1 ATGCGAACCCTACATGTTATTT
1216956 ATGCGAACCCTACA
1 ATGCGAACCCTACA
1216970 CATGGTATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
22 13 0.45
23 14 0.48
24 2 0.07
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (22 bp):
ATGCGAACCCTACATGTTATTT
Found at i:1216999 original size:16 final size:16
Alignment explanation
Indices: 1216978--1217035 Score: 77
Period size: 15 Copynumber: 3.8 Consensus size: 16
1216968 CACATGGTAT
1216978 ATGCGAACCCT-GATG
1 ATGCGAACCCTAGATG
1216993 CATGCGAACCCTAGATG
1 -ATGCGAACCCTAGATG
*
1217010 -TGCGAACCCTAAATG
1 ATGCGAACCCTAGATG
1217025 -TGCGAACCCTA
1 ATGCGAACCCTA
1217036 TATGTGTGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
15 25 0.62
16 11 0.28
17 4 0.10
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.19
Consensus pattern (16 bp):
ATGCGAACCCTAGATG
Found at i:1217015 original size:15 final size:15
Alignment explanation
Indices: 1216998--1217152 Score: 125
Period size: 15 Copynumber: 10.3 Consensus size: 15
1216988 TGATGCATGC
*
1216998 GAACCCTAGATGTGC
1 GAACCCTAGATGTGT
* *
1217013 GAACCCTAAATGTGC
1 GAACCCTAGATGTGT
*
1217028 GAACCCTATATGTGT
1 GAACCCTAGATGTGT
** *
1217043 GAAATCTATATGTGT
1 GAACCCTAGATGTGT
*
1217058 AAACCCTAGATGTGT
1 GAACCCTAGATGTGT
*
1217073 GAACCCTA-ATGCATGC
1 GAACCCTAGATG--TGT
* * *
1217089 AAACTCTATATGTGT
1 GAACCCTAGATGTGT
1217104 GAACCCT-GTATGTGT
1 GAACCCTAG-ATGTGT
* *
1217119 GAACTCTATATGTGT
1 GAACCCTAGATGTGT
* *
1217134 GAACCCTAAATGTAT
1 GAACCCTAGATGTGT
1217149 GAAC
1 GAAC
1217153 TCTGTATGGG
Statistics
Matches: 113, Mismatches: 22, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
14 3 0.03
15 99 0.88
16 8 0.07
17 3 0.03
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (15 bp):
GAACCCTAGATGTGT
Found at i:1217031 original size:30 final size:30
Alignment explanation
Indices: 1216995--1217237 Score: 157
Period size: 30 Copynumber: 8.1 Consensus size: 30
1216985 CCCTGATGCA
* *
1216995 TGCGAACCCTAGATGTGCGAACCCTAAATG
1 TGCGAACCCTATATGTGTGAACCCTAAATG
** *
1217025 TGCGAACCCTATATGTGTGAAATCTATATG
1 TGCGAACCCTATATGTGTGAACCCTAAATG
** *
1217055 TGTAAACCCTAGATGTGTGAACCCT-AATG
1 TGCGAACCCTATATGTGTGAACCCTAAATG
* * **
1217084 CATGCAAACTCTATATGTGTGAACCCTGTATG
1 --TGCGAACCCTATATGTGTGAACCCTAAATG
* *
1217116 TGTGAACTCTATATGTGTGAACCCTAAATG
1 TGCGAACCCTATATGTGTGAACCCTAAATG
** * * * ** *
1217146 TATGAACTCTGTATGGGCAAACCCTATATG
1 TGCGAACCCTATATGTGTGAACCCTAAATG
* ** * * * *
1217176 GGTAAAACCTATATATATGAACCCTATATG
1 TGCGAACCCTATATGTGTGAACCCTAAATG
* * *
1217206 TGCAAAGCCC-ATATGTGCGAACCCTATATG
1 TGCGAA-CCCTATATGTGTGAACCCTAAATG
1217236 TG
1 TG
1217238 AACCTATTAT
Statistics
Matches: 167, Mismatches: 42, Indels: 8
0.77 0.19 0.04
Matches are distributed among these distances:
29 3 0.02
30 137 0.82
31 24 0.14
32 3 0.02
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.29
Consensus pattern (30 bp):
TGCGAACCCTATATGTGTGAACCCTAAATG
Found at i:1217169 original size:91 final size:91
Alignment explanation
Indices: 1216983--1217171 Score: 200
Period size: 91 Copynumber: 2.1 Consensus size: 91
1216973 GGTATATGCG
* * *
1216983 AACCCTGATGCATGCGAACCCTAGATGTGCGAACCCTAAATGTGCGAACCCTATATGTGTGAAAT
1 AACCCTAATGCATGCAAACCCTAGATGTGCGAACCCTAAATGTGCGAACCCTATATGTGTGAAAC
* * * **
1217048 CTATATGTGTAAACCCTAGATGTGTG
66 CTAAATGTATAAACCCTAGATGGGCA
* * * ** * * *
1217074 AACCCTAATGCATGCAAACTCTATATGTGTGAACCCTGTATGTGTGAACTCTATATGTGTGAACC
1 AACCCTAATGCATGCAAACCCTAGATGTGCGAACCCTAAATGTGCGAACCCTATATGTGTGAAAC
* *
1217139 CTAAATGTATGAACTCT-GTATGGGCA
66 CTAAATGTATAAACCCTAG-ATGGGCA
1217165 AACCCTA
1 AACCCTA
1217172 TATGGGTAAA
Statistics
Matches: 79, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
90 1 0.01
91 78 0.99
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (91 bp):
AACCCTAATGCATGCAAACCCTAGATGTGCGAACCCTAAATGTGCGAACCCTATATGTGTGAAAC
CTAAATGTATAAACCCTAGATGGGCA
Found at i:1217173 original size:45 final size:46
Alignment explanation
Indices: 1217124--1217236 Score: 131
Period size: 45 Copynumber: 2.5 Consensus size: 46
1217114 TGTGTGAACT
* * *
1217124 CTATATGTGTGAACCCTAAATGTATGAACTCTGTATGGGCAAA-CC
1 CTATATGTGTGAACCCTATATGTATGAACCCTATATGGGCAAAGCC
* * * * *
1217169 CTATATGGGTAAAACCTATATATATGAACCCTATATGTGCAAAGCC
1 CTATATGTGTGAACCCTATATGTATGAACCCTATATGGGCAAAGCC
*
1217215 C-ATATGTGCGAACCCTATATGT
1 CTATATGTGTGAACCCTATATGT
1217237 GAACCTATTA
Statistics
Matches: 54, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
45 51 0.94
46 3 0.06
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (46 bp):
CTATATGTGTGAACCCTATATGTATGAACCCTATATGGGCAAAGCC
Found at i:1217177 original size:15 final size:15
Alignment explanation
Indices: 1216999--1217237 Score: 115
Period size: 15 Copynumber: 15.9 Consensus size: 15
1216989 GATGCATGCG
* *
1216999 AACCCTAGATGTGCG
1 AACCCTATATGTGCA
* *
1217014 AACCCTAAATGTGCG
1 AACCCTATATGTGCA
*
1217029 AACCCTATATGTGTGA
1 AACCCTATATGTG-CA
* *
1217045 AA-TCTATATGTGTA
1 AACCCTATATGTGCA
* **
1217059 AACCCTAGATGTGTG
1 AACCCTATATGTGCA
1217074 AACCCTA-ATGCATGCA
1 AACCCTATATG--TGCA
* **
1217090 AACTCTATATGTGTG
1 AACCCTATATGTGCA
* **
1217105 AACCCTGTATGTGTG
1 AACCCTATATGTGCA
* **
1217120 AACTCTATATGTGTG
1 AACCCTATATGTGCA
* ***
1217135 AACCCTAAATGTATG
1 AACCCTATATGTGCA
* * *
1217150 AACTCTGTATGGGCA
1 AACCCTATATGTGCA
* *
1217165 AACCCTATATGGGTA
1 AACCCTATATGTGCA
* * ***
1217180 AAACCTATATATATG
1 AACCCTATATGTGCA
1217195 AACCCTATATGTGCA
1 AACCCTATATGTGCA
*
1217210 AAGCCC-ATATGTGCG
1 AA-CCCTATATGTGCA
1217225 AACCCTATATGTG
1 AACCCTATATGTG
1217238 AACCTATTAT
Statistics
Matches: 175, Mismatches: 42, Indels: 14
0.76 0.18 0.06
Matches are distributed among these distances:
14 9 0.05
15 150 0.86
16 13 0.07
17 3 0.02
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (15 bp):
AACCCTATATGTGCA
Found at i:1217744 original size:18 final size:18
Alignment explanation
Indices: 1217721--1217756 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1217711 TTTGGTGTGT
1217721 CAAGCGATACTCAAGGGC
1 CAAGCGATACTCAAGGGC
1217739 CAAGCGATACTCAAGGGC
1 CAAGCGATACTCAAGGGC
1217757 GAATAGGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.28, T:0.11
Consensus pattern (18 bp):
CAAGCGATACTCAAGGGC
Found at i:1218614 original size:21 final size:23
Alignment explanation
Indices: 1218574--1218621 Score: 73
Period size: 21 Copynumber: 2.2 Consensus size: 23
1218564 AGTTAAAAGG
*
1218574 AAAAAGATGAAAAGTAAAGAAAT
1 AAAAACATGAAAAGTAAAGAAAT
1218597 AAAAACAT-AAAA-TAAAGAAAT
1 AAAAACATGAAAAGTAAAGAAAT
1218618 AAAA
1 AAAA
1218622 CGATGGTGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 13 0.54
22 4 0.17
23 7 0.29
ACGTcount: A:0.75, C:0.02, G:0.10, T:0.12
Consensus pattern (23 bp):
AAAAACATGAAAAGTAAAGAAAT
Found at i:1225290 original size:13 final size:14
Alignment explanation
Indices: 1225265--1225293 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1225255 AATTAATACT
1225265 AAAAAGAATAAAGA
1 AAAAAGAATAAAGA
1225279 AAAAAGAA-AAAGA
1 AAAAAGAATAAAGA
1225292 AA
1 AA
1225294 TTGTGTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (14 bp):
AAAAAGAATAAAGA
Found at i:1230742 original size:11 final size:11
Alignment explanation
Indices: 1230726--1230750 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1230716 ATATTGAAAC
1230726 CTATGCAGTTT
1 CTATGCAGTTT
1230737 CTATGCAGTTT
1 CTATGCAGTTT
1230748 CTA
1 CTA
1230751 AGTTCTCCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.44
Consensus pattern (11 bp):
CTATGCAGTTT
Found at i:1231236 original size:26 final size:26
Alignment explanation
Indices: 1231200--1231253 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
1231190 TTGGGTATAG
1231200 TCAGATACAGGTAATGTTCAGTTTGT
1 TCAGATACAGGTAATGTTCAGTTTGT
1231226 TCAGATACAGGTAATGTTCAGTTTGT
1 TCAGATACAGGTAATGTTCAGTTTGT
1231252 TC
1 TC
1231254 TAAGCTTTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.39
Consensus pattern (26 bp):
TCAGATACAGGTAATGTTCAGTTTGT
Found at i:1234936 original size:59 final size:59
Alignment explanation
Indices: 1234832--1234948 Score: 153
Period size: 59 Copynumber: 2.0 Consensus size: 59
1234822 TTACATTTTG
* * * * *
1234832 GTACCTGAACTTGGCTTATGATTCAAATTGGTATCTAATGATTTTTTTTGTCCAATTAA
1 GTACCTGAACTTGGCTTAAGACTCAAATTAGTACCTAACGATTTTTTTTGTCCAATTAA
* * * *
1234891 GTACTTGAACTTGGCTTAAGGCTCAATTTAGTACCTAACGTTTTTTTTTGTCCAATTA
1 GTACCTGAACTTGGCTTAAGACTCAAATTAGTACCTAACGATTTTTTTTGTCCAATTA
1234949 GGGTTACGAA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 49 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (59 bp):
GTACCTGAACTTGGCTTAAGACTCAAATTAGTACCTAACGATTTTTTTTGTCCAATTAA
Found at i:1235716 original size:29 final size:30
Alignment explanation
Indices: 1235675--1235738 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
1235665 AAAGTTATTA
*
1235675 TTTAGTCCATATAC-TTTGATTTGATCAAT
1 TTTAGTCCATATACTTTTGAATTGATCAAT
* *
1235704 TTTAGTCCCTATACTTTTTGAATTGGTCAAT
1 TTTAGTCCATATAC-TTTTGAATTGATCAAT
1235735 TTTA
1 TTTA
1235739 ATACTTGTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 13 0.43
31 17 0.57
ACGTcount: A:0.25, C:0.14, G:0.11, T:0.50
Consensus pattern (30 bp):
TTTAGTCCATATACTTTTGAATTGATCAAT
Found at i:1236162 original size:3 final size:3
Alignment explanation
Indices: 1236154--1236199 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
1236144 ATATACTATC
1236154 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1236200 CCTTTTAGCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1246512 original size:5 final size:5
Alignment explanation
Indices: 1246504--1246528 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1246494 TTTTTGTTAA
1246504 TAATT TAATT TAATT TAATT TAATT
1 TAATT TAATT TAATT TAATT TAATT
1246529 AATAAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TAATT
Found at i:1250482 original size:3 final size:3
Alignment explanation
Indices: 1250476--1250521 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
1250466 TTTAAAAGAA
1250476 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1250522 GGAAAAGATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1261058 original size:44 final size:44
Alignment explanation
Indices: 1260995--1261081 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 44
1260985 ATAGGTTAAA
*
1260995 TAATATTAAAATAAACTACA-TTAATTAAAGTTTAAGTGGGAAAT
1 TAATATTAAAATAAACTACACTT-ATCAAAGTTTAAGTGGGAAAT
* *
1261039 TAATATTAAAATAACCTACACTTATCAGAGTTTAAGTGGGAAA
1 TAATATTAAAATAAACTACACTTATCAAAGTTTAAGTGGGAAA
1261082 CTAAAAACCA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
44 37 0.95
45 2 0.05
ACGTcount: A:0.47, C:0.08, G:0.13, T:0.32
Consensus pattern (44 bp):
TAATATTAAAATAAACTACACTTATCAAAGTTTAAGTGGGAAAT
Found at i:1262881 original size:23 final size:22
Alignment explanation
Indices: 1262835--1262881 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
1262825 AGATAAAACT
*
1262835 AAACCCCAAAACCTAAAAATAA
1 AAACCCCAAAACCTAAAAACAA
* *
1262857 AAACCCTCAAAACGTAAACACAA
1 AAACCC-CAAAACCTAAAAACAA
1262880 AA
1 AA
1262882 TTCTCTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.62, C:0.28, G:0.02, T:0.09
Consensus pattern (22 bp):
AAACCCCAAAACCTAAAAACAA
Found at i:1264053 original size:107 final size:107
Alignment explanation
Indices: 1263851--1264140 Score: 469
Period size: 107 Copynumber: 2.7 Consensus size: 107
1263841 TTTAAGAGGG
* * *
1263851 TATTTGG-CTAAACG-AGAAATCGAAACCCAGCGCATTAGGGCACGTTTTCTTGAATTTCCAAAC
1 TATTTGGTC-AAACGAAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAAC
* *
1263914 GCAAAATATTGCCTTACTTTGAAATTTTAAAAGTATATTTGGC
65 GCAAAATATTGCCATACTTTGAAATTTTAAAAGGATATTTGGC
1263957 TATTTGGTCAAACGAAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAACG
1 TATTTGGTCAAACGAAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAAC-
1264022 GCAAAATATT-CCATACTTTGAAATTTTAAAAGGATATTTGGC
65 GCAAAATATTGCCATACTTTGAAATTTTAAAAGGATATTTGGC
* * *
1264064 TATTTGGTCAAACAAAAAAATCGAAACCCAGCACATTAGGGCACGTTTTTTCGAATTTTCAAACG
1 TATTTGGTCAAACGAAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAACG
1264129 CAAAATATTGCC
66 CAAAATATTGCC
1264141 TTTATTATTT
Statistics
Matches: 172, Mismatches: 8, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
106 22 0.13
107 140 0.81
108 10 0.06
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.30
Consensus pattern (107 bp):
TATTTGGTCAAACGAAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAACG
CAAAATATTGCCATACTTTGAAATTTTAAAAGGATATTTGGC
Found at i:1266820 original size:183 final size:183
Alignment explanation
Indices: 1266545--1266961 Score: 692
Period size: 183 Copynumber: 2.3 Consensus size: 183
1266535 ATAGGATTCA
* * * * * * *
1266545 TATCTTCAAACTTGCCCCACT-CAACTTCAGGGGGATAAGGCTTGATATGATAAGATTTAATCCG
1 TATCTTC-AACCTGCTCCACTGCGACCTCAGGGAGATAAGGTTTGATATGATAAGATTTAATCCA
* *
1266609 ACCCTCTGCAACTTCAAAGGTGTAGGATTCATCGTTTTAATCCGCTCCATTGCAACTTTAGGGAG
65 ACCCTCTGCAACTTCAAAGGTATAGGATTCATCGTTTTAATCCGCTCCATTACAACTTTAGGGAG
*
1266674 ATAGGATTAGTAGCTTCAGTCTGTTCCACTGTAACTTCAGGGAGATAAGACTTG
130 ATAGGATTAGTAGCTTCAGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTTG
*
1266728 TATCTTCAACCTGCTCCATTGCGACCTCAGGGAGATAAGGTTTGATATGATAAGATTTAATCCAA
1 TATCTTCAACCTGCTCCACTGCGACCTCAGGGAGATAAGGTTTGATATGATAAGATTTAATCCAA
* *
1266793 CCCTTTGCAACTTCAAAGGTATAGGATTTATCGTTTTAATCCGCTCCATTACAACTTTAGGGAGA
66 CCCTCTGCAACTTCAAAGGTATAGGATTCATCGTTTTAATCCGCTCCATTACAACTTTAGGGAGA
1266858 TAGGATTAGTAGCTTCAGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTTG
131 TAGGATTAGTAGCTTCAGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTTG
*
1266911 TATCTTCAACCTGCTCCACTGCGACCTCAGGAAGATAAGGTTTGATATGAT
1 TATCTTCAACCTGCTCCACTGCGACCTCAGGGAGATAAGGTTTGATATGAT
1266962 CTTCTTTCTA
Statistics
Matches: 218, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
182 10 0.05
183 208 0.95
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (183 bp):
TATCTTCAACCTGCTCCACTGCGACCTCAGGGAGATAAGGTTTGATATGATAAGATTTAATCCAA
CCCTCTGCAACTTCAAAGGTATAGGATTCATCGTTTTAATCCGCTCCATTACAACTTTAGGGAGA
TAGGATTAGTAGCTTCAGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTTG
Found at i:1266918 original size:44 final size:44
Alignment explanation
Indices: 1266835--1266949 Score: 115
Period size: 44 Copynumber: 2.6 Consensus size: 44
1266825 GTTTTAATCC
* * * * **
1266835 GCTCCATTACAACTTTAGGGAGATAGGATTAGTAGCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTCAACCT
* *
1266879 GCTCCACTGTAACTTCAGGGAGATAAGACTT-GTATCTTCAACCT
1 GCTCCACTGCAACTTCAGGGAGATAAGA-TTAGTAGCTTCAACCT
* * *
1266923 GCTCCACTGCGACCTCAGGAAGATAAG
1 GCTCCACTGCAACTTCAGGGAGATAAG
1266950 GTTTGATATG
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
44 56 0.97
45 2 0.03
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTCAACCT
Found at i:1267124 original size:41 final size:45
Alignment explanation
Indices: 1267079--1267183 Score: 119
Period size: 45 Copynumber: 2.4 Consensus size: 45
1267069 CGCTCCACTA
* * * *
1267079 CAACTTTAGGGAGATAAGAT-T-C-ATCGT-GGTCTGTTCTACTG
1 CAACTTCAGAGAGATAAGATCTGCTATCGTCAGTCTATTCTACTG
* *
1267120 CAACTTCAGAGAGATAATATCTGCTATCTTCAGTCTATTCTACTG
1 CAACTTCAGAGAGATAAGATCTGCTATCGTCAGTCTATTCTACTG
*
1267165 CAACTTCAGTGAGATAAGA
1 CAACTTCAGAGAGATAAGA
1267184 CTTGTAATTT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
41 17 0.33
42 1 0.02
43 1 0.02
44 4 0.08
45 29 0.56
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (45 bp):
CAACTTCAGAGAGATAAGATCTGCTATCGTCAGTCTATTCTACTG
Found at i:1267387 original size:148 final size:146
Alignment explanation
Indices: 1267161--1267436 Score: 367
Period size: 148 Copynumber: 1.9 Consensus size: 146
1267151 AGTCTATTCT
* * ** * **
1267161 ACTGCAACTTCAGTGAGATAAGACTTGTAATTTCAATAAAGTCTGATGCGATCTGTTTTACTGTA
1 ACTGCAACTTCAGTGAGATAAGACTTGTAATTTCAATAAAGTCAGACGCGATCCATTCTACTACA
* * *
1267226 ACTTCAGATAGATAAGGTCCATCATTTTGATCCAT-TCCACTGCAACTTCAGGGAGATAGGACTC
66 AATTCAGAGAGATAAGATCCATCATTTTGA-CC-TCTCCACTGCAACTTCAGGGAGATAGGACTC
1267290 ATATCTTCAACTTGCCCC
129 ATATCTTCAACTTGCCCC
* * *
1267308 ACTGCAACTTTAG-GGGCATAAGACTTGTAATTTTCAATAAAGTCAGACGTGATCCATTCTACTA
1 ACTGCAACTTCAGTGAG-ATAAGACTTGTAA-TTTCAATAAAGTCAGACGCGATCCATTCTACTA
*
1267372 CAAATTCAGAGAGATAAGATCTATCATTTTGACCTGCTCCACTGCAACTTCAGGGAGATAGGACT
64 CAAATTCAGAGAGATAAGATCCATCATTTTGACCT-CTCCACTGCAACTTCAGGGAGATAGGACT
1267437 TATAATTTTC
Statistics
Matches: 111, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
146 3 0.03
147 27 0.24
148 81 0.73
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (146 bp):
ACTGCAACTTCAGTGAGATAAGACTTGTAATTTCAATAAAGTCAGACGCGATCCATTCTACTACA
AATTCAGAGAGATAAGATCCATCATTTTGACCTCTCCACTGCAACTTCAGGGAGATAGGACTCAT
ATCTTCAACTTGCCCC
Found at i:1267437 original size:104 final size:104
Alignment explanation
Indices: 1267306--1267540 Score: 292
Period size: 104 Copynumber: 2.3 Consensus size: 104
1267296 TCAACTTGCC
* * * *
1267306 CCACTGCAACTTTAGGG-GCATAAGACTTGTAATTTTCAATAAAGTCAGACGTGATCCATTCTAC
1 CCACTGCAACTTCAGGGAG-ATAGGACTTATAATTTTCAATAAAGTCAGACGTGATACATTCTAC
* *
1267370 TACAAATTCAGAGAGATAAGATCTATCATTTTGACCTGCT
65 TACAAATTCAGAGAGATAAGATCCATCATTTTGACCCGCT
* * * **
1267410 CCACTGCAACTTCAGGGAGATAGGACTTATAATTTTCAATAAATTCTGATGTGATATGTTCTACT
1 CCACTGCAACTTCAGGGAGATAGGACTTATAATTTTCAATAAAGTCAGACGTGATACATTCTACT
*** * *
1267475 GTTACTTTAGAGAGATAAGATCCATCATTTTGACCCGCT
66 ACAAATTCAGAGAGATAAGATCCATCATTTTGACCCGCT
* *
1267514 CCACTACAACTTCAGGGAAATAGGACT
1 CCACTGCAACTTCAGGGAGATAGGACT
1267541 CGTATCTTCA
Statistics
Matches: 112, Mismatches: 18, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
104 111 0.99
105 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (104 bp):
CCACTGCAACTTCAGGGAGATAGGACTTATAATTTTCAATAAAGTCAGACGTGATACATTCTACT
ACAAATTCAGAGAGATAAGATCCATCATTTTGACCCGCT
Found at i:1267627 original size:44 final size:44
Alignment explanation
Indices: 1267546--1267637 Score: 112
Period size: 44 Copynumber: 2.1 Consensus size: 44
1267536 GGACTCGTAT
* ** * *
1267546 CTTCAACTTGCCCCACTGCAACTTCAGGGGGATAAGGTTAGTGA
1 CTTCAACCTGCCCCACTGCAACTTCAAAGAGACAAGGTTAGTGA
* * *
1267590 CTTCAACCTGCTCTACTGCAACTTCAAAGAGACAAGGTTTGTGA
1 CTTCAACCTGCCCCACTGCAACTTCAAAGAGACAAGGTTAGTGA
1267634 CTTC
1 CTTC
1267638 GCTGATCTGT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (44 bp):
CTTCAACCTGCCCCACTGCAACTTCAAAGAGACAAGGTTAGTGA
Found at i:1267946 original size:24 final size:24
Alignment explanation
Indices: 1267910--1267968 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
1267900 ACGGATTGCC
*
1267910 TCCACTGTAATCTTCAAAGTTTAA
1 TCCACTGTAATCTTCAAAGTTCAA
* * *
1267934 TCCGCTGTAATCTTCAAGGTTCAG
1 TCCACTGTAATCTTCAAAGTTCAA
1267958 TCCACTGTAAT
1 TCCACTGTAAT
1267969 TTTGGGACAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.36
Consensus pattern (24 bp):
TCCACTGTAATCTTCAAAGTTCAA
Found at i:1268614 original size:108 final size:107
Alignment explanation
Indices: 1268440--1268644 Score: 284
Period size: 108 Copynumber: 1.9 Consensus size: 107
1268430 GAAAAATGCT
* *
1268440 TGAAAAAGATTATCACAATGACAAGATGAAATTTTATTTAGGGCAAAACTCCAAACAAATAAATT
1 TGAAAAAGATTATCACAATGACAAGATGAAATTTTATTGAGAGCAAAACTCCAAACAAATAAATT
* *
1268505 AATCAGGATAGCAAATTTTGCTAAAATTCAAAGTGAATAAGA
66 AATCAAGATAGCAAATTTTGCTAAAATACAAAGTGAATAAGA
* * * ** * * *
1268547 TGAAAAAGATTATCACAATGGACAAGATGGAATTTTGTTGAGAGCAAAGCTTGAGACGAATAGAT
1 TGAAAAAGATTATCACAAT-GACAAGATGAAATTTTATTGAGAGCAAAACTCCAAACAAATAAAT
*
1268612 TAATCAAGATAGCAAATTTTGCTAGAATACAAA
65 TAATCAAGATAGCAAATTTTGCTAAAATACAAA
1268645 AATGATAATA
Statistics
Matches: 84, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
107 19 0.23
108 65 0.77
ACGTcount: A:0.46, C:0.11, G:0.17, T:0.26
Consensus pattern (107 bp):
TGAAAAAGATTATCACAATGACAAGATGAAATTTTATTGAGAGCAAAACTCCAAACAAATAAATT
AATCAAGATAGCAAATTTTGCTAAAATACAAAGTGAATAAGA
Found at i:1268990 original size:12 final size:12
Alignment explanation
Indices: 1268970--1269019 Score: 77
Period size: 12 Copynumber: 4.3 Consensus size: 12
1268960 GGCCTCTCAT
1268970 TTTTC-TTTTTC
1 TTTTCTTTTTTC
1268981 TTTTCTTTTTTC
1 TTTTCTTTTTTC
*
1268993 TTTT-TTTATTC
1 TTTTCTTTTTTC
1269004 TTTTCTTTTTTC
1 TTTTCTTTTTTC
1269016 TTTT
1 TTTT
1269020 TTCTATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
11 15 0.43
12 20 0.57
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:1268991 original size:7 final size:7
Alignment explanation
Indices: 1268969--1269029 Score: 65
Period size: 7 Copynumber: 8.7 Consensus size: 7
1268959 TGGCCTCTCA
1268969 TTTTTC-
1 TTTTTCT
1268975 TTTTTC-
1 TTTTTCT
1268981 -TTTTCT
1 TTTTTCT
1268987 TTTTTCTT
1 TTTTTC-T
*
1268995 TTTTTAT
1 TTTTTCT
1269002 TCTTTTCT
1 T-TTTTCT
1269010 TTTTTCT
1 TTTTTCT
1269017 TTTTTCT
1 TTTTTCT
1269024 ATTTTT
1 -TTTTT
1269030 TTTAACATTC
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
5 5 0.10
6 6 0.12
7 20 0.42
8 17 0.35
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTCT
Found at i:1269004 original size:23 final size:23
Alignment explanation
Indices: 1268969--1269031 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1268959 TGGCCTCTCA
*
1268969 TTTTTCTTTTTCTTTTCTTTTTTC
1 TTTTT-TTATTCTTTTCTTTTTTC
1268993 TTTTTTTATTCTTTTCTTTTTTC
1 TTTTTTTATTCTTTTCTTTTTTC
*
1269016 TTTTTTCTATTTTTTT
1 TTTTTT-TATTCTTTT
1269032 TAACATTCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 23 0.64
24 13 0.36
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (23 bp):
TTTTTTTATTCTTTTCTTTTTTC
Found at i:1269017 original size:30 final size:30
Alignment explanation
Indices: 1268972--1269030 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
1268962 CCTCTCATTT
1268972 TTCTTTTTCTTTTCTTTTTTCT-TTTTTTA
1 TTCTTTTTCTTTTCTTTTTTCTATTTTTTA
*
1269001 TTCTTTTCTTTTTTCTTTTTTCTATTTTTT
1 TTCTTTT-TCTTTTCTTTTTTCTATTTTTT
1269031 TTAACATTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 7 0.26
30 14 0.52
31 6 0.22
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (30 bp):
TTCTTTTTCTTTTCTTTTTTCTATTTTTTA
Found at i:1269621 original size:22 final size:20
Alignment explanation
Indices: 1269585--1269643 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
1269575 GGCCCGACCT
1269585 ATTT-TTTTAATAAATACCAAAA
1 ATTTATTTTAA-AAATA--AAAA
1269607 ATTTATTTTAAAAATTAAAAA
1 ATTTATTTTAAAAA-TAAAAA
**
1269628 AAGTATTTTAAAAATA
1 ATTTATTTTAAAAATA
1269644 TTTTAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 2 0.06
21 16 0.48
22 7 0.21
23 8 0.24
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (20 bp):
ATTTATTTTAAAAATAAAAA
Found at i:1273350 original size:107 final size:107
Alignment explanation
Indices: 1273214--1273489 Score: 453
Period size: 107 Copynumber: 2.6 Consensus size: 107
1273204 GCTAAACGAG
* *
1273214 AAATCGAAACCTAGCGCATTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAATATTGCCTTACT
1 AAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAATATTGCCTTACT
* * *
1273279 TTGAAATTTTAAAAGTATATTTGGCTATTTGGTCGAACGAAA
66 TTGAAATTTTAAAAGGATATTTGGCTACTTGGTCAAACGAAA
*
1273321 AAATCGAAACCCAGCACATTAGGGTACGTTTTCTCGAATTTCCAAACGCAAAATATTGCCTTACT
1 AAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAATATTGCCTTACT
1273386 TTGAAATTTTAAAAGGATATTTGGCTACTTGGTCAAACGAAA
66 TTGAAATTTTAAAAGGATATTTGGCTACTTGGTCAAACGAAA
* * * * *
1273428 AAATCAAAACCCGGCACATTAGGGCATGTTTTCTCGAATTTTCAAACGCAAAATATAGCCTT
1 AAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAATATTGCCTT
1273490 TATTATTTTT
Statistics
Matches: 157, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
107 157 1.00
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (107 bp):
AAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAATATTGCCTTACT
TTGAAATTTTAAAAGGATATTTGGCTACTTGGTCAAACGAAA
Found at i:1274077 original size:14 final size:14
Alignment explanation
Indices: 1274058--1274092 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
1274048 ATGCATATAG
1274058 ATATATATAGATAT
1 ATATATATAGATAT
1274072 ATATATATAGATAT
1 ATATATATAGATAT
*
1274086 GTATATA
1 ATATATA
1274093 AATTATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (14 bp):
ATATATATAGATAT
Found at i:1274090 original size:10 final size:10
Alignment explanation
Indices: 1274052--1274076 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1274042 TAAAAAATGC
1274052 ATATAGATAT
1 ATATAGATAT
1274062 ATATAGATAT
1 ATATAGATAT
1274072 ATATA
1 ATATA
1274077 TATAGATATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (10 bp):
ATATAGATAT
Found at i:1274153 original size:29 final size:31
Alignment explanation
Indices: 1274120--1274194 Score: 91
Period size: 29 Copynumber: 2.5 Consensus size: 31
1274110 ACATATATAA
*
1274120 GTATGTATATATATAAATAGATTAT-AAAAT
1 GTATGTATGTATATAAATAGATTATAAAAAT
* * * *
1274150 -TATGTACGTGTATATATATATTATAAAAAT
1 GTATGTATGTATATAAATAGATTATAAAAAT
1274180 GTATGTATGTATATA
1 GTATGTATGTATATA
1274195 TATGTATAAC
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
29 19 0.53
30 5 0.14
31 12 0.33
ACGTcount: A:0.44, C:0.01, G:0.12, T:0.43
Consensus pattern (31 bp):
GTATGTATGTATATAAATAGATTATAAAAAT
Found at i:1274282 original size:19 final size:19
Alignment explanation
Indices: 1274238--1274274 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1274228 TGAATGAGTA
*
1274238 AATAGTAATGATAATAATT
1 AATAATAATGATAATAATT
1274257 AATAATAATGATAATAAT
1 AATAATAATGATAATAAT
1274275 AGCAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (19 bp):
AATAATAATGATAATAATT
Found at i:1275820 original size:44 final size:43
Alignment explanation
Indices: 1275734--1275876 Score: 150
Period size: 44 Copynumber: 3.4 Consensus size: 43
1275724 AATCCGACCT
* * * *
1275734 ACTGCAACTTCAGAGG-TATAGGATT-CATCTTCAATCTTCTCC
1 ACTGCAACTTCAG-GGAGATAAGATTGGATCTTCAATCTGCTCC
* *
1275776 ACTGCAAGTTCAGGGAGATAAGATTGGTATCTTCAACCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGATTGG-ATCTTCAATCTGCTCC
* * * *
1275820 ATTGCAACTTCAGTGAGATAAGATTGGA--TGCAATCTGCTCT
1 ACTGCAACTTCAGGGAGATAAGATTGGATCTTCAATCTGCTCC
1275861 ACTGCAACTTCAGGGA
1 ACTGCAACTTCAGGGA
1275877 CGAGATTTGT
Statistics
Matches: 84, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
41 26 0.31
42 19 0.23
43 1 0.01
44 38 0.45
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.29
Consensus pattern (43 bp):
ACTGCAACTTCAGGGAGATAAGATTGGATCTTCAATCTGCTCC
Found at i:1276051 original size:132 final size:132
Alignment explanation
Indices: 1275906--1276279 Score: 579
Period size: 132 Copynumber: 2.8 Consensus size: 132
1275896 TTACTTCCCT
1275906 ACTACCTTGGGAAGATAAGATTCACCATATTTGATCTGCTCCACTACTGCTTAGGGAGACAGAAT
1 ACTACCTTGGGAAGATAAGATTCACCATATTTGATCTGCTCCACTACTGCTTAGGGAGACAGAAT
* *
1275971 CTGCAATCTTCAACCTACTGCACTACTGCTTAGGGAGATAGGGCTAATGGCTTAAATCTGCTTCT
66 CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGGCTAATGGCTTAAATATGCTTCT
1276036 CC
131 CC
* * *
1276038 ACTATCTTGGGAAGATAAGATTCACCATCTTTGATTTGCTCCACTACTGCTTAGGGAGACAGAAT
1 ACTACCTTGGGAAGATAAGATTCACCATATTTGATCTGCTCCACTACTGCTTAGGGAGACAGAAT
*
1276103 CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATATGCTTCT
66 CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGGCTAATGGCTTAAATATGCTTCT
*
1276168 CT
131 CC
* * ** * *
1276170 TCTACCTTAGGAAGATAAGATTCACTTTTTTTGATCTGCTCCACTACTGCTTAGGGAGATA-AGA
1 ACTACCTTGGGAAGATAAGATTCACCATATTTGATCTGCTCCACTACTGCTTAGGGAGACAGA-A
* * * *
1276234 TCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGCT
65 TCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGGCT
1276280 TGATATGATG
Statistics
Matches: 221, Mismatches: 20, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
131 1 0.00
132 220 1.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.30
Consensus pattern (132 bp):
ACTACCTTGGGAAGATAAGATTCACCATATTTGATCTGCTCCACTACTGCTTAGGGAGACAGAAT
CTGCAATCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGGCTAATGGCTTAAATATGCTTCT
CC
Found at i:1276256 original size:44 final size:44
Alignment explanation
Indices: 1275944--1276276 Score: 152
Period size: 44 Copynumber: 7.6 Consensus size: 44
1275934 ATTTGATCTG
* *
1275944 CTCCACTACTGCTTAGGGAGA-CAGAATCTGCAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGAGATAAG-ATCTACAATCTTCAACCTA
* ** * *
1275988 CTGCACTACTGCTTAGGGAGAT-AGGGCT--AATGGCTTAAATCTGCTT
1 CTCCACTACTGCTTAGGGAGATAAGATCTACAAT--CTTCAA-C--CTA
* ** ** *
1276034 CTCCACTA-T-CTT-GGGAAGATAAGAT-TCACCATCTTTGATTTG
1 CTCCACTACTGCTTAGGG-AGATAAGATCT-ACAATCTTCAACCTA
* *
1276076 CTCCACTACTGCTTAGGGAGA-CAGAATCTGCAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGAGATAAG-ATCTACAATCTTCAACCTA
* * ** *
1276120 CTCCACTACTGCTTAGGGAGATAGGA-CT--AATGGCTTAAATATG
1 CTCCACTACTGCTTAGGGAGATAAGATCTACAAT--CTTCAACCTA
* * * * * ** * ** * *
1276163 CTTCTCTTCTACCTTAGGAAGATAAGAT-TCACTTTTTTTGATCTG
1 CTCCACTACT-GCTTAGGGAGATAAGATCT-ACAATCTTCAACCTA
1276208 CTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTA
* *
1276252 CTCCACTGCTGCTCAGGGAGATAAG
1 CTCCACTACTGCTTAGGGAGATAAG
1276277 GCTTGATATG
Statistics
Matches: 210, Mismatches: 54, Indels: 50
0.67 0.17 0.16
Matches are distributed among these distances:
41 6 0.03
42 9 0.04
43 28 0.13
44 129 0.61
45 26 0.12
46 9 0.04
47 3 0.01
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (44 bp):
CTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTA
Found at i:1277614 original size:17 final size:14
Alignment explanation
Indices: 1277587--1277662 Score: 73
Period size: 14 Copynumber: 5.3 Consensus size: 14
1277577 TGGCCTCTCC
1277587 TTTTCTTTTTCTTTT
1 TTTTCTTTTT-TTTT
* *
1277602 ATCTTCTTTTTTCTT
1 -TTTTCTTTTTTTTT
*
1277617 TTTTCTTTGTTTTT
1 TTTTCTTTTTTTTT
*
1277631 CTTTC-TTTTTTTT
1 TTTTCTTTTTTTTT
*
1277644 TTCTCTTTTTTCTTT
1 TTTTCTTTTTT-TTT
1277659 TTTT
1 TTTT
1277663 TTAGATATTT
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
13 10 0.21
14 20 0.42
15 9 0.19
16 9 0.19
ACGTcount: A:0.01, C:0.14, G:0.01, T:0.83
Consensus pattern (14 bp):
TTTTCTTTTTTTTT
Found at i:1277629 original size:10 final size:10
Alignment explanation
Indices: 1277594--1277660 Score: 52
Period size: 10 Copynumber: 6.9 Consensus size: 10
1277584 TCCTTTTCTT
1277594 TTTCTTTTATC
1 TTTCTTTT-TC
1277605 -TTCTTTTT-
1 TTTCTTTTTC
*
1277613 TCT-TTTTTC
1 TTTCTTTTTC
*
1277622 TTTGTTTTTC
1 TTTCTTTTTC
*
1277632 TTTCTTTTTTT
1 TTTC-TTTTTC
*
1277643 TTTCTCTTT-
1 TTTCTTTTTC
1277652 TTTCTTTTT
1 TTTCTTTTT
1277661 TTTTAGATAT
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
8 5 0.11
9 12 0.26
10 20 0.43
11 9 0.20
ACGTcount: A:0.01, C:0.15, G:0.01, T:0.82
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:1277633 original size:34 final size:34
Alignment explanation
Indices: 1277592--1277664 Score: 96
Period size: 34 Copynumber: 2.1 Consensus size: 34
1277582 TCTCCTTTTC
1277592 TTTTTCTTT-TATCTTCTTTTT-TCTTTTTTCTTTG
1 TTTTTCTTTCT-T-TTCTTTTTCTCTTTTTTCTTTG
* *
1277626 TTTTTCTTTCTTTTTTTTTTCTCTTTTTTCTTTT
1 TTTTTCTTTCTTTTCTTTTTCTCTTTTTTCTTTG
1277660 TTTTT
1 TTTTT
1277665 AGATATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 7 0.20
34 27 0.77
35 1 0.03
ACGTcount: A:0.01, C:0.14, G:0.01, T:0.84
Consensus pattern (34 bp):
TTTTTCTTTCTTTTCTTTTTCTCTTTTTTCTTTG
Found at i:1277663 original size:24 final size:24
Alignment explanation
Indices: 1277587--1277664 Score: 86
Period size: 24 Copynumber: 3.2 Consensus size: 24
1277577 TGGCCTCTCC
* *
1277587 TTTTCTTTT-TCTTTTATCTTCTTT
1 TTTTTTTTTCTCTTTTTTCTT-TTT
* *
1277611 TTTCTTTTTTCTTTGTTTTTCTTTCT
1 TTT-TTTTTTCTCT-TTTTTCTTTTT
1277637 TTTTTTTTTCTCTTTTTTCTTTTT
1 TTTTTTTTTCTCTTTTTTCTTTTT
1277661 TTTT
1 TTTT
1277665 AGATATTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
24 17 0.38
25 14 0.31
26 7 0.16
27 7 0.16
ACGTcount: A:0.01, C:0.14, G:0.01, T:0.83
Consensus pattern (24 bp):
TTTTTTTTTCTCTTTTTTCTTTTT
Found at i:1277673 original size:21 final size:20
Alignment explanation
Indices: 1277608--1277675 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 20
1277598 TTTTATCTTC
*
1277608 TTTTTTCTTTTTTCTTTG-TT
1 TTTTTTCTTTTTT-TTTGATA
** *
1277628 TTTCTTTCTTTTTTTTTTCTC
1 TTT-TTTCTTTTTTTTTGATA
1277649 TTTTTTCTTTTTTTTTAGATA
1 TTTTTTCTTTTTTTTT-GATA
1277670 TTTTTT
1 TTTTTT
1277676 ATTGAACCTG
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
20 19 0.47
21 21 0.52
ACGTcount: A:0.04, C:0.10, G:0.03, T:0.82
Consensus pattern (20 bp):
TTTTTTCTTTTTTTTTGATA
Found at i:1277674 original size:34 final size:33
Alignment explanation
Indices: 1277608--1277675 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 33
1277598 TTTTATCTTC
*** *
1277608 TTTTTTCTTTTTTCTTTGTTTTTCTTTCTTTTT
1 TTTTTTCTTTTTTCTTTGTTTTTAGATATTTTT
*
1277641 TTTTTCTCTTTTTTCTTTTTTTTTAGATATTTTT
1 TTTTT-TCTTTTTTCTTTGTTTTTAGATATTTTT
1277675 T
1 T
1277676 ATTGAACCTG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
33 5 0.17
34 24 0.83
ACGTcount: A:0.04, C:0.10, G:0.03, T:0.82
Consensus pattern (33 bp):
TTTTTTCTTTTTTCTTTGTTTTTAGATATTTTT
Found at i:1288646 original size:43 final size:43
Alignment explanation
Indices: 1288504--1288658 Score: 154
Period size: 43 Copynumber: 3.6 Consensus size: 43
1288494 TTTCGAGATG
* * *
1288504 TGATATCGTGTAAGACCATGTCTGGGACATTGGCATCGATCTGA
1 TGATAACGTGTAAGACCATGTCTGGGACATTGGCATTGATAT-A
* **
1288548 -GATCACGTGTAAGACCATGTCTGGGACATTGG--TGTCCTATA
1 TGATAACGTGTAAGACCATGTCTGGGACATTGGCAT-TGATATA
*** * *
1288589 TGATTTTGTGTAAGACCCTGTCTGGGACAGTGGCATTGATATA
1 TGATAACGTGTAAGACCATGTCTGGGACATTGGCATTGATATA
* *
1288632 TGATAACATGTAAGACCATATCTGGGA
1 TGATAACGTGTAAGACCATGTCTGGGA
1288659 TATAGCATTG
Statistics
Matches: 88, Mismatches: 19, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
41 2 0.02
42 29 0.33
43 56 0.64
44 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (43 bp):
TGATAACGTGTAAGACCATGTCTGGGACATTGGCATTGATATA
Found at i:1292669 original size:114 final size:114
Alignment explanation
Indices: 1292510--1293117 Score: 982
Period size: 114 Copynumber: 5.3 Consensus size: 114
1292500 AAAATAAGCA
* * * * *
1292510 TTAGCGGCGTTTTTAAGAAAGCACCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGAGAAAGCGC
1 TTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTGGGAAAGCGC
* * * *
1292575 CACAAAAAAATCTAAGCCTAACGACGCCGTCTTCTGAGCTTTCGGGGAT
66 CGCAAAAATACCTAAGCCTAACGACGCCGTTTTCTGAGCTTTCGGGGAT
* *
1292624 TTAGTGGCGTTTTTAGGTAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTAGGAAAGCGC
1 TTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTGGGAAAGCGC
*
1292689 CGCAAAAATACCTAAGTCTAACGACGCCGTTTTCTGAGCTTTCGGGGAT
66 CGCAAAAATACCTAAGCCTAACGACGCCGTTTTCTGAGCTTTCGGGGAT
*
1292738 TTAGTGGCATTTTTAAGTAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTGGGAAAGCGC
1 TTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTGGGAAAGCGC
* *
1292803 CGTAAAAATACCTAAGCCTAACGACGCCGTTTTTTGAGCTTTCGGGGAT
66 CGCAAAAATACCTAAGCCTAACGACGCCGTTTTCTGAGCTTTCGGGGAT
* *
1292852 TTAGTGGCGTTTTTAAGTAAGCGCCGTTGATGCTCAGGTCTTTAGCGGCGTTTTTGGGAAAGCGC
1 TTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTGGGAAAGCGC
* *
1292917 CGCAAAAATACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGAGGAT
66 CGCAAAAATACCTAAGCCTAACGACGCCGTTTTCTGAGCTTTCGGGGAT
* * ** *
1292966 TTAGTGGCATTTTTAAGTAAGTGCCGCTGTTGCTCAGGTCTTTAGTGGCGTTTTTGGGAAAGCGC
1 TTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTGGGAAAGCGC
* *
1293031 CGCAAAAATACCTAAGCCCAACGACGCCGTTTTCTAAGCTTTCGGGGAT
66 CGCAAAAATACCTAAGCCTAACGACGCCGTTTTCTGAGCTTTCGGGGAT
1293080 TTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGG
1 TTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGG
1293118 GATTTAAAAT
Statistics
Matches: 458, Mismatches: 36, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 458 1.00
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (114 bp):
TTAGTGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTGGGAAAGCGC
CGCAAAAATACCTAAGCCTAACGACGCCGTTTTCTGAGCTTTCGGGGAT
Found at i:1294155 original size:21 final size:21
Alignment explanation
Indices: 1294102--1294155 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 21
1294092 TAAAGATTAT
1294102 TAATTTAAAA-TTGATATGCAA
1 TAATTTAAAATTTGATAT-CAA
*
1294123 T-ATATAATAATTTGAATAT-AA
1 TAATTTAA-AATTTG-ATATCAA
1294144 TAATTTAAAATT
1 TAATTTAAAATT
1294156 GTAAAATTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
20 5 0.19
21 10 0.37
22 8 0.30
23 4 0.15
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.43
Consensus pattern (21 bp):
TAATTTAAAATTTGATATCAA
Found at i:1294206 original size:18 final size:18
Alignment explanation
Indices: 1294185--1294224 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
1294175 TAAAAATTAC
*
1294185 AAAAAATAAAATA-AAAT
1 AAAAAATAAAAAAGAAAT
1294202 AAAAAATAAAAAAGAAAT
1 AAAAAATAAAAAAGAAAT
1294220 AAAAA
1 AAAAA
1294225 CACTAACATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (18 bp):
AAAAAATAAAAAAGAAAT
Found at i:1294207 original size:12 final size:11
Alignment explanation
Indices: 1294185--1294224 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
1294175 TAAAAATTAC
1294185 AAAAAATAAAAT
1 AAAAAA-AAAAT
1294197 AAAATAAAAAAT
1 AAAA-AAAAAAT
*
1294209 AAAAAAGAAAT
1 AAAAAAAAAAT
1294220 AAAAA
1 AAAAA
1294225 CACTAACATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 11 0.42
12 13 0.50
13 2 0.08
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (11 bp):
AAAAAAAAAAT
Found at i:1294240 original size:68 final size:70
Alignment explanation
Indices: 1294168--1294305 Score: 235
Period size: 70 Copynumber: 2.0 Consensus size: 70
1294158 AAAATTGTAA
1294168 AAAATTGTAAAAATTACAAAAAATAAAA-TAAAA-TAAAAAATAAAAAAGAAATAAAAACACTAA
1 AAAATTGTAAAAATTACAAAAAATAAAATTAAAATTAAAAAATAAAAAAGAAATAAAAACACTAA
*
1294231 CATTT
66 AATTT
* *
1294236 AAAATTGTAAAAATTATAAAAAATAAAATTAAAATTAAAAAATTAAAAAGAAATAAAAACACTAA
1 AAAATTGTAAAAATTACAAAAAATAAAATTAAAATTAAAAAATAAAAAAGAAATAAAAACACTAA
1294301 AATTT
66 AATTT
1294306 TTATTTTTAC
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
68 27 0.42
69 5 0.08
70 33 0.51
ACGTcount: A:0.70, C:0.04, G:0.03, T:0.23
Consensus pattern (70 bp):
AAAATTGTAAAAATTACAAAAAATAAAATTAAAATTAAAAAATAAAAAAGAAATAAAAACACTAA
AATTT
Found at i:1294270 original size:30 final size:30
Alignment explanation
Indices: 1294234--1294293 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
1294224 ACACTAACAT
* *
1294234 TTAAAATTGTAAAAATTATAAA-AAATAAAA
1 TTAAAATT-AAAAAATTAAAAAGAAATAAAA
1294264 TTAAAATTAAAAAATTAAAAAGAAATAAAA
1 TTAAAATTAAAAAATTAAAAAGAAATAAAA
1294294 ACACTAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (30 bp):
TTAAAATTAAAAAATTAAAAAGAAATAAAA
Found at i:1294284 original size:21 final size:21
Alignment explanation
Indices: 1294245--1294283 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1294235 TAAAATTGTA
1294245 AAAATTATAAAAAATAAAATT
1 AAAATTATAAAAAATAAAATT
*
1294266 AAAATTA-AAAAATTAAAA
1 AAAATTATAAAAAATAAAA
1294284 AGAAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAATTATAAAAAATAAAATT
Found at i:1294361 original size:47 final size:48
Alignment explanation
Indices: 1294289--1294387 Score: 137
Period size: 47 Copynumber: 2.1 Consensus size: 48
1294279 TAAAAAGAAA
** * *
1294289 TAAAAACACTAAAATTTTTATTTTTACCTAATTTTTATAAATACTACT
1 TAAAAACACTAAAATTGATAATTTTACCTAATTTTTATAAATACTACC
* *
1294337 TAAAAA-ACTAAAATTGATAATTTTATCTAATTTTTATAAATATTACC
1 TAAAAACACTAAAATTGATAATTTTACCTAATTTTTATAAATACTACC
1294384 TAAA
1 TAAA
1294388 CAAAACTATG
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
47 39 0.87
48 6 0.13
ACGTcount: A:0.45, C:0.10, G:0.01, T:0.43
Consensus pattern (48 bp):
TAAAAACACTAAAATTGATAATTTTACCTAATTTTTATAAATACTACC
Found at i:1294796 original size:192 final size:193
Alignment explanation
Indices: 1294462--1294994 Score: 807
Period size: 192 Copynumber: 2.7 Consensus size: 193
1294452 CGTTTCTAAC
*
1294462 AAAAACGCCACAAAATATTCTTAATAATGAAGACAAAACGGTGCAGTTTTTGGCTGCGAATTTAA
1 AAAAACGCCGCAAAATATTCTTAATAATGAAG-----A-GGTGCAGTTTTTGGCTGCGAATTTAA
*
1294527 TGGGTTTTGCGGCGCTAAGGGAAAAACGCCGCTAAAGGTGGTCATTAGCGACGCTAAGGAAAAAA
60 TGGGTTTTGCGGCGCTAAGGGAAAAACGCCGCTAAAGGTGGTCATTAGCGGCGCTAAGGAAAAAA
* *
1294592 CGCTGCAAAGTTCTGTTATCAGTTTTCGTAAAACGGTGTCGTTTTGCCTGGGCATTAGTGGCGCT
125 CGCCGCAAAGTTCTATTATCAGTTTTCGTAAAACGGTGTCGTTTTGCCTGGGCATTAGTGGCGCT
1294657 ACTA
190 ACTA
*
1294661 AAAAACGCCGCAAAATATTCTTAATAATGAAG-GGTGCAGTTTTTGGCTGTGAATTTAATGGGTT
1 AAAAACGCCGCAAAATATTCTTAATAATGAAGAGGTGCAGTTTTTGGCTGCGAATTTAATGGGTT
* * *
1294725 TTGCAGCGCTAAGGGAAAAATGCCGCTAAAGGTGGTCATTAGCGGCGCTAAGGAAAAAAAGCCGC
66 TTGCGGCGCTAAGGGAAAAACGCCGCTAAAGGTGGTCATTAGCGGCGCTAAGGAAAAAACGCCGC
* *
1294790 AAAGTTCTATTCTCAGTTTTCGTAAAATGGTGTCGTTTTGCCTGGGCATTAGTGGCGCTACTA
131 AAAGTTCTATTATCAGTTTTCGTAAAACGGTGTCGTTTTGCCTGGGCATTAGTGGCGCTACTA
*
1294853 AAAAACGCCGCAAAATATTCTTAATAATGAAGACAAAACGGTGCAATTTTTGGCTGCGAATTTAA
1 AAAAACGCCGCAAAATATTCTTAATAATGAAG-----A-GGTGCAGTTTTTGGCTGCGAATTTAA
* * ** *
1294918 TGGGTTTTGCGGCGCTAAGGTAAAAACACCGCTAAATATGGTCATTAGCGGCGCTAAGGAACAAA
60 TGGGTTTTGCGGCGCTAAGGGAAAAACGCCGCTAAAGGTGGTCATTAGCGGCGCTAAGGAAAAAA
1294983 CGCCGCAAAGTT
125 CGCCGCAAAGTT
1294995 AGTACTGAAA
Statistics
Matches: 307, Mismatches: 20, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
192 183 0.60
199 124 0.40
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (193 bp):
AAAAACGCCGCAAAATATTCTTAATAATGAAGAGGTGCAGTTTTTGGCTGCGAATTTAATGGGTT
TTGCGGCGCTAAGGGAAAAACGCCGCTAAAGGTGGTCATTAGCGGCGCTAAGGAAAAAACGCCGC
AAAGTTCTATTATCAGTTTTCGTAAAACGGTGTCGTTTTGCCTGGGCATTAGTGGCGCTACTA
Found at i:1298236 original size:174 final size:174
Alignment explanation
Indices: 1297946--1299436 Score: 2982
Period size: 174 Copynumber: 8.6 Consensus size: 174
1297936 TTAATATCGT
1297946 AACATGGCCTTTAGCGGTGTTTTCAGGAAAAGCGCCGCTAAAGAACATGGCCTTTAGCGGCGTTT
1 AACATGGCCTTTAGCGGTGTTTTCAGGAAAAGCGCCGCTAAAGAACATGGCCTTTAGCGGCGTTT
1298011 GCGGGAAAAGCGCCGCTAAAGAACATGACCTTTAACGGCGTTTGTGGGAAAAAAATGCCGCTAAA
66 GCGGGAAAAGCGCCGCTAAAGAACATGACCTTTAACGGCGTTTGTGGGAAAAAAATGCCGCTAAA
1298076 GGACATGGCCTTTAGCGGCATTTTCGGGAAAAGAGCCGCTAAAG
131 GGACATGGCCTTTAGCGGCATTTTCGGGAAAAGAGCCGCTAAAG
1298120 AACATGGCCTTTAGCGGTGTTTTCAGGAAAAGCGCCGCTAAAGAACATGGCCTTTAGCGGCGTTT
1 AACATGGCCTTTAGCGGTGTTTTCAGGAAAAGCGCCGCTAAAGAACATGGCCTTTAGCGGCGTTT
1298185 GCGGGAAAAGCGCCGCTAAAGAACATGACCTTTAACGGCGTTTGTGGGAAAAAAATGCCGCTAAA
66 GCGGGAAAAGCGCCGCTAAAGAACATGACCTTTAACGGCGTTTGTGGGAAAAAAATGCCGCTAAA
1298250 GGACATGGCCTTTAGCGGCATTTTCGGGAAAAGAGCCGCTAAAG
131 GGACATGGCCTTTAGCGGCATTTTCGGGAAAAGAGCCGCTAAAG
1298294 AACATGGCCTTTAGCGGTGTTTTCAGGAAAAGCGCCGCTAAAGAACATGGCCTTTAGCGGCGTTT
1 AACATGGCCTTTAGCGGTGTTTTCAGGAAAAGCGCCGCTAAAGAACATGGCCTTTAGCGGCGTTT
1298359 GCGGGAAAAGCGCCGCTAAAGAACATGACCTTTAACGGCGTTTGTGGGAAAAAAATGCCGCTAAA
66 GCGGGAAAAGCGCCGCTAAAGAACATGACCTTTAACGGCGTTTGTGGGAAAAAAATGCCGCTAAA
1298424 GGACATGGCCTTTAGCGGCATTTTCGGGAAAAGAGCCGCTAAAG
131 GGACATGGCCTTTAGCGGCATTTTCGGGAAAAGAGCCGCTAAAG
1298468 AACATGGCCTTTAGCGGTGTTTTCAGGAAAAGCGCCGCTAAAGAACATGGCCTTTAGCGGCGTTT
1 AACATGGCCTTTAGCGGTGTTTTCAGGAAAAGCGCCGCTAAAGAACATGGCCTTTAGCGGCGTTT
1298533 GCGGGAAAAGCGCCGCTAAAGAACATGACCTTTAACGGCGTTTGTGGGAAAAAAATGCCGCTAAA
66 GCGGGAAAAGCGCCGCTAAAGAACATGACCTTTAACGGCGTTTGTGGGAAAAAAATGCCGCTAAA
1298598 GGACATGGCCTTTAGCGGCATTTTCGGGAAAAGAGCCGCTAAAG
131 GGACATGGCCTTTAGCGGCATTTTCGGGAAAAGAGCCGCTAAAG
1298642 AACATGGCCTTTAGCGGTGTTTTCAGGAAAAGCGCCGCTAAAGAACATGGCCTTTAGCGGCGTTT
1 AACATGGCCTTTAGCGGTGTTTTCAGGAAAAGCGCCGCTAAAGAACATGGCCTTTAGCGGCGTTT
1298707 GCGGGAAAAGCGCCGCTAAAGAACATGACCTTTAACGGCGTTTGTGGGAAAAAAATGCCGCTAAA
66 GCGGGAAAAGCGCCGCTAAAGAACATGACCTTTAACGGCGTTTGTGGGAAAAAAATGCCGCTAAA
1298772 GGACATGGCCTTTAGCGGCATTTTCGGGAAAAGAGCCGCTAAAG
131 GGACATGGCCTTTAGCGGCATTTTCGGGAAAAGAGCCGCTAAAG
1298816 AACATGGCCTTTAGCGGTGTTTTCAGGAAAAGCGCCGCTAAAGAACATGGCCTTTAGCGGCGTTT
1 AACATGGCCTTTAGCGGTGTTTTCAGGAAAAGCGCCGCTAAAGAACATGGCCTTTAGCGGCGTTT
1298881 GCGGGAAAAGCGCCGCTAAAGAACATGACCTTTAACGGCGTTTGTGGGAAAAAAATGCCGCTAAA
66 GCGGGAAAAGCGCCGCTAAAGAACATGACCTTTAACGGCGTTTGTGGGAAAAAAATGCCGCTAAA
1298946 GGACATGGCCTTTAGCGGCATTTTCGGGAAAAGAGCCGCTAAAG
131 GGACATGGCCTTTAGCGGCATTTTCGGGAAAAGAGCCGCTAAAG
1298990 AACATGGCCTTTAGCGGTGTTTTCAGGAAAAGCGCCGCTAAAGAACATGGCCTTTAGCGGCGTTT
1 AACATGGCCTTTAGCGGTGTTTTCAGGAAAAGCGCCGCTAAAGAACATGGCCTTTAGCGGCGTTT
1299055 GCGGGAAAAGCGCCGCTAAAGAACATGACCTTTAACGGCGTTTGTGGGAAAAAAATGCCGCTAAA
66 GCGGGAAAAGCGCCGCTAAAGAACATGACCTTTAACGGCGTTTGTGGGAAAAAAATGCCGCTAAA
1299120 GGACATGGCCTTTAGCGGCATTTTCGGGAAAAGAGCCGCTAAAG
131 GGACATGGCCTTTAGCGGCATTTTCGGGAAAAGAGCCGCTAAAG
1299164 AACATGGCCTTTAGCGGTGTTTTCAGGAAAAGCGCCGCTAAAGAACATGGCCTTTAGCGGCGTTT
1 AACATGGCCTTTAGCGGTGTTTTCAGGAAAAGCGCCGCTAAAGAACATGGCCTTTAGCGGCGTTT
1299229 GCGGGAAAAGCGCCGCTAAAGAACATGACCTTTAACGGCGTTTGTGGGAAAAAAATGCCGCTAAA
66 GCGGGAAAAGCGCCGCTAAAGAACATGACCTTTAACGGCGTTTGTGGGAAAAAAATGCCGCTAAA
1299294 GGACATGGCCTTTAGCGGCATTTTCGGGAAAAGAGCCGCTAAAG
131 GGACATGGCCTTTAGCGGCATTTTCGGGAAAAGAGCCGCTAAAG
1299338 AACATGGCCTTTAGCGGTGTTTTCAGGAAAAGCGCCGCTAAAGAACATGGCCTTTAGCGGCGTTT
1 AACATGGCCTTTAGCGGTGTTTTCAGGAAAAGCGCCGCTAAAGAACATGGCCTTTAGCGGCGTTT
1299403 GCGGGAAAAGCGCCGCTAAAGAACATGACCTTTA
66 GCGGGAAAAGCGCCGCTAAAGAACATGACCTTTA
1299437 GCTGCATTTA
Statistics
Matches: 1317, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
174 1317 1.00
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (174 bp):
AACATGGCCTTTAGCGGTGTTTTCAGGAAAAGCGCCGCTAAAGAACATGGCCTTTAGCGGCGTTT
GCGGGAAAAGCGCCGCTAAAGAACATGACCTTTAACGGCGTTTGTGGGAAAAAAATGCCGCTAAA
GGACATGGCCTTTAGCGGCATTTTCGGGAAAAGAGCCGCTAAAG
Found at i:1301328 original size:15 final size:15
Alignment explanation
Indices: 1301308--1301337 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1301298 GTGAGAAATG
1301308 TTCGTAAACTAATTT
1 TTCGTAAACTAATTT
1301323 TTCGTAAACTAATTT
1 TTCGTAAACTAATTT
1301338 GATCGTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.47
Consensus pattern (15 bp):
TTCGTAAACTAATTT
Found at i:1302611 original size:33 final size:33
Alignment explanation
Indices: 1302569--1302636 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
1302559 TTCGTGTAAG
*
1302569 ACCCTGTATGGGCAGTGACATCGGTATATGATA
1 ACCCTGTATGGGCAGTGACATCAGTATATGATA
1302602 ACCCTGTATGGGCAGTGACATCAGTATATGATA
1 ACCCTGTATGGGCAGTGACATCAGTATATGATA
1302635 AC
1 AC
1302637 ATGTATGACC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.26
Consensus pattern (33 bp):
ACCCTGTATGGGCAGTGACATCAGTATATGATA
Found at i:1309942 original size:28 final size:27
Alignment explanation
Indices: 1309876--1309942 Score: 62
Period size: 28 Copynumber: 2.4 Consensus size: 27
1309866 CTTTAATAGT
* * *
1309876 AACAGTACAGTGTGGGCCTTAGCCCTA
1 AACAGTACAGTGTAGGCCTAAGCCCGA
* **
1309903 TACAAAAACAGTGTAGGCCTAAGCCCGA
1 AAC-AGTACAGTGTAGGCCTAAGCCCGA
1309931 AACAGTATCAGT
1 AACAGTA-CAGT
1309943 ATGTTGTAAG
Statistics
Matches: 29, Mismatches: 9, Indels: 3
0.71 0.22 0.07
Matches are distributed among these distances:
27 4 0.14
28 25 0.86
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.19
Consensus pattern (27 bp):
AACAGTACAGTGTAGGCCTAAGCCCGA
Found at i:1310161 original size:22 final size:22
Alignment explanation
Indices: 1310088--1310161 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
1310078 CAGCAGAGCT
*
1310088 GCCAGTAATCAGAATGGCTAAAA
1 GCCA-TAAACAGAATGGCTAAAA
* * * *
1310111 GCCGTAAATAGGATAGCTATAAA
1 GCCATAAACAGAATGGCTA-AAA
* *
1310134 -CTATAAACAGAATGGCTACAA
1 GCCATAAACAGAATGGCTAAAA
1310155 GCCATAA
1 GCCATAA
1310162 GTATAGTAAT
Statistics
Matches: 37, Mismatches: 12, Indels: 5
0.69 0.22 0.09
Matches are distributed among these distances:
21 2 0.05
22 29 0.78
23 6 0.16
ACGTcount: A:0.45, C:0.18, G:0.19, T:0.19
Consensus pattern (22 bp):
GCCATAAACAGAATGGCTAAAA
Found at i:1310208 original size:32 final size:32
Alignment explanation
Indices: 1310153--1310354 Score: 228
Period size: 32 Copynumber: 6.4 Consensus size: 32
1310143 GAATGGCTAC
* * *
1310153 AAGCCATAAGT-ATAGTAATATGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * *
1310184 AAGCCATCAGTAGCAGTTATATGATCAGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * *
1310216 CAGCCATCAGTAACGGTAATATGATCGACACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * *
1310248 AAGCCATCAG-AGCAGTTATATGATCAGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * *
1310279 CAGCCATCAGTAACGGTAATATGATCGACACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
** *
1310311 AAGCCATCAGTAATGGTAATATGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
1310343 AAGCCATCAGTA
1 AAGCCATCAGTA
1310355 GCATCGCAGC
Statistics
Matches: 141, Mismatches: 28, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
31 35 0.25
32 106 0.75
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATCGGCACA
Found at i:1310272 original size:63 final size:64
Alignment explanation
Indices: 1310167--1310354 Score: 288
Period size: 63 Copynumber: 3.0 Consensus size: 64
1310157 CATAAGTATA
* *
1310167 GTAATATGATTGGCACAAAGCCATCAGTAGCAGTTATATGATCAGCACACAGCCATCAGTAACG
1 GTAATATGATCGACACAAAGCCATCAGTAGCAGTTATATGATCAGCACACAGCCATCAGTAACG
1310231 GTAATATGATCGACACAAAGCCATCAG-AGCAGTTATATGATCAGCACACAGCCATCAGTAACG
1 GTAATATGATCGACACAAAGCCATCAGTAGCAGTTATATGATCAGCACACAGCCATCAGTAACG
*** * ** *
1310294 GTAATATGATCGACACAAAGCCATCAGTAATGGTAATATGATTGGCACAAAGCCATCAGTA
1 GTAATATGATCGACACAAAGCCATCAGTAGCAGTTATATGATCAGCACACAGCCATCAGTA
1310355 GCATCGCAGC
Statistics
Matches: 114, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
63 63 0.55
64 51 0.45
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (64 bp):
GTAATATGATCGACACAAAGCCATCAGTAGCAGTTATATGATCAGCACACAGCCATCAGTAACG
Found at i:1310316 original size:95 final size:96
Alignment explanation
Indices: 1310153--1310357 Score: 263
Period size: 95 Copynumber: 2.2 Consensus size: 96
1310143 GAATGGCTAC
* * * ** * * *
1310153 AAGCCATAAGTA-TAGTAATATGATTGGCACAAAGCCATCAGTAGCAGTTATATGATCAGCACAC
1 AAGCCATCAGTAGCAGTTATATGATCAGCACAAAGCCATCAGTAACAGTAATATGATCAGCACAA
1310217 AGCCATCAGTAACGGTAATATGATCGACACA
66 AGCCATCAGTAACGGTAATATGATCGACACA
* *
1310248 AAGCCATCAG-AGCAGTTATATGATCAGCACACAGCCATCAGTAACGGTAATATGATC-GACACA
1 AAGCCATCAGTAGCAGTTATATGATCAGCACAAAGCCATCAGTAACAGTAATATGATCAG-CACA
* * *
1310311 AAGCCATCAGTAATGGTAATATGATTGGCACA
65 AAGCCATCAGTAACGGTAATATGATCGACACA
1310343 AAGCCATCAGTAGCA
1 AAGCCATCAGTAGCA
1310358 TCGCAGCAAA
Statistics
Matches: 94, Mismatches: 13, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
94 2 0.02
95 88 0.94
96 4 0.04
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.21
Consensus pattern (96 bp):
AAGCCATCAGTAGCAGTTATATGATCAGCACAAAGCCATCAGTAACAGTAATATGATCAGCACAA
AGCCATCAGTAACGGTAATATGATCGACACA
Found at i:1310570 original size:24 final size:24
Alignment explanation
Indices: 1310515--1310581 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
1310505 TCATACCAAA
* *
1310515 CACAAACAAAGCAATCATTTACAT
1 CACAGACAAATCAATCATTTACAT
*
1310539 CA-AGGACAAATCAATCATTTATAT
1 CACA-GACAAATCAATCATTTACAT
* *
1310563 CACAGACAATTCAAACATT
1 CACAGACAAATCAATCATT
1310582 AACCTCGAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 1 0.03
24 34 0.94
25 1 0.03
ACGTcount: A:0.48, C:0.22, G:0.06, T:0.24
Consensus pattern (24 bp):
CACAGACAAATCAATCATTTACAT
Found at i:1310703 original size:27 final size:27
Alignment explanation
Indices: 1310673--1310960 Score: 203
Period size: 27 Copynumber: 10.7 Consensus size: 27
1310663 ACCCTACAAA
**
1310673 GGTATTACTATCATTTTACCCTATAGG
1 GGTATTACGGTCATTTTACCCTATAGG
* * * * *
1310700 GGTA-TATCGATCAATTCA-CCTAACAGA
1 GGTATTA-CGGTCATTTTACCCT-ATAGG
* *
1310727 AGTATTACGG-CTATTTTACCTTATAGG
1 GGTATTACGGTC-ATTTTACCCTATAGG
* * *
1310754 GGCATTACGGTCATTTTACCTTACAGG
1 GGTATTACGGTCATTTTACCCTATAGG
1310781 GGTATTAC-GTCATTTTACCCTATAGG
1 GGTATTACGGTCATTTTACCCTATAGG
* *
1310807 GGTATTATGGTCATTTTACCCTAT-GAA
1 GGTATTACGGTCATTTTACCCTATAG-G
** * * * *
1310834 GGTATTTTGATCAATTCA-CCTA-ACTGA
1 GGTATTACGGTCATTTTACCCTATA--GG
* * *
1310861 AGTGTTACGGTCATTTTACTCTATAGG
1 GGTATTACGGTCATTTTACCCTATAGG
* * * *
1310888 GGCATTACGATTATTTTACCCTACAGG
1 GGTATTACGGTCATTTTACCCTATAGG
* *
1310915 GGTATTACGGTCATTTTATCCTACAGG
1 GGTATTACGGTCATTTTACCCTATAGG
*
1310942 GGCATTACGGTCATTTTAC
1 GGTATTACGGTCATTTTAC
1310961 AAACATTAGG
Statistics
Matches: 202, Mismatches: 46, Indels: 26
0.74 0.17 0.09
Matches are distributed among these distances:
26 34 0.17
27 158 0.78
28 9 0.04
29 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.37
Consensus pattern (27 bp):
GGTATTACGGTCATTTTACCCTATAGG
Found at i:1310846 original size:134 final size:135
Alignment explanation
Indices: 1310660--1310960 Score: 394
Period size: 134 Copynumber: 2.2 Consensus size: 135
1310650 TTATAGTAAC
** * ** *
1310660 TTTACCCTACAAAGGTATTACTATCATTTTACCCTATAGGGGTATATCGATCAATTCACCTAACA
1 TTTACCCTACAGGGGCATTACGGTCATTTTACCCTATAGAGGTATATCGATCAATTCACCTAACA
* *
1310725 GAAGTATTACGG-CTATTTTAC-CTTATAGGGGCATTACGGTCATTTTACCTTACAGGGGTATTA
66 GAAGTATTACGGTC-ATTTTACTC-TATAGGGGCATTACGATCATTTTACCCTACAGGGGTATTA
1310788 C-GTCAT
129 CGGTCAT
* * * * *
1310794 TTTACCCTATAGGGGTATTATGGTCATTTTACCCTAT-GAAGGTATTTTGATCAATTCACCTAAC
1 TTTACCCTACAGGGGCATTACGGTCATTTTACCCTATAG-AGGTATATCGATCAATTCACCTAAC
* * *
1310858 TGAAGTGTTACGGTCATTTTACTCTATAGGGGCATTACGATTATTTTACCCTACAGGGGTATTAC
65 AGAAGTATTACGGTCATTTTACTCTATAGGGGCATTACGATCATTTTACCCTACAGGGGTATTAC
1310923 GGTCAT
130 GGTCAT
*
1310929 TTTATCCTACAGGGGCATTACGGTCATTTTAC
1 TTTACCCTACAGGGGCATTACGGTCATTTTAC
1310961 AAACATTAGG
Statistics
Matches: 145, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
133 1 0.01
134 109 0.75
135 35 0.24
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (135 bp):
TTTACCCTACAGGGGCATTACGGTCATTTTACCCTATAGAGGTATATCGATCAATTCACCTAACA
GAAGTATTACGGTCATTTTACTCTATAGGGGCATTACGATCATTTTACCCTACAGGGGTATTACG
GTCAT
Found at i:1311344 original size:18 final size:18
Alignment explanation
Indices: 1311317--1311354 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1311307 CTATGTGGCT
1311317 CACAAGCCTA-CTAGGCC
1 CACAAGCCTATCTAGGCC
*
1311334 CACATAGCCTATTTAGGCC
1 CACA-AGCCTATCTAGGCC
1311353 CA
1 CA
1311355 ATAAGACCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 6 0.33
19 8 0.44
ACGTcount: A:0.29, C:0.37, G:0.16, T:0.18
Consensus pattern (18 bp):
CACAAGCCTATCTAGGCC
Found at i:1315568 original size:43 final size:44
Alignment explanation
Indices: 1315501--1315600 Score: 123
Period size: 44 Copynumber: 2.3 Consensus size: 44
1315491 AATGTTGAAG
* *
1315501 TAAAATTAAAAAATAGTTACGTGTTT-TTTTATAAGTAACTATA
1 TAAAATTAAAAAATAGTGACGTGTTTCTTTTATAAATAACTATA
* * *
1315544 TAAAATTAAAAAATTA-TGATGTGTTTCTTTTATAAATAATTTTA
1 TAAAATTAAAAAA-TAGTGACGTGTTTCTTTTATAAATAACTATA
*
1315588 TGAAATTAAAAAA
1 TAAAATTAAAAAA
1315601 ATCCACAATC
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
43 21 0.43
44 28 0.57
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (44 bp):
TAAAATTAAAAAATAGTGACGTGTTTCTTTTATAAATAACTATA
Found at i:1316220 original size:67 final size:65
Alignment explanation
Indices: 1316141--1316273 Score: 212
Period size: 67 Copynumber: 2.0 Consensus size: 65
1316131 TTTTTATGGA
* **
1316141 TCTTGCAAGAAAGAGTAACGCAATACACCAGCATTATTGTGTCAATTTTAGACCATAAATATAGT
1 TCTTGCAAGAAAGAGTAACGCAATACACCACCATTA--CAGTCAATTTTAGACCATAAATATAGT
1316206 AT
64 AT
*
1316208 TCTTGCAAGAAAGAGTAACGCAATACACCACCATTACAGTCAATTTTAGCCCATAAATATAGTAT
1 TCTTGCAAGAAAGAGTAACGCAATACACCACCATTACAGTCAATTTTAGACCATAAATATAGTAT
1316273 T
1 T
1316274 TCTATTTATG
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
65 27 0.44
67 35 0.56
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.29
Consensus pattern (65 bp):
TCTTGCAAGAAAGAGTAACGCAATACACCACCATTACAGTCAATTTTAGACCATAAATATAGTAT
Found at i:1319734 original size:61 final size:60
Alignment explanation
Indices: 1319640--1319755 Score: 160
Period size: 61 Copynumber: 1.9 Consensus size: 60
1319630 TACAGATGTT
* * *
1319640 TTTAAATTTTTTTATATATATGTATAATTTAATTTTTAGTTTGTTGATAAATTATATACA
1 TTTAAATTTTTTTACATAAATGTATAATCTAATTTTTAGTTTGTTGATAAATTATATACA
* * * *
1319700 TTTAAATATTTTTTACATAAATTTATAGTCTAATTTTTATTTTGTTTATAAATTAT
1 TTTAAAT-TTTTTTACATAAATGTATAATCTAATTTTTAGTTTGTTGATAAATTAT
1319756 TTGTTATTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
60 7 0.15
61 41 0.85
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (60 bp):
TTTAAATTTTTTTACATAAATGTATAATCTAATTTTTAGTTTGTTGATAAATTATATACA
Found at i:1319775 original size:23 final size:22
Alignment explanation
Indices: 1319732--1319775 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
1319722 TTATAGTCTA
*
1319732 ATTTTTATTTTGTTTATAAATT
1 ATTTTTATTTTGTTTAAAAATT
1319754 ATTTGTTATTTTAG-TTAAAAAT
1 ATTT-TTATTTT-GTTTAAAAAT
1319776 AAATTATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 14 0.74
24 1 0.05
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
ATTTTTATTTTGTTTAAAAATT
Found at i:1321904 original size:28 final size:28
Alignment explanation
Indices: 1321872--1321928 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
1321862 TATGTTAGGA
1321872 ATTCTACTTTACCTACGAAAAGTAAGAT
1 ATTCTACTTTACCTACGAAAAGTAAGAT
1321900 ATTCTACTTTACCTACGAAAAGTAAGAT
1 ATTCTACTTTACCTACGAAAAGTAAGAT
1321928 A
1 A
1321929 CTTTGCATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.32
Consensus pattern (28 bp):
ATTCTACTTTACCTACGAAAAGTAAGAT
Found at i:1324366 original size:16 final size:16
Alignment explanation
Indices: 1324341--1324375 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1324331 AGTAAAACTG
1324341 GAAAACTTGTTATCTC
1 GAAAACTTGTTATCTC
*
1324357 GAAAATTTGTTATCTC
1 GAAAACTTGTTATCTC
1324373 GAA
1 GAA
1324376 GGTTGGGTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37
Consensus pattern (16 bp):
GAAAACTTGTTATCTC
Found at i:1343123 original size:23 final size:22
Alignment explanation
Indices: 1343080--1343123 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
1343070 TTATTGTCTA
*
1343080 ATTTTTATTTTGTTTATAAATT
1 ATTTTTATTTTGTTTAAAAATT
1343102 ATTTGTTATTTTAG-TTAAAAAT
1 ATTT-TTATTTT-GTTTAAAAAT
1343124 AAATTATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 14 0.74
24 1 0.05
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
ATTTTTATTTTGTTTAAAAATT
Found at i:1351604 original size:32 final size:32
Alignment explanation
Indices: 1351568--1351657 Score: 144
Period size: 32 Copynumber: 2.8 Consensus size: 32
1351558 ATCAGTAACT
**
1351568 GTAATATGATCGACACAAAGCCATCGGTAATG
1 GTAATATGATCGACACAAAGCCATCAATAATG
1351600 GTAATATGATCGACACAAAGCCATCAATAATG
1 GTAATATGATCGACACAAAGCCATCAATAATG
* *
1351632 GTAATATGATTGGCACAAAGCCATCA
1 GTAATATGATCGACACAAAGCCATCA
1351658 GTAGTATCAC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 54 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (32 bp):
GTAATATGATCGACACAAAGCCATCAATAATG
Found at i:1351707 original size:27 final size:25
Alignment explanation
Indices: 1351672--1351742 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 25
1351662 TATCACAGTA
*
1351672 AAGCTACCAGTAATAGTATATGTGGCC
1 AAGCCACCAGTAATAGTAT-TGTGG-C
1351699 AAGCCACCAGTAATAGTGATTGTGGC
1 AAGCCACCAGTAATAGT-ATTGTGGC
*
1351725 AGAGCCACCAAT-ATAGTA
1 A-AGCCACCAGTAATAGTA
1351743 CTTCCTCCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
25 1 0.03
26 7 0.17
27 30 0.75
28 2 0.05
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.23
Consensus pattern (25 bp):
AAGCCACCAGTAATAGTATTGTGGC
Found at i:1351877 original size:24 final size:24
Alignment explanation
Indices: 1351822--1351888 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
1351812 TCATACCAAA
*
1351822 CACAGACAAAGCAATCATTTACAT
1 CACAGACAAATCAATCATTTACAT
*
1351846 CA-AGGACAAATCAATCATTTATAT
1 CACA-GACAAATCAATCATTTACAT
* *
1351870 CACAGACAATTCAAACATT
1 CACAGACAAATCAATCATT
1351889 AACCTCGAGG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
23 1 0.03
24 35 0.95
25 1 0.03
ACGTcount: A:0.46, C:0.22, G:0.07, T:0.24
Consensus pattern (24 bp):
CACAGACAAATCAATCATTTACAT
Found at i:1352100 original size:27 final size:27
Alignment explanation
Indices: 1352034--1352152 Score: 109
Period size: 27 Copynumber: 4.4 Consensus size: 27
1352024 CCTAACAGAA
*
1352034 GTATTAC-AGTCATTTTACCCTATA-GA
1 GTATTACGA-TCATTTTACCCTATAGGG
* * * * *
1352060 GCATTATGGTCATTTTATCCTACAGGG
1 GTATTACGATCATTTTACCCTATAGGG
*
1352087 GTATTACGATCATTTTACCCTATAAGG
1 GTATTACGATCATTTTACCCTATAGGG
* * *
1352114 GTATTATGGTCATTTTACCCTATGGGG
1 GTATTACGATCATTTTACCCTATAGGG
1352141 GTA-TATCGATCA
1 GTATTA-CGATCA
1352153 ATTCACCTAA
Statistics
Matches: 72, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
26 20 0.28
27 52 0.72
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (27 bp):
GTATTACGATCATTTTACCCTATAGGG
Found at i:1352144 original size:54 final size:54
Alignment explanation
Indices: 1352034--1352239 Score: 172
Period size: 54 Copynumber: 3.8 Consensus size: 54
1352024 CCTAACAGAA
* *
1352034 GTATTAC-AGTCATTTTACCCTAT-AGAGCATTATGGTCATTTTATCCTACAGGG
1 GTATTACGA-TCATTTTACCCTATAAGAGCATTATGGTCATTTTACCCTATAGGG
* * *
1352087 GTATTACGATCATTTTACCCTATAAGGGTATTATGGTCATTTTACCCTATGGGG
1 GTATTACGATCATTTTACCCTATAAGAGCATTATGGTCATTTTACCCTATAGGG
* * * * * **
1352141 GTA-TATCGATCAATTCA-CCTAACTAA-AGTATTATGGTCATTTCACTCTATAAAG
1 GTATTA-CGATCATTTTACCCT-A-TAAGAGCATTATGGTCATTTTACCCTATAGGG
* * * * *
1352195 GCATTACGGTCATTTTACCCTA-CAGGGACATTACGGTCATTTTAC
1 GTATTACGATCATTTTACCCTATAAGAG-CATTATGGTCATTTTAC
1352240 AAACATTAGG
Statistics
Matches: 122, Mismatches: 22, Indels: 17
0.76 0.14 0.11
Matches are distributed among these distances:
52 1 0.01
53 27 0.22
54 86 0.70
55 8 0.07
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (54 bp):
GTATTACGATCATTTTACCCTATAAGAGCATTATGGTCATTTTACCCTATAGGG
Found at i:1352147 original size:134 final size:135
Alignment explanation
Indices: 1351993--1352239 Score: 372
Period size: 134 Copynumber: 1.8 Consensus size: 135
1351983 ATTACAATTA
* *
1351993 TTTACCGTATGGGGGTATATCGATCAATTCACCTAAC-AGAAGTATTACAGTCATTTTACCCTAT
1 TTTACCCTATGGGGGTATATCGATCAATTCACCTAACTA-AAGTATTACAGTCATTTCACCCTAT
* * * **
1352057 AGA-GCATTATGGTCATTTTATCCTACAGGGGTATTACGATCATTTTACCCTATAAGGGTATTAT
65 AAAGGCATTACGGTCATTTTACCCTACAGGGACATTACGATCATTTTACCCTATAAGGGTATTAT
1352121 GGTCAT
130 GGTCAT
** *
1352127 TTTACCCTATGGGGGTATATCGATCAATTCACCTAACTAAAGTATTATGGTCATTTCACTCTATA
1 TTTACCCTATGGGGGTATATCGATCAATTCACCTAACTAAAGTATTACAGTCATTTCACCCTATA
*
1352192 AAGGCATTACGGTCATTTTACCCTACAGGGACATTACGGTCATTTTAC
66 AAGGCATTACGGTCATTTTACCCTACAGGGACATTACGATCATTTTAC
1352240 AAACATTAGG
Statistics
Matches: 100, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
134 59 0.59
135 41 0.41
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.35
Consensus pattern (135 bp):
TTTACCCTATGGGGGTATATCGATCAATTCACCTAACTAAAGTATTACAGTCATTTCACCCTATA
AAGGCATTACGGTCATTTTACCCTACAGGGACATTACGATCATTTTACCCTATAAGGGTATTATG
GTCAT
Found at i:1375901 original size:10 final size:10
Alignment explanation
Indices: 1375887--1375925 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
1375877 TTGGAAAATA
1375887 AATATGATAT
1 AATATGATAT
*
1375897 GATATGATAT
1 AATATGATAT
*
1375907 AATATAATAT
1 AATATGATAT
1375917 AATAT-ATAT
1 AATATGATAT
1375926 TCATTTAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
9 4 0.15
10 22 0.85
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (10 bp):
AATATGATAT
Found at i:1378035 original size:42 final size:44
Alignment explanation
Indices: 1377988--1378086 Score: 123
Period size: 44 Copynumber: 2.3 Consensus size: 44
1377978 AATGTTGAAG
* *
1377988 TAAAATTAAAAAA-TAGTTACGTG-TT-TTTTATAAGTAACTATA
1 TAAAATTAAAAAATTA-TGACGTGTTTCTTTTATAAATAACTATA
* *
1378030 TAAAATTAAAAAATTATGATGTGTTTCTTTTATAAATAATTATA
1 TAAAATTAAAAAATTATGACGTGTTTCTTTTATAAATAACTATA
*
1378074 TGAAATTAAAAAA
1 TAAAATTAAAAAA
1378087 AATCCACAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
42 18 0.37
43 4 0.08
44 27 0.55
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.40
Consensus pattern (44 bp):
TAAAATTAAAAAATTATGACGTGTTTCTTTTATAAATAACTATA
Found at i:1380131 original size:61 final size:61
Alignment explanation
Indices: 1380063--1380179 Score: 189
Period size: 61 Copynumber: 1.9 Consensus size: 61
1380053 TACCGATGTT
* * *
1380063 TTTAAATATTTTTTATATATATTTTTAGTTTAATTTTTAGTTTGTTGATAAATTATATACA
1 TTTAAATATTTTTTACATATATCTATAGTTTAATTTTTAGTTTGTTGATAAATTATATACA
* *
1380124 TTTAAATATTTTTTACATATATCTATAGTTTAATTTTTATTTTGTTTATAAATTAT
1 TTTAAATATTTTTTACATATATCTATAGTTTAATTTTTAGTTTGTTGATAAATTAT
1380180 TTGTTATTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.60
Consensus pattern (61 bp):
TTTAAATATTTTTTACATATATCTATAGTTTAATTTTTAGTTTGTTGATAAATTATATACA
Found at i:1380199 original size:23 final size:22
Alignment explanation
Indices: 1380156--1380199 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
1380146 CTATAGTTTA
*
1380156 ATTTTTATTTTGTTTATAAATT
1 ATTTTTATTTTGTTTAAAAATT
1380178 ATTTGTTATTTTAG-TTAAAAAT
1 ATTT-TTATTTT-GTTTAAAAAT
1380200 AAATTATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 14 0.74
24 1 0.05
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
ATTTTTATTTTGTTTAAAAATT
Found at i:1387060 original size:26 final size:26
Alignment explanation
Indices: 1387031--1387082 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
1387021 CCCTTACACC
* *
1387031 AATATCGCAGCATAGCTGCCAGTAGT
1 AATAACGCAGCAGAGCTGCCAGTAGT
*
1387057 AATAACGCAGTAGAGCTGCCAGTAGT
1 AATAACGCAGCAGAGCTGCCAGTAGT
1387083 CAGAATGGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (26 bp):
AATAACGCAGCAGAGCTGCCAGTAGT
Found at i:1387137 original size:22 final size:22
Alignment explanation
Indices: 1387083--1387147 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 22
1387073 TGCCAGTAGT
*
1387083 CAGAATGGCTAAAAGCCGTAAA
1 CAGAATGGCTAAAAGCCATAAA
* * * * *
1387105 TAGGATAGCTATAAGCTATAAA
1 CAGAATGGCTAAAAGCCATAAA
*
1387127 CAGAATGGCTACAAGCCATAA
1 CAGAATGGCTAAAAGCCATAA
1387148 GTACAGTAAT
Statistics
Matches: 32, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.45, C:0.17, G:0.20, T:0.18
Consensus pattern (22 bp):
CAGAATGGCTAAAAGCCATAAA
Found at i:1387267 original size:32 final size:32
Alignment explanation
Indices: 1387139--1387277 Score: 145
Period size: 32 Copynumber: 4.4 Consensus size: 32
1387129 GAATGGCTAC
* *
1387139 AAGCCATAAGT-ACAGTAATATGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATTGACACA
* ** * *
1387170 AAACCATCAGTAGTAGTGATATGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATTGACACA
* * * * *
1387202 CAGACATCAATAACGGTAATATGATCGACACA
1 AAGCCATCAGTAACAGTAATATGATTGACACA
*
1387234 AAGCCATCAGTAACAATAATATGATTGACACA
1 AAGCCATCAGTAACAGTAATATGATTGACACA
*
1387266 AAGCCATTAGTA
1 AAGCCATCAGTA
1387278 GCATTGCAGC
Statistics
Matches: 85, Mismatches: 22, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
31 9 0.11
32 76 0.89
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.22
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATTGACACA
Found at i:1387629 original size:27 final size:27
Alignment explanation
Indices: 1387599--1387884 Score: 184
Period size: 27 Copynumber: 10.6 Consensus size: 27
1387589 TAGGAGAGGC
* *
1387599 ATTACGGTCACTTTACGCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * *
1387626 ATTACGATTATTTTACCCTAAAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * * * * **
1387653 A-TATTGATCAATTCA-TCTAACAGAAGT
1 ATTA-CGGTCATTTTACCCT-ACAGGGGT
* *
1387680 ATTACGGTCATTTTACCCTATAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
* * *
1387707 ATTATGGTTATTTTACCCTACAAGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * * **
1387734 ATTATGGTCGTTTTATCCTATGGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * * * **
1387761 A-TATCGATCAATTCA-CCTAACCGAAGT
1 ATTA-CGGTCATTTTACCCT-ACAGGGGT
* * *
1387788 ATTACGGTCATTTTACCCTATAGGTGC
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
1387815 ATTACGGTCATTTCACCCTACAAGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
** *
1387842 ATTACATTCATTTTACCCTACAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
1387869 ATTACGGTCATTTTAC
1 ATTACGGTCATTTTAC
1387885 AAATATTGGG
Statistics
Matches: 189, Mismatches: 62, Indels: 16
0.71 0.23 0.06
Matches are distributed among these distances:
26 9 0.05
27 171 0.90
28 9 0.05
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.35
Consensus pattern (27 bp):
ATTACGGTCATTTTACCCTACAGGGGT
Found at i:1387734 original size:81 final size:80
Alignment explanation
Indices: 1387567--1387735 Score: 203
Period size: 81 Copynumber: 2.1 Consensus size: 80
1387557 TTACCTTTTG
* ** * * *
1387567 AGGGTATATCGGTCAATTCACCTAGGAGAGGCATTACGGTCACTTTACGCTACAGGGGTATTACG
1 AGGGTATATCGATCAATTCACCTAACAGAAGCATTACGGTCACTTTACCCTACAGGGGCATTACG
1387632 ATTATTTTACCCTAA
66 ATTATTTTACCCTAA
* * * * * *
1387647 AGGGGTATATTGATCAATTCATCTAACAGAAGTATTACGGTCATTTTACCCTATAGGGGCATTAT
1 A-GGGTATATCGATCAATTCACCTAACAGAAGCATTACGGTCACTTTACCCTACAGGGGCATTAC
*
1387712 GGTTATTTTACCCTACA
65 GATTATTTTACCCTA-A
1387729 AGGGTAT
1 AGGGTAT
1387736 TATGGTCGTT
Statistics
Matches: 74, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
80 1 0.01
81 71 0.96
82 2 0.03
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (80 bp):
AGGGTATATCGATCAATTCACCTAACAGAAGCATTACGGTCACTTTACCCTACAGGGGCATTACG
ATTATTTTACCCTAA
Found at i:1387736 original size:54 final size:54
Alignment explanation
Indices: 1387596--1387881 Score: 219
Period size: 54 Copynumber: 5.3 Consensus size: 54
1387586 ACCTAGGAGA
* * * * *
1387596 GGCATTACGGTCACTTT-ACGCTACAGGGGTATTACGATTATTTTACCCTAAAGG
1 GGCATTACGGTCA-TTTCACCCTACAAGGGTATTACGGTCATTTTACCCTATAGG
* * * * * *
1387650 GGTA-TATTGATCAATTCA-TCTA-ACAGAAGTATTACGGTCATTTTACCCTATAGG
1 GGCATTA-CGGTCATTTCACCCTACA-AG-GGTATTACGGTCATTTTACCCTATAGG
* * * * * * *
1387704 GGCATTATGGTTATTTTACCCTACAAGGGTATTATGGTCGTTTTATCCTATGGG
1 GGCATTACGGTCATTTCACCCTACAAGGGTATTACGGTCATTTTACCCTATAGG
* * *
1387758 GGTA-TATCGATCAATTCA-CCTAACCGAA--GTATTACGGTCATTTTACCCTATAGG
1 GGCATTA-CGGTCATTTCACCCT-A-C-AAGGGTATTACGGTCATTTTACCCTATAGG
* ** *
1387812 TGCATTACGGTCATTTCACCCTACAAGGGTATTACATTCATTTTACCCTACAGG
1 GGCATTACGGTCATTTCACCCTACAAGGGTATTACGGTCATTTTACCCTATAGG
1387866 GGCATTACGGTCATTT
1 GGCATTACGGTCATTT
1387882 TACAAATATT
Statistics
Matches: 178, Mismatches: 39, Indels: 30
0.72 0.16 0.12
Matches are distributed among these distances:
52 3 0.02
53 14 0.08
54 145 0.81
55 13 0.07
56 3 0.02
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (54 bp):
GGCATTACGGTCATTTCACCCTACAAGGGTATTACGGTCATTTTACCCTATAGG
Found at i:1387856 original size:108 final size:107
Alignment explanation
Indices: 1387596--1387867 Score: 357
Period size: 108 Copynumber: 2.5 Consensus size: 107
1387586 ACCTAGGAGA
* * *
1387596 GGCATTACGGTCACTTTACGCTACAGGGGTATTACGATT-ATTTTACCCTAAAGGGGTATATTGA
1 GGCATTACGGTCA-TTTACCCTACAAGGGTATTAC-ATTCATTTTACCCTAAAGGGGTATATCGA
*
1387660 TCAATTCATCTAACAGAAGTATTACGGTCATTTTACCCTATAGG
64 TCAATTCACCTAACAGAAGTATTACGGTCATTTTACCCTATAGG
* * *** * * **
1387704 GGCATTATGGTTATTTTACCCTACAAGGGTATTATGGTCGTTTTATCCTATGGGGGTATATCGAT
1 GGCATTACGGTCA-TTTACCCTACAAGGGTATTACATTCATTTTACCCTAAAGGGGTATATCGAT
*
1387769 CAATTCACCTAACCGAAGTATTACGGTCATTTTACCCTATAGG
65 CAATTCACCTAACAGAAGTATTACGGTCATTTTACCCTATAGG
* *
1387812 TGCATTACGGTCATTTCACCCTACAAGGGTATTACATTCATTTTACCCTACAGGGG
1 GGCATTACGGTCATTT-ACCCTACAAGGGTATTACATTCATTTTACCCTAAAGGGG
1387868 CATTACGGTC
Statistics
Matches: 137, Mismatches: 25, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
107 4 0.03
108 133 0.97
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.34
Consensus pattern (107 bp):
GGCATTACGGTCATTTACCCTACAAGGGTATTACATTCATTTTACCCTAAAGGGGTATATCGATC
AATTCACCTAACAGAAGTATTACGGTCATTTTACCCTATAGG
Found at i:1389110 original size:18 final size:18
Alignment explanation
Indices: 1389055--1389125 Score: 90
Period size: 18 Copynumber: 3.8 Consensus size: 18
1389045 TAGTCACTGG
1389055 GCTATAAAATACTTTATA
1 GCTATAAAATACTTTATA
* *
1389073 GCCTA-AAACCAAAATTTATA
1 G-CTATAAA--ATACTTTATA
1389093 GCTATAAAATACTTTATA
1 GCTATAAAATACTTTATA
1389111 GCTATAAAATACTTT
1 GCTATAAAATACTTT
1389126 GGTCAGACCT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
18 27 0.60
19 6 0.13
20 12 0.27
ACGTcount: A:0.45, C:0.14, G:0.06, T:0.35
Consensus pattern (18 bp):
GCTATAAAATACTTTATA
Found at i:1393059 original size:123 final size:123
Alignment explanation
Indices: 1392840--1393084 Score: 481
Period size: 123 Copynumber: 2.0 Consensus size: 123
1392830 GTGGAAAATC
1392840 CAAATTAAATTTTAGATTTTAGGCCAATTTGTTTGGTGAGTTCTTTGTACAAGATTGTAGCAAAG
1 CAAATTAAATTTTAGATTTTAGGCCAATTTGTTTGGTGAGTTCTTTGTACAAGATTGTAGCAAAG
1392905 GTATTGTCTCGAAGGTTAAGGGAGATAGTCACAATGGTGATGAGTGACACACAATGTA
66 GTATTGTCTCGAAGGTTAAGGGAGATAGTCACAATGGTGATGAGTGACACACAATGTA
1392963 CAAATTAAATTTTAGATTTTAGGCCAATTTGTTTGGTGAGTTCTTTGTACAAGATTGTAGCAAAG
1 CAAATTAAATTTTAGATTTTAGGCCAATTTGTTTGGTGAGTTCTTTGTACAAGATTGTAGCAAAG
*
1393028 GTATTGTCTCGAAGGTTAAGGGAGATAGTCACAATGGTGGTGAGTGACACACAATGT
66 GTATTGTCTCGAAGGTTAAGGGAGATAGTCACAATGGTGATGAGTGACACACAATGT
1393085 GCTTTTATCG
Statistics
Matches: 121, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
123 121 1.00
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (123 bp):
CAAATTAAATTTTAGATTTTAGGCCAATTTGTTTGGTGAGTTCTTTGTACAAGATTGTAGCAAAG
GTATTGTCTCGAAGGTTAAGGGAGATAGTCACAATGGTGATGAGTGACACACAATGTA
Found at i:1399672 original size:66 final size:66
Alignment explanation
Indices: 1399590--1399722 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
1399580 CTTTTATGGA
1399590 TCTTGCAAGAAAGAGTAACGCAATACACCACCATTACAGTCAATTTTAGACCATTAAATATAGTA
1 TCTTGCAAGAAAGAGTAACGCAATACACCACCATTACAGTCAATTTTAGACCATTAAATATAGTA
1399655 T
66 T
1399656 TCTTGCAAGAAAGAGTAACGCAATACACCACCATTACAGTCAATTTTAGACCATTAAATATAGTA
1 TCTTGCAAGAAAGAGTAACGCAATACACCACCATTACAGTCAATTTTAGACCATTAAATATAGTA
1399721 T
66 T
1399722 T
1 T
1399723 TCTATTTATG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.28
Consensus pattern (66 bp):
TCTTGCAAGAAAGAGTAACGCAATACACCACCATTACAGTCAATTTTAGACCATTAAATATAGTA
T
Found at i:1400291 original size:26 final size:25
Alignment explanation
Indices: 1400244--1400293 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1400234 AAATTTTAAA
*
1400244 ATATTTATAAAAAATTTCAAAATTT
1 ATATTTATAAAAAATTTAAAAATTT
1400269 ATATTT-TAAAAAAGTTATAAAAATT
1 ATATTTATAAAAAA-TT-TAAAAATT
1400294 AAGAATTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 7 0.32
25 8 0.36
26 7 0.32
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (25 bp):
ATATTTATAAAAAATTTAAAAATTT
Found at i:1400844 original size:61 final size:61
Alignment explanation
Indices: 1400770--1400886 Score: 173
Period size: 61 Copynumber: 1.9 Consensus size: 61
1400760 TTATCGATGT
** *
1400770 TTTTAAATATTTTTTTATATATTTTTAGTTTAATTTTTAGTTTGTTGATAAATTATATACA
1 TTTTAAATATTTTTACATATATTTATAGTTTAATTTTTAGTTTGTTGATAAATTATATACA
* *
1400831 TTTT-AATATTTTTTACATATATTTATAGTTTAATTTTTATTTTGTTTATAAATTAT
1 TTTTAAATA-TTTTTACATATATTTATAGTTTAATTTTTAGTTTGTTGATAAATTAT
1400887 TTGTTATTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
60 4 0.08
61 46 0.92
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (61 bp):
TTTTAAATATTTTTACATATATTTATAGTTTAATTTTTAGTTTGTTGATAAATTATATACA
Found at i:1400906 original size:23 final size:22
Alignment explanation
Indices: 1400863--1400906 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
1400853 TTATAGTTTA
*
1400863 ATTTTTATTTTGTTTATAAATT
1 ATTTTTATTTTGTTTAAAAATT
1400885 ATTTGTTATTTTAG-TTAAAAAT
1 ATTT-TTATTTT-GTTTAAAAAT
1400907 AAATTATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 14 0.74
24 1 0.05
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
ATTTTTATTTTGTTTAAAAATT
Found at i:1401465 original size:296 final size:296
Alignment explanation
Indices: 1400930--1401513 Score: 1060
Period size: 296 Copynumber: 2.0 Consensus size: 296
1400920 TATTAACTTA
1400930 CAAATATATCTCAATTATATTCATATAAATATATTTATATTTAAATATAAGTTTTAAAATTATTA
1 CAAATATATCTCAATTATATTCATATAAATATATTTATATTTAAATATAAGTTTTAAAATTATTA
1400995 ATTAGGTTGAATAATTCAATTTAACTTTTCATTTTAAATATAATTTTGAAAAATTAAAATGGTTA
66 ATTAGGTTGAATAATTCAATTTAACTTTTCATTTTAAATATAATTTTGAAAAATTAAAATGGTTA
* * *
1401060 ATAAAAAATTTTAAAATTTGGTTTAAAATGCCAATATTTTGTATCAACTGATTTGGGCCAATACA
131 AGAAAAAATTTTAAAATTTAGTTTAAAATGCCAATATTTTGTATCAACCGATTTGGGCCAATACA
*
1401125 TACTGATTACAAACCGAAACAGATTGAAATACACTGAAATAGCCGAAGCACACCAAAATTTTAAC
196 TACTGATTACAAACCAAAACAGATTGAAATACACTGAAATAGCCGAAGCACACCAAAATTTTAAC
* *
1401190 AAGAACGAAACATAACCTAATTAATACTTTAACATG
261 AAGAACAAAACATAAACTAATTAATACTTTAACATG
1401226 CAAATATATCTCAATTATATTCATATAAATATATTTATATTTAAATATAAGTTTTAAAATTATTA
1 CAAATATATCTCAATTATATTCATATAAATATATTTATATTTAAATATAAGTTTTAAAATTATTA
1401291 ATTAGGTTGAATAATTCAATTTAACTTTTCATTTTAAATATAATTTTGAAAAATTAAAATGGTTA
66 ATTAGGTTGAATAATTCAATTTAACTTTTCATTTTAAATATAATTTTGAAAAATTAAAATGGTTA
* *
1401356 AGAAAAAATTTTAAAATTTAGTTTAAAATGTCAATATTTTGTATCAACCGATTTGGGCCGATACA
131 AGAAAAAATTTTAAAATTTAGTTTAAAATGCCAATATTTTGTATCAACCGATTTGGGCCAATACA
* * * *
1401421 TACTGATTACAGACCAAAACAGATTGACATACACTGATATAGCCGAAGCACACCGAAATTTTAAC
196 TACTGATTACAAACCAAAACAGATTGAAATACACTGAAATAGCCGAAGCACACCAAAATTTTAAC
1401486 AAGAACAAAACATAAACTAATTAATACT
261 AAGAACAAAACATAAACTAATTAATACT
1401514 GATTTAGGAC
Statistics
Matches: 276, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
296 276 1.00
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.35
Consensus pattern (296 bp):
CAAATATATCTCAATTATATTCATATAAATATATTTATATTTAAATATAAGTTTTAAAATTATTA
ATTAGGTTGAATAATTCAATTTAACTTTTCATTTTAAATATAATTTTGAAAAATTAAAATGGTTA
AGAAAAAATTTTAAAATTTAGTTTAAAATGCCAATATTTTGTATCAACCGATTTGGGCCAATACA
TACTGATTACAAACCAAAACAGATTGAAATACACTGAAATAGCCGAAGCACACCAAAATTTTAAC
AAGAACAAAACATAAACTAATTAATACTTTAACATG
Found at i:1402112 original size:61 final size:60
Alignment explanation
Indices: 1402032--1402147 Score: 169
Period size: 61 Copynumber: 1.9 Consensus size: 60
1402022 TACAGATGTT
* *
1402032 TTTAAATTTTTTTATATATATGTATAATTTAATTTTTAGTTTGTTGATAAATTATATACA
1 TTTAAATTTTTTTACATATATGTATAATCTAATTTTTAGTTTGTTGATAAATTATATACA
* * * *
1402092 TTTAAATATTTTTTACATATATTTATAGTCTAATTTTTATTTTGTTTATAAATTAT
1 TTTAAAT-TTTTTTACATATATGTATAATCTAATTTTTAGTTTGTTGATAAATTAT
1402148 TTGTTATTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
60 7 0.14
61 42 0.86
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.59
Consensus pattern (60 bp):
TTTAAATTTTTTTACATATATGTATAATCTAATTTTTAGTTTGTTGATAAATTATATACA
Found at i:1402167 original size:23 final size:22
Alignment explanation
Indices: 1402124--1402167 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
1402114 TTATAGTCTA
*
1402124 ATTTTTATTTTGTTTATAAATT
1 ATTTTTATTTTGTTTAAAAATT
1402146 ATTTGTTATTTTAG-TTAAAAAT
1 ATTT-TTATTTT-GTTTAAAAAT
1402168 AAATTATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 14 0.74
24 1 0.05
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
ATTTTTATTTTGTTTAAAAATT
Found at i:1402516 original size:4 final size:4
Alignment explanation
Indices: 1402507--1402790 Score: 568
Period size: 4 Copynumber: 71.0 Consensus size: 4
1402497 TATTAAATCA
1402507 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1402555 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1402603 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1402651 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1402699 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1402747 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1402791 ATCTATTGTA
Statistics
Matches: 280, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 280 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:1403792 original size:42 final size:42
Alignment explanation
Indices: 1403731--1403942 Score: 275
Period size: 42 Copynumber: 5.1 Consensus size: 42
1403721 TTTTGTGTAT
* * * * * * *
1403731 GTGAAATAATTTCAAACTTTACGTCTAGTAGGTTTATTGCTA
1 GTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCA
* *
1403773 GTGAAACAATATCAGACTTTACGTTTAGCAGGCTTAATGCCG
1 GTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCA
*
1403815 GTGAAACAATATTAGACTTTACGTCTAGCAGGCTTAATGCCA
1 GTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCA
*
1403857 GTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCG
1 GTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCA
* * *
1403899 GTGAAAC-ATTTCAGACTATATGTCTAGCAGGC-TAAGTGCCA
1 GTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAA-TGCCA
1403940 GTG
1 GTG
1403943 TACTGAATCA
Statistics
Matches: 151, Mismatches: 18, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
40 3 0.02
41 29 0.19
42 119 0.79
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (42 bp):
GTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCA
Found at i:1403984 original size:82 final size:84
Alignment explanation
Indices: 1403750--1403985 Score: 250
Period size: 84 Copynumber: 2.8 Consensus size: 84
1403740 TTTCAAACTT
* * * * * ** *
1403750 TACGTCTAGTAGGTTTATTGCTAGTGAAACAATATCAGACTTTACGTTTAGCAGGCTTAATGCCG
1 TACGTCTAGCAGGCTTAATGCCAGTGAAACAATATCAGACTTTAAGCCTAGCAAGCTTAATGCCG
*
1403815 GTGAAACAATATTAGACTT
66 GTGAAACAATATTAGACTA
* * *
1403834 TACGTCTAGCAGGCTTAATGCCAGTGAAACAATATCAGACTTTACGTCTAGCAGGCTTAATGCCG
1 TACGTCTAGCAGGCTTAATGCCAGTGAAACAATATCAGACTTTAAGCCTAGCAAGCTTAATGCCG
1403899 GTGAAAC-AT-TTCAGACTA
66 GTGAAACAATATT-AGACTA
* * * *
1403917 TATGTCTAGCAGGC-TAAGTGCCAGTG-TACTGA-ATCAGGCTTTAAGCCTAGCAAGC-TAAGTG
1 TACGTCTAGCAGGCTTAA-TGCCAGTGAAAC-AATATCAGACTTTAAGCCTAGCAAGCTTAA-TG
1403978 CCGGTGAA
63 CCGGTGAA
1403986 TCTGTTTAAA
Statistics
Matches: 135, Mismatches: 13, Indels: 10
0.85 0.08 0.06
Matches are distributed among these distances:
81 3 0.02
82 36 0.27
83 29 0.21
84 67 0.50
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28
Consensus pattern (84 bp):
TACGTCTAGCAGGCTTAATGCCAGTGAAACAATATCAGACTTTAAGCCTAGCAAGCTTAATGCCG
GTGAAACAATATTAGACTA
Found at i:1405284 original size:143 final size:143
Alignment explanation
Indices: 1405014--1405641 Score: 882
Period size: 143 Copynumber: 4.4 Consensus size: 143
1405004 AGTGTTACAT
* * *
1405014 TGGTTGCTTCAATCTACTCCACTGCAACTTCAGGAAGATAAGATCCGCCATAATTTGTAGCTTTA
1 TGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCTGCCATAATTTGTAGCTTTA
* *
1405079 ATCTGTTCCACTGCAACGCCAAGGAAATAAGATTTGTTGTCTTCAGTCTGCTCCGCTGCAACTTC
66 ATCTGTTCCACTGCAACGCCAAGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTC
1405144 AGGGAGATAAGGC
131 AGGGAGATAAGGC
1405157 TGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCTGCCATAATTTGTAGCTTTA
1 TGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCTGCCATAATTTGTAGCTTTA
* * * * * * *
1405222 ATATGTTCCACTGCAACGCCAAGGAAATAAGATTTGTTGTCTTCAGTTTGCTCCTCTACAACTTT
66 ATCTGTTCCACTGCAACGCCAAGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTC
*
1405287 AGAGAGATAAGGC
131 AGGGAGATAAGGC
* * *
1405300 TGGTGGCTTCAATCTGCTCCAATGCAACTTCAAGAAGATAAGATCCT-CCATAATTTGTAACTTT
1 TGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGAT-CTGCCATAATTTGTAGCTTT
* * * * * *
1405364 AATCTGTTCCACTACAACGTCAGGGAAATAAGATTCGCTGACTTCAATCTGTTCCGCTGCAACTT
65 AATCTGTTCCACTGCAACGCCAAGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTT
1405429 CAGGGAGATAAGGC
130 CAGGGAGATAAGGC
* * * * **
1405443 TAGTGGCTTCAATCTACTCCACTGGAACTTCA-GAAGGATAAGATCCGCCATAATCAGTAGCTTT
1 TGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAA-GATAAGATCTGCCATAATTTGTAGCTTT
* * * * ** *
1405507 AATCTGTTCTACTGCAATGCCAGGGAAATAAGATTCACTGTCTTCAGTCTGCAACACTGCAACTT
65 AATCTGTTCCACTGCAACGCCAAGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTT
*
1405572 CATGGAGATAAGGC
130 CAGGGAGATAAGGC
* *
1405586 TGGTGGCTTCAATCTGCTCTACTGCAACTTCAGAAAGATAAGATCTGCCATAATTT
1 TGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCTGCCATAATTT
1405642 CTTCAATCAA
Statistics
Matches: 427, Mismatches: 54, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
142 4 0.01
143 419 0.98
144 4 0.01
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (143 bp):
TGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATCTGCCATAATTTGTAGCTTTA
ATCTGTTCCACTGCAACGCCAAGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTC
AGGGAGATAAGGC
Found at i:1406491 original size:17 final size:17
Alignment explanation
Indices: 1406469--1406533 Score: 67
Period size: 17 Copynumber: 3.7 Consensus size: 17
1406459 TGGCCTCTCC
*
1406469 TTTTTCTTTTTCTTTCA
1 TTTTTCTTTTTTTTTCA
*
1406486 TTTTTCTCCTTTTTTTTCT
1 TTTTTCT--TTTTTTTTCA
* **
1406505 TTTTTGTTTTTTTTTTG
1 TTTTTCTTTTTTTTTCA
1406522 TTTTTCTTTTTT
1 TTTTTCTTTTTT
1406534 ATTTTTTTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
17 26 0.65
19 14 0.35
ACGTcount: A:0.02, C:0.12, G:0.03, T:0.83
Consensus pattern (17 bp):
TTTTTCTTTTTTTTTCA
Found at i:1406515 original size:26 final size:26
Alignment explanation
Indices: 1406464--1406540 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 26
1406454 CACCTTGGCC
*
1406464 TCTCCTTTTTCTTT-TTCTTTCA-TTTT
1 TCTCCTTTTT-TTTCTT-TTTTATTTTT
*
1406490 TCTCCTTTTTTTTCTTTTTTGTTTTT
1 TCTCCTTTTTTTTCTTTTTTATTTTT
1406516 T-T--TTTGTTTTTCTTTTTTATTTTT
1 TCTCCTTT-TTTTTCTTTTTTATTTTT
1406540 T
1 T
1406541 TAAAAGTGGA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
23 3 0.07
24 18 0.40
25 7 0.16
26 17 0.38
ACGTcount: A:0.03, C:0.14, G:0.03, T:0.81
Consensus pattern (26 bp):
TCTCCTTTTTTTTCTTTTTTATTTTT
Found at i:1406516 original size:18 final size:18
Alignment explanation
Indices: 1406475--1406539 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 18
1406465 CTCCTTTTTC
* *
1406475 TTTTTCTTTCATTTTTCTC
1 TTTTTTTTTC-TTTTTCTT
*
1406494 CTTTTTTTTCTTTTT-TGT
1 TTTTTTTTTCTTTTTCT-T
*
1406512 TTTTTTTTTGTTTTTCTT
1 TTTTTTTTTCTTTTTCTT
1406530 TTTTATTTTT
1 TTTT-TTTTT
1406540 TTAAAAGTGG
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
17 1 0.03
18 23 0.61
19 14 0.37
ACGTcount: A:0.03, C:0.11, G:0.03, T:0.83
Consensus pattern (18 bp):
TTTTTTTTTCTTTTTCTT
Found at i:1409251 original size:23 final size:22
Alignment explanation
Indices: 1409212--1409256 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
1409202 ATTTAGTGCA
1409212 TATGATGCAATGCAATGTTAATG
1 TATGATGCAATGCAATG-TAATG
1409235 TATGAATGCAATG-AATGTAATG
1 TATG-ATGCAATGCAATGTAATG
1409257 AATGCAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.24
23 8 0.38
24 8 0.38
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.33
Consensus pattern (22 bp):
TATGATGCAATGCAATGTAATG
Found at i:1409259 original size:18 final size:18
Alignment explanation
Indices: 1409220--1409263 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
1409210 CATATGATGC
1409220 AATGCAATGTTAATGTATG
1 AATGCAATG-TAATGTATG
1409239 AATGCAATG-AATGTAATG
1 AATGCAATGTAATGT-ATG
1409257 AATGCAA
1 AATGCAA
1409264 AAAAGAAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.21
18 10 0.42
19 9 0.38
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (18 bp):
AATGCAATGTAATGTATG
Found at i:1414244 original size:60 final size:61
Alignment explanation
Indices: 1414143--1414284 Score: 144
Period size: 60 Copynumber: 2.3 Consensus size: 61
1414133 CCTTTTCTTT
* * * * * ** *
1414143 TTGAAATTTTTAGAATTAGAGCTAAATTGTCATATTATGTAAATGTTGAGAGCTAAATTTA
1 TTGAATTTTTTAGAATTAGAACTAAAATGACAAATTATGTAAACATTAAGAGCTAAATTTA
* * * *
1414204 TTG-ATTTTTTAGAATTCA-AACTAAAATGACAAATTTTGTAAACATTAAGGGTTAAATTTG
1 TTGAATTTTTTAGAATT-AGAACTAAAATGACAAATTATGTAAACATTAAGAGCTAAATTTA
*
1414264 TTGAATTTTTTAGATTTAGAA
1 TTGAATTTTTTAGAATTAGAA
1414285 TCAAACCGAT
Statistics
Matches: 65, Mismatches: 13, Indels: 6
0.77 0.15 0.07
Matches are distributed among these distances:
60 47 0.72
61 18 0.28
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (61 bp):
TTGAATTTTTTAGAATTAGAACTAAAATGACAAATTATGTAAACATTAAGAGCTAAATTTA
Found at i:1415842 original size:509 final size:509
Alignment explanation
Indices: 1414885--1415902 Score: 2036
Period size: 509 Copynumber: 2.0 Consensus size: 509
1414875 CATGGCCTTG
1414885 AATTTAACATACCAAGTATCCAATTTGAACTACTAATAAAATTACTTGATATGATAATCTAATGC
1 AATTTAACATACCAAGTATCCAATTTGAACTACTAATAAAATTACTTGATATGATAATCTAATGC
1414950 ATTTATTGCAGATTTTAATGTATTTATTGTAACTTCTTTGTTTTTATTCTAATATAGCTTGGAAA
66 ATTTATTGCAGATTTTAATGTATTTATTGTAACTTCTTTGTTTTTATTCTAATATAGCTTGGAAA
1415015 GAGTATTTTTCAAGTATGGAAAGGTATTAATTTGTTTCTTGCTTTAGCAAAGTTCGAGAATCCTT
131 GAGTATTTTTCAAGTATGGAAAGGTATTAATTTGTTTCTTGCTTTAGCAAAGTTCGAGAATCCTT
1415080 TGACATCAAGCTTCTCTTTATATAAACTAACACAAACGGCAAATCATATAAGAAAAACCTAACTA
196 TGACATCAAGCTTCTCTTTATATAAACTAACACAAACGGCAAATCATATAAGAAAAACCTAACTA
1415145 AACCCCATACCAAATCTAGCTTATTTGAGTTCAATTTTGGGTCCTTTTTTGCTTTAGAAATCAAT
261 AACCCCATACCAAATCTAGCTTATTTGAGTTCAATTTTGGGTCCTTTTTTGCTTTAGAAATCAAT
1415210 GACCATGATTCAAGGTCTTGTTTTAAGTTTGATTAAAGACGAATTGGGTTTGTCGGCAGCAATAG
326 GACCATGATTCAAGGTCTTGTTTTAAGTTTGATTAAAGACGAATTGGGTTTGTCGGCAGCAATAG
1415275 AAGATCTCCTAGAAGAAAATAAACATCAGGTTAACAATCACAAGGGAAATCAAGTAGACCGTGGC
391 AAGATCTCCTAGAAGAAAATAAACATCAGGTTAACAATCACAAGGGAAATCAAGTAGACCGTGGC
1415340 GATGAAACCGATGAAGGTGTTGATTCAAGTAAGGTTGAAACGTTACAAATAAGT
456 GATGAAACCGATGAAGGTGTTGATTCAAGTAAGGTTGAAACGTTACAAATAAGT
1415394 AATTTAACATACCAAGTATCCAATTTGAACTACTAATAAAATTACTTGATATGATAATCTAATGC
1 AATTTAACATACCAAGTATCCAATTTGAACTACTAATAAAATTACTTGATATGATAATCTAATGC
1415459 ATTTATTGCAGATTTTAATGTATTTATTGTAACTTCTTTGTTTTTATTCTAATATAGCTTGGAAA
66 ATTTATTGCAGATTTTAATGTATTTATTGTAACTTCTTTGTTTTTATTCTAATATAGCTTGGAAA
1415524 GAGTATTTTTCAAGTATGGAAAGGTATTAATTTGTTTCTTGCTTTAGCAAAGTTCGAGAATCCTT
131 GAGTATTTTTCAAGTATGGAAAGGTATTAATTTGTTTCTTGCTTTAGCAAAGTTCGAGAATCCTT
1415589 TGACATCAAGCTTCTCTTTATATAAACTAACACAAACGGCAAATCATATAAGAAAAACCTAACTA
196 TGACATCAAGCTTCTCTTTATATAAACTAACACAAACGGCAAATCATATAAGAAAAACCTAACTA
1415654 AACCCCATACCAAATCTAGCTTATTTGAGTTCAATTTTGGGTCCTTTTTTGCTTTAGAAATCAAT
261 AACCCCATACCAAATCTAGCTTATTTGAGTTCAATTTTGGGTCCTTTTTTGCTTTAGAAATCAAT
1415719 GACCATGATTCAAGGTCTTGTTTTAAGTTTGATTAAAGACGAATTGGGTTTGTCGGCAGCAATAG
326 GACCATGATTCAAGGTCTTGTTTTAAGTTTGATTAAAGACGAATTGGGTTTGTCGGCAGCAATAG
1415784 AAGATCTCCTAGAAGAAAATAAACATCAGGTTAACAATCACAAGGGAAATCAAGTAGACCGTGGC
391 AAGATCTCCTAGAAGAAAATAAACATCAGGTTAACAATCACAAGGGAAATCAAGTAGACCGTGGC
1415849 GATGAAACCGATGAAGGTGTTGATTCAAGTAAGGTTGAAACGTTACAAATAAGT
456 GATGAAACCGATGAAGGTGTTGATTCAAGTAAGGTTGAAACGTTACAAATAAGT
1415903 CCGATATACT
Statistics
Matches: 509, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
509 509 1.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (509 bp):
AATTTAACATACCAAGTATCCAATTTGAACTACTAATAAAATTACTTGATATGATAATCTAATGC
ATTTATTGCAGATTTTAATGTATTTATTGTAACTTCTTTGTTTTTATTCTAATATAGCTTGGAAA
GAGTATTTTTCAAGTATGGAAAGGTATTAATTTGTTTCTTGCTTTAGCAAAGTTCGAGAATCCTT
TGACATCAAGCTTCTCTTTATATAAACTAACACAAACGGCAAATCATATAAGAAAAACCTAACTA
AACCCCATACCAAATCTAGCTTATTTGAGTTCAATTTTGGGTCCTTTTTTGCTTTAGAAATCAAT
GACCATGATTCAAGGTCTTGTTTTAAGTTTGATTAAAGACGAATTGGGTTTGTCGGCAGCAATAG
AAGATCTCCTAGAAGAAAATAAACATCAGGTTAACAATCACAAGGGAAATCAAGTAGACCGTGGC
GATGAAACCGATGAAGGTGTTGATTCAAGTAAGGTTGAAACGTTACAAATAAGT
Found at i:1425528 original size:60 final size:61
Alignment explanation
Indices: 1425443--1425584 Score: 146
Period size: 60 Copynumber: 2.3 Consensus size: 61
1425433 CCTTTCCTTT
* * * * **
1425443 TTGAAATTTTTAGAATTAGAGCTAAA-TTATCATATTATGTAAATGTTGAGAGCTAAATTTA
1 TTGAATTTTTTAGAATTAGAACTAAAGTGA-CAAATTATGTAAACATTGAGAGCTAAATTTA
* * * *
1425504 TTG-ATTTTTTAGAATTCA-AACTAAAGTGACAAATTTTGTAAACATTGAGGGTTAAATTTG
1 TTGAATTTTTTAGAATT-AGAACTAAAGTGACAAATTATGTAAACATTGAGAGCTAAATTTA
*
1425564 TTGAATTTTTTAGATTTAGAA
1 TTGAATTTTTTAGAATTAGAA
1425585 TCAAAACGAT
Statistics
Matches: 66, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
60 46 0.70
61 20 0.30
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.42
Consensus pattern (61 bp):
TTGAATTTTTTAGAATTAGAACTAAAGTGACAAATTATGTAAACATTGAGAGCTAAATTTA
Found at i:1428464 original size:6 final size:6
Alignment explanation
Indices: 1428453--1428482 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
1428443 AAGGTTGTCA
1428453 AATTTT AATTTT AATTTT AATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT
1428483 TTAAGAGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
AATTTT
Found at i:1433273 original size:23 final size:22
Alignment explanation
Indices: 1433223--1433274 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
1433213 TTTACCATGT
1433223 AATTTTTTAAGGGACTAAATAG
1 AATTTTTTAAGGGACTAAATAG
1433245 AATTTTTTAAGGGACTAAATAG
1 AATTTTTTAAGGGACTAAATAG
1433267 AATTTTTT
1 AATTTTTT
1433275 TCATTTTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.04, G:0.15, T:0.42
Consensus pattern (22 bp):
AATTTTTTAAGGGACTAAATAG
Found at i:1441195 original size:20 final size:20
Alignment explanation
Indices: 1441170--1441209 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1441160 GAATGAACTT
*
1441170 ATTATTTTGCTTTTTAACCA
1 ATTATTTTGCTTTTGAACCA
*
1441190 ATTATTTTGGTTTTGAACCA
1 ATTATTTTGCTTTTGAACCA
1441210 TCCCTATCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.25, C:0.12, G:0.10, T:0.53
Consensus pattern (20 bp):
ATTATTTTGCTTTTGAACCA
Done.