Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold400
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: 2847997
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 9 of 17
Found at i:1238762 original size:15 final size:15
Alignment explanation
Indices: 1238742--1238780 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1238732 ACCATCCAAG
* *
1238742 TTGGAAAGCTTTTTT
1 TTGGAAAACATTTTT
1238757 TTGGAAAAACATTTTT
1 TTGG-AAAACATTTTT
1238773 TTGGAAAA
1 TTGGAAAA
1238781 AGTTAAGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (15 bp):
TTGGAAAACATTTTT
Found at i:1241014 original size:21 final size:22
Alignment explanation
Indices: 1240974--1241015 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1240964 GATAAGTATA
1240974 AATGTTTTCAAGGCTTAAAATG
1 AATGTTTTCAAGGCTTAAAATG
1240996 AATGATTTTCAA-G-TTAAAAT
1 AATG-TTTTCAAGGCTTAAAAT
1241016 ATATCAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 5 0.26
23 7 0.37
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.38
Consensus pattern (22 bp):
AATGTTTTCAAGGCTTAAAATG
Found at i:1241153 original size:13 final size:13
Alignment explanation
Indices: 1241135--1241159 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1241125 ATAATGCACA
1241135 GTATCGATACATT
1 GTATCGATACATT
1241148 GTATCGATACAT
1 GTATCGATACAT
1241160 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1241172 original size:20 final size:21
Alignment explanation
Indices: 1241147--1241199 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
1241137 ATCGATACAT
*
1241147 TGTATCGATACATG-ACCA-AA
1 TGTATCGATACATGCA-AAGAA
*
1241167 TGTATCGATACTTGCAAAGAA
1 TGTATCGATACATGCAAAGAA
1241188 TGTATCGATACA
1 TGTATCGATACA
1241200 GGTGATTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGCAAAGAA
Found at i:1241277 original size:13 final size:13
Alignment explanation
Indices: 1241259--1241284 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1241249 TACACACAAG
1241259 ATGTATCGATACA
1 ATGTATCGATACA
1241272 ATGTATCGATACA
1 ATGTATCGATACA
1241285 TCCCAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1241301 original size:33 final size:32
Alignment explanation
Indices: 1241241--1241304 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
1241231 CTTAACTGTT
*
1241241 TGTATCGATACACACAAGATGTATCGATACAA
1 TGTATCGATACACACAAAATGTATCGATACAA
*
1241273 TGTATCGATACATCCCAAAATGTATCGATACA
1 TGTATCGATACA-CACAAAATGTATCGATACA
1241305 TTGGCTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAA
Found at i:1247421 original size:20 final size:21
Alignment explanation
Indices: 1247391--1247430 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1247381 CTAGAAAAAT
*
1247391 TTCAGAATGTATCGATACATG
1 TTCAGAATGTATCAATACATG
1247412 TTCA-AATGTATCAATACAT
1 TTCAGAATGTATCAATACAT
1247431 CTGGAAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (21 bp):
TTCAGAATGTATCAATACATG
Found at i:1247483 original size:13 final size:13
Alignment explanation
Indices: 1247465--1247502 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
1247455 AAGCATTCTC
1247465 TGTATCGATACAT
1 TGTATCGATACAT
* *
1247478 TGTATCAATATAT
1 TGTATCGATACAT
1247491 TGTATCGATACA
1 TGTATCGATACA
1247503 AAGGGTTTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1247673 original size:19 final size:21
Alignment explanation
Indices: 1247635--1247674 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1247625 AAATTTCTTG
*
1247635 TTTTTCACTCCAAATACATCA
1 TTTTTCACTCAAAATACATCA
1247656 TTTTTCA-TCAAAAT-CATCA
1 TTTTTCACTCAAAATACATCA
1247675 ACAAAAACAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 6 0.33
21 7 0.39
ACGTcount: A:0.35, C:0.25, G:0.00, T:0.40
Consensus pattern (21 bp):
TTTTTCACTCAAAATACATCA
Found at i:1249935 original size:20 final size:19
Alignment explanation
Indices: 1249906--1249944 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
1249896 AGGTCAAAAC
*
1249906 CCTTAAATGTATTGATACA
1 CCTTAAATGTATCGATACA
1249925 CCTTCAAATGTATCGATACA
1 CCTT-AAATGTATCGATACA
1249945 TAATGCACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (19 bp):
CCTTAAATGTATCGATACA
Found at i:1250069 original size:53 final size:53
Alignment explanation
Indices: 1250007--1250124 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
1249997 TTGCAAAGAA
1250007 TGTATCGATACAGGTGATTGGCAGTAGATTGGCAATAGCCACCCTTAACTGTT
1 TGTATCGATACAGGTGATTGGCAGTAGATTGGCAATAGCCACCCTTAACTGTT
* *
1250060 TGTATCGATACAGGTGATTGGCAGTAGCTTGGCAGTAGCCACCCTTAACTGTT
1 TGTATCGATACAGGTGATTGGCAGTAGATTGGCAATAGCCACCCTTAACTGTT
1250113 TGTATCGATACA
1 TGTATCGATACA
1250125 CACAAGATGT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
53 63 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (53 bp):
TGTATCGATACAGGTGATTGGCAGTAGATTGGCAATAGCCACCCTTAACTGTT
Found at i:1250176 original size:33 final size:32
Alignment explanation
Indices: 1250113--1250176 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
1250103 CTTAACTGTT
*
1250113 TGTATCGATACACACAAGATGTATCGATACAA
1 TGTATCGATACACACAAAATGTATCGATACAA
* * *
1250145 TGTATCGATATATCCCAAAATGTATCTATACA
1 TGTATCGATACA-CACAAAATGTATCGATACA
1250177 TTGGCTTGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.30
Consensus pattern (32 bp):
TGTATCGATACACACAAAATGTATCGATACAA
Found at i:1256169 original size:20 final size:21
Alignment explanation
Indices: 1256146--1256191 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
1256136 GCCTGTATTG
1256146 ATACATCT-ACTTA-TGTATCC
1 ATACAT-TAACTTATTGTATCC
*
1256166 ATACATTAACTTATTGTATCG
1 ATACATTAACTTATTGTATCC
1256187 ATACA
1 ATACA
1256192 AATTATAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 11 0.48
21 11 0.48
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.39
Consensus pattern (21 bp):
ATACATTAACTTATTGTATCC
Found at i:1264007 original size:20 final size:20
Alignment explanation
Indices: 1263965--1264015 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1263955 AGCTAATTGC
* **
1263965 CTTGGTTTTAACCTAAGTGA
1 CTTGGTTTTGACCTAAGCAA
1263985 CTTGGTTTTGACCTAAGCAA
1 CTTGGTTTTGACCTAAGCAA
*
1264005 CTTGATTTTGA
1 CTTGGTTTTGA
1264016 TTCTAAATGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.41
Consensus pattern (20 bp):
CTTGGTTTTGACCTAAGCAA
Found at i:1265194 original size:6 final size:6
Alignment explanation
Indices: 1265183--1265223 Score: 73
Period size: 6 Copynumber: 6.7 Consensus size: 6
1265173 GCTGCTGCCT
1265183 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA CTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA -TTTT
1265224 CACTTAACTT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 30 0.88
7 4 0.12
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTA
Found at i:1266487 original size:5 final size:5
Alignment explanation
Indices: 1266472--1266501 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
1266462 TTATTTATCT
1266472 TTTAA -TTAA TTTAA TTTAA TTTAA TTTAA T
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA T
1266502 ATAAAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTTAA
Found at i:1266885 original size:15 final size:15
Alignment explanation
Indices: 1266867--1266899 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1266857 ATGTATATTT
1266867 TTTAAAAATTTAATA
1 TTTAAAAATTTAATA
*
1266882 TTTAATAATTTAATA
1 TTTAAAAATTTAATA
1266897 TTT
1 TTT
1266900 TTATTAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTAAAAATTTAATA
Found at i:1267015 original size:53 final size:53
Alignment explanation
Indices: 1266936--1267047 Score: 127
Period size: 55 Copynumber: 2.1 Consensus size: 53
1266926 ATTTTTCTTA
* * * * *
1266936 ATATTTATATTATAATATTACATATAT-TTTTTTATAATAAAAATTATCTACT
1 ATATATATATTATAATATTACATATATAATTTATAAAATAAAAATTACCTACT
* * *
1266988 ATATATATATTTTAATGTTTACATATATAAATTTATAAAATAAAAATTGCCTACT
1 ATATATATATTATAAT-ATTACATATAT-AATTTATAAAATAAAAATTACCTACT
1267043 ATATA
1 ATATA
1267048 AAAATATAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
52 14 0.29
53 10 0.20
55 25 0.51
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (53 bp):
ATATATATATTATAATATTACATATATAATTTATAAAATAAAAATTACCTACT
Found at i:1267731 original size:2 final size:2
Alignment explanation
Indices: 1267724--1267760 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1267714 TGAAAACAGA
1267724 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1267761 AAGAGTTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1269019 original size:7 final size:7
Alignment explanation
Indices: 1269009--1269043 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
1268999 AAAGAAACAC
*
1269009 AAATGTT
1 AAATTTT
1269016 AAATTTT
1 AAATTTT
1269023 AAAATTTT
1 -AAATTTT
1269031 AAATTTT
1 AAATTTT
1269038 AAATTT
1 AAATTT
1269044 ATCAATTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
7 19 0.73
8 7 0.27
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (7 bp):
AAATTTT
Found at i:1269050 original size:15 final size:15
Alignment explanation
Indices: 1269009--1269040 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1268999 AAAGAAACAC
*
1269009 AAATGTTAAATTTTA
1 AAATTTTAAATTTTA
1269024 AAATTTTAAATTTTA
1 AAATTTTAAATTTTA
1269039 AA
1 AA
1269041 TTTATCAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
AAATTTTAAATTTTA
Found at i:1271124 original size:3 final size:3
Alignment explanation
Indices: 1271103--1271151 Score: 73
Period size: 3 Copynumber: 16.7 Consensus size: 3
1271093 GCCAAGTGAA
* *
1271103 AAG AAA AAG AA- AGG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1271150 AA
1 AA
1271152 TGAACTGATA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 1 0.02
3 40 0.98
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1272723 original size:28 final size:28
Alignment explanation
Indices: 1272692--1272745 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
1272682 ATTATTTTTA
**
1272692 AAAAATAAATTATTATCTTTAAAAGTTT
1 AAAAATAAAAAATTATCTTTAAAAGTTT
*
1272720 AAAATTAAAAAATTATCTTTAAAAGT
1 AAAAATAAAAAATTATCTTTAAAAGT
1272746 CATCTTCTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.39
Consensus pattern (28 bp):
AAAAATAAAAAATTATCTTTAAAAGTTT
Found at i:1273578 original size:2 final size:2
Alignment explanation
Indices: 1273571--1273615 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1273561 AATTTTGGAC
*
1273571 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1273613 TA T
1 TA T
1273616 TACTTTTCAG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1275145 original size:2 final size:2
Alignment explanation
Indices: 1275138--1275189 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1275128 ATAATAAATA
1275138 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1275180 AT AT AT AT AT
1 AT AT AT AT AT
1275190 GCAAATCGTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1276209 original size:74 final size:76
Alignment explanation
Indices: 1276079--1276221 Score: 186
Period size: 75 Copynumber: 1.9 Consensus size: 76
1276069 ATGGATTAAC
* * *
1276079 CAAAGTGAAATTTTTCCTTCTTTTGCTTAGCTAAAGAAAACTTGCCACTGGTGA-TTTTCTTGAA
1 CAAAGTGAAATTTTTCCCTCTTTTGCTTAGCTAAAGAAAACTTACCACT-GTGATTTTTCCTGAA
1276143 TTTAAGAGGGAT
65 TTTAAGAGGGAT
* *
1276155 CAAAGTGAAATTTTTCCCT-TTTTGCTTAG-TTAAGAAAGCTTACCAACAT-TGATTTTTCCTGA
1 CAAAGTGAAATTTTTCCCTCTTTTGCTTAGCTAAAGAAAACTTACC-AC-TGTGATTTTTCCTGA
1276217 ATTTA
64 ATTTA
1276222 TGGGGGGGGG
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
74 15 0.25
75 25 0.42
76 19 0.32
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.40
Consensus pattern (76 bp):
CAAAGTGAAATTTTTCCCTCTTTTGCTTAGCTAAAGAAAACTTACCACTGTGATTTTTCCTGAAT
TTAAGAGGGAT
Found at i:1276404 original size:19 final size:19
Alignment explanation
Indices: 1276380--1276417 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1276370 TTTTTAAAAT
*
1276380 TTTTTAAAATAATTTTTAA
1 TTTTTAAAATAATTATTAA
1276399 TTTTTAAAATAATTATTAA
1 TTTTTAAAATAATTATTAA
1276418 CTACGTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTTTAAAATAATTATTAA
Found at i:1277051 original size:18 final size:18
Alignment explanation
Indices: 1277028--1277071 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1277018 AAAAAAAATA
1277028 ATTTTTAAGTAAATAATT
1 ATTTTTAAGTAAATAATT
* * **
1277046 ATTTTTTAGTGAATGGTT
1 ATTTTTAAGTAAATAATT
1277064 ATTTTTAA
1 ATTTTTAA
1277072 AAATAAAAAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (18 bp):
ATTTTTAAGTAAATAATT
Found at i:1278508 original size:11 final size:11
Alignment explanation
Indices: 1278474--1278517 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
1278464 GTATTATAAA
1278474 TTAAATTTATCAT
1 TTAAATTTAT--T
* *
1278487 TAAAATATATT
1 TTAAATTTATT
1278498 TTAAATTTATT
1 TTAAATTTATT
1278509 TTAAATTTA
1 TTAAATTTA
1278518 AAAATTAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 19 0.70
13 8 0.30
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (11 bp):
TTAAATTTATT
Found at i:1278511 original size:29 final size:27
Alignment explanation
Indices: 1278451--1278511 Score: 68
Period size: 29 Copynumber: 2.2 Consensus size: 27
1278441 CATATATGTT
*
1278451 TTTTATATTAAATGTATTATAAATTAA
1 TTTTATATTAAATATATTATAAATTAA
* * *
1278478 ATTTATCATTAAAATATATTTTAAATTTA
1 TTTTAT-ATT-AAATATATTATAAATTAA
1278507 TTTTA
1 TTTTA
1278512 AATTTAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 5 0.19
28 3 0.11
29 19 0.70
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (27 bp):
TTTTATATTAAATATATTATAAATTAA
Found at i:1280029 original size:21 final size:20
Alignment explanation
Indices: 1280003--1280045 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
1279993 TTTGAATAAA
1280003 AATTTTAAAATATATAATCAT
1 AATTTTAAAATATATAAT-AT
*
1280024 AATTTTATAATATATAATAT
1 AATTTTAAAATATATAATAT
1280044 AA
1 AA
1280046 CAATAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
AATTTTAAAATATATAATAT
Found at i:1280467 original size:79 final size:79
Alignment explanation
Indices: 1280336--1280496 Score: 313
Period size: 79 Copynumber: 2.0 Consensus size: 79
1280326 ACAAATTTTT
1280336 AAACCCGAAATGATGAGTCAGAGTTATTCTTGAACAAGTAAAACTTTGATATTATATTTTCAAAG
1 AAACCCGAAATGATGAGTCAGAGTTATTCTTGAACAAGTAAAACTTTGATATTATATTTTCAAAG
*
1280401 TAACCTAAAGAATA
66 TAACCTAAAAAATA
1280415 AAACCCGAAATGATGAGTCAGAGTTATTCTTGAACAAGTAAAACTTTGATATTATATTTTCAAAG
1 AAACCCGAAATGATGAGTCAGAGTTATTCTTGAACAAGTAAAACTTTGATATTATATTTTCAAAG
1280480 TAACCTAAAAAATA
66 TAACCTAAAAAATA
1280494 AAA
1 AAA
1280497 TTTACTTTGG
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 81 1.00
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.30
Consensus pattern (79 bp):
AAACCCGAAATGATGAGTCAGAGTTATTCTTGAACAAGTAAAACTTTGATATTATATTTTCAAAG
TAACCTAAAAAATA
Found at i:1281037 original size:2 final size:2
Alignment explanation
Indices: 1281030--1281072 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1281020 TACAATGGGA
1281030 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1281072 A
1 A
1281073 ATGATTACGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1283002 original size:22 final size:21
Alignment explanation
Indices: 1282947--1283002 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 21
1282937 CATTATTTTT
1282947 AATTAAATTAA-TATTTAAAA
1 AATTAAATTAATTATTTAAAA
1282967 AATTATAATATAATTAATTTAAAA
1 AATTA-AAT-TAATT-ATTTAAAA
**
1282991 TTTTAAATTAAT
1 AATTAAATTAAT
1283003 CTGAATCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 5 0.17
21 3 0.10
22 7 0.23
23 4 0.13
24 11 0.37
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AATTAAATTAATTATTTAAAA
Found at i:1283756 original size:16 final size:16
Alignment explanation
Indices: 1283724--1283779 Score: 53
Period size: 17 Copynumber: 3.6 Consensus size: 16
1283714 TTTATATTAA
*
1283724 AAATTTTTTAAAA--T
1 AAATTATTTAAAATTT
*
1283738 AAATAATTTAAAATTT
1 AAATTATTTAAAATTT
* *
1283754 AAAATTTTTTATAATTT
1 -AAATTATTTAAAATTT
1283771 AAATTATTT
1 AAATTATTT
1283780 TGAATTTGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
14 11 0.33
16 9 0.27
17 13 0.39
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AAATTATTTAAAATTT
Found at i:1283780 original size:17 final size:17
Alignment explanation
Indices: 1283723--1283773 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
1283713 TTTTATATTA
1283723 AAAATTTTTTAAAA--T
1 AAAATTTTTTAAAATTT
**
1283738 -AAATAATTTAAAATTT
1 AAAATTTTTTAAAATTT
*
1283754 AAAATTTTTTATAATTT
1 AAAATTTTTTAAAATTT
1283771 AAA
1 AAA
1283774 TTATTTTGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
14 11 0.39
16 1 0.04
17 16 0.57
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AAAATTTTTTAAAATTT
Found at i:1284554 original size:110 final size:111
Alignment explanation
Indices: 1284438--1284657 Score: 363
Period size: 111 Copynumber: 2.0 Consensus size: 111
1284428 AAGAGATGAT
*
1284438 AAGATAATAC-AAAAAAGTACTCTTATTAATTATTATTTTATTATTTATCCTAATAATTTAATCT
1 AAGATAATACAAAAAAAGTACTCCTATTAATTATTATTTTATTATTTATCCTAATAATTTAATCT
* *
1284502 TAATTAAAAACTAAATTTT-TCAAAAAATCATGATGAAAATTACTTG
66 TAACTAAAAACTAAATTTTCT-AAAAAATCATAATGAAAATTACTTG
*
1284548 AAGATAATACAAAAAAAGTACTCCTATTAATTATTATTTTATTATTTATCTTAATAATTTAATCT
1 AAGATAATACAAAAAAAGTACTCCTATTAATTATTATTTTATTATTTATCCTAATAATTTAATCT
* *
1284613 TAACTAAAAATTAAATTTTCTAAAAAATCATAATTAAAATTACTT
66 TAACTAAAAACTAAATTTTCTAAAAAATCATAATGAAAATTACTT
1284658 AATATATAGT
Statistics
Matches: 102, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
110 10 0.10
111 91 0.89
112 1 0.01
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.41
Consensus pattern (111 bp):
AAGATAATACAAAAAAAGTACTCCTATTAATTATTATTTTATTATTTATCCTAATAATTTAATCT
TAACTAAAAACTAAATTTTCTAAAAAATCATAATGAAAATTACTTG
Found at i:1285269 original size:23 final size:23
Alignment explanation
Indices: 1285221--1285267 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
1285211 ACAATTGTAG
1285221 TTATTATTCGTATTTTGATAAAT
1 TTATTATTCGTATTTTGATAAAT
*
1285244 TTATTATT-TTATTTT-ATATAAT
1 TTATTATTCGTATTTTGATA-AAT
1285266 TT
1 TT
1285268 TAAAAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 3 0.14
22 11 0.50
23 8 0.36
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (23 bp):
TTATTATTCGTATTTTGATAAAT
Found at i:1287631 original size:32 final size:33
Alignment explanation
Indices: 1287595--1287657 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
1287585 TTTTATATTT
* *
1287595 TATATAAATTTTAATTTATTAATA-ATTTATAC
1 TATATAAAATTTAATATATTAATATATTTATAC
*
1287627 TATATAAAATTTAATATATTTATATATTTAT
1 TATATAAAATTTAATATATTAATATATTTAT
1287658 TGTTACCTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 21 0.78
33 6 0.22
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (33 bp):
TATATAAAATTTAATATATTAATATATTTATAC
Found at i:1288910 original size:13 final size:13
Alignment explanation
Indices: 1288886--1288918 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1288876 GACTTTTTAC
1288886 TGTATT-TATATT
1 TGTATTATATATT
1288898 TGTATTATATATT
1 TGTATTATATATT
*
1288911 TGAATTAT
1 TGTATTAT
1288919 TTTATATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (13 bp):
TGTATTATATATT
Found at i:1289402 original size:16 final size:17
Alignment explanation
Indices: 1289345--1289402 Score: 59
Period size: 16 Copynumber: 3.6 Consensus size: 17
1289335 AAATAAATAC
* *
1289345 ATTTT-AATTGATTTGA
1 ATTTTAAATTAATTTAA
*
1289361 ATTTGAAA-TAATTTAA
1 ATTTTAAATTAATTTAA
*
1289377 AATTTAAATTAA-TTAA
1 ATTTTAAATTAATTTAA
1289393 ATTTTAAATT
1 ATTTTAAATT
1289403 TATAAATTCA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
16 29 0.85
17 5 0.15
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (17 bp):
ATTTTAAATTAATTTAA
Found at i:1289534 original size:20 final size:21
Alignment explanation
Indices: 1289481--1289534 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 21
1289471 TTTAATTTTA
1289481 AAAATATA-AATT-ATTAATCT
1 AAAATATATAATTAATTAA-CT
**
1289501 AAAA-ATATTTTTAATTAA-T
1 AAAATATATAATTAATTAACT
1289520 AAAATATATAATTAA
1 AAAATATATAATTAA
1289535 ATTGATGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
19 8 0.30
20 14 0.52
21 5 0.19
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
AAAATATATAATTAATTAACT
Found at i:1290006 original size:21 final size:19
Alignment explanation
Indices: 1289966--1290016 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 19
1289956 ATATATCAAA
1289966 ATTAATATAATCTAAATTATT
1 ATTAATAT-ATCTAAATTA-T
1289987 ATTAATATAT-TAAAATTTAT
1 ATTAATATATCT-AAA-TTAT
*
1290007 ATAAATATAT
1 ATTAATATAT
1290017 AATATTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 1 0.04
20 15 0.56
21 11 0.41
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTAATATATCTAAATTAT
Found at i:1290013 original size:20 final size:20
Alignment explanation
Indices: 1289990--1290053 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 20
1289980 AATTATTATT
1289990 AATATATTAAAATTTATATA
1 AATATATTAAAATTTATATA
*
1290010 AATATA-TAATA-TT-T-TA
1 AATATATTAAAATTTATATA
* * *
1290026 AATATGATTATAATATATAAA
1 AATAT-ATTAAAATTTATATA
1290047 AATATAT
1 AATATAT
1290054 AAATATGATA
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
16 7 0.21
17 2 0.06
18 5 0.15
19 5 0.15
20 9 0.26
21 6 0.18
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
AATATATTAAAATTTATATA
Found at i:1291441 original size:14 final size:13
Alignment explanation
Indices: 1291422--1291452 Score: 53
Period size: 13 Copynumber: 2.3 Consensus size: 13
1291412 TTTGCCTACT
1291422 AAAAAGGAAAAAAG
1 AAAAAGG-AAAAAG
1291436 AAAAAGGAAAAAG
1 AAAAAGGAAAAAG
1291449 AAAA
1 AAAA
1291453 TCTTTCCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (13 bp):
AAAAAGGAAAAAG
Found at i:1292488 original size:20 final size:20
Alignment explanation
Indices: 1292460--1292534 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
1292450 TTTTACCTTG
1292460 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1292480 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
1292500 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
1292520 ATGTATCGATACATT
1 ATGTATCGATACATT
1292535 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1292527 original size:40 final size:39
Alignment explanation
Indices: 1292460--1292537 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1292450 TTTTACCTTG
* *
1292460 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
1292500 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
1292538 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:1293507 original size:22 final size:23
Alignment explanation
Indices: 1293443--1293501 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
1293433 AGCCTTTGAC
1293443 CATGCA-TTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
1293465 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
*
1293488 CATG-TTTTTTTTTA
1 CATGCATTTTTTTTA
1293502 ACATGTCCAG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
22 15 0.43
23 20 0.57
ACGTcount: A:0.17, C:0.08, G:0.08, T:0.66
Consensus pattern (23 bp):
CATGCATTTTTTTTATTATGTTT
Found at i:1299655 original size:23 final size:24
Alignment explanation
Indices: 1299603--1299648 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
1299593 CCTTTAAATG
*
1299603 ACAAAAAAAGTCAAAAGCAAAAGC
1 ACAAAAAAAGTCAAAAGAAAAAGC
*
1299627 ACAAAAAAA-TGAAAAGAAAAAG
1 ACAAAAAAAGTCAAAAGAAAAAG
1299649 TGCAAAAGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.72, C:0.11, G:0.13, T:0.04
Consensus pattern (24 bp):
ACAAAAAAAGTCAAAAGAAAAAGC
Found at i:1301030 original size:27 final size:27
Alignment explanation
Indices: 1301000--1301371 Score: 483
Period size: 27 Copynumber: 13.6 Consensus size: 27
1300990 TTTAAAGCCT
*
1301000 ACAACTCCGTGACACCCTTTTAAGTCC
1 ACAACTCCGTGGCACCCTTTTAAGTCC
1301027 ACAACTCCGTGGCACCCTTTTAAGTCC
1 ACAACTCCGTGGCACCCTTTTAAGTCC
1301054 ACAACTCCGTGGCACCCTTTTAAGTCC
1 ACAACTCCGTGGCACCCTTTTAAGTCC
1301081 ACAACTCCGTGGCACCCTTTTAAGTCC
1 ACAACTCCGTGGCACCCTTTTAAGTCC
* * *
1301108 ACAACTCTGTGGCATCCTTTTAAGACC
1 ACAACTCCGTGGCACCCTTTTAAGTCC
* * *
1301135 GCAACTCCGTGGCAACCTTTTAAGACC
1 ACAACTCCGTGGCACCCTTTTAAGTCC
* * *
1301162 GCAACTACGTGGTACCCTTTTAAGTCC
1 ACAACTCCGTGGCACCCTTTTAAGTCC
* * *
1301189 ATAACTCCGTGGCATCCTTTTAAGACC
1 ACAACTCCGTGGCACCCTTTTAAGTCC
1301216 ACAACTCCGTGGCACCCTTTTAAGTCC
1 ACAACTCCGTGGCACCCTTTTAAGTCC
* * * * *
1301243 ATAACTCTGTGACATCTCTTTTGAGTCC
1 ACAACTCCGTGGCA-CCCTTTTAAGTCC
* * *
1301271 ATAACTCTGTGGCACCCTTTTAAAATCC
1 ACAACTCCGTGGCACCCTTTT-AAGTCC
*
1301299 ACAACTCCGTGGCACCCTTTTAAAATCC
1 ACAACTCCGTGGCACCCTTTT-AAGTCC
* *
1301327 ACAACTCCGTGGCACTCTTTTAAAATCC
1 ACAACTCCGTGGCACCCTTTT-AAGTCC
*
1301355 ACAACTCTGTGGCACCC
1 ACAACTCCGTGGCACCC
1301372 ATTTCAAAGC
Statistics
Matches: 309, Mismatches: 34, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
27 213 0.69
28 96 0.31
ACGTcount: A:0.25, C:0.33, G:0.14, T:0.28
Consensus pattern (27 bp):
ACAACTCCGTGGCACCCTTTTAAGTCC
Found at i:1301789 original size:28 final size:28
Alignment explanation
Indices: 1301279--1302478 Score: 1135
Period size: 28 Copynumber: 40.8 Consensus size: 28
1301269 CCATAACTCT
* ** * *
1301279 GTGGCACCCTTTTAAAATCCACAACTCC
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
* ** * *
1301307 GTGGCACCCTTTTAAAATCCACAACTCC
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
* * ** * *
1301335 GTGGCACTCTTTTAAAATCCACAACTCT
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
*
1301363 GTGGCACCCATTTCAAAGCCCACACAAGTCG
1 GTGGCACCC-TTTCAAAG-CC-CACAAGTCA
*
1301394 GTGGCAACCCATTTCAAAGCCCACACAAGTCG
1 GTGGC-ACCC-TTTCAAAG-CC-CACAAGTCA
* *
1301426 GTGGCAACCATTTTCAAAGCCCACACAAGTCG
1 GTGGC-ACC-CTTTCAAAG-CC-CACAAGTCA
* *
1301458 GTGGCAACCATTTTCAAAGCCCACACAAGTCG
1 GTGGC-ACC-CTTTCAAAG-CC-CACAAGTCA
1301490 GTGGCAACCCTTTTCAAAGCCCACATAAGTCA
1 GTGGC-ACCC-TTTCAAAGCCCAC--AAGTCA
*
1301522 GTGGCACCCTTTCAAAGCCCACACAAGTCG
1 GTGGCACCCTTTCAAAG-CC-CACAAGTCA
*
1301552 GTGGCAACCCTTTTCAAAGCCCACACAAGTCG
1 GTGGC-ACCC-TTTCAAAG-CC-CACAAGTCA
1301584 GTGGCAACCCATTTCAAAGCCCACACAAGTCA
1 GTGGC-ACCC-TTTCAAAG-CC-CACAAGTCA
* * *
1301616 GTGGCAACCCATTCCAAAGTCCACATAAGTCG
1 GTGGC-ACCC-TTTCAAAG-CC-CACAAGTCA
*
1301648 GTGGCAACCCATTTCAAAGCCCACACAAGTCG
1 GTGGC-ACCC-TTTCAAAG-CC-CACAAGTCA
*
1301680 GTGGCAACCTATTTCAAAGCCCACAAGTCA
1 GTGGC-ACC-CTTTCAAAGCCCACAAGTCA
* *
1301710 GTGGCACTCTTTTCAAAGCCCACAAATCA
1 GTGGCAC-CCTTTCAAAGCCCACAAGTCA
* *
1301739 GTGGCACTCTTTTCTAAGCCCACAAGTCA
1 GTGGCAC-CCTTTCAAAGCCCACAAGTCA
1301768 GTGGCACCCTTTCAAAGCCCACAAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
*
1301796 TTGGCACTCCTTTCAAAGCCCACAAGTCA
1 GTGGCAC-CCTTTCAAAGCCCACAAGTCA
** * *
1301825 GTGGCACTTTTTTCAAAGCCCATAAATCA
1 GTGGCAC-CCTTTCAAAGCCCACAAGTCA
*
1301854 GTGGCACTCTTTTCAAAGCCCACAAGTCA
1 GTGGCAC-CCTTTCAAAGCCCACAAGTCA
* *
1301883 ATGGCACCCTTTCAAAGCCCACAAGTTA
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
*
1301911 GTGGCACCCTTTCAGAGCCCACAAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
*
1301939 GTGGCACCCTTTCGAAGCCCACAAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
* * * * *
1301967 GTGGCACCATTGCGAAGCCCACAATTTA
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
*
1301995 GTGGCACTCTTTCAAAGCCCACAAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
*
1302023 GTGGCACCCTTTTAAAGCCCACACAAGTCA
1 GTGGCACCCTTTCAAAG-CC-CACAAGTCA
* * *
1302053 GTGGCACTCCTTTTAAAGCTCACGCAAGTCG
1 GTGGCAC-CCTTTCAAAGC-C-CACAAGTCA
* * *
1302084 GTGGTACCTTTTCAAAGCCCACGAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
* *
1302112 GTGGCACTCTTTCAAAGCCCACAAGTTA
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
** * *
1302140 GTGGCGTCCTTTCAAAGCCCACGAGTTA
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
*
1302168 GTGGCATCCTTTCAAAGCCCACACAAGTCA
1 GTGGCACCCTTTCAAAG-CC-CACAAGTCA
1302198 GTGGCACTCCTTTCAAAGCCCACGCAAGTCA
1 GTGGCAC-CCTTTCAAAGCCCA--CAAGTCA
* *
1302229 GTGGCACCTTTTCAAAGCCCACGAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
* *
1302257 GTGGCACTCTTTCATAGCCCACAAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
**
1302285 GTGGCACCCTTTC-AAGCCCATGAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
* * *
1302312 GTGGTACCTTTTCAAAGCCCACGAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
1302340 GTGGCA-CCTTTCAAAGCCCACAAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
* *
1302367 GTGGCACTCTTTCAAAGCCCACGAGTCA
1 GTGGCACCCTTTCAAAGCCCACAAGTCA
*
1302395 GTGGCATCCTTTCAAAGCCCACGCAAGTCA
1 GTGGCACCCTTTCAAAGCCCA--CAAGTCA
* *
1302425 GTGGCACCTTTTTAAAGCCCACGCAAGTCA
1 GTGGCACCCTTTCAAAGCCCA--CAAGTCA
** *
1302455 GTAACACTCTTTTCAAAGCCCACA
1 GTGGCAC-CCTTTCAAAGCCCACA
1302479 TGTGTCAGTG
Statistics
Matches: 1037, Mismatches: 106, Indels: 57
0.86 0.09 0.05
Matches are distributed among these distances:
27 47 0.05
28 385 0.37
29 146 0.14
30 128 0.12
31 88 0.08
32 243 0.23
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (28 bp):
GTGGCACCCTTTCAAAGCCCACAAGTCA
Found at i:1302141 original size:145 final size:145
Alignment explanation
Indices: 1301298--1302529 Score: 1164
Period size: 145 Copynumber: 8.3 Consensus size: 145
1301288 TTTTAAAATC
* * * ** * * ** *
1301298 CACAACTCCGTGGCACCCTTTTAAAATC-CACAACTCCGTGGCACTCTTTT-AAAATCCACAACT
1 CACAAGTCAGTGGCACCCTTTCAAAGCCACACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGT
* * * * * *
1301361 CTGTGGCACCCATTTCAAAGCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAGTCG
65 CAGTGGCACTC-TTTCAAAG-CC-CACAAGTCAGTGGC-ACTCTTTTCAAAG-CC-CACAAGTCA
*
1301426 GTGGCAACCATTTTCAAAGCCCA
124 GTGGC-ACCCTTTTCAAAGCCCA
* * *
1301449 CACAAGTCGGTGGCAACCATTTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCAC
1 CACAAGTCAGTGGC-ACC-CTTTCAAAG-CCACACAAGTCAGTGGC-A-CCTTTTCAAAGCCCAC
* * *
1301514 ATAAGTCAGTGGCACCCTTTCAAAGCCCACACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACA
61 --AAGTCAGTGGCACTCTTTCAAAG-CC-CACAAGTCAGTGGC-ACTCTTTTCAAAG-CC-CACA
* *
1301579 AGTCGGTGGCAACCCATTTCAAAGCCCA
119 AGTCAGTGGC-ACCCTTTTCAAAGCCCA
* * * *
1301607 CACAAGTCAGTGGCAACCCATTCCAAAGTCCACATAAGTCGGTGGCAACCCATTTCAAAGCCCAC
1 CACAAGTCAGTGGC-ACCC-TTTCAAAG-CCACACAAGTCAGTGGC-A-CCTTTTCAAAG-CC-C
* * *
1301672 ACAAGTCGGTGGCAACCTATTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAAT
59 ACAAGTCAGTGGC-A-CTCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGT
* *
1301737 CAGTGGCACTCTTTTCTAAG-CC-
122 CAGTGGCACCCTTTTCAAAGCCCA
* *
1301759 CACAAGTCAGTGGCACCCTTTCAAAGCC-CACAAGTCATTGGCACTCCTTTCAAAGCCCACAAGT
1 CACAAGTCAGTGGCACCCTTTCAAAGCCACACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGT
* * * *
1301823 CAGTGGCACTTTTTTCAAAGCCCATAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAATGGC
65 CAGTGGCAC-TCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGC
1301888 ACCC-TTTCAAAG-CC-
129 ACCCTTTTCAAAGCCCA
* * * *
1301902 CACAAGTTAGTGGCACCCTTTCAGAGCC-CACAAGTCAGTGGCACCCTTTCGAAGCCCACAAGTC
1 CACAAGTCAGTGGCACCCTTTCAAAGCCACACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTC
* * * *
1301966 AGTGGCAC-CATTGCGAAGCCCACAATTTAGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGGCA
66 AGTGGCACTC-TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCA
1302029 CCCTTTT-AAAGCCCA
130 CCCTTTTCAAAGCCCA
* * * * *
1302044 CACAAGTCAGTGGCACTCCTTTTAAAGCTCACGCAAGTCGGTGGTACCTTTTCAAAGCCCACGAG
1 CACAAGTCAGTGGCAC-CCTTTCAAAGC-CACACAAGTCAGTGGCACCTTTTCAAAGCCCACAAG
* * * * *
1302109 TCAGTGGCACTCTTTCAAAGCCCACAAGTTAGTGGC-GTCCTTTCAAAGCCCACGAGTTAGTGGC
64 TCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGC
*
1302173 ATCC-TTTCAAAGCCCA
129 ACCCTTTTCAAAGCCCA
* *
1302189 CACAAGTCAGTGGCACTCCTTTCAAAGCCCACGCAAGTCAGTGGCACCTTTTCAAAGCCCACGAG
1 CACAAGTCAGTGGCAC-CCTTTCAAAG-CCACACAAGTCAGTGGCACCTTTTCAAAGCCCACAAG
* * ** *
1302254 TCAGTGGCACTCTTTCATAGCCCACAAGTCAGTGGCAC-CCTTTC-AAGCCCATGAGTCAGTGGT
64 TCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGC
1302317 A-CCTTTTCAAAG-CC-
129 ACCCTTTTCAAAGCCCA
* *
1302331 CACGAGTCAGTGGCA-CCTTTCAAAGCC-CACAAGTCAGTGGCA-CTCTTTCAAAGCCCACGAGT
1 CACAAGTCAGTGGCACCCTTTCAAAGCCACACAAGTCAGTGGCACCT-TTTCAAAGCCCACAAGT
*
1302393 CAGTGGCA-TCCTTTCAAAGCCCACGCAAGTCAGTGGCAC-CTTTTTAAAGCCCACGCAAGTCAG
65 CAGTGGCACT-CTTTCAAAGCCCA--CAAGTCAGTGGCACTCTTTTCAAAGCCCA--CAAGTCAG
** *
1302456 TAACACTCTTTTCAAAGCCCA
125 TGGCACCCTTTTCAAAGCCCA
*** ** *
1302477 CATGTGTCAGTGGCAACTTTTCTCAAAGCCTACACAAG-CTAGTGGCACATTTT
1 CACAAGTCAGTGGC-ACCCTT-TCAAAGCC-ACACAAGTC-AGTGGCACCTTTT
1302530 TTTTAAAAAA
Statistics
Matches: 939, Mismatches: 96, Indels: 92
0.83 0.09 0.08
Matches are distributed among these distances:
137 3 0.00
138 51 0.05
139 2 0.00
140 59 0.06
141 35 0.04
142 56 0.06
143 72 0.08
144 95 0.10
145 207 0.22
146 17 0.02
147 11 0.01
148 13 0.01
149 10 0.01
150 8 0.01
151 32 0.03
152 18 0.02
153 8 0.01
154 11 0.01
155 24 0.03
156 8 0.01
157 20 0.02
158 149 0.16
159 18 0.02
160 12 0.01
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (145 bp):
CACAAGTCAGTGGCACCCTTTCAAAGCCACACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTC
AGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC
CCTTTTCAAAGCCCA
Found at i:1303117 original size:20 final size:20
Alignment explanation
Indices: 1303089--1303163 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
1303079 TTTTACCTTG
1303089 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1303109 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
1303129 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
1303149 ATGTATCGATACATT
1 ATGTATCGATACATT
1303164 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1303156 original size:40 final size:39
Alignment explanation
Indices: 1303089--1303166 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1303079 TTTTACCTTG
* *
1303089 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
1303129 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
1303167 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:1304107 original size:23 final size:23
Alignment explanation
Indices: 1304071--1304128 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
1304061 AGCCTTTGAC
1304071 CATGCA-TTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
1304093 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
1304116 CATG--TTTTTTTTA
1 CATGCATTTTTTTTA
1304129 ACATGTCCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
21 9 0.26
22 6 0.17
23 20 0.57
ACGTcount: A:0.17, C:0.09, G:0.09, T:0.66
Consensus pattern (23 bp):
CATGCATTTTTTTTATTATGTTT
Found at i:1306851 original size:4 final size:4
Alignment explanation
Indices: 1306842--1306871 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
1306832 GACATCATCA
1306842 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1306872 CACAAAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1307024 original size:18 final size:18
Alignment explanation
Indices: 1306998--1307032 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1306988 TCATTATTGA
1306998 GGTTAAAAATCTATAATT
1 GGTTAAAAATCTATAATT
* *
1307016 GGTTGAAAATCTGTAAT
1 GGTTAAAAATCTATAAT
1307033 CAATATGTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.37
Consensus pattern (18 bp):
GGTTAAAAATCTATAATT
Found at i:1307064 original size:17 final size:18
Alignment explanation
Indices: 1307036--1307092 Score: 66
Period size: 17 Copynumber: 3.2 Consensus size: 18
1307026 CTGTAATCAA
1307036 TATGTAATTTTTAAAAATT
1 TATG-AATTTTTAAAAATT
1307055 TATG-ATTTTTAAAAA-T
1 TATGAATTTTTAAAAATT
*
1307071 TATGTAATTCTT-AAAATT
1 TATG-AATTTTTAAAAATT
1307089 TATG
1 TATG
1307093 GTTGATGTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
16 5 0.15
17 15 0.44
18 10 0.29
19 4 0.12
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (18 bp):
TATGAATTTTTAAAAATT
Found at i:1307084 original size:18 final size:18
Alignment explanation
Indices: 1307036--1307092 Score: 73
Period size: 18 Copynumber: 3.2 Consensus size: 18
1307026 CTGTAATCAA
1307036 TATGTAATTTTTAAAAATT
1 TATGTAATTTTTAAAAA-T
1307055 TATG--ATTTTTAAAAAT
1 TATGTAATTTTTAAAAAT
* *
1307071 TATGTAATTCTTAAAATT
1 TATGTAATTTTTAAAAAT
1307089 TATG
1 TATG
1307093 GTTGATGTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
16 5 0.15
17 11 0.32
18 14 0.41
19 4 0.12
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (18 bp):
TATGTAATTTTTAAAAAT
Found at i:1307882 original size:14 final size:14
Alignment explanation
Indices: 1307863--1307890 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1307853 TTTTTCGATT
1307863 TTAAATATATTTTA
1 TTAAATATATTTTA
1307877 TTAAATATATTTTA
1 TTAAATATATTTTA
1307891 AATATTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTAAATATATTTTA
Found at i:1308546 original size:2 final size:2
Alignment explanation
Indices: 1308539--1308584 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1308529 TGCTTGCTGC
1308539 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1308581 AT AT
1 AT AT
1308585 GTGTGTGTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1308589 original size:2 final size:2
Alignment explanation
Indices: 1308584--1308632 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
1308574 TATATATATA
* * *
1308584 TG TG TG TG TG TG TG TG TG TG TG TG TG TA TG TG TG CG TG TG CG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1308626 TG TG TG T
1 TG TG TG T
1308633 ATAATATTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.02, C:0.04, G:0.47, T:0.47
Consensus pattern (2 bp):
TG
Found at i:1309713 original size:158 final size:158
Alignment explanation
Indices: 1309425--1309750 Score: 476
Period size: 158 Copynumber: 2.1 Consensus size: 158
1309415 AAATATAACA
* *
1309425 AAGTCATAAATTTTTAAATAGAATAACGAAAATTACAAAATAAAAATATTCTTTTTATAAGCAAT
1 AAGTCATAAATTTTTAAATAGAATAACGAAAATGACAAAATAAAAATAGTCTTTTTATAAGCAAT
* *
1309490 ATAAAGTCACCTTTATAAGTAACTTATCTGTAAGGTAAAAGTTATATTTTTACGCAACATGTCTT
66 ATAAAGTCACATTTATAAGTAACTTATCTGTAAGGTAAAAGTTATATTTTTACACAACATGTCTT
1309555 TTAGTTAGATGTTATGTCTTTACACAAC
131 TTAGTTAGATGTTATGTCTTTACACAAC
* * * * * *
1309583 AAGTCATAAATTTTTGAATAGAATAGCGAAAATGACATAATAGAAAT-GTCGTTTTTATAGGTAA
1 AAGTCATAAATTTTTAAATAGAATAACGAAAATGACAAAATAAAAATAGTC-TTTTTATAAGCAA
* * * * * *
1309647 TGTAAAGTCACATTTGTAAGTAACTTATCTGTAGGGTAAAAGTTATGTTTTTACATAATATGTCT
65 TATAAAGTCACATTTATAAGTAACTTATCTGTAAGGTAAAAGTTATATTTTTACACAACATGTCT
*
1309712 TTTAGTTAGATGTTATGTCTTTACATAAC
130 TTTAGTTAGATGTTATGTCTTTACACAAC
1309741 AAGTC-TAAAT
1 AAGTCATAAAT
1309751 GTTGTATTTT
Statistics
Matches: 150, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
157 7 0.05
158 143 0.95
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (158 bp):
AAGTCATAAATTTTTAAATAGAATAACGAAAATGACAAAATAAAAATAGTCTTTTTATAAGCAAT
ATAAAGTCACATTTATAAGTAACTTATCTGTAAGGTAAAAGTTATATTTTTACACAACATGTCTT
TTAGTTAGATGTTATGTCTTTACACAAC
Found at i:1311154 original size:2 final size:2
Alignment explanation
Indices: 1311147--1311177 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1311137 TTAAAAATGC
1311147 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1311178 ATTCCTTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1313269 original size:20 final size:17
Alignment explanation
Indices: 1313244--1313289 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
1313234 AATTTTTATT
1313244 TAAAATTTAATTATAAAATA
1 TAAAATTTAA--ATAAAA-A
1313264 TAAAATTTTAAATAAAAA
1 TAAAA-TTTAAATAAAAA
1313282 TAAAATTT
1 TAAAATTT
1313290 TTATATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 3 0.12
18 6 0.24
19 6 0.24
20 5 0.20
21 5 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAAATTTAAATAAAAA
Found at i:1314116 original size:13 final size:13
Alignment explanation
Indices: 1314073--1314116 Score: 70
Period size: 13 Copynumber: 3.4 Consensus size: 13
1314063 AAAGGTGAAA
1314073 AAAAATTATTCTT
1 AAAAATTATTCTT
*
1314086 AATAATTATTCTT
1 AAAAATTATTCTT
*
1314099 TAAAATTATTCTT
1 AAAAATTATTCTT
1314112 AAAAA
1 AAAAA
1314117 CGATATTCGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (13 bp):
AAAAATTATTCTT
Found at i:1318953 original size:15 final size:15
Alignment explanation
Indices: 1318933--1318962 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1318923 AAAAACTTGA
1318933 AAAAAATTAAACATT
1 AAAAAATTAAACATT
1318948 AAAAAATTAAACATT
1 AAAAAATTAAACATT
1318963 CCCATATCAA
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:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAAAATTAAACATT
Found at i:1323204 original size:3 final size:3
Alignment explanation
Indices: 1323196--1323227 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1323186 AGCATAACCA
1323196 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1323228 CAGATTATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1323601 original size:14 final size:15
Alignment explanation
Indices: 1323582--1323627 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 15
1323572 ATATTTTAAA
*
1323582 TTATTTTTAA-TATT
1 TTATTTTAAATTATT
1323596 TTATTTTAAATTATT
1 TTATTTTAAATTATT
* *
1323611 TT-TATTAAATTAAT
1 TTATTTTAAATTATT
1323625 TTA
1 TTA
1323628 AATTTAGATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 21 0.78
15 6 0.22
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTATTTTAAATTATT
Found at i:1323627 original size:24 final size:24
Alignment explanation
Indices: 1323576--1323631 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
1323566 AAATTAATAT
** *
1323576 TTTAAATTATTTTTAATATTTTAT
1 TTTAAATTATTTTTAATAAATTAA
*
1323600 TTTAAATTATTTTTATTAAATTAA
1 TTTAAATTATTTTTAATAAATTAA
1323624 TTTAAATT
1 TTTAAATT
1323632 TAGATTGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTAAATTATTTTTAATAAATTAA
Found at i:1324650 original size:3 final size:3
Alignment explanation
Indices: 1324642--1324669 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1324632 GTTCGAATTT
1324642 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1324670 GTAATTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1326628 original size:4 final size:4
Alignment explanation
Indices: 1326613--1326646 Score: 59
Period size: 4 Copynumber: 8.2 Consensus size: 4
1326603 TTAATTTATT
1326613 TTAA TTACA TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TTA-A TTAA TTAA TTAA TTAA TTAA TTAA T
1326647 GTGTAACATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (4 bp):
TTAA
Found at i:1334474 original size:26 final size:26
Alignment explanation
Indices: 1334445--1334495 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
1334435 ACTTTTTAGC
*
1334445 ACTTCCTTTTGTTAATAGTGTTACAG
1 ACTTCCTTTTGTTAATAGTCTTACAG
*
1334471 ACTTCCTTTTGTTAATGGTCTTACA
1 ACTTCCTTTTGTTAATAGTCTTACA
1334496 AATATGTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.22, C:0.18, G:0.14, T:0.47
Consensus pattern (26 bp):
ACTTCCTTTTGTTAATAGTCTTACAG
Found at i:1335108 original size:31 final size:30
Alignment explanation
Indices: 1335063--1335207 Score: 98
Period size: 31 Copynumber: 4.7 Consensus size: 30
1335053 AAGCATTGGT
* *
1335063 AAATATTAAGTATAATAAAAAAATATTTATA
1 AAATAATAAATATAATAAAAAAATATTT-TA
* *
1335094 AAATAATAAATATAATATATAAATATTTTA
1 AAATAATAAATATAATAAAAAAATATTTTA
* * * * *
1335124 AAAT-TTATATATTATAAATTATTAATATATTA
1 AAATAATAAATATAATAAA--A-AAATATTTTA
*
1335156 AAAT-ATATATA-AATATAAAAAATATTTTA
1 AAATAATAAATATAATA-AAAAAATATTTTA
*
1335185 AATATAATTTTAATATAATAAAA
1 AA-ATAA--TAAATATAATAAAA
1335208 TATATAAATA
Statistics
Matches: 88, Mismatches: 17, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
29 20 0.23
30 9 0.10
31 28 0.32
32 20 0.23
33 7 0.08
34 4 0.05
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.41
Consensus pattern (30 bp):
AAATAATAAATATAATAAAAAAATATTTTA
Found at i:1335141 original size:16 final size:17
Alignment explanation
Indices: 1335084--1335244 Score: 58
Period size: 16 Copynumber: 9.6 Consensus size: 17
1335074 ATAATAAAAA
1335084 AATAT-TTATAAA-A-T
1 AATATATTATAAATATT
*
1335098 AATA-AATAT-AATATAT
1 AATATATTATAAATAT-T
*
1335114 AA-ATATTTTAAA-ATT
1 AATATATTATAAATATT
*
1335129 TATATATTATAAATTATT
1 AATATATTATAAA-TATT
1335147 AATATATTA-AAATATAT
1 AATATATTATAAATAT-T
* * *
1335164 ATAAATATAAAAAATATT
1 A-ATATATTATAAATATT
* * *
1335182 -TTA-AATAT-AATTTT
1 AATATATTATAAATATT
*
1335196 AATATAATA-AAATATAT
1 AATATATTATAAATAT-T
*
1335213 AAATATAATATAAATATAT
1 -AATATATTATAAATAT-T
1335232 CAATTATATTATA
1 -AA-TATATTATA
1335245 GACACATTTT
Statistics
Matches: 110, Mismatches: 18, Indels: 32
0.69 0.11 0.20
Matches are distributed among these distances:
13 2 0.02
14 13 0.12
15 7 0.06
16 29 0.26
17 8 0.07
18 27 0.25
19 16 0.15
20 8 0.07
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.43
Consensus pattern (17 bp):
AATATATTATAAATATT
Found at i:1335151 original size:18 final size:19
Alignment explanation
Indices: 1335130--1335231 Score: 75
Period size: 18 Copynumber: 5.9 Consensus size: 19
1335120 TTTAAAATTT
*
1335130 ATATATTATAAAT-TATTA
1 ATATAATATAAATATATTA
*
1335148 ATATATTA-AAATATATATAA
1 ATATAATATAAATATAT-T-A
1335168 ATATAA-A-AAATAT-TT-
1 ATATAATATAAATATATTA
1335183 -TA-AATAT-AAT-T-TTA
1 ATATAATATAAATATATTA
*
1335197 ATATAATA-AAATATATAA
1 ATATAATATAAATATATTA
1335215 ATATAATATAAATATAT
1 ATATAATATAAATATAT
1335232 CAATTATATT
Statistics
Matches: 70, Mismatches: 2, Indels: 23
0.74 0.02 0.24
Matches are distributed among these distances:
13 5 0.07
14 6 0.09
15 2 0.03
16 7 0.10
17 6 0.09
18 22 0.31
19 16 0.23
20 6 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATATAATATAAATATATTA
Found at i:1335199 original size:29 final size:29
Alignment explanation
Indices: 1335091--1335230 Score: 100
Period size: 29 Copynumber: 5.0 Consensus size: 29
1335081 AAAAATATTT
*
1335091 ATAAAATA-ATAAATATAATATATAAATATT
1 ATAAAATATATAAATAT-A-ATATAAATATA
* *
1335121 TTAAAAT-T-T--ATATATTATAAAT-TA
1 ATAAAATATATAAATATAATATAAATATA
* *
1335145 TTAATATAT-TAAAATAT-ATATAAATATA
1 ATAAAATATAT-AAATATAATATAAATATA
* * * *
1335173 AAAAATAT-TTTAAATATAATTTTAATATA
1 ATAAA-ATATATAAATATAATATAAATATA
1335202 ATAAAATATATAAATATAATATAAATATA
1 ATAAAATATATAAATATAATATAAATATA
1335231 TCAATTATAT
Statistics
Matches: 86, Mismatches: 14, Indels: 21
0.71 0.12 0.17
Matches are distributed among these distances:
24 7 0.08
25 9 0.10
26 1 0.01
27 11 0.13
28 17 0.20
29 35 0.41
30 6 0.07
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (29 bp):
ATAAAATATATAAATATAATATAAATATA
Found at i:1335239 original size:20 final size:19
Alignment explanation
Indices: 1335098--1335231 Score: 73
Period size: 18 Copynumber: 6.9 Consensus size: 19
1335088 TTTATAAAAT
1335098 AATA-AATAT-AATATATA
1 AATATAATATAAATATATA
** *
1335115 AATATTTTA-AAATTTATA
1 AATATAATATAAATATATA
* *
1335133 TATTATAAATTATTAATATATTA
1 -AATAT-AA-TATAAATATA-TA
1335156 AA-ATATATATAAATATA-A
1 AATATA-ATATAAATATATA
* * * *
1335174 AAAATATTTTAAATATAATTTT
1 AATATAATATAAATAT-A--TA
1335196 AATATAATA-AAATATATA
1 AATATAATATAAATATATA
1335214 AATATAATATAAATATAT
1 AATATAATATAAATATAT
1335232 CAATTATATT
Statistics
Matches: 86, Mismatches: 17, Indels: 26
0.67 0.13 0.20
Matches are distributed among these distances:
17 4 0.05
18 30 0.35
19 16 0.19
20 11 0.13
21 11 0.13
22 12 0.14
23 2 0.02
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AATATAATATAAATATATA
Found at i:1335484 original size:2 final size:2
Alignment explanation
Indices: 1335477--1335508 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
1335467 ATCTTAAGCT
1335477 TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
1335509 TATTTATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1335623 original size:24 final size:25
Alignment explanation
Indices: 1335598--1335654 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
1335588 TAAAAATATA
*
1335598 AAAT-ATTTTAAAT-TTTATTTTTT
1 AAATAATTTTAAATATATATTTTTT
1335621 AAATAATTTTAAATATATA-TTTTT
1 AAATAATTTTAAATATATATTTTTT
1335645 AAATTAATTT
1 AAA-TAATTT
1335655 AATACATCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 4 0.13
24 17 0.57
25 9 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
AAATAATTTTAAATATATATTTTTT
Found at i:1337590 original size:2 final size:2
Alignment explanation
Indices: 1337583--1337614 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1337573 GTAGAAAAGG
1337583 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1337615 TATTTGCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1340590 original size:29 final size:28
Alignment explanation
Indices: 1340498--1340607 Score: 98
Period size: 29 Copynumber: 3.9 Consensus size: 28
1340488 GATAAAAGCT
* * *
1340498 AATCTCTAAAGTTT-GCGGTTAACTACA
1 AATCCCTAAAGTTTAGTGATTAACTACA
** *
1340525 AATCCCTAAAGTTTAGTGATTAGAAAAGCC
1 AATCCCTAAAGTTTAGTGATTA-ACTA-CA
1340555 AA-CCCTAAAGTTTAGTGATTTAACTACA
1 AATCCCTAAAGTTTAGTGA-TTAACTACA
* * *
1340583 AATTCCTAAAGTTCAATGATTAACT
1 AATCCCTAAAGTTTAGTGATTAACT
1340608 TGAGAATTCT
Statistics
Matches: 66, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
27 13 0.20
28 14 0.21
29 33 0.50
30 6 0.09
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (28 bp):
AATCCCTAAAGTTTAGTGATTAACTACA
Found at i:1343563 original size:37 final size:37
Alignment explanation
Indices: 1343521--1343715 Score: 194
Period size: 37 Copynumber: 5.2 Consensus size: 37
1343511 TTAAGAATAG
** * *
1343521 TTTTTGTTTTGAACCGTGCCACCGGTAAGAATTGTGG
1 TTTTTGTTCCGAACCGTGCCACCGGTAAGAATAGTGA
* * * *
1343558 TTTTTGTCCCGATCCGTGCCACCGGTAAAAATTGTGA
1 TTTTTGTTCCGAACCGTGCCACCGGTAAGAATAGTGA
* * *
1343595 TTTTTGTCCCGATCCGTGCCACCAGTAAGAATAGTGA
1 TTTTTGTTCCGAACCGTGCCACCGGTAAGAATAGTGA
* * *
1343632 TTTCTGTTTCAAACCGTGCCACCGGTTAAGAATAGTGA
1 TTTTTGTTCCGAACCGTGCCACCGG-TAAGAATAGTGA
* * *
1343670 TTTTTGTTCCAAAACCGTGCCATCGGTTAAAAATAGT-A
1 TTTTTGTTCC-GAACCGTGCCACCGG-TAAGAATAGTGA
1343708 GTTTTTGT
1 -TTTTTGT
1343716 CAAATAGTAG
Statistics
Matches: 136, Mismatches: 19, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
37 84 0.62
38 21 0.15
39 31 0.23
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.35
Consensus pattern (37 bp):
TTTTTGTTCCGAACCGTGCCACCGGTAAGAATAGTGA
Found at i:1343722 original size:17 final size:17
Alignment explanation
Indices: 1343700--1343732 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1343690 CATCGGTTAA
1343700 AAATAGTAGTTTTTGTC
1 AAATAGTAGTTTTTGTC
1343717 AAATAGTAGTTTTTGT
1 AAATAGTAGTTTTTGT
1343733 TCCAAACCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.03, G:0.18, T:0.48
Consensus pattern (17 bp):
AAATAGTAGTTTTTGTC
Found at i:1351316 original size:6 final size:6
Alignment explanation
Indices: 1351301--1351377 Score: 82
Period size: 6 Copynumber: 12.8 Consensus size: 6
1351291 TTGTGGATTA
* * * ** * * *
1351301 TATATT TATATG TATATG TATACG CATGCG TATACG TATACG TATACG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1351349 TATATG TATATG TATATG TATATG TATAT
1 TATATG TATATG TATATG TATATG TATAT
1351378 TGGGGACAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 64 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (6 bp):
TATATG
Found at i:1358183 original size:28 final size:28
Alignment explanation
Indices: 1358151--1358216 Score: 132
Period size: 28 Copynumber: 2.4 Consensus size: 28
1358141 AAAGTATAAT
1358151 AGAAAATTAAATTTAACTAAAAGTGGTA
1 AGAAAATTAAATTTAACTAAAAGTGGTA
1358179 AGAAAATTAAATTTAACTAAAAGTGGTA
1 AGAAAATTAAATTTAACTAAAAGTGGTA
1358207 AGAAAATTAA
1 AGAAAATTAA
1358217 TTATTATATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.56, C:0.03, G:0.14, T:0.27
Consensus pattern (28 bp):
AGAAAATTAAATTTAACTAAAAGTGGTA
Found at i:1364540 original size:15 final size:14
Alignment explanation
Indices: 1364516--1364567 Score: 72
Period size: 13 Copynumber: 3.8 Consensus size: 14
1364506 AAAAAAAGCT
1364516 AAAA-TAAAAAATG
1 AAAATTAAAAAATG
*
1364529 GAAATTACAAAAATG
1 AAAATTA-AAAAATG
1364544 AAAATT-AAAAATG
1 AAAATTAAAAAATG
1364557 AAAATTAAAAA
1 AAAATTAAAAA
1364568 CAAACATTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
13 16 0.47
14 6 0.18
15 12 0.35
ACGTcount: A:0.71, C:0.02, G:0.08, T:0.19
Consensus pattern (14 bp):
AAAATTAAAAAATG
Found at i:1364671 original size:15 final size:15
Alignment explanation
Indices: 1364643--1364680 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1364633 ATTATCATTT
1364643 ATTAAAAA-ATAAAAA
1 ATTAAAAACA-AAAAA
1364658 ATTTAAAAACAAAAAA
1 A-TTAAAAACAAAAAA
1364674 ATTAAAA
1 ATTAAAA
1364681 TAATTAAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 7 0.33
16 13 0.62
17 1 0.05
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (15 bp):
ATTAAAAACAAAAAA
Found at i:1364958 original size:20 final size:20
Alignment explanation
Indices: 1364895--1364963 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 20
1364885 TGAAAATTTC
*
1364895 TTTTAAAGAAAGTTTTAAATT
1 TTTTAAATAAA-TTTTAAATT
* *
1364916 TTTTAAATTCAATTTTAATTT
1 TTTTAAA-TAAATTTTAAATT
*
1364937 TTTTAAA-AAATTTTAAAAT
1 TTTTAAATAAATTTTAAATT
*
1364956 TTTAAAAT
1 TTTTAAAT
1364964 TTTTTATTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
19 15 0.38
21 22 0.56
22 2 0.05
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (20 bp):
TTTTAAATAAATTTTAAATT
Found at i:1365356 original size:14 final size:14
Alignment explanation
Indices: 1365337--1365387 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
1365327 GTTAGGGATA
1365337 AAATTTAATTATTT
1 AAATTTAATTATTT
*
1365351 AAATTTAAATCGA-TT
1 AAATTT-AAT-TATTT
*
1365366 AAATTTAATTATAT
1 AAATTTAATTATTT
1365380 AAATTTAA
1 AAATTTAA
1365388 ATTTAAGTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 1 0.03
14 18 0.58
15 11 0.35
16 1 0.03
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (14 bp):
AAATTTAATTATTT
Found at i:1366116 original size:4 final size:4
Alignment explanation
Indices: 1366107--1366147 Score: 66
Period size: 4 Copynumber: 10.2 Consensus size: 4
1366097 GGAAAAACAG
1366107 AGAA AGAA AGAA AGAAA AGAA AGAA AGAA AGAA AG-A AGAA A
1 AGAA AGAA AGAA AG-AA AGAA AGAA AGAA AGAA AGAA AGAA A
1366148 AAAATGAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 3 0.09
4 28 0.80
5 4 0.11
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:1366124 original size:21 final size:21
Alignment explanation
Indices: 1366100--1366143 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1366090 ACGCTACGGA
*
1366100 AAAACAGAGAAAGAAAGAAAG
1 AAAACAAAGAAAGAAAGAAAG
*
1366121 AAAAGAAAGAAAGAAAGAAAG
1 AAAACAAAGAAAGAAAGAAAG
1366142 AA
1 AA
1366144 GAAAAAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.75, C:0.02, G:0.23, T:0.00
Consensus pattern (21 bp):
AAAACAAAGAAAGAAAGAAAG
Found at i:1366239 original size:27 final size:27
Alignment explanation
Indices: 1366192--1366250 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
1366182 TTTATTTAAA
*
1366192 ATATTATAATTTTTGTATATTTTTTAT
1 ATATTATAATTTTTGTATATTTTATAT
1366219 ATATTAATAATTTATT-T-TATTTTATAT
1 ATATT-ATAATTT-TTGTATATTTTATAT
1366246 ATATT
1 ATATT
1366251 TTTATATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 19 0.66
28 8 0.28
29 2 0.07
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (27 bp):
ATATTATAATTTTTGTATATTTTATAT
Found at i:1366559 original size:20 final size:20
Alignment explanation
Indices: 1366534--1366582 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
1366524 ATAATTAGTA
1366534 TTATATATATTATGA-CATAT
1 TTATATATATTAT-ATCATAT
*
1366554 TTATATAT-TTATATCATCT
1 TTATATATATTATATCATAT
1366573 TTATAT-TATT
1 TTATATATATT
1366583 TTTTTCATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 2 0.08
19 16 0.62
20 8 0.31
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (20 bp):
TTATATATATTATATCATAT
Found at i:1366649 original size:22 final size:22
Alignment explanation
Indices: 1366624--1366669 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1366614 ATTTCATTTG
*
1366624 TATTATGTCTTGATTTATC-TTA
1 TATTATGT-ATGATTTATCATTA
*
1366646 TATTTTGTATGATTTATCATTA
1 TATTATGTATGATTTATCATTA
1366668 TA
1 TA
1366670 ATTTAACAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.26, C:0.07, G:0.09, T:0.59
Consensus pattern (22 bp):
TATTATGTATGATTTATCATTA
Found at i:1367416 original size:19 final size:20
Alignment explanation
Indices: 1367392--1367431 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1367382 TTATTATTTA
*
1367392 ATATAATTT-AATTTAAATT
1 ATATAATTTGAAATTAAATT
1367411 ATATAATTTGAAATTAAATT
1 ATATAATTTGAAATTAAATT
1367431 A
1 A
1367432 AAATTTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
ATATAATTTGAAATTAAATT
Found at i:1367712 original size:40 final size:42
Alignment explanation
Indices: 1367646--1367725 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 42
1367636 TTCAAAATTG
* *
1367646 ATTAAATTAAATTCAAATTTTTTTAATCAAACTC-AATAATA
1 ATTAAATCAAATTCAAATTATTTTAATCAAACTCGAATAATA
*
1367687 ATTAAATCAAATT-AAATTATTTTAATTAAACTCGAATAA
1 ATTAAATCAAATTCAAATTATTTTAATCAAACTCGAATAA
1367726 CTTAATAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
40 18 0.51
41 17 0.49
ACGTcount: A:0.50, C:0.09, G:0.01, T:0.40
Consensus pattern (42 bp):
ATTAAATCAAATTCAAATTATTTTAATCAAACTCGAATAATA
Found at i:1370720 original size:80 final size:80
Alignment explanation
Indices: 1370629--1370790 Score: 297
Period size: 80 Copynumber: 2.0 Consensus size: 80
1370619 AATGTTTTCC
*
1370629 ACCAAAAAAAAATCAAAATGTTTATATTAAGTAACTTTATATGGTCCCAAGAGAACTCCCAACTC
1 ACCAAAAAAAAATCAAAATGTTTATATTAAGTAACGTTATATGGTCCCAAGAGAACTCCCAACTC
1370694 AAACTTAAAACTCCA
66 AAACTTAAAACTCCA
*
1370709 ACCAAAAAAAAATCAAAATGTTTATCTTAAGTAACGTTATATGGTCCCAAGAGAACTCCCAACTC
1 ACCAAAAAAAAATCAAAATGTTTATATTAAGTAACGTTATATGGTCCCAAGAGAACTCCCAACTC
*
1370774 AAACTTCAAACTCCA
66 AAACTTAAAACTCCA
1370789 AC
1 AC
1370791 TTAGACGTCT
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.45, C:0.23, G:0.08, T:0.24
Consensus pattern (80 bp):
ACCAAAAAAAAATCAAAATGTTTATATTAAGTAACGTTATATGGTCCCAAGAGAACTCCCAACTC
AAACTTAAAACTCCA
Found at i:1378433 original size:250 final size:250
Alignment explanation
Indices: 1377957--1378456 Score: 806
Period size: 250 Copynumber: 2.0 Consensus size: 250
1377947 CATTCTTATC
*
1377957 TTTTTTTGCTCTAAATTAACTGCAGAATACTGATCTTAAATAGCTTTCTAAAACTTCAAGAAAAT
1 TTTTTTTGCTCTAAATAAACTGCAGAATACTGATCTTAAATAGCTTTCTAAAACTTCAAGAAAAT
* * * *
1378022 TAACTCCACATTCACCAAACAATCCCAATCCTCAATCAAATTCACTAAATCTATACTCTTTCTGT
66 TAACTCCACATTCACCAAACAAGCCCAATCCTCAATCAAATTAACTAAATCAATACTCTTTCTGC
* * *
1378087 GAAATATATTTTATTGTCAGAGAATTTTCTGCATTATTGCTTTGTGATTTTATGATGCAAACAAA
131 GAAATATATTTTATTGTCAGAGAATTTTCAGCATTATTGCTTCGTGATTGTATGATGCAAACAAA
* * *
1378152 CTTAGGTGCGACTTCAAAGGAACCTTAGTGTGGTGTTTAGAGATTGCTTTTTTTTT
196 CTTAGGTGCGACTCCAAAGGAACCCTAGTGTGGTGTTTAGAGATTG-TTTTATTTT
* *
1378208 TTTTTTTGCTCTCAATAAACCTGTAGAATACTGATCTTAAATAGCTTTCTAAAACTTCAAGAAAA
1 TTTTTTTGCTCTAAATAAA-CTGCAGAATACTGATCTTAAATAGCTTTCTAAAACTTCAAGAAAA
*
1378273 TTAATTCCACA-TCACCAAACAAGCCCAATCCTCAATCAAATTAACTAAATCAATACTCTTTCTG
65 TTAACTCCACATTCACCAAACAAGCCCAATCCTCAATCAAATTAACTAAATCAATACTCTTTCTG
*
1378337 CGAAATATA-TTTATTGTCAGAGAATTTTCAGCATTATTGCTTCGTGATTGTATGATGCAATCAA
130 CGAAATATATTTTATTGTCAGAGAATTTTCAGCATTATTGCTTCGTGATTGTATGATGCAAACAA
* * *
1378401 ACTTATGTGTGACTCCAAAGGAACCCTAGTGTGGTGTTTAGGGATTGTTTTATTTT
195 ACTTAGGTGCGACTCCAAAGGAACCCTAGTGTGGTGTTTAGAGATTGTTTTATTTT
1378457 GCATTTCCTT
Statistics
Matches: 230, Mismatches: 18, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
249 8 0.03
250 93 0.40
251 75 0.33
252 54 0.23
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (250 bp):
TTTTTTTGCTCTAAATAAACTGCAGAATACTGATCTTAAATAGCTTTCTAAAACTTCAAGAAAAT
TAACTCCACATTCACCAAACAAGCCCAATCCTCAATCAAATTAACTAAATCAATACTCTTTCTGC
GAAATATATTTTATTGTCAGAGAATTTTCAGCATTATTGCTTCGTGATTGTATGATGCAAACAAA
CTTAGGTGCGACTCCAAAGGAACCCTAGTGTGGTGTTTAGAGATTGTTTTATTTT
Found at i:1380158 original size:22 final size:18
Alignment explanation
Indices: 1380126--1380177 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 18
1380116 ATTTAGTTTT
*
1380126 AATTTATAAATTAAAAATTA
1 AATTTTTAAATT--AAATTA
1380146 TAATTATTTAAATTAAATTA
1 -AATT-TTTAAATTAAATTA
1380166 AATTTTTAAATT
1 AATTTTTAAATT
1380178 TTTATAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 8 0.28
19 4 0.14
20 6 0.21
21 4 0.14
22 7 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
AATTTTTAAATTAAATTA
Found at i:1380855 original size:18 final size:17
Alignment explanation
Indices: 1380822--1380861 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
1380812 ATTAAACTTT
1380822 TTAA-ATATTTAATATA
1 TTAATATATTTAATATA
1380838 TTAATATATTTAAATATA
1 TTAATATATTT-AATATA
*
1380856 CTAATA
1 TTAATA
1380862 AAATAAACTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.19
17 6 0.29
18 11 0.52
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAATATATTTAATATA
Found at i:1392442 original size:39 final size:39
Alignment explanation
Indices: 1392386--1392496 Score: 134
Period size: 39 Copynumber: 2.8 Consensus size: 39
1392376 AAAAGTTCAC
* *
1392386 AAGACCAATCAAATTCATATAAATCCAAATATGTATCAA
1 AAGATCAATCAAATTCATATAAAACCAAATATGTATCAA
* * * * *
1392425 GATG-TCAATTAAATTCATATAAAGCCAAATATTTATTAA
1 -AAGATCAATCAAATTCATATAAAACCAAATATGTATCAA
*
1392464 AAGATCAATCAAGTTCATATAAAACCAAATATG
1 AAGATCAATCAAATTCATATAAAACCAAATATG
1392497 CCTAAAAAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
38 2 0.03
39 55 0.93
40 2 0.03
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (39 bp):
AAGATCAATCAAATTCATATAAAACCAAATATGTATCAA
Found at i:1396768 original size:20 final size:21
Alignment explanation
Indices: 1396730--1396781 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 21
1396720 CTATAATTTG
*
1396730 TATCGATACAAATAGTAAATA
1 TATCGATACATATAGTAAATA
*
1396751 TATCGATACATA-AGTAAATG
1 TATCGATACATATAGTAAATA
1396771 TATCGATACAT
1 TATCGATACAT
1396782 GCATGAAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.31
Consensus pattern (21 bp):
TATCGATACATATAGTAAATA
Found at i:1403378 original size:13 final size:13
Alignment explanation
Indices: 1403360--1403384 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1403350 CATAAAGTGT
1403360 TGTATCGATACAA
1 TGTATCGATACAA
1403373 TGTATCGATACA
1 TGTATCGATACA
1403385 TATTTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1403400 original size:32 final size:33
Alignment explanation
Indices: 1403340--1403405 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
1403330 TTCAACGATT
1403340 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
** *
1403373 TGTATCGATACAT-ATTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
1403405 T
1 T
1403406 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.39
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:1403439 original size:85 final size:86
Alignment explanation
Indices: 1403340--1403523 Score: 352
Period size: 86 Copynumber: 2.2 Consensus size: 86
1403330 TTCAACGATT
1403340 TGTATCGATACATAAAGTGTTGTATCGATACAATGTATCGATACATA-TTTTTTGTATCGATACA
1 TGTATCGATACATAAAGTGTTGTATCGATACAATGTATCGATACATATTTTTTTGTATCGATACA
1403404 ATTTAAGCTACTGCCAAAAAA
66 ATTTAAGCTACTGCCAAAAAA
*
1403425 TGTATTGATACATAAAGTGTTGTATCGATACAATGTATCGATACATATTTTTTTGTATCGATACA
1 TGTATCGATACATAAAGTGTTGTATCGATACAATGTATCGATACATATTTTTTTGTATCGATACA
1403490 ATTTAAGCTACTGCCAAAAAA
66 ATTTAAGCTACTGCCAAAAAA
1403511 TGTATCGATACAT
1 TGTATCGATACAT
1403524 TACTCAAATG
Statistics
Matches: 96, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
85 46 0.48
86 50 0.52
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (86 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAATGTATCGATACATATTTTTTTGTATCGATACA
ATTTAAGCTACTGCCAAAAAA
Found at i:1403460 original size:33 final size:33
Alignment explanation
Indices: 1403423--1403491 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
1403413 ACTGCCAAAA
*
1403423 AATGTATTGATACATAAAGTGTTGTATCGATAC
1 AATGTATCGATACATAAAGTGTTGTATCGATAC
*** *
1403456 AATGTATCGATACATATTTTTTTGTATCGATAC
1 AATGTATCGATACATAAAGTGTTGTATCGATAC
1403489 AAT
1 AAT
1403492 TTAAGCTACT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (33 bp):
AATGTATCGATACATAAAGTGTTGTATCGATAC
Found at i:1403463 original size:13 final size:13
Alignment explanation
Indices: 1403445--1403469 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1403435 CATAAAGTGT
1403445 TGTATCGATACAA
1 TGTATCGATACAA
1403458 TGTATCGATACA
1 TGTATCGATACA
1403470 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1403594 original size:52 final size:51
Alignment explanation
Indices: 1403531--1403732 Score: 289
Period size: 52 Copynumber: 3.9 Consensus size: 51
1403521 CATTACTCAA
* * *
1403531 ATGTATCGATACACTGATCT-TTGTATCGATACATGTAGGCAAATTTGCCCAG
1 ATGTATCGATACACT-AT-TAATGTATCGATACATGCAGGCAAATTTACCCAG
* * *
1403583 ATGTATCGATACATTATAAAATGTATTGATACATGCAGGCAAATTTACCCAG
1 ATGTATCGATACACTAT-TAATGTATCGATACATGCAGGCAAATTTACCCAG
1403635 ATGTATCGATACACTATTAAATGTATCGATACATGCAGGCAAATTTACCCAG
1 ATGTATCGATACACTATT-AATGTATCGATACATGCAGGCAAATTTACCCAG
*
1403687 ATGTATCGATACACTATTAAATGTATCGATACATGCAGGTAAATTT
1 ATGTATCGATACACTATT-AATGTATCGATACATGCAGGCAAATTT
1403733 TCATATTTCG
Statistics
Matches: 137, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
51 2 0.01
52 135 0.99
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (51 bp):
ATGTATCGATACACTATTAATGTATCGATACATGCAGGCAAATTTACCCAG
Found at i:1405878 original size:24 final size:27
Alignment explanation
Indices: 1405851--1405901 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1405841 TATCAAAATT
1405851 TATTCAT-CG-GGG-ACACTCCAACCC
1 TATTCATCCGAGGGAACACTCCAACCC
*
1405875 TATTCCTCCGAGGGAACACTCCAACCC
1 TATTCATCCGAGGGAACACTCCAACCC
1405902 CGTTTTCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 6 0.26
25 2 0.09
26 3 0.13
27 12 0.52
ACGTcount: A:0.25, C:0.39, G:0.16, T:0.20
Consensus pattern (27 bp):
TATTCATCCGAGGGAACACTCCAACCC
Found at i:1408882 original size:42 final size:42
Alignment explanation
Indices: 1408791--1409064 Score: 229
Period size: 42 Copynumber: 6.5 Consensus size: 42
1408781 TCCTCATATT
* * * * *
1408791 TCCTTTGTACTCAAGGAGCAGGACCCA-TTACATTCTCCTTTT-
1 TCCTTTGTCCTCAAAGAGCAAGACACACTT-TATT-TCCTTTTC
* * * *
1408833 TGCTTTGTCCTCAAAGAGAAAAACACACTTTATTTTCTTTTC
1 TCCTTTGTCCTCAAAGAGCAAGACACACTTTATTTCCTTTTC
* *
1408875 TCTTTTGTCCTTAAAGAGCAAGA-A-ACTTTATTTCCTTTTC
1 TCCTTTGTCCTCAAAGAGCAAGACACACTTTATTTCCTTTTC
** * *
1408915 TCCTTTGTCCTCAAAGAGCAAGATGC-GTTTAATTTCCTTTTT
1 TCCTTTGTCCTCAAAGAGCAAGACACACTTT-ATTTCCTTTTC
*
1408957 TCCCTTTGGCCTCAAAGAGCAAGACACACTTTATTT-CTTATTC
1 T-CCTTTGTCCTCAAAGAGCAAGACACACTTTATTTCCTT-TTC
* * ** **
1409000 TCCTTTGTCCTCAAAGGGCAGGATGCA-TTTCATTTTATTTTC
1 TCCTTTGTCCTCAAAGAGCAAGACACACTTT-ATTTCCTTTTC
* *
1409042 TCCTTTTTCCTCAAAGAGGAAGA
1 TCCTTTGTCCTCAAAGAGCAAGA
1409065 TGCATTTTAT
Statistics
Matches: 187, Mismatches: 35, Indels: 20
0.77 0.14 0.08
Matches are distributed among these distances:
40 36 0.19
41 13 0.07
42 102 0.55
43 33 0.18
44 3 0.02
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.39
Consensus pattern (42 bp):
TCCTTTGTCCTCAAAGAGCAAGACACACTTTATTTCCTTTTC
Found at i:1409007 original size:85 final size:82
Alignment explanation
Indices: 1408826--1409103 Score: 255
Period size: 85 Copynumber: 3.4 Consensus size: 82
1408816 CATTACATTC
* * * ** * * *
1408826 TCCTTTT-TGCTTTGTCCTCAAAGAGAAAAACACACTTT-ATTTTCTTTTCTCTTTTGTCCTTAA
1 TCCTTTTCTCCTTTGTCCTCAAAGAGCAAGATGCA-TTTAATTTTATTTTCTCCTTTGTCCTCAA
1408889 AGAGCAAGAAACTTTATT
65 AGAGCAAGAAACTTTATT
* * *
1408907 TCCTTTTCTCCTTTGTCCTCAAAGAGCAAGATGCGTTTAATTTCCTTTTTTC-CCTTTGGCCTCA
1 TCCTTTTCTCCTTTGTCCTCAAAGAGCAAGATGCATTTAATTT--TATTTTCTCCTTTGTCCTCA
1408971 AAGAGCAAGACACACTTTATT
64 AAGAGCAAGA-A-ACTTTATT
* * * *
1408992 T-CTTATTCTCCTTTGTCCTCAAAGGGCAGGATGCATTTCATTTTATTTTCTCCTTTTTCCTCAA
1 TCCTT-TTCTCCTTTGTCCTCAAAGAGCAAGATGCATTTAATTTTATTTTCTCCTTTGTCCTCAA
* **
1409056 AGAGGAAG--A-TGCATT
65 AGAGCAAGAAACTTTATT
** * *
1409071 TTATTTTCTCCTTTGTCTTCAAAGAGCATGATG
1 TCCTTTTCTCCTTTGTCCTCAAAGAGCAAGATG
1409104 ACTTCCTTTT
Statistics
Matches: 164, Mismatches: 24, Indels: 20
0.79 0.12 0.10
Matches are distributed among these distances:
79 30 0.18
80 3 0.02
81 10 0.06
82 25 0.15
83 25 0.15
84 28 0.17
85 43 0.26
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.42
Consensus pattern (82 bp):
TCCTTTTCTCCTTTGTCCTCAAAGAGCAAGATGCATTTAATTTTATTTTCTCCTTTGTCCTCAAA
GAGCAAGAAACTTTATT
Found at i:1409067 original size:42 final size:41
Alignment explanation
Indices: 1408835--1409103 Score: 221
Period size: 42 Copynumber: 6.6 Consensus size: 41
1408825 CTCCTTTTTG
* * **
1408835 CTTTGTCCTCAAAGAGAAAAACACACTTTATTT-TCTTTTCTC
1 CTTTGTCCTCAAAGAGCAAGATGCA-TTTATTTCT-TTTTCTC
* * ** *
1408877 TTTTGTCCTTAAAGAGCAAGAAAC-TTTATTTCCTTTTCTC
1 CTTTGTCCTCAAAGAGCAAGATGCATTTATTTCTTTTTCTC
*
1408917 CTTTGTCCTCAAAGAGCAAGATGCGTTTAATTTCCTTTTT-TCC
1 CTTTGTCCTCAAAGAGCAAGATGCATTT-ATTT-CTTTTTCT-C
* ** *
1408960 CTTTGGCCTCAAAGAGCAAGACACACTTTATTTCTTATTCTC
1 CTTTGTCCTCAAAGAGCAAGATGCA-TTTATTTCTTTTTCTC
* *
1409002 CTTTGTCCTCAAAGGGCAGGATGCATTTCATTT-TATTTTCTC
1 CTTTGTCCTCAAAGAGCAAGATGCATTT-ATTTCT-TTTTCTC
* * *
1409044 CTTTTTCCTCAAAGAGGAAGATGCA--T-TTT-ATTTTCTC
1 CTTTGTCCTCAAAGAGCAAGATGCATTTATTTCTTTTTCTC
* *
1409081 CTTTGTCTTCAAAGAGCATGATG
1 CTTTGTCCTCAAAGAGCAAGATG
1409104 ACTTCCTTTT
Statistics
Matches: 187, Mismatches: 31, Indels: 23
0.78 0.13 0.10
Matches are distributed among these distances:
37 26 0.14
38 3 0.02
40 35 0.19
41 7 0.04
42 81 0.43
43 32 0.17
44 3 0.02
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.41
Consensus pattern (41 bp):
CTTTGTCCTCAAAGAGCAAGATGCATTTATTTCTTTTTCTC
Found at i:1409692 original size:87 final size:87
Alignment explanation
Indices: 1409425--1409943 Score: 650
Period size: 87 Copynumber: 6.0 Consensus size: 87
1409415 CGATGCCCAA
* * *
1409425 GTCAAA-CCCTACACGAGTTGGTGGCACCTAAGTTCAAGTTAAGTCCACATTAATTGGCACCTGT
1 GTCAAAGCCC-ACACGAGTTGGTGGCACCTAAGTTTAAGTCAAGTCCACATTAGTTGGCACCTGT
*
1409489 CTAAGGAGGTTAAGCCTTAGAAT
65 CTAAAGAGGTTAAGCCTTAGAAT
* * * * * *
1409512 GTCAAAGCCCACACAAGTTGGTGACACTTAAGTTTGAGTCAAGACCACA--AGTTGGCACTTGTC
1 GTCAAAGCCCACACGAGTTGGTGGCACCTAAGTTTAAGTCAAGTCCACATTAGTTGGCACCTGTC
*
1409575 AAAAGAGGTTAAGCCTTAGAAT
66 TAAAGAGGTTAAGCCTTAGAAT
* * * *
1409597 GTCGAAGCCCACATGAGTTGGTGGCACCCAAGTTTAAGTCAAGTCCACGTTAGTTGGCACCTGTC
1 GTCAAAGCCCACACGAGTTGGTGGCACCTAAGTTTAAGTCAAGTCCACATTAGTTGGCACCTGTC
* *
1409662 TAAGGAGGTTAAGCCTTAAAAT
66 TAAAGAGGTTAAGCCTTAGAAT
* * *
1409684 GTCAAAGCCCACACGAGTTGGTGGCACCTAAGTTTGAGTCAAGTACATATTAGTTGGCACCTGTC
1 GTCAAAGCCCACACGAGTTGGTGGCACCTAAGTTTAAGTCAAGTCCACATTAGTTGGCACCTGTC
* *
1409749 TAAAGAAGTTAAGCCTTAAAAT
66 TAAAGAGGTTAAGCCTTAGAAT
** ** *
1409771 GTCAAAGCCCACACGAGTTGGTGGCACCTAAGTTCGAGTCAAGTCCATGTTAGTTGGCACTTGTC
1 GTCAAAGCCCACACGAGTTGGTGGCACCTAAGTTTAAGTCAAGTCCACATTAGTTGGCACCTGTC
** *
1409836 TAAAGAACTTAAACCTTAGAAT
66 TAAAGAGGTTAAGCCTTAGAAT
* * * *
1409858 GTCAAAACCCACACAAGCTT-GTGGCACCTAAGTCTAAGTCAAGTCCGCATTAGTTGGCACCTGT
1 GTCAAAGCCCACACGAG-TTGGTGGCACCTAAGTTTAAGTCAAGTCCACATTAGTTGGCACCTGT
* * * *
1409922 CTGAGGGGGTCAAGCCTTAGAA
65 CTAAAGAGGTTAAGCCTTAGAA
1409944 AAACTAAAAC
Statistics
Matches: 372, Mismatches: 56, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
85 72 0.19
87 295 0.79
88 5 0.01
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (87 bp):
GTCAAAGCCCACACGAGTTGGTGGCACCTAAGTTTAAGTCAAGTCCACATTAGTTGGCACCTGTC
TAAAGAGGTTAAGCCTTAGAAT
Found at i:1411727 original size:24 final size:24
Alignment explanation
Indices: 1411695--1411743 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1411685 GAAATTTCCA
1411695 GCACATTAGTTGTTGTTAGAACAT
1 GCACATTAGTTGTTGTTAGAACAT
1411719 GCACATTAGTTGTTGTTAGAACAT
1 GCACATTAGTTGTTGTTAGAACAT
1411743 G
1 G
1411744 TTCATATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (24 bp):
GCACATTAGTTGTTGTTAGAACAT
Found at i:1414588 original size:706 final size:706
Alignment explanation
Indices: 1413237--1414645 Score: 2818
Period size: 706 Copynumber: 2.0 Consensus size: 706
1413227 TTATGGGTTG
1413237 TCCATATTCTTATTCATCATTTTCCTTGTGTTATATCATTACATTAGTCACATGTCTCCTATTAT
1 TCCATATTCTTATTCATCATTTTCCTTGTGTTATATCATTACATTAGTCACATGTCTCCTATTAT
1413302 AATAATTGTTATGCATTTATGTGTTATTAATTGTTTTCTAAAAAATCATTAAGGCAATGTTCCGT
66 AATAATTGTTATGCATTTATGTGTTATTAATTGTTTTCTAAAAAATCATTAAGGCAATGTTCCGT
1413367 ATTGGTATCCCTTTAATGCTCAATGTGGAATATCCTTTTTAAATTCAAACCGAAACATTTTATCC
131 ATTGGTATCCCTTTAATGCTCAATGTGGAATATCCTTTTTAAATTCAAACCGAAACATTTTATCC
1413432 TTACGTTTCTCCATTTCCTTGAGATATGTAATGGTGCCAAATTATTTTTTTAAAAATCGAGTCCT
196 TTACGTTTCTCCATTTCCTTGAGATATGTAATGGTGCCAAATTATTTTTTTAAAAATCGAGTCCT
1413497 ATTTTCTTTATAAAAATCATGCATTAATAAAAGGGATTATATTCAAGTACTAACATTGAAAGCCG
261 ATTTTCTTTATAAAAATCATGCATTAATAAAAGGGATTATATTCAAGTACTAACATTGAAAGCCG
1413562 AGAAAATTGAGATCAGGATAGTATATGGATAAGAGGTACCTATTTTGGGCGTCCTAGGGGTACTA
326 AGAAAATTGAGATCAGGATAGTATATGGATAAGAGGTACCTATTTTGGGCGTCCTAGGGGTACTA
1413627 ATCCTTCTCTACACGTAACCGACTCTCGGACACTACTAGCAAATTCTGAAGTACGCAGACCACGA
391 ATCCTTCTCTACACGTAACCGACTCTCGGACACTACTAGCAAATTCTGAAGTACGCAGACCACGA
1413692 AACCAAATCTTCATGTTTAACAATTTAGGACAACGATTTCGATAGGTTATCGGTCACACCTAACC
456 AACCAAATCTTCATGTTTAACAATTTAGGACAACGATTTCGATAGGTTATCGGTCACACCTAACC
1413757 CAAATGATCAGTGGCGACTCCCAATCTTTGGTCATTTCGTGGTGACCATTGAAGATTAATTAGAT
521 CAAATGATCAGTGGCGACTCCCAATCTTTGGTCATTTCGTGGTGACCATTGAAGATTAATTAGAT
1413822 GGGCGATTCGTCTAATGATCTTCCCTAATTACACATTTTCATCACGCCACAAAAATCCCTAATCG
586 GGGCGATTCGTCTAATGATCTTCCCTAATTACACATTTTCATCACGCCACAAAAATCCCTAATCG
1413887 TGAAGGATATTAAGTCAGGCACACCTGATTCCCTATCACCGGGGCGAGCACACATT
651 TGAAGGATATTAAGTCAGGCACACCTGATTCCCTATCACCGGGGCGAGCACACATT
1413943 TCCATATTCTTATTCATCATTTTCCTTGTGTTATATCATTACATTAGTCACATGTCTCCTATTAT
1 TCCATATTCTTATTCATCATTTTCCTTGTGTTATATCATTACATTAGTCACATGTCTCCTATTAT
1414008 AATAATTGTTATGCATTTATGTGTTATTAATTGTTTTCTAAAAAATCATTAAGGCAATGTTCCGT
66 AATAATTGTTATGCATTTATGTGTTATTAATTGTTTTCTAAAAAATCATTAAGGCAATGTTCCGT
1414073 ATTGGTATCCCTTTAATGCTCAATGTGGAATATCCTTTTTAAATTCAAACCGAAACATTTTATCC
131 ATTGGTATCCCTTTAATGCTCAATGTGGAATATCCTTTTTAAATTCAAACCGAAACATTTTATCC
1414138 TTACGTTTCTCCATTTCCTTGAGATATGTAATGGTGCCAAATTATTTTTTTAAAAATCGAGTCCT
196 TTACGTTTCTCCATTTCCTTGAGATATGTAATGGTGCCAAATTATTTTTTTAAAAATCGAGTCCT
1414203 ATTTTCTTTATAAAAATCATGCATTAATAAAAGGGATTATATTCAAGTACTAACATTGAAAGCCG
261 ATTTTCTTTATAAAAATCATGCATTAATAAAAGGGATTATATTCAAGTACTAACATTGAAAGCCG
1414268 AGAAAATTGAGATCAGGATAGTATATGGATAAGAGGTACCTATTTTGGGCGTCCTAGGGGTACTA
326 AGAAAATTGAGATCAGGATAGTATATGGATAAGAGGTACCTATTTTGGGCGTCCTAGGGGTACTA
1414333 ATCCTTCTCTACACGTAACCGACTCTCGGACACTACTAGCAAATTCTGAAGTACGCAGACCACGA
391 ATCCTTCTCTACACGTAACCGACTCTCGGACACTACTAGCAAATTCTGAAGTACGCAGACCACGA
1414398 AACCAAATCTTCATGTTTAACAATTTAGGACAACGATTTCGATAGGTTATCGGTCACACCTAACC
456 AACCAAATCTTCATGTTTAACAATTTAGGACAACGATTTCGATAGGTTATCGGTCACACCTAACC
1414463 CAAATGATCAGTGGCGACTCCCAATCTTTGGTCATTTCGTGGTGACCATTGAAGATTAATTAGAT
521 CAAATGATCAGTGGCGACTCCCAATCTTTGGTCATTTCGTGGTGACCATTGAAGATTAATTAGAT
1414528 GGGCGATTCGTCTAATGATCTTCCCTAATTACACATTTTCATCACGCCACAAAAATCCCTAATCG
586 GGGCGATTCGTCTAATGATCTTCCCTAATTACACATTTTCATCACGCCACAAAAATCCCTAATCG
1414593 TGAAGGATATTAAGTCAGGCACACCTGATTCCCTATCACCGGGGCGAGCACAC
651 TGAAGGATATTAAGTCAGGCACACCTGATTCCCTATCACCGGGGCGAGCACAC
1414646 GTTGTGACAA
Statistics
Matches: 703, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
706 703 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.34
Consensus pattern (706 bp):
TCCATATTCTTATTCATCATTTTCCTTGTGTTATATCATTACATTAGTCACATGTCTCCTATTAT
AATAATTGTTATGCATTTATGTGTTATTAATTGTTTTCTAAAAAATCATTAAGGCAATGTTCCGT
ATTGGTATCCCTTTAATGCTCAATGTGGAATATCCTTTTTAAATTCAAACCGAAACATTTTATCC
TTACGTTTCTCCATTTCCTTGAGATATGTAATGGTGCCAAATTATTTTTTTAAAAATCGAGTCCT
ATTTTCTTTATAAAAATCATGCATTAATAAAAGGGATTATATTCAAGTACTAACATTGAAAGCCG
AGAAAATTGAGATCAGGATAGTATATGGATAAGAGGTACCTATTTTGGGCGTCCTAGGGGTACTA
ATCCTTCTCTACACGTAACCGACTCTCGGACACTACTAGCAAATTCTGAAGTACGCAGACCACGA
AACCAAATCTTCATGTTTAACAATTTAGGACAACGATTTCGATAGGTTATCGGTCACACCTAACC
CAAATGATCAGTGGCGACTCCCAATCTTTGGTCATTTCGTGGTGACCATTGAAGATTAATTAGAT
GGGCGATTCGTCTAATGATCTTCCCTAATTACACATTTTCATCACGCCACAAAAATCCCTAATCG
TGAAGGATATTAAGTCAGGCACACCTGATTCCCTATCACCGGGGCGAGCACACATT
Found at i:1416069 original size:34 final size:34
Alignment explanation
Indices: 1416030--1416101 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
1416020 CCCAGTGGCA
1416030 TTTTTTCTTTTAAAGTCCACAACTCCGTGGCACC
1 TTTTTTCTTTTAAAGTCCACAACTCCGTGGCACC
** * * *
1416064 TTTTTTCTTTTTTAGTTCACAACTCTGTGGCATC
1 TTTTTTCTTTTAAAGTCCACAACTCCGTGGCACC
1416098 TTTT
1 TTTT
1416102 AGTCCTTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.17, C:0.24, G:0.11, T:0.49
Consensus pattern (34 bp):
TTTTTTCTTTTAAAGTCCACAACTCCGTGGCACC
Found at i:1416246 original size:42 final size:42
Alignment explanation
Indices: 1416200--1416455 Score: 282
Period size: 42 Copynumber: 6.4 Consensus size: 42
1416190 CTTTTTGCTC
* *
1416200 TGTCCTCAAAGAGCAAAACACACTTTATTTCTTTTTCTCTTT
1 TGTCCTCAAAGAGCAAGACACACTTTATTTCTTTTTCTCCTT
* * *
1416242 TGTCCTCAAAGAGTAGGACACACTTTATATCTTTTTCTCCTT
1 TGTCCTCAAAGAGCAAGACACACTTTATTTCTTTTTCTCCTT
* * *
1416284 TGTCCTCAAAGAGCAAGACGCGCTCTA-TT-TTTTT-TCCTT
1 TGTCCTCAAAGAGCAAGACACACTTTATTTCTTTTTCTCCTT
* *
1416323 TGTCCTCAAAAAGCAAG--ACATTTTATTT-TTTTTCTCCTT
1 TGTCCTCAAAGAGCAAGACACACTTTATTTCTTTTTCTCCTT
* * *
1416362 TGTCCTCAAAGGGCAAGACGCACTTTATTTCTATTTCTCCTT
1 TGTCCTCAAAGAGCAAGACACACTTTATTTCTTTTTCTCCTT
* * *
1416404 TGTCCTCAAAAAGTAAGACGCACTTTA-----TTTTCTCCTT
1 TGTCCTCAAAGAGCAAGACACACTTTATTTCTTTTTCTCCTT
*
1416441 TGTCTTCAAAGAGCA
1 TGTCCTCAAAGAGCA
1416456 GGACTATTTC
Statistics
Matches: 181, Mismatches: 28, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
37 25 0.14
38 7 0.04
39 41 0.23
40 5 0.03
41 10 0.06
42 93 0.51
ACGTcount: A:0.25, C:0.24, G:0.12, T:0.40
Consensus pattern (42 bp):
TGTCCTCAAAGAGCAAGACACACTTTATTTCTTTTTCTCCTT
Found at i:1416372 original size:120 final size:119
Alignment explanation
Indices: 1416191--1416464 Score: 325
Period size: 120 Copynumber: 2.3 Consensus size: 119
1416181 TTCATTCTCC
* * * * * *
1416191 TTTTTGCTCTGTCCTCAAAGAGCAAAACACACTTTATTTCTTTTTCTCTTTTGTCCTCAAAGAGT
1 TTTTTCCTTTGTCCTCAAAGAGC--AAGACATTTTATTTCTTTTTCTCCTTTGTCCTCAAAGAGC
* * * * *
1416256 AGGACACACTTTATATCTTTTTCTCCTTTGTCCTCAAAGAGCAAGACGCGCTCTATTT
64 AAGACACACTTTATATCTATTTCTCCTTTGTCCTCAAAAAGCAAGACGCACT-T-TAT
* *
1416314 TTTTTCCTTTGTCCTCAAAAAGCAAGACATTTTATTT-TTTTTCTCCTTTGTCCTCAAAGGGCAA
1 TTTTTCCTTTGTCCTCAAAGAGCAAGACATTTTATTTCTTTTTCTCCTTTGTCCTCAAAGAGCAA
* * *
1416378 GACGCACTTTATTTCTATTTCTCCTTTGTCCTCAAAAAGTAAGACGCACTTTAT
66 GACACACTTTATATCTATTTCTCCTTTGTCCTCAAAAAGCAAGACGCACTTTAT
* * *
1416432 TTTCTCCTTTGTCTTCAAAGAGCAGGACTATTT
1 TTTTTCCTTTGTCCTCAAAGAGCAAGAC-ATTT
1416465 CCTTTTTCCT
Statistics
Matches: 130, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
118 26 0.20
119 5 0.04
120 67 0.52
121 12 0.09
123 20 0.15
ACGTcount: A:0.24, C:0.23, G:0.12, T:0.41
Consensus pattern (119 bp):
TTTTTCCTTTGTCCTCAAAGAGCAAGACATTTTATTTCTTTTTCTCCTTTGTCCTCAAAGAGCAA
GACACACTTTATATCTATTTCTCCTTTGTCCTCAAAAAGCAAGACGCACTTTAT
Found at i:1417050 original size:86 final size:87
Alignment explanation
Indices: 1416782--1417298 Score: 628
Period size: 87 Copynumber: 6.0 Consensus size: 87
1416772 TGCCCGACTT
* * * * * * *
1416782 AAAGCCCACATGAGTTGGTGGCACGTATGTTCAAGTTAAGTCCACACTAGTTGGCACCTATCTAA
1 AAAGCCCACATGAGTTGGTGACACCTAAGTTCGAGTCAAGTCCACATTAGTTGGCACCTGTCTAA
* *
1416847 GGAGGTTAAGCATTAGAATGTC
66 AGAGGTTAAGCCTTAGAATGTC
* * * *
1416869 AAAGCCCATAGGAGTTGGCGGA-A-CTAAAGTTCGAGTCAAGTCCACATTAGTTGGCACCTATCT
1 AAAGCCCACATGAGTTGG-TGACACCT-AAGTTCGAGTCAAGTCCACATTAGTTGGCACCTGTCT
*
1416932 AAAGAGATTAAGCCTTAGAATGTC
64 AAAGAGGTTAAGCCTTAGAATGTC
* ** *
1416956 GAAGCCCACACAAGTTGGTGACACCTAAGTTCGAGTCAAGTCCACGTTAGTTGG-ACCTGTCTAA
1 AAAGCCCACATGAGTTGGTGACACCTAAGTTCGAGTCAAGTCCACATTAGTTGGCACCTGTCTAA
1417020 AGAGGTTAAGCCTTAGAATGTC
66 AGAGGTTAAGCCTTAGAATGTC
* * * *
1417042 GAAGCCCACATGAGTTGGTGGCACCTAAGTTCGAGTCAAGTCCATATTAGTTGGCACTTGTCTAA
1 AAAGCCCACATGAGTTGGTGACACCTAAGTTCGAGTCAAGTCCACATTAGTTGGCACCTGTCTAA
* *
1417107 AGAAGTTAAGCCTTAGAATGTTA
66 AGAGGTTAAGCCTTAGAATG-TC
* * * *
1417130 AAAGCCCACACGAGTTGGTGACATCTAAGTTCGAGTCAAGTCTACGTTAGTTGGCACCTGTCTAA
1 AAAGCCCACATGAGTTGGTGACACCTAAGTTCGAGTCAAGTCCACATTAGTTGGCACCTGTCTAA
** *
1417195 AGAACTTAAGCCTTAGAATATC
66 AGAGGTTAAGCCTTAGAATGTC
* * * * *
1417217 AAAGCCCACATAAGCTGCTG-CACCTAAGTCCAAGTCAAGTCCACATTAGTTGGCACCTGTCTAA
1 AAAGCCCACATGAGTTGGTGACACCTAAGTTCGAGTCAAGTCCACATTAGTTGGCACCTGTCTAA
* * *
1417281 GGAGGTCAAGCTTTAGAA
66 AGAGGTTAAGCCTTAGAA
1417299 AAACCAAAAC
Statistics
Matches: 371, Mismatches: 53, Indels: 13
0.85 0.12 0.03
Matches are distributed among these distances:
86 134 0.36
87 158 0.43
88 79 0.21
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (87 bp):
AAAGCCCACATGAGTTGGTGACACCTAAGTTCGAGTCAAGTCCACATTAGTTGGCACCTGTCTAA
AGAGGTTAAGCCTTAGAATGTC
Done.