Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 3 of 93
Found at i:1105569 original size:5 final size:5
Alignment explanation
Indices: 1105559--1105583 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1105549 TAAATTAATT
1105559 ACCTA ACCTA ACCTA ACCTA ACCTA
1 ACCTA ACCTA ACCTA ACCTA ACCTA
1105584 CATCTGCCTT
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:0.40, G:0.00, T:0.20
Consensus pattern (5 bp):
ACCTA
Found at i:1108467 original size:33 final size:33
Alignment explanation
Indices: 1108430--1108496 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
1108420 GGAGCAATGA
* *
1108430 TTTAGTTTAGTTTTCACTAGAATCTATACTTTG
1 TTTAGTTTAGTTTTCACTAAAACCTATACTTTG
1108463 TTTAGTTTAGTTTTCACTAAAACCTATACTTTG
1 TTTAGTTTAGTTTTCACTAAAACCTATACTTTG
1108496 T
1 T
1108497 CAATGGATCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.25, C:0.13, G:0.10, T:0.51
Consensus pattern (33 bp):
TTTAGTTTAGTTTTCACTAAAACCTATACTTTG
Found at i:1118050 original size:13 final size:13
Alignment explanation
Indices: 1118034--1118058 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1118024 TTTAGAACAA
1118034 AATAAAACTGATG
1 AATAAAACTGATG
1118047 AATAAAACTGAT
1 AATAAAACTGAT
1118059 AAAGCAGTTT
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:0.56, C:0.08, G:0.12, T:0.24
Consensus pattern (13 bp):
AATAAAACTGATG
Found at i:1119746 original size:18 final size:18
Alignment explanation
Indices: 1119713--1119747 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1119703 TCAAGAAGCA
*
1119713 GCAGAAGAGGAAGAAGAT
1 GCAGAAGAAGAAGAAGAT
*
1119731 GCAGAAGAAGATGAAGA
1 GCAGAAGAAGAAGAAGA
1119748 ATTTATATTA
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:0.51, C:0.06, G:0.37, T:0.06
Consensus pattern (18 bp):
GCAGAAGAAGAAGAAGAT
Found at i:1129428 original size:3 final size:3
Alignment explanation
Indices: 1129422--1129455 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
1129412 AGTAAGTAAA
* *
1129422 CAG CAG CAG CAG CAG CAG CAC CAG CAC CAG CAG C
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG C
1129456 CACTGAGTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.32, C:0.41, G:0.26, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:1131678 original size:2 final size:2
Alignment explanation
Indices: 1131671--1131699 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1131661 AGAGGTCCAA
1131671 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 A
1131700 CACACCAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1143733 original size:32 final size:32
Alignment explanation
Indices: 1143697--1143757 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
1143687 AACATCACCA
1143697 AAGTTCCACTAA-CATTCAAAGTTTAAAACCTT
1 AAGTTCCA-TAAGCATTCAAAGTTTAAAACCTT
*
1143729 AAGTTCCATAAGTATTCAAAGTTTAAAAC
1 AAGTTCCATAAGCATTCAAAGTTTAAAAC
1143758 GTTGTATTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 3 0.11
32 24 0.89
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.31
Consensus pattern (32 bp):
AAGTTCCATAAGCATTCAAAGTTTAAAACCTT
Found at i:1147626 original size:29 final size:30
Alignment explanation
Indices: 1147588--1147655 Score: 102
Period size: 29 Copynumber: 2.3 Consensus size: 30
1147578 ATAGTTATCA
*
1147588 ATATTGTATTATACGTAATAAATTATA-TT
1 ATATTATATTATACGTAATAAATTATATTT
*
1147617 ATATTATATTATACGTGATAAATTATATTT
1 ATATTATATTATACGTAATAAATTATATTT
*
1147647 ATAATATAT
1 ATATTATAT
1147656 ATAAAAATAC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
29 25 0.71
30 10 0.29
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (30 bp):
ATATTATATTATACGTAATAAATTATATTT
Found at i:1152365 original size:44 final size:44
Alignment explanation
Indices: 1152312--1152402 Score: 137
Period size: 44 Copynumber: 2.1 Consensus size: 44
1152302 AATTGTGTTG
* *
1152312 TATGATAATAATAAAAAATAATAACAATATAGTATTTAATTANA
1 TATGATAATAATAAAAAATAATAACAATATAATATTTAATTAAA
* * *
1152356 TATGATAATAGTAAAAAATAATAATAATATAATTTTTAATTAAA
1 TATGATAATAATAAAAAATAATAACAATATAATATTTAATTAAA
1152400 TAT
1 TAT
1152403 TGAAAATTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.37
Consensus pattern (44 bp):
TATGATAATAATAAAAAATAATAACAATATAATATTTAATTAAA
Found at i:1152831 original size:21 final size:20
Alignment explanation
Indices: 1152777--1152831 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
1152767 ATTTGATGAA
1152777 ATATCAAAAATATATCTTACG
1 ATAT-AAAAATATATCTTACG
* * *
1152798 ATACACGATATATATCTTACG
1 ATATA-AAAATATATCTTACG
1152819 ATATAAAACATAT
1 ATATAAAA-ATAT
1152832 GGTATCATAT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
20 2 0.08
21 24 0.92
ACGTcount: A:0.47, C:0.15, G:0.05, T:0.33
Consensus pattern (20 bp):
ATATAAAAATATATCTTACG
Found at i:1158388 original size:29 final size:29
Alignment explanation
Indices: 1158313--1158380 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
1158303 TGACTTTTTA
*
1158313 TAGAAACAAAAATTATTTATAAAGTGTTAATT
1 TAGAAA-AAAAA--ATTCATAAAGTGTTAATT
*
1158345 TAGAAAAAAAAATTCATAAGGTGTTAA-T
1 TAGAAAAAAAAATTCATAAAGTGTTAATT
1158373 TA-AAAAAA
1 TAGAAAAAA
1158381 TAACATTCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
27 6 0.18
28 3 0.09
29 14 0.41
31 5 0.15
32 6 0.18
ACGTcount: A:0.56, C:0.03, G:0.10, T:0.31
Consensus pattern (29 bp):
TAGAAAAAAAAATTCATAAAGTGTTAATT
Found at i:1200563 original size:2 final size:2
Alignment explanation
Indices: 1200556--1200602 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
1200546 TTCAATCCTC
* *
1200556 CT CT CT CT CA CT -T CA CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
1200597 CC CT CT
1 CT CT CT
1200603 TTTTNCGCTG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.04, C:0.51, G:0.00, T:0.45
Consensus pattern (2 bp):
CT
Found at i:1204158 original size:18 final size:19
Alignment explanation
Indices: 1204103--1204159 Score: 53
Period size: 24 Copynumber: 2.8 Consensus size: 19
1204093 TAATTAATTG
*
1204103 AAAAAACTAAATAAATATA
1 AAAAAATTAAATAAATATA
1204122 AATAATAATAGTAATATAAATA-A
1 AA-AA-AAT--TAA-ATAAATATA
1204145 AAAAAATTAAATAAA
1 AAAAAATTAAATAAA
1204160 AACTTTACTT
Statistics
Matches: 32, Mismatches: 1, Indels: 11
0.73 0.02 0.25
Matches are distributed among these distances:
18 5 0.16
19 5 0.16
20 2 0.06
21 5 0.16
22 2 0.06
23 6 0.19
24 7 0.22
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (19 bp):
AAAAAATTAAATAAATATA
Found at i:1229102 original size:26 final size:26
Alignment explanation
Indices: 1229051--1229102 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
1229041 ATATTACGTG
*
1229051 TTATTATTTATATTTTTTAATTAAAT
1 TTATTATTTATATTTTTTAATAAAAT
*
1229077 TTATTATTTTTTATTTTTTAA-AAAAT
1 TTATTA-TTTATATTTTTTAATAAAAT
1229103 ATAAAGTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (26 bp):
TTATTATTTATATTTTTTAATAAAAT
Found at i:1234633 original size:2 final size:2
Alignment explanation
Indices: 1234628--1234654 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1234618 AAAAAAAAAA
1234628 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 A
1234655 GTAGTATACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1235425 original size:23 final size:23
Alignment explanation
Indices: 1235395--1235440 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
1235385 TGAATATAGA
1235395 ATAGGAATCACAAAAAGTTTTCT
1 ATAGGAATCACAAAAAGTTTTCT
*
1235418 ATAGGAATCACAAAATGTTTTCT
1 ATAGGAATCACAAAAAGTTTTCT
1235441 TACATGTAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (23 bp):
ATAGGAATCACAAAAAGTTTTCT
Found at i:1241300 original size:18 final size:17
Alignment explanation
Indices: 1241277--1241312 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
1241267 TACTACTTAA
1241277 AAAAATTTTAAATTATTT
1 AAAAATTTTAAATT-TTT
*
1241295 AAAAATTTTTAATTTTT
1 AAAAATTTTAAATTTTT
1241312 A
1 A
1241313 TTATATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AAAAATTTTAAATTTTT
Found at i:1241319 original size:26 final size:28
Alignment explanation
Indices: 1241290--1241342 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
1241280 AATTTTAAAT
*
1241290 TATTTAA-AAATTTTTA-ATTTTTATTA
1 TATTTAATAAAGTTTTATATTTTTATTA
*
1241316 TATTTAATTAAGTTTTATATTTTTATT
1 TATTTAATAAAGTTTTATATTTTTATT
1241343 TTAAATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 7 0.30
27 7 0.30
28 9 0.39
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (28 bp):
TATTTAATAAAGTTTTATATTTTTATTA
Found at i:1241346 original size:20 final size:21
Alignment explanation
Indices: 1241301--1241346 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 21
1241291 ATTTAAAAAT
*
1241301 TTTTAATTTTTATTATATTTA
1 TTTTAAGTTTTATTATATTTA
* *
1241322 -ATTAAGTTTTA-TATTTTTA
1 TTTTAAGTTTTATTATATTTA
1241341 TTTTAA
1 TTTTAA
1241347 ATTAAATAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTAAGTTTTATTATATTTA
Found at i:1241364 original size:30 final size:30
Alignment explanation
Indices: 1241281--1241364 Score: 75
Period size: 30 Copynumber: 2.8 Consensus size: 30
1241271 ACTTAAAAAA
**
1241281 ATTTTAAATTATTTAAAAATTTT-TAATTTTT
1 ATTTTAAATTAAAT-AAAATTTTAT-ATTTTT
* * * *
1241312 A--TTATATTTAATTAAGTTTTATATTTTT
1 ATTTTAAATTAAATAAAATTTTATATTTTT
1241340 ATTTTAAATTAAATAAAATTTTATA
1 ATTTTAAATTAAATAAAATTTTATA
1241365 ATTAATTAAT
Statistics
Matches: 40, Mismatches: 10, Indels: 7
0.70 0.18 0.12
Matches are distributed among these distances:
28 13 0.32
29 8 0.20
30 18 0.45
31 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (30 bp):
ATTTTAAATTAAATAAAATTTTATATTTTT
Found at i:1241870 original size:105 final size:105
Alignment explanation
Indices: 1241687--1241879 Score: 232
Period size: 105 Copynumber: 1.8 Consensus size: 105
1241677 CACGTTCAGG
* * *
1241687 ACCGTGACATCCAAAGCGAACAATACCTCATAGGAGTTAGTGTGGATCGTGACAATTGATGTCAC
1 ACCGTGACATCCAAAGCGAACAATACCTCACAAGAGTTAGTGTAGATCGTGACAATTGATGTCAC
*
1241752 AGTCTTCGCGTGGACGTGAATCTTTCAGGTCTACACTAGA
66 AGTCCTCGCGTGGACGTGAATCTTTCAGGTCTACACTAGA
* * * *
1241792 ACCGTGACATCCAAAGTGGACAATATCTCACAAGAGTTGGTGTAGA-C-TGTAGCAATTCG-TGT
1 ACCGTGACATCCAAAGCGAACAATACCTCACAAGAGTTAGTGTAGATCGTG-A-CAATT-GATGT
* *
1241854 CAC-GATCCTCGTGTGGATGTGAATCT
63 CACAG-TCCTCGCGTGGACGTGAATCT
1241880 CACATTGTTG
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
103 2 0.03
104 3 0.04
105 68 0.92
106 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.26
Consensus pattern (105 bp):
ACCGTGACATCCAAAGCGAACAATACCTCACAAGAGTTAGTGTAGATCGTGACAATTGATGTCAC
AGTCCTCGCGTGGACGTGAATCTTTCAGGTCTACACTAGA
Found at i:1251446 original size:22 final size:22
Alignment explanation
Indices: 1251420--1251463 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1251410 AACTAGTAAA
1251420 GCGGTATCAAACAGTTACATAC
1 GCGGTATCAAACAGTTACATAC
1251442 GCGGTATCAAACAGTTACATAC
1 GCGGTATCAAACAGTTACATAC
1251464 ATTCGAAGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (22 bp):
GCGGTATCAAACAGTTACATAC
Found at i:1258578 original size:14 final size:15
Alignment explanation
Indices: 1258554--1258582 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1258544 TTTGACTACT
1258554 TATTAAATTATAAAA
1 TATTAAATTATAAAA
1258569 TATT-AATTATAAAA
1 TATTAAATTATAAAA
1258583 GTTATAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TATTAAATTATAAAA
Found at i:1258602 original size:23 final size:23
Alignment explanation
Indices: 1258553--1258605 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
1258543 TTTTGACTAC
* *
1258553 TTATTAAA-TTATAAAATATTAA
1 TTATAAAAGTTATAAAATATCAA
1258575 TTATAAAAGTTATAAAATATC-A
1 TTATAAAAGTTATAAAATATCAA
1258597 TATATAAAA
1 T-TATAAAA
1258606 AATTAAAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 9 0.33
23 18 0.67
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
TTATAAAAGTTATAAAATATCAA
Found at i:1264743 original size:2 final size:2
Alignment explanation
Indices: 1264732--1264772 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
1264722 GCATAATTTT
*
1264732 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1264773 AGCGTGGATC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1267200 original size:2 final size:2
Alignment explanation
Indices: 1267193--1267237 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1267183 ACAATATGCC
1267193 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1267235 TA T
1 TA T
1267238 TGCTTAATGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1277542 original size:25 final size:25
Alignment explanation
Indices: 1277513--1277578 Score: 96
Period size: 25 Copynumber: 2.6 Consensus size: 25
1277503 AAATACTTAA
* *
1277513 ATTTTAACTTTATTTAAAATCAAAT
1 ATTTTAATTTTATTAAAAATCAAAT
*
1277538 ATTTTAATTTTATTAAAAATTAAAT
1 ATTTTAATTTTATTAAAAATCAAAT
*
1277563 ATCTTAATTTTATTAA
1 ATTTTAATTTTATTAA
1277579 CTATTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.52
Consensus pattern (25 bp):
ATTTTAATTTTATTAAAAATCAAAT
Found at i:1278450 original size:15 final size:15
Alignment explanation
Indices: 1278431--1278473 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
1278421 ATATATATAT
1278431 ATATATATTATAA-G
1 ATATATATTATAATG
*
1278445 AT-TATATAAATAATG
1 ATATATAT-TATAATG
1278460 ATATATATTATAAT
1 ATATATATTATAAT
1278474 TAATAAGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 5 0.21
14 6 0.25
15 8 0.33
16 5 0.21
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (15 bp):
ATATATATTATAATG
Found at i:1278545 original size:19 final size:19
Alignment explanation
Indices: 1278520--1278573 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
1278510 CACAAAATAA
1278520 AAAATAAATATATTTATAT
1 AAAATAAATATATTTATAT
* *
1278539 TAAATAAATATATATATAT
1 AAAATAAATATATTTATAT
*
1278558 AATAATAATTATATTT
1 AA-AATAAATATATTT
1278574 TTTATAATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AAAATAAATATATTTATAT
Found at i:1293140 original size:15 final size:15
Alignment explanation
Indices: 1293122--1293173 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
1293112 TATTAGATTT
1293122 TTTAAATATTTATAA
1 TTTAAATATTTATAA
1293137 TTTAAA-ATTT-T-A
1 TTTAAATATTTATAA
* *
1293149 TTAAAATATTAATAA
1 TTTAAATATTTATAA
1293164 TTTAAATATT
1 TTTAAATATT
1293174 NATAGAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
12 6 0.19
13 4 0.13
14 5 0.16
15 16 0.52
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTTAAATATTTATAA
Found at i:1293140 original size:27 final size:27
Alignment explanation
Indices: 1293118--1293169 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
1293108 TTTTTATTAG
1293118 ATTTT-TT-AAATATTTATAATTTAAA
1 ATTTTATTAAAATATTTATAATTTAAA
*
1293143 ATTTTATTAAAATATTAATAATTTAAA
1 ATTTTATTAAAATATTTATAATTTAAA
1293170 TATTNATAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 5 0.21
26 2 0.08
27 17 0.71
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
ATTTTATTAAAATATTTATAATTTAAA
Found at i:1293364 original size:27 final size:27
Alignment explanation
Indices: 1293334--1293386 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
1293324 ATTTTTTATT
*
1293334 TTTAAAACATTAATAATTTATAATTTG
1 TTTAAAACATTAATAATTGATAATTTG
* *
1293361 TTTAATATATTAATAATTGATAATTT
1 TTTAAAACATTAATAATTGATAATTT
1293387 AAATGTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (27 bp):
TTTAAAACATTAATAATTGATAATTTG
Found at i:1293464 original size:38 final size:38
Alignment explanation
Indices: 1293396--1293501 Score: 106
Period size: 38 Copynumber: 2.6 Consensus size: 38
1293386 TAAATGTTAA
*
1293396 TATTTTATTTATAATTTAATCATTAGTATTAT-ATAATATTAT
1 TATTTTATTT-TAATTTAA--A-TATTATTATGATAAT-TTAT
* *
1293438 TATTTTATTTTAATTTAAATATTATTATGATTATTTTT
1 TATTTTATTTTAATTTAAATATTATTATGATAATTTAT
*
1293476 TATTTTATTTTATTTTTTAAATATTA
1 TATTTTATTTTA--ATTTAAATATTA
1293502 ATAATTGAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
38 23 0.40
39 5 0.09
40 11 0.19
41 8 0.14
42 10 0.18
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.63
Consensus pattern (38 bp):
TATTTTATTTTAATTTAAATATTATTATGATAATTTAT
Found at i:1293550 original size:27 final size:26
Alignment explanation
Indices: 1293494--1293553 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
1293484 TTTATTTTTT
** *
1293494 AAATATTAATAATTGAAATTTTATTT
1 AAATATTAATAATTGAAATTCAATTA
1293520 AAATATTAATAATTGATAATTCAATTA
1 AAATATTAATAATTGA-AATTCAATTA
1293547 AAATATT
1 AAATATT
1293554 TTTTATATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 16 0.53
27 14 0.47
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (26 bp):
AAATATTAATAATTGAAATTCAATTA
Found at i:1293676 original size:25 final size:25
Alignment explanation
Indices: 1293644--1293696 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
1293634 TTTATGAATA
1293644 ATTTATAATTAAATATTAATATTTT
1 ATTTATAATTAAATATTAATATTTT
*
1293669 ATTTATAATTTAATATTAATATTTT
1 ATTTATAATTAAATATTAATATTTT
1293694 ATT
1 ATT
1293697 AAAAATTGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
ATTTATAATTAAATATTAATATTTT
Found at i:1293687 original size:32 final size:31
Alignment explanation
Indices: 1293631--1293691 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
1293621 ATTTATAATT
1293631 TATTTTATGAATAATTTATAATTAAATATTAA
1 TATTTTATGAATAATTTATAATT-AATATTAA
**
1293663 TATTTTATTTATAATTTA-ATATTAATATT
1 TATTTTATGAATAATTTATA-ATTAATATT
1293692 TTATTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 7 0.27
32 19 0.73
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (31 bp):
TATTTTATGAATAATTTATAATTAATATTAA
Found at i:1293703 original size:25 final size:25
Alignment explanation
Indices: 1293650--1293703 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
1293640 AATAATTTAT
* *
1293650 AATTAAATATTAATATTTTATTTAT
1 AATTAAATATTAATATTTTATTAAA
*
1293675 AATTTAATATTAATATTTTATTAAA
1 AATTAAATATTAATATTTTATTAAA
1293700 AATT
1 AATT
1293704 GGAATCAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
AATTAAATATTAATATTTTATTAAA
Found at i:1296798 original size:87 final size:87
Alignment explanation
Indices: 1296652--1296816 Score: 285
Period size: 87 Copynumber: 1.9 Consensus size: 87
1296642 TACCATCGAA
*
1296652 GAGAATCAAGACTAACATAACACATACTTTAAATGCAGTTTATGAAATGATTGAGAAGGGTCATG
1 GAGAATCAAGACTAACATAACACATACTTTAAATGCAGCTTATGAAATGATTGAGAAGGGTCATG
*
1296717 CTGCGAAGTTGCCTTAGCCATT
66 CTGCCAAGTTGCCTTAGCCATT
* * *
1296739 GAGAATCAAGACTAACATAACACCTACTTTAAATGCAGCTTCTGAAATGATTGAGAAGGGTCTTG
1 GAGAATCAAGACTAACATAACACATACTTTAAATGCAGCTTATGAAATGATTGAGAAGGGTCATG
1296804 CTGCCAAGTTGCC
66 CTGCCAAGTTGCC
1296817 ATAGTTAGCA
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 73 1.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.27
Consensus pattern (87 bp):
GAGAATCAAGACTAACATAACACATACTTTAAATGCAGCTTATGAAATGATTGAGAAGGGTCATG
CTGCCAAGTTGCCTTAGCCATT
Found at i:1297272 original size:14 final size:15
Alignment explanation
Indices: 1297255--1297321 Score: 55
Period size: 16 Copynumber: 4.1 Consensus size: 15
1297245 ACAATTACGG
1297255 TAAAA-AAAATATTT
1 TAAAATAAAATATTT
1297269 TAAAATAAAATATTATTT
1 TAAAAT-AAA-A-TATTT
*
1297287 TATAAATAAAATAATAT
1 TA-AAATAAAAT-ATTT
*
1297304 TAAAATATTAATATTT
1 TAAAATA-AAATATTT
1297320 TA
1 TA
1297322 TATGTTATCA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
14 5 0.12
16 14 0.33
17 10 0.23
18 10 0.23
19 4 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAAAATAAAATATTT
Found at i:1297277 original size:19 final size:20
Alignment explanation
Indices: 1297255--1297297 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
1297245 ACAATTACGG
1297255 TAAAAAAAATATTTTA-AAA
1 TAAAAAAAATATTTTATAAA
* *
1297274 T-AAAATATTATTTTATAAA
1 TAAAAAAAATATTTTATAAA
1297293 TAAAA
1 TAAAA
1297298 TAATATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 12 0.60
19 5 0.25
20 3 0.15
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
TAAAAAAAATATTTTATAAA
Found at i:1297278 original size:18 final size:19
Alignment explanation
Indices: 1297257--1297304 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
1297247 AATTACGGTA
*
1297257 AAAAAAATATTTTA-AAAT
1 AAAATAATATTTTATAAAT
*
1297275 AAAATATTATTTTATAAAT
1 AAAATAATATTTTATAAAT
1297294 AAAATAATATT
1 AAAATAATATT
1297305 AAAATATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 12 0.46
19 14 0.54
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAATAATATTTTATAAAT
Found at i:1297700 original size:16 final size:15
Alignment explanation
Indices: 1297658--1297699 Score: 66
Period size: 16 Copynumber: 2.7 Consensus size: 15
1297648 TATTATTTTA
1297658 AAAAAATAAAATAAT
1 AAAAAATAAAATAAT
*
1297673 AAAATGATAAAATAAT
1 AAAA-AATAAAATAAT
1297689 AAAAAATAAAA
1 AAAAAATAAAA
1297700 AGAATTGAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (15 bp):
AAAAAATAAAATAAT
Found at i:1298525 original size:2 final size:2
Alignment explanation
Indices: 1298520--1298571 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
1298510 GGGAAAAAAA
1298520 AT AT AT AT AT AT AT AT AT AT AT A- 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
1298561 AT AT AT AT AT A
1 AT AT AT AT AT A
1298572 GTGGGTTGCT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1299399 original size:60 final size:58
Alignment explanation
Indices: 1299245--1299415 Score: 186
Period size: 59 Copynumber: 2.9 Consensus size: 58
1299235 AAGAGAGATT
* *
1299245 TGAAGTCTCGATTTATATTGGGTGACGTGGGTAGTTCTCACGAATAAGTAAAAGGGACC
1 TGAAGTCTCGATTTATATT-GGTGACGTGAGTAGTTCTCACGAATAGGTAAAAGGGACC
* ** * *
1299304 TGAAATC-CTGATTTATATGTGGTGGTGTGAATAGTTCTCACGAATAGGTAAAGGGAGACC
1 TGAAGTCTC-GATTTATAT-TGGTGACGTGAGTAGTTCTCACGAATAGGTAAAAGG-GACC
*
1299364 TGAAGTCTCGATTTATATATAGTGACGTGAGTAGTT-TCCAC-AAGTAGGTAAA
1 TGAAGTCTCGATTTATAT-TGGTGACGTGAGTAGTTCT-CACGAA-TAGGTAAA
1299416 TGAGGACTTG
Statistics
Matches: 93, Mismatches: 13, Indels: 11
0.79 0.11 0.09
Matches are distributed among these distances:
58 1 0.01
59 47 0.51
60 44 0.47
61 1 0.01
ACGTcount: A:0.30, C:0.12, G:0.27, T:0.30
Consensus pattern (58 bp):
TGAAGTCTCGATTTATATTGGTGACGTGAGTAGTTCTCACGAATAGGTAAAAGGGACC
Found at i:1315445 original size:27 final size:27
Alignment explanation
Indices: 1315394--1315457 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
1315384 TTTAAAATTT
*
1315394 TTAAA-TAAATTTTTATTTTTATTATA
1 TTAAATTAAATTTTTATTATTATTATA
* *
1315420 TTGAATTAAATTTTTATATATT-TTATT
1 TTAAATTAAATTTTTAT-TATTATTATA
1315447 TTAAATTAAAT
1 TTAAATTAAAT
1315458 AAAATTTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 4 0.12
27 25 0.78
28 3 0.09
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (27 bp):
TTAAATTAAATTTTTATTATTATTATA
Found at i:1315466 original size:31 final size:28
Alignment explanation
Indices: 1315394--1315468 Score: 73
Period size: 31 Copynumber: 2.6 Consensus size: 28
1315384 TTTAAAATTT
*
1315394 TTAAAT-AAATTTT-TATTTTTATTATA
1 TTAAATAAAATTTTATATTTTTATTAAA
* *
1315420 TTGAATTAAATTTTTATATATTTTATTTTAAA
1 TT-AAATAAAATTTTATAT-TTTTA--TTAAA
1315452 TTAAATAAAATTTTATA
1 TTAAATAAAATTTTATA
1315469 ATTAACTATT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
26 2 0.05
27 3 0.08
28 6 0.16
29 3 0.08
30 5 0.13
31 13 0.34
32 6 0.16
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (28 bp):
TTAAATAAAATTTTATATTTTTATTAAA
Found at i:1328654 original size:27 final size:27
Alignment explanation
Indices: 1328617--1328682 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
1328607 CAGGACAGGT
1328617 CTCAGGCTTCTTACCATCTTTCTTCGG
1 CTCAGGCTTCTTACCATCTTTCTTCGG
* *
1328644 GTCAGGCTTCTTATCATCTTTCTTCGG
1 CTCAGGCTTCTTACCATCTTTCTTCGG
*
1328671 CTCGGGCTTCTT
1 CTCAGGCTTCTT
1328683 CTCTTCGGGC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.09, C:0.30, G:0.18, T:0.42
Consensus pattern (27 bp):
CTCAGGCTTCTTACCATCTTTCTTCGG
Found at i:1330492 original size:319 final size:304
Alignment explanation
Indices: 1329883--1330502 Score: 839
Period size: 319 Copynumber: 2.0 Consensus size: 304
1329873 CTACATGAAT
1329883 CTGAATCTATAGTAAATAGATATCTCTTTTATACTTAAATGTTTAAATTTCAATAAATATCAATC
1 CTGAATCTATAGTAAATAGATATCTCTTTTATACTTAAATGTTTAAATTTCAATAAATATCAATC
* *
1329948 CAATTCATTATATAAAAGTAAGATAATTTATTAGGTCAATTGATCGACACATCAATTGAATTAAT
66 CAATTCATTATATAAAAGTAAGATAATTGATTAGGTCAATAGATCGACACATCAATTGAATTAAT
*
1330013 TTTTTTTTACACCTTATATCAAAACTACATTGCTTTGGACATTTGAAAGTTTTTTTTTTTTACTT
131 TTTTTTTTACACCTTATATCAAAACTACATTGCTTTGAACATTTGAAAGTTTTTTTTTTTTACTT
*
1330078 TTATTTATATCAGTAAAAAAATACTTGAAAACAATAATTTCTAACTTTTAATACCTAGAAGATAA
196 GTATTTATATCAGTAAAAAAATACTTGAAAACAATAATTTCTAACTTTTAATACCTAGAAGATAA
*
1330143 ATTTATTTAATATTTATCAGTTACAATTTAATATTATTTTTATC
261 ATTTATTTAATATTTATCAATTACAATTTAATATTATTTTTATC
*
1330187 CTGAATTTATAGTAAATAGATATCTCTTTTATACTTAAATAGATGTTTAAA-TTCTAATAAATAT
1 CTGAATCTATAGTAAATAGATATCTCTTTTATACTT--A-A-ATGTTTAAATTTC-AATAAATAT
* * * * ** *
1330251 CCATCCAATTCATTATATATAAGTAAGATAATTGATTGGGTCAATAGATTGACATTTGTCATTCT
61 CAATCCAATTCATTATATAAAAGTAAGATAATTGATTAGGTCAATAGATCGACA--CATCAAT-T
* * * * *
1330316 TAATTAAATTAATTTTTTTACACCTTATGTCAAAACTACATTGTTTTTAACATTTGAAGGGTTTT
123 GAATT-AATT--TTTTTTTACACCTTATATCAAAACTACATTGCTTTGAACATTTGAA-AG----
* * *
1330381 TTTTTTCTTTTTTACTTGTATTTATTTTAGT-AAAAAATATTTGAAAACAATAATTTCTAACTTT
180 TTTTTT-TTTTTTACTTGTATTTATATCAGTAAAAAAATACTTGAAAACAATAATTTCTAACTTT
* * * **
1330445 TAATACTTATAAGATAGATTTATTTAATATTTATCAATTGTAATTTAATATTATTTTT
244 TAATACCTAGAAGATAAATTTATTTAATATTTATCAATTACAATTTAATATTATTTTT
1330503 TNNNNNNNNN
Statistics
Matches: 273, Mismatches: 26, Indels: 19
0.86 0.08 0.06
Matches are distributed among these distances:
304 35 0.13
306 1 0.00
307 4 0.01
308 66 0.24
310 4 0.01
311 5 0.02
312 4 0.01
314 42 0.15
315 1 0.00
319 90 0.33
320 21 0.08
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.46
Consensus pattern (304 bp):
CTGAATCTATAGTAAATAGATATCTCTTTTATACTTAAATGTTTAAATTTCAATAAATATCAATC
CAATTCATTATATAAAAGTAAGATAATTGATTAGGTCAATAGATCGACACATCAATTGAATTAAT
TTTTTTTTACACCTTATATCAAAACTACATTGCTTTGAACATTTGAAAGTTTTTTTTTTTTACTT
GTATTTATATCAGTAAAAAAATACTTGAAAACAATAATTTCTAACTTTTAATACCTAGAAGATAA
ATTTATTTAATATTTATCAATTACAATTTAATATTATTTTTATC
Found at i:1334100 original size:41 final size:41
Alignment explanation
Indices: 1334016--1334101 Score: 95
Period size: 41 Copynumber: 2.1 Consensus size: 41
1334006 TAAATCAAAG
* * *
1334016 CCTATCATAATATATTATATCTTAACAATTTAACCTAATAA
1 CCTATCATAATATATTATATCTCAACAATTTAACCGAACAA
* *
1334057 CCTATCATAA-AGTATTATATCTCAATAATTCT-ATCGAACAA
1 CCTATCATAATA-TATTATATCTCAACAATT-TAACCGAACAA
1334098 CCTA
1 CCTA
1334102 ATATATTAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
40 1 0.03
41 36 0.95
42 1 0.03
ACGTcount: A:0.42, C:0.20, G:0.02, T:0.36
Consensus pattern (41 bp):
CCTATCATAATATATTATATCTCAACAATTTAACCGAACAA
Found at i:1336832 original size:36 final size:36
Alignment explanation
Indices: 1336776--1336864 Score: 117
Period size: 36 Copynumber: 2.5 Consensus size: 36
1336766 TTTATTGTGA
* * *
1336776 TTCAAGGTTAAACTATTTCTTTGATCTTCTAGTTG-
1 TTCAGGGTAAAACTATTTCTTTGATCTTCTAGATGC
*
1336811 TATCAGGGTAAAACTATTTCTTTGATCTTTTAGATGC
1 T-TCAGGGTAAAACTATTTCTTTGATCTTCTAGATGC
*
1336848 TTCAGGGTAAAAGTATT
1 TTCAGGGTAAAACTATT
1336865 CCTTGTATTG
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
35 1 0.02
36 45 0.96
37 1 0.02
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44
Consensus pattern (36 bp):
TTCAGGGTAAAACTATTTCTTTGATCTTCTAGATGC
Found at i:1339487 original size:135 final size:134
Alignment explanation
Indices: 1339244--1339503 Score: 468
Period size: 135 Copynumber: 1.9 Consensus size: 134
1339234 TGGATAAAAT
1339244 TATTTAAATATAATATGTTTTGATAAGCTATTAGGTTGGACTACTAAGATGTAATATATTATGAT
1 TATTTAAATATAATATGTTTTGATAAGCTATTAGGTTGGACTACTAAGATGTAATATATTATGAT
* *
1339309 AGACTTAAATTTATATTAAAACTTAATGGGTTTTGATTAGTAGACTCACTTTTATTTTTTATNAT
66 AGACTTAAATTTAAATTAAAACTTAATGGGTTCTGATTAGTAGACTCACTTTTATTTTTTAT-AT
1339374 GGAAC
130 GGAAC
1339379 TATTTAAATATAATATGTTTTGATAAGCTATTAGGTTGGACTACTAAGATGTAATATATTATGAT
1 TATTTAAATATAATATGTTTTGATAAGCTATTAGGTTGGACTACTAAGATGTAATATATTATGAT
*
1339444 AGACTTAAATTTAAATTAAAACTTAATGGG-TCTGAATTGGTAGACTCACTTTTATTTTTT
66 AGACTTAAATTTAAATTAAAACTTAATGGGTTCTG-ATTAGTAGACTCACTTTTATTTTTT
1339504 TATAAATTTG
Statistics
Matches: 121, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
134 3 0.02
135 118 0.98
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.43
Consensus pattern (134 bp):
TATTTAAATATAATATGTTTTGATAAGCTATTAGGTTGGACTACTAAGATGTAATATATTATGAT
AGACTTAAATTTAAATTAAAACTTAATGGGTTCTGATTAGTAGACTCACTTTTATTTTTTATATG
GAAC
Found at i:1340071 original size:18 final size:18
Alignment explanation
Indices: 1340035--1340072 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1340025 GAATAAATAG
*
1340035 AATATAAATAATAATAAT
1 AATATAAATAATAAAAAT
1340053 AATATAAATTAA-AAAAAT
1 AATATAAA-TAATAAAAAT
1340071 AA
1 AA
1340073 AAAAACTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AATATAAATAATAAAAAT
Found at i:1342031 original size:35 final size:35
Alignment explanation
Indices: 1341985--1342261 Score: 220
Period size: 35 Copynumber: 7.9 Consensus size: 35
1341975 TCTTTAAGAA
***
1341985 GCCCAATTAACTTAATTGTTTAATTTAATCAATTAG
1 GCCCAA-TAACTTAATTAAATAATTTAATCAATTAG
* * *
1342021 GCTCAATAACTTAATTAAATAATTTAATTAATTAA
1 GCCCAATAACTTAATTAAATAATTTAATCAATTAG
* * * *
1342056 GCCCAACAATTTAATTAAACAATTTTAATCAAGTAG
1 GCCCAATAACTTAATTAAATAA-TTTAATCAATTAG
* * * *
1342092 GCCTAATGACTTAATTAAACAAATTCAATCAATTAG
1 GCCCAATAACTTAATTAAA-TAATTTAATCAATTAG
* *** *
1342128 GCCCAATAATTTAATTGTTTAATTTAATTAATTAG
1 GCCCAATAACTTAATTAAATAATTTAATCAATTAG
* * * *
1342163 GCCCAATGACTTAATAAAACAATTTAATTAATTAG
1 GCCCAATAACTTAATTAAATAATTTAATCAATTAG
* * * *
1342198 GCCCAATGA-TTCAATTAAACAATTTAGTTAATTAG
1 GCCCAATAACTT-AATTAAATAATTTAATCAATTAG
* *
1342233 G--C-ACAACTTAATTAAACAATTTTAATCAA
1 GCCCAATAACTTAATTAAATAA-TTTAATCAA
1342262 GTGCTTGAGA
Statistics
Matches: 194, Mismatches: 42, Indels: 13
0.78 0.17 0.05
Matches are distributed among these distances:
32 12 0.06
33 10 0.05
34 2 0.01
35 114 0.59
36 54 0.28
37 2 0.01
ACGTcount: A:0.43, C:0.14, G:0.08, T:0.36
Consensus pattern (35 bp):
GCCCAATAACTTAATTAAATAATTTAATCAATTAG
Found at i:1342135 original size:107 final size:106
Alignment explanation
Indices: 1342006--1342219 Score: 277
Period size: 107 Copynumber: 2.0 Consensus size: 106
1341996 TTAATTGTTT
* * *
1342006 AATTTAATCAATTAGGCTCAATAACTTAATTAAATAATTTAATTAATTAAGCCCAACAATTTAAT
1 AATTCAATCAATTAGGCCCAATAACTTAATTAAATAATTTAATTAATTAAGCCCAACAACTTAAT
* *
1342071 TAAACAATTTTAATCAAGTAGGCCTAATGACTT-AATTAAACA
66 AAAACAA-TTTAATCAAGTAGGCCCAATGA-TTCAATTAAACA
* *** * **
1342113 AATTCAATCAATTAGGCCCAATAATTTAATTGTTTAATTTAATTAATTAGGCCCAATGACTTAAT
1 AATTCAATCAATTAGGCCCAATAACTTAATTAAATAATTTAATTAATTAAGCCCAACAACTTAAT
* *
1342178 AAAACAATTTAATTAATTAGGCCCAATGATTCAATTAAACA
66 AAAACAATTTAATCAAGTAGGCCCAATGATTCAATTAAACA
1342219 A
1 A
1342220 TTTAGTTAAT
Statistics
Matches: 92, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
105 2 0.02
106 29 0.32
107 61 0.66
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.35
Consensus pattern (106 bp):
AATTCAATCAATTAGGCCCAATAACTTAATTAAATAATTTAATTAATTAAGCCCAACAACTTAAT
AAAACAATTTAATCAAGTAGGCCCAATGATTCAATTAAACA
Found at i:1346502 original size:25 final size:25
Alignment explanation
Indices: 1346468--1346520 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
1346458 TTGAGTTTAT
*
1346468 TTCGACCCTTGTATCTCTTATGAGG
1 TTCGACCCTTATATCTCTTATGAGG
*
1346493 TTCGACCCTTATATCTCTTATGGGG
1 TTCGACCCTTATATCTCTTATGAGG
1346518 TTC
1 TTC
1346521 ACACATCAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.15, C:0.25, G:0.19, T:0.42
Consensus pattern (25 bp):
TTCGACCCTTATATCTCTTATGAGG
Found at i:1347308 original size:122 final size:123
Alignment explanation
Indices: 1347158--1347394 Score: 352
Period size: 122 Copynumber: 1.9 Consensus size: 123
1347148 CAAAAGCTTA
* *
1347158 AAAATTTTATAATTTTGTCTTTGTTTTGTTTTAAAATTTTATAATTTTAC-TCT-TTTTTAAAAA
1 AAAACTTTATAATTTTGTCTTTGTTTTGTTTTAAAAATTTATAATTTTACTTCTATTTTTAAAAA
** *
1347221 AAATTTATAATTTCATCCCTTTAAATATTAAATTTTTTATTTTTACCTCCTAAAGTTGC
66 AAATTTATAATTTCATCCCTCCAAATATTAAAATTTTT-TTTTTACCTCCTAAAGTTGC
* *
1347280 AAAACTTTATAATTTTGTCTTTGTTTTGTTTTAAAAATTTATAATTTTACTTTTATTTTTTAAAA
1 AAAACTTTATAATTTTGTCTTTGTTTTGTTTTAAAAATTTATAATTTTACTTCTATTTTTAAAAA
* * * *
1347345 AATTTTATAGTTTCATTCCTCCAAATATTAAAATTTTTTTTTTATCTCCT
66 AAATTTATAATTTCATCCCTCCAAATATTAAAATTTTTTTTTTACCTCCT
1347395 CAAATATGAA
Statistics
Matches: 102, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
122 48 0.47
123 13 0.13
124 41 0.40
ACGTcount: A:0.31, C:0.10, G:0.04, T:0.55
Consensus pattern (123 bp):
AAAACTTTATAATTTTGTCTTTGTTTTGTTTTAAAAATTTATAATTTTACTTCTATTTTTAAAAA
AAATTTATAATTTCATCCCTCCAAATATTAAAATTTTTTTTTTACCTCCTAAAGTTGC
Found at i:1350138 original size:27 final size:26
Alignment explanation
Indices: 1350098--1350155 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
1350088 TATAATATTA
**
1350098 AAAAATAATTTTAT-TTTTTTTATTTT
1 AAAAATAATTTTATATAATTTT-TTTT
*
1350124 AAAAATTATTATTATATAATTTTTTTT
1 AAAAATAATT-TTATATAATTTTTTTT
1350151 AAAAA
1 AAAAA
1350156 AATCAGGGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 9 0.33
27 13 0.48
28 5 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
AAAAATAATTTTATATAATTTTTTTT
Found at i:1354743 original size:20 final size:21
Alignment explanation
Indices: 1354718--1354758 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1354708 ATAATGTATA
*
1354718 TTAAT-AATTATATTACAAAT
1 TTAATAAATTAAATTACAAAT
1354738 TTAATAAAATTAAATTACAAA
1 TTAAT-AAATTAAATTACAAA
1354759 ATCAATCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
22 13 0.72
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (21 bp):
TTAATAAATTAAATTACAAAT
Found at i:1355410 original size:22 final size:22
Alignment explanation
Indices: 1355389--1355429 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1355379 AAACATAGTA
1355389 ACGTACA-GAAAGAAAATAAGT
1 ACGTACAGGAAAGAAAATAAGT
* *
1355410 ATGTATAGGAAAGAAAATAA
1 ACGTACAGGAAAGAAAATAA
1355430 CCTCTGCCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.59, C:0.05, G:0.20, T:0.17
Consensus pattern (22 bp):
ACGTACAGGAAAGAAAATAAGT
Found at i:1360811 original size:38 final size:37
Alignment explanation
Indices: 1360739--1360812 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 37
1360729 CTACCTGGAT
*
1360739 TTGAAATACTTTATCTACTTTTTCTAAAATATTTGAC
1 TTGAAATACTTTATCTACTTTTTCTAAAACATTTGAC
1360776 TTGAAATACTCTTATCTA-TTTTTC-AAGAGACATTTGA
1 TTGAAATACT-TTATCTACTTTTTCTAA-A-ACATTTGA
1360813 TGTGATACAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
36 2 0.06
37 17 0.52
38 14 0.42
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (37 bp):
TTGAAATACTTTATCTACTTTTTCTAAAACATTTGAC
Found at i:1368970 original size:2 final size:2
Alignment explanation
Indices: 1368963--1369014 Score: 95
Period size: 2 Copynumber: 25.5 Consensus size: 2
1368953 GCAACAAATT
1368963 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1369005 GTA TA TA TA T
1 -TA TA TA TA T
1369015 TAAATCATTG
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 47 0.96
3 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1370772 original size:16 final size:16
Alignment explanation
Indices: 1370751--1370784 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1370741 TTTACTTTTT
*
1370751 TTTAAAGATTGTAGTC
1 TTTAAACATTGTAGTC
*
1370767 TTTAAACATTGTCGTC
1 TTTAAACATTGTAGTC
1370783 TT
1 TT
1370785 ATTGTAAGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.26, C:0.12, G:0.15, T:0.47
Consensus pattern (16 bp):
TTTAAACATTGTAGTC
Found at i:1378560 original size:3 final size:3
Alignment explanation
Indices: 1378544--1378623 Score: 58
Period size: 3 Copynumber: 26.0 Consensus size: 3
1378534 TTTTCTTCCA
*
1378544 ATT A-T ATT ATTT ATT ATT ATT ATTT ATTT ATT TTT CATT -TT ATT ATT
1 ATT ATT ATT A-TT ATT ATT ATT A-TT A-TT ATT ATT -ATT ATT ATT ATT
* * *
1378591 ATC ATT ATT TTT TTT ATT ATT ATT -TT ATAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
1378624 TTTTTATTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
2 6 0.09
3 43 0.67
4 15 0.23
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (3 bp):
ATT
Found at i:1378585 original size:29 final size:28
Alignment explanation
Indices: 1378553--1378634 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 28
1378543 AATTATATTA
1378553 TTTATTATTATTATTTATTTATTTTTCAT
1 TTTATTATTATTATTTATTTATTTTT-AT
*
1378582 TTTATTATTATCA-TTATTT-TTTTTAT
1 TTTATTATTATTATTTATTTATTTTTAT
*
1378608 TATTATT-TTATATATTTTTTTATTTTT
1 T-TTATTATTAT-TATTTATTTATTTTT
1378635 TTATCTAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
26 7 0.15
27 11 0.24
28 11 0.24
29 17 0.37
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (28 bp):
TTTATTATTATTATTTATTTATTTTTAT
Found at i:1378590 original size:32 final size:31
Alignment explanation
Indices: 1378544--1378638 Score: 102
Period size: 32 Copynumber: 3.0 Consensus size: 31
1378534 TTTTCTTCCA
* *
1378544 ATTATATTATTTATTATTATTATTTATTTATT
1 ATTATTTTA-TTATTATTATTATTTTTTTATT
* *
1378576 TTTCATTTTATTATTATCATTATTTTTTTTATT
1 ATT-ATTTTATTATTATTATTA-TTTTTTTATT
*
1378609 ATTATTTTATATATT-TTTTTATTTTTTTAT
1 ATTATTTTAT-TATTATTATTATTTTTTTAT
1378639 CTAAAAATAT
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
31 9 0.17
32 24 0.45
33 20 0.38
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (31 bp):
ATTATTTTATTATTATTATTATTTTTTTATT
Found at i:1378614 original size:24 final size:23
Alignment explanation
Indices: 1378544--1378628 Score: 82
Period size: 24 Copynumber: 3.5 Consensus size: 23
1378534 TTTTCTTCCA
* *
1378544 ATTATATTATTTATTATTATTAT
1 ATTATTTTTTTTATTATTATTAT
1378567 -TTATTTATTTTTCATTTTATTATTAT
1 ATTATTT-TTTTT-A--TTATTATTAT
*
1378593 CATTATTTTTTTTATTATTATTTT
1 -ATTATTTTTTTTATTATTATTAT
1378617 ATATATTTTTTT
1 AT-TATTTTTTT
1378629 ATTTTTTTAT
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
22 5 0.10
23 6 0.12
24 19 0.37
26 11 0.21
27 5 0.10
28 6 0.12
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (23 bp):
ATTATTTTTTTTATTATTATTAT
Found at i:1378624 original size:9 final size:8
Alignment explanation
Indices: 1378544--1378638 Score: 63
Period size: 8 Copynumber: 11.6 Consensus size: 8
1378534 TTTTCTTCCA
*
1378544 ATTATATT
1 ATTATTTT
1378552 ATTTATTATT
1 A-TTATT-TT
1378562 ATTA-TTT
1 ATTATTTT
1378569 ATTTATTTT
1 A-TTATTTT
*
1378578 -TCATTTT
1 ATTATTTT
*
1378585 ATTATTATC
1 ATTATT-TT
1378594 ATTATTTT
1 ATTATTTT
1378602 -TT-TTATT
1 ATTATT-TT
1378609 ATTATTTT
1 ATTATTTT
1378617 ATATATTTT
1 AT-TATTTT
*
1378626 TTTATTTT
1 ATTATTTT
*
1378634 TTTAT
1 ATTAT
1378639 CTAAAAATAT
Statistics
Matches: 71, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
6 2 0.03
7 13 0.18
8 27 0.38
9 26 0.37
10 3 0.04
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (8 bp):
ATTATTTT
Found at i:1378628 original size:50 final size:49
Alignment explanation
Indices: 1378544--1378638 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 49
1378534 TTTTCTTCCA
1378544 ATTATATTATTTATTATTATTATTTATTTATTTTTCATTTTATTATTATC
1 ATTATATTATTTATTATTATTATTTATTTATTTTT-ATTTTATTATTATC
* * *
1378594 ATTATTTTTTTTATTATTATT-TTATATATT-TTTTTATTTTTTTAT
1 ATTATATTATTTATTATTATTATT-TAT-TTATTTTTATTTTATTAT
1378639 CTAAAAATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
49 11 0.28
50 27 0.68
51 2 0.05
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (49 bp):
ATTATATTATTTATTATTATTATTTATTTATTTTTATTTTATTATTATC
Found at i:1379347 original size:39 final size:39
Alignment explanation
Indices: 1379227--1379349 Score: 167
Period size: 39 Copynumber: 3.1 Consensus size: 39
1379217 GACGATCCTT
* *
1379227 CCCTTCCCGTCGGCCTCTCTCTCTCTCCTTTCAGATCTCA
1 CCCTT-CCGTCGGCCTCTCTCTCTTTCCTCTCAGATCTCA
* * *
1379267 CCATTCCGTCGGTCTCTCTCTCTCTT-CGCTCAGATCTCA
1 CCCTTCCGTCGGCCTCTCTCTCT-TTCCTCTCAGATCTCA
*
1379306 CCCTTCCGTCAGCCTCTCTCTCTTTCCTCTCAGATCTCA
1 CCCTTCCGTCGGCCTCTCTCTCTTTCCTCTCAGATCTCA
1379345 CCCTT
1 CCCTT
1379350 TTCTCCTTGT
Statistics
Matches: 72, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
38 2 0.03
39 65 0.90
40 5 0.07
ACGTcount: A:0.09, C:0.46, G:0.10, T:0.36
Consensus pattern (39 bp):
CCCTTCCGTCGGCCTCTCTCTCTTTCCTCTCAGATCTCA
Found at i:1379350 original size:20 final size:19
Alignment explanation
Indices: 1379295--1379350 Score: 51
Period size: 20 Copynumber: 2.9 Consensus size: 19
1379285 TCTCTCTTCG
1379295 CTCAGATCTCACCC-TTCC
1 CTCAGATCTCACCCTTTCC
* * * *
1379313 GTCAGCCTCTCTCTCTTTCC
1 CTCAG-ATCTCACCCTTTCC
1379333 TCTCAGATCTCACCCTTT
1 -CTCAGATCTCACCCTTT
1379351 TCTCCTTGTT
Statistics
Matches: 27, Mismatches: 8, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
18 4 0.15
19 6 0.22
20 13 0.48
21 4 0.15
ACGTcount: A:0.12, C:0.45, G:0.07, T:0.36
Consensus pattern (19 bp):
CTCAGATCTCACCCTTTCC
Found at i:1379589 original size:4 final size:4
Alignment explanation
Indices: 1379580--1379655 Score: 50
Period size: 4 Copynumber: 18.0 Consensus size: 4
1379570 CATCCCCAAT
* *
1379580 TTTA TTTA TTTT TATTA ATTA -TTA -TTA TTTTA TTTA TTTTA TTTTA
1 TTTA TTTA TTTA T-TTA TTTA TTTA TTTA -TTTA TTTA -TTTA -TTTA
1379626 TTTAA TTTA TTTAA TTT- TTATA TTTA TTTA
1 TTT-A TTTA TTT-A TTTA TT-TA TTTA TTTA
1379656 GGTGTCTACA
Statistics
Matches: 61, Mismatches: 3, Indels: 16
0.76 0.04 0.20
Matches are distributed among these distances:
3 8 0.13
4 29 0.48
5 24 0.39
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:1379592 original size:10 final size:10
Alignment explanation
Indices: 1379579--1379655 Score: 56
Period size: 10 Copynumber: 7.9 Consensus size: 10
1379569 CCATCCCCAA
1379579 TTTTATTTAT
1 TTTTATTTAT
*
1379589 TTTTATTAAT
1 TTTTATTTAT
*
1379599 TATTA-TTA-
1 TTTTATTTAT
1379607 TTTTATTTA-
1 TTTTATTTAT
1379616 TTTTATTT-T
1 TTTTATTTAT
*
1379625 ATTTAATTTAT
1 -TTTTATTTAT
1379636 TTAATT-TTTAT
1 TT--TTATTTAT
*
1379647 ATTTATTTA
1 TTTTATTTA
1379656 GGTGTCTACA
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
8 4 0.08
9 15 0.28
10 26 0.49
11 7 0.13
12 1 0.02
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTTATTTAT
Found at i:1379618 original size:9 final size:9
Alignment explanation
Indices: 1379578--1379654 Score: 77
Period size: 9 Copynumber: 8.4 Consensus size: 9
1379568 GCCATCCCCA
1379578 ATTTTATTT
1 ATTTTATTT
*
1379587 ATTTTTATTA
1 A-TTTTATTT
1379597 ATTATTA-TT
1 ATT-TTATTT
1379606 ATTTTATTT
1 ATTTTATTT
1379615 ATTTTATTTT
1 ATTTTA-TTT
*
1379625 ATTTAATTT
1 ATTTTATTT
*
1379634 ATTTAATTT
1 ATTTTATTT
*
1379643 -TTATATTT
1 ATTTTATTT
1379651 ATTT
1 ATTT
1379655 AGGTGTCTAC
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
8 9 0.16
9 29 0.51
10 19 0.33
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (9 bp):
ATTTTATTT
Found at i:1379618 original size:28 final size:24
Alignment explanation
Indices: 1379578--1379655 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 24
1379568 GCCATCCCCA
1379578 ATTTTATTTATTTTTATTAATTATTATT
1 ATTTTATTTATTTTTATT--TTA-T-TT
1379606 ATTTTATTTA-TTTTATTTTATTT
1 ATTTTATTTATTTTTATTTTATTT
*
1379629 AATTTATTTAATTTTTATATTTATTT
1 ATTTTATTT-ATTTTTAT-TTTATTT
1379655 A
1 A
1379656 GGTGTCTACA
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
23 10 0.22
24 2 0.04
25 9 0.20
26 8 0.17
27 7 0.15
28 10 0.22
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (24 bp):
ATTTTATTTATTTTTATTTTATTT
Found at i:1382865 original size:2 final size:2
Alignment explanation
Indices: 1382858--1382899 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1382848 GGACTTCCCT
1382858 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1382900 CATTTTCTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1397272 original size:37 final size:38
Alignment explanation
Indices: 1397231--1397307 Score: 122
Period size: 38 Copynumber: 2.1 Consensus size: 38
1397221 AATCAACCTG
1397231 GACTTGAAATACT-TTATCTACTTTTTCT-AAAATATTT
1 GACTTGAAATACTCTTATCTACTTTTTCTGAAAA-ATTT
*
1397268 GACTTGAAATACTCTTATCTATTTTTTCTGAAAAATTT
1 GACTTGAAATACTCTTATCTACTTTTTCTGAAAAATTT
1397306 GA
1 GA
1397308 TGTGATTCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
37 13 0.35
38 20 0.54
39 4 0.11
ACGTcount: A:0.32, C:0.13, G:0.08, T:0.47
Consensus pattern (38 bp):
GACTTGAAATACTCTTATCTACTTTTTCTGAAAAATTT
Found at i:1415733 original size:19 final size:19
Alignment explanation
Indices: 1415709--1415758 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
1415699 GACATATATG
*
1415709 AAAATTATTGATTATAATT
1 AAAATTATTAATTATAATT
*
1415728 AAAATTTTTAATTATAATT
1 AAAATTATTAATTATAATT
*
1415747 ATAATCTATTAA
1 AAAAT-TATTAA
1415759 AAAAACACTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 21 0.81
20 5 0.19
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (19 bp):
AAAATTATTAATTATAATT
Found at i:1419862 original size:15 final size:16
Alignment explanation
Indices: 1419844--1419899 Score: 64
Period size: 15 Copynumber: 3.5 Consensus size: 16
1419834 TTATTTTATT
1419844 TTTAAAT-ATTAATAA
1 TTTAAATAATTAATAA
1419859 TTTATAATTAATTAA-AA
1 TTTA-AA-TAATTAATAA
1419876 TATT-AATAATTAATAA
1 T-TTAAATAATTAATAA
1419892 TTTAAATA
1 TTTAAATA
1419900 TCAATATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
15 13 0.37
16 11 0.31
17 4 0.11
18 7 0.20
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TTTAAATAATTAATAA
Found at i:1420508 original size:17 final size:16
Alignment explanation
Indices: 1420467--1420530 Score: 50
Period size: 17 Copynumber: 4.2 Consensus size: 16
1420457 GGTGCCACTT
1420467 AGAGAGAG-AATGAGA
1 AGAGAGAGAAATGAGA
*
1420482 A-AGGAAAGAACATGAGA
1 AGA-GAGAGAA-ATGAGA
1420499 AGAGAGAGAAA-GAAGA
1 AGAGAGAGAAATG-AGA
1420515 AG-G-GA-AAATGAGA
1 AGAGAGAGAAATGAGA
1420528 AGA
1 AGA
1420531 AAAAAAAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 15
0.70 0.04 0.26
Matches are distributed among these distances:
13 8 0.20
14 4 0.10
15 7 0.17
16 7 0.17
17 13 0.32
18 1 0.03
ACGTcount: A:0.58, C:0.02, G:0.36, T:0.05
Consensus pattern (16 bp):
AGAGAGAGAAATGAGA
Found at i:1443148 original size:33 final size:33
Alignment explanation
Indices: 1443111--1443185 Score: 105
Period size: 33 Copynumber: 2.3 Consensus size: 33
1443101 GTTATTATAT
* * *
1443111 TATATTAATATGTCATATTATTATTAATTATGA
1 TATATTAATATGTCATATAATCATCAATTATGA
*
1443144 TATATTAACATGTCATATAATCATCAATTATGA
1 TATATTAATATGTCATATAATCATCAATTATGA
*
1443177 TATTTTAAT
1 TATATTAAT
1443186 CAGAGTTACA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (33 bp):
TATATTAATATGTCATATAATCATCAATTATGA
Found at i:1444477 original size:18 final size:18
Alignment explanation
Indices: 1444447--1444483 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1444437 AAAAGAAACG
1444447 GGCCACTAGGGCCCACAA
1 GGCCACTAGGGCCCACAA
1444465 GGCCTACTA-GGCCCACAA
1 GGCC-ACTAGGGCCCACAA
1444483 G
1 G
1444484 CTTAACAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.27, C:0.38, G:0.27, T:0.08
Consensus pattern (18 bp):
GGCCACTAGGGCCCACAA
Found at i:1473348 original size:17 final size:17
Alignment explanation
Indices: 1473326--1473362 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
1473316 TTTTTGTCGT
1473326 TATGGCATGTTCGTAAA
1 TATGGCATGTTCGTAAA
1473343 TATGGCATGTTCGTAAA
1 TATGGCATGTTCGTAAA
1473360 TAT
1 TAT
1473363 TCGCATATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.38
Consensus pattern (17 bp):
TATGGCATGTTCGTAAA
Found at i:1492152 original size:5 final size:5
Alignment explanation
Indices: 1492142--1492169 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1492132 TTGGACCATA
1492142 TTTGG TTTGG TTTGG TTTGG TTTGG TTT
1 TTTGG TTTGG TTTGG TTTGG TTTGG TTT
1492170 CTTTCTTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.36, T:0.64
Consensus pattern (5 bp):
TTTGG
Found at i:1511305 original size:23 final size:22
Alignment explanation
Indices: 1511260--1511306 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
1511250 ATTTTGTATC
* *
1511260 ATAAAAAAATTAAAATTATAAT
1 ATAAAAAAATTAAAATCAAAAT
1511282 ATAAAATAAATTAAAATCAAAAT
1 ATAAAA-AAATTAAAATCAAAAT
1511305 AT
1 AT
1511307 TTATTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (22 bp):
ATAAAAAAATTAAAATCAAAAT
Found at i:1511325 original size:21 final size:20
Alignment explanation
Indices: 1511292--1511330 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1511282 ATAAAATAAA
1511292 TTAAAATCAAAATATTTATT
1 TTAAAATCAAAATATTTATT
*
1511312 TTAAACTCTAAAATATTTA
1 TTAAAATC-AAAATATTTA
1511331 AACAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAAAATCAAAATATTTATT
Found at i:1513772 original size:15 final size:15
Alignment explanation
Indices: 1513754--1513804 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
1513744 TTATTTTTTC
1513754 TGTAATTATATTATT
1 TGTAATTATATTATT
* * *
1513769 TGTAATCACATTACT
1 TGTAATTATATTATT
*
1513784 TATAATTATATTATT
1 TGTAATTATATTATT
1513799 TGTAAT
1 TGTAAT
1513805 CACATTATAT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (15 bp):
TGTAATTATATTATT
Found at i:1513811 original size:15 final size:15
Alignment explanation
Indices: 1513763--1513812 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
1513753 CTGTAATTAT
1513763 ATTATTTGTAATCAC
1 ATTATTTGTAATCAC
* * * *
1513778 ATTACTTATAATTAT
1 ATTATTTGTAATCAC
1513793 ATTATTTGTAATCAC
1 ATTATTTGTAATCAC
1513808 ATTAT
1 ATTAT
1513813 ATTATAAAAT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.36, C:0.10, G:0.04, T:0.50
Consensus pattern (15 bp):
ATTATTTGTAATCAC
Found at i:1530627 original size:13 final size:13
Alignment explanation
Indices: 1530609--1530636 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1530599 GTTTTAAATG
1530609 AAAGTAATTAATA
1 AAAGTAATTAATA
1530622 AAAGTAATTAATA
1 AAAGTAATTAATA
1530635 AA
1 AA
1530637 GGGTAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (13 bp):
AAAGTAATTAATA
Found at i:1534202 original size:64 final size:63
Alignment explanation
Indices: 1534101--1534231 Score: 228
Period size: 64 Copynumber: 2.1 Consensus size: 63
1534091 AAGCTTTTTT
*
1534101 CAGCCTACCTGTTTTCTTCCTTTGGAGGGCTTGCCTTAATCACATCCGT-TAAAACCCCAATTAA
1 CAGCCTACCTGTTTTCCTCCTTTGGAGGGCTTGCCTTAATCACATCC-TCTAAAACCCC-ATTAA
1534165 CAGCCTACCTGTTTTCCTCCTTTGGAGGGCTTGCCTTAATCACATCCTCTAAAACCCCATTAA
1 CAGCCTACCTGTTTTCCTCCTTTGGAGGGCTTGCCTTAATCACATCCTCTAAAACCCCATTAA
1534228 CAGC
1 CAGC
1534232 TCTAATAACG
Statistics
Matches: 65, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
63 10 0.15
64 55 0.85
ACGTcount: A:0.23, C:0.32, G:0.14, T:0.31
Consensus pattern (63 bp):
CAGCCTACCTGTTTTCCTCCTTTGGAGGGCTTGCCTTAATCACATCCTCTAAAACCCCATTAA
Found at i:1548195 original size:18 final size:18
Alignment explanation
Indices: 1548172--1548206 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1548162 TGGTGGGGTT
1548172 TTTCTTTTCTTT-TTCTTC
1 TTTCTTTT-TTTGTTCTTC
1548190 TTTCTTTTTTTGTTCTT
1 TTTCTTTTTTTGTTCTT
1548207 TCATCTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (18 bp):
TTTCTTTTTTTGTTCTTC
Found at i:1552339 original size:13 final size:13
Alignment explanation
Indices: 1552323--1552347 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1552313 GGGATTTTCC
1552323 TTTTTTATTTTTA
1 TTTTTTATTTTTA
1552336 TTTTTTATTTTT
1 TTTTTTATTTTT
1552348 TAGTGAAAGG
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTATTTTTA
Found at i:1578754 original size:76 final size:74
Alignment explanation
Indices: 1578628--1578792 Score: 249
Period size: 76 Copynumber: 2.2 Consensus size: 74
1578618 TCTCCTTATC
1578628 TGATGGTATGATGGTGAGGAAGATAAGGCTCTCAAGGTATTTCAAGACTGCTAAGTCTAATTTTT
1 TGATGGTATGATGGTGAGGAAGATAAGGCTCTCAAGGTATTTCAAGACTGCTAAGTCTAA--TTT
*
1578693 TTTTAGTTTTG
64 TTTTAGTTTTA
* * * * *
1578704 TGATGATATGATGGTGAGGAGGATAAGGTTGTCAAGGTATTTCATGACTGCTAAGTCTAATTTTT
1 TGATGGTATGATGGTGAGGAAGATAAGGCTCTCAAGGTATTTCAAGACTGCTAAGTCTAATTTTT
*
1578769 TTATTTTTA
66 TTAGTTTTA
1578778 TGATGGTATGATGGT
1 TGATGGTATGATGGT
1578793 TGTGATGGTA
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
74 26 0.32
76 55 0.68
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.41
Consensus pattern (74 bp):
TGATGGTATGATGGTGAGGAAGATAAGGCTCTCAAGGTATTTCAAGACTGCTAAGTCTAATTTTT
TTAGTTTTA
Found at i:1578787 original size:8 final size:8
Alignment explanation
Indices: 1578776--1578809 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
1578766 TTTTTATTTT
1578776 TATGATGG
1 TATGATGG
1578784 TATGATGG
1 TATGATGG
*
1578792 TTGTGATGG
1 -TATGATGG
1578801 TATGATGG
1 TATGATGG
1578809 T
1 T
1578810 GATTTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.41
Consensus pattern (8 bp):
TATGATGG
Found at i:1580372 original size:35 final size:36
Alignment explanation
Indices: 1580333--1580420 Score: 87
Period size: 35 Copynumber: 2.5 Consensus size: 36
1580323 AAATAATTTA
1580333 AATATTTTTAATTTTTAATA-TTT-AAA-TTAAATATT
1 AATATTTTTAATTTTTAATATTTTCAAACTT-AATA-T
*
1580368 AATATTTATTAA-ATTT-ATATTTTCAAACTTAATAT
1 AATATTT-TTAATTTTTAATATTTTCAAACTTAATAT
* *
1580403 AATTTTTTTATTTTTTAA
1 AATATTTTTAATTTTTAA
1580421 AAAATTTGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
34 6 0.14
35 23 0.53
36 12 0.28
37 2 0.05
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (36 bp):
AATATTTTTAATTTTTAATATTTTCAAACTTAATAT
Found at i:1580389 original size:15 final size:17
Alignment explanation
Indices: 1580333--1580389 Score: 57
Period size: 19 Copynumber: 3.4 Consensus size: 17
1580323 AAATAATTTA
* *
1580333 AATATTT-TTAATTTTT
1 AATATTTATTAAATATT
1580349 AATATTTAAATTAAATATT
1 AATATTT--ATTAAATATT
1580368 AATATTTATTAAAT-TT
1 AATATTTATTAAATATT
1580384 -ATATTT
1 AATATTT
1580390 TCAAACTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
15 6 0.17
16 9 0.25
17 7 0.19
19 14 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
AATATTTATTAAATATT
Found at i:1581286 original size:21 final size:21
Alignment explanation
Indices: 1581257--1581305 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1581247 ATCATATTCG
* * *
1581257 GTTGCTGCCGTTGCCGTCGTC
1 GTTGTTGCCGTCGCCGTCGCC
1581278 GTTGTTGCCGTCGCCGTCGCC
1 GTTGTTGCCGTCGCCGTCGCC
*
1581299 GGTGTTG
1 GTTGTTG
1581306 AGTTCCAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.00, C:0.31, G:0.37, T:0.33
Consensus pattern (21 bp):
GTTGTTGCCGTCGCCGTCGCC
Found at i:1581366 original size:23 final size:23
Alignment explanation
Indices: 1581316--1581368 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
1581306 AGTTCCAGTT
* * *
1581316 AGAGAGAGAATGAGAGAGGGAGA
1 AGAGAGAGAAAGAGAAAGGGAAA
1581339 AGAGAGAGAAAGA-AAAGGGAAA
1 AGAGAGAGAAAGAGAAAGGGAAA
1581361 ATGAGAGA
1 A-GAGAGA
1581369 AAAAAAGTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 8 0.31
23 18 0.69
ACGTcount: A:0.55, C:0.00, G:0.42, T:0.04
Consensus pattern (23 bp):
AGAGAGAGAAAGAGAAAGGGAAA
Found at i:1594215 original size:19 final size:19
Alignment explanation
Indices: 1594179--1594217 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1594169 CCCTCTGTCT
*
1594179 TATTCACATTACATTCCTC
1 TATTCACATTACAGTCCTC
1594198 TATT-ACATTCACAGTCCTC
1 TATTCACATT-ACAGTCCTC
1594217 T
1 T
1594218 TCTTTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.26, C:0.31, G:0.03, T:0.41
Consensus pattern (19 bp):
TATTCACATTACAGTCCTC
Found at i:1596019 original size:123 final size:123
Alignment explanation
Indices: 1595799--1596054 Score: 351
Period size: 123 Copynumber: 2.1 Consensus size: 123
1595789 ATTTAATATT
* * * *
1595799 ATTATAAAAA-ATCGATATATTTTACTGTTTTATCAAATTATTAAAATAGAGCATTTAATAATAT
1 ATTATAAAAATATCAATATATTTAACTGTTATATAAAATTATTAAAATAGAGCATTTAATAATAT
*
1595863 AAAACATAGATGTAACTAGATACTGAAAGAATATATTAAATATTATTATAATTAAGTTA
66 AAAACATAGATATAACTAGATACTGAAAGAATATATTAAA-ATTATTATAATTAAGTTA
* **
1595922 ATTATAAAAATATCAATATTATTTAACTGTTATATAAAATTATT-AAA-AGAGTATTTTGTAATA
1 ATTATAAAAATATCAATA-TATTTAACTGTTATATAAAATTATTAAAATAGAGCATTTAATAATA
* * * *
1595985 TAAAACATAGATATAACTCGATATTGAAATAATATATTAAAATTATTATAATTACGTTA
65 TAAAACATAGATATAACTAGATACTGAAAGAATATATTAAAATTATTATAATTAAGTTA
1596044 A-TA-AAAAATAT
1 ATTATAAAAATAT
1596055 TGACCTTAAT
Statistics
Matches: 119, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
120 8 0.07
121 2 0.02
122 18 0.15
123 60 0.50
124 9 0.08
125 22 0.18
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (123 bp):
ATTATAAAAATATCAATATATTTAACTGTTATATAAAATTATTAAAATAGAGCATTTAATAATAT
AAAACATAGATATAACTAGATACTGAAAGAATATATTAAAATTATTATAATTAAGTTA
Found at i:1596140 original size:186 final size:183
Alignment explanation
Indices: 1595922--1596265 Score: 435
Period size: 182 Copynumber: 1.9 Consensus size: 183
1595912 AATTAAGTTA
1595922 ATTATAAAAATATCAATATTATTTAACTGTTATATAAAATTATT-AAA-AGAGTATTTTGTAATA
1 ATTATAAAAATATCAATATTATTTAACTGTTATATAAAATTATTAAAATAGAGTA--TT-T-A-A
* *
1595985 TAAAACATAGATA-TAACTCGATATTGAAATAATATATTAAAATTATTATAATTACGTTAATA-A
61 T--AACATAGATATTAACTAGATATTGAAATAATATATTAAAATTATTATAATTAAGTTAATATA
** * *
1596048 AAAATATTGACCTTAATAATTATATTATATAATAAAAATAATAATTAAATTACTTTTATT
124 AAAATATCAACATTAATAATTATATTAGATAATAAAAATAATAATTAAATTACTTTTATT
* ** ** *
1596108 ATTATTAAAATATTGATATTATTTTGCTGTTATATAAAATTATTAAAATAGAGTATTTAATAATA
1 ATTATAAAAATATCAATATTATTTAACTGTTATATAAAATTATTAAAATAGAGTATTTAATAACA
* * * * *
1596173 TAGTTATTAAGTAGATTTTGAAATAATATATTAATATTATTATAATTAAGTTATTATAAAAATAT
66 TAGATATTAACTAGATATTGAAATAATATATTAAAATTATTATAATTAAGTTAATATAAAAATAT
*
1596238 CAACATTAATAATTATGTTAGATAATAA
131 CAACATTAATAATTATATTAGATAATAA
1596266 TAAAAATTAA
Statistics
Matches: 136, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
181 8 0.06
182 43 0.32
183 33 0.24
184 1 0.01
185 1 0.01
186 41 0.30
187 3 0.02
188 6 0.04
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (183 bp):
ATTATAAAAATATCAATATTATTTAACTGTTATATAAAATTATTAAAATAGAGTATTTAATAACA
TAGATATTAACTAGATATTGAAATAATATATTAAAATTATTATAATTAAGTTAATATAAAAATAT
CAACATTAATAATTATATTAGATAATAAAAATAATAATTAAATTACTTTTATT
Found at i:1608051 original size:26 final size:26
Alignment explanation
Indices: 1608022--1608081 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
1608012 CATTGAATAG
*
1608022 GATAACTTTTATAATTTTAAAAATTA
1 GATAACATTTATAATTTTAAAAATTA
* *
1608048 GATAAAATTTATAATTTTGAAAATTA
1 GATAACATTTATAATTTTAAAAATTA
*
1608074 AATAACAT
1 GATAACAT
1608082 AAATTAGATA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (26 bp):
GATAACATTTATAATTTTAAAAATTA
Found at i:1608149 original size:57 final size:56
Alignment explanation
Indices: 1608088--1608231 Score: 150
Period size: 57 Copynumber: 2.6 Consensus size: 56
1608078 ACATAAATTA
* * *
1608088 GATAAATTTTAAAATTTTGAAGAGACAAATAAGAAAAAAAACATTTAT-ATTGAATAT
1 GATAAATTTTATAATTTTGAAGAGACAAAGAAGAAAAAAAACATTT-TCA-TGAATAG
* * *
1608145 GATAAATTTCT-TAATTTTGAA-ATGACGAAGAAGAAAAATAGCATTTTCATGAATAG
1 GATAAATTT-TATAATTTTGAAGA-GACAAAGAAGAAAAAAAACATTTTCATGAATAG
** *
1608201 GATAAATTCCATAATTTTGAAGAGGCAAAGA
1 GATAAATTTTATAATTTTGAAGAGACAAAGA
1608232 TTGAATAAGA
Statistics
Matches: 72, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
56 32 0.44
57 39 0.54
58 1 0.01
ACGTcount: A:0.49, C:0.06, G:0.15, T:0.31
Consensus pattern (56 bp):
GATAAATTTTATAATTTTGAAGAGACAAAGAAGAAAAAAAACATTTTCATGAATAG
Found at i:1608298 original size:94 final size:92
Alignment explanation
Indices: 1608136--1608446 Score: 370
Period size: 94 Copynumber: 3.3 Consensus size: 92
1608126 AAACATTTAT
* * * *
1608136 ATTGAATATGATAAATTTCTTAATTTTGAAATGACGAAGAAGAAAAATAGCATTTTCATGAATAG
1 ATTGAATAAGATAAATTCCATAATTTTGAAA-GATG-AGAAGAAAAATAGCATTTTCATGAATAG
*
1608201 GATAAATTCCATAATTTTGAAGAGGCAAA
64 GATAAATTTCATAATTTTGAAGAGGCAAA
* *
1608230 GATTGAATAAGATAAATTCCATAATTTTGAAGGATGAGTAAGAAAGATAGCATTTTCATGAATAG
1 -ATTGAATAAGATAAATTCCATAATTTTGAAAGATGAG-AAGAAAAATAGCATTTTCATGAATAG
*
1608295 GATAAATTTCATAATTTTGAAGAGGTGAAA
64 GATAAATTTCATAATTTTGAAGAGG-CAAA
* * * ** *
1608325 ATTGAATAGGAAAAATTCCATAATTTCGAAAGATTTGCAAGAAAAATAGCATTCTCATGAATAGG
1 ATTGAATAAGATAAATTCCATAATTTTGAAAGATGAG-AAGAAAAATAGCATTTTCATGAATAGG
* * *
1608390 ATGATTTTCATAATTTTGAAGAGACAAA
65 ATAAATTTCATAATTTTGAAGAGGCAAA
* * *
1608418 CATCGAAGAAAAATAAATTCCATAATTTT
1 -ATTGAA-TAAGATAAATTCCATAATTTT
1608447 AATAGCATAA
Statistics
Matches: 185, Mismatches: 27, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
93 5 0.03
94 134 0.72
95 46 0.25
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.31
Consensus pattern (92 bp):
ATTGAATAAGATAAATTCCATAATTTTGAAAGATGAGAAGAAAAATAGCATTTTCATGAATAGGA
TAAATTTCATAATTTTGAAGAGGCAAA
Found at i:1612552 original size:42 final size:44
Alignment explanation
Indices: 1612472--1612563 Score: 116
Period size: 45 Copynumber: 2.1 Consensus size: 44
1612462 TTATTTCACC
* * * *
1612472 ATAATAAATATTATAAAGCATATTACTTAATATTATTATTTGAAT
1 ATAATAAATATAATAAAGAATATTACTT-ATAGTATTATTTAAAT
1612517 ATAATAAATATAATAAAGAATATTA-TT-TAGTATTATTTAAAT
1 ATAATAAATATAATAAAGAATATTACTTATAGTATTATTTAAAT
*
1612559 TTAAT
1 ATAAT
1612564 GAAAAATATA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
42 17 0.40
44 2 0.05
45 23 0.55
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (44 bp):
ATAATAAATATAATAAAGAATATTACTTATAGTATTATTTAAAT
Found at i:1612644 original size:20 final size:21
Alignment explanation
Indices: 1612591--1612663 Score: 76
Period size: 23 Copynumber: 3.3 Consensus size: 21
1612581 TCTTAATATT
1612591 AAATATTATTGAATTATAAT-A
1 AAATATTATT-AATTATAATAA
* *
1612612 AAATGTTTAATTATCTTATAATACA
1 AAAT-ATT-ATTA-ATTATAATA-A
1612637 AAATATTATTAATTATAATAA
1 AAATATTATTAATTATAATAA
1612658 AAATAT
1 AAATAT
1612664 GTTTGTATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
21 11 0.26
22 11 0.26
23 14 0.33
24 2 0.05
25 5 0.12
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (21 bp):
AAATATTATTAATTATAATAA
Found at i:1615022 original size:44 final size:44
Alignment explanation
Indices: 1614952--1615043 Score: 148
Period size: 44 Copynumber: 2.1 Consensus size: 44
1614942 ATTCTAACTA
* *
1614952 TGAAAAACTATTAGTCATCGGCTTATACTATCATGGCCGATGTT
1 TGAAAAACTATTAGTCATCCGCTTATACTATCATGGCCGATATT
* *
1614996 TGAAAAACTATTAGTCATCCGTTTATACTATCATTGCCGATATT
1 TGAAAAACTATTAGTCATCCGCTTATACTATCATGGCCGATATT
1615040 TGAA
1 TGAA
1615044 GTCATATACA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (44 bp):
TGAAAAACTATTAGTCATCCGCTTATACTATCATGGCCGATATT
Found at i:1616831 original size:16 final size:16
Alignment explanation
Indices: 1616810--1616840 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1616800 CCAGATGGCG
*
1616810 GATGTTGTTTTCTGCT
1 GATGTTGTGTTCTGCT
1616826 GATGTTGTGTTCTGC
1 GATGTTGTGTTCTGC
1616841 CAAGAAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.06, C:0.13, G:0.29, T:0.52
Consensus pattern (16 bp):
GATGTTGTGTTCTGCT
Found at i:1620256 original size:20 final size:19
Alignment explanation
Indices: 1620223--1620264 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1620213 AAATTTTTGT
1620223 AATTAACAAATTTTTAAATAA
1 AATTAAC-AATTTTTAAA-AA
1620244 AATT-ACAATTTTTAAAAA
1 AATTAACAATTTTTAAAAA
1620262 AAT
1 AAT
1620265 GTATTGGACA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.24
19 10 0.48
20 2 0.10
21 4 0.19
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTAACAATTTTTAAAAA
Found at i:1620664 original size:20 final size:20
Alignment explanation
Indices: 1620639--1620712 Score: 93
Period size: 20 Copynumber: 3.8 Consensus size: 20
1620629 TAAATTTGAT
1620639 AAATATTAATATTTAATTTA
1 AAATATTAATATTTAATTTA
*
1620659 AAATATTAA-A--AAATTTAA
1 AAATATTAATATTTAATTT-A
1620677 AAATATTAATATTTAATTTA
1 AAATATTAATATTTAATTTA
1620697 AAA-ATTTAATATTTAA
1 AAATA-TTAATATTTAA
1620713 ATTATTCAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
17 5 0.11
18 10 0.21
19 3 0.06
20 24 0.51
21 5 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATATTAATATTTAATTTA
Found at i:1623629 original size:30 final size:29
Alignment explanation
Indices: 1623527--1623629 Score: 79
Period size: 29 Copynumber: 3.5 Consensus size: 29
1623517 AACAAAATTT
* *
1623527 AAATAAATTTTTATATTTTTA-TTAC-GTTC
1 AAATAAATTCTTATA-TTTTAGTTTCAG-TC
*
1623556 -AATCAAATTCTTATATTTTATTTTCAGTC
1 AAAT-AAATTCTTATATTTTAGTTTCAGTC
* * *
1623585 AGATAAGTTTTTATACTTTT-GTTTCAAGTC
1 AAATAAATTCTTATA-TTTTAGTTTC-AGTC
1623615 AAATAAATTCTTATA
1 AAATAAATTCTTATA
1623630 ACTAATAATT
Statistics
Matches: 59, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
28 8 0.14
29 28 0.47
30 23 0.39
ACGTcount: A:0.34, C:0.10, G:0.06, T:0.50
Consensus pattern (29 bp):
AAATAAATTCTTATATTTTAGTTTCAGTC
Found at i:1633728 original size:2 final size:2
Alignment explanation
Indices: 1633721--1633790 Score: 70
Period size: 2 Copynumber: 34.0 Consensus size: 2
1633711 AGAGCAGGAT
* * **
1633721 AG AG AG AG AG AG AG AG AG AG AG AG ACG AC NG TCT AG AG CAG -G
1 AG AG AG AG AG AG AG AG AG AG AG AG A-G AG AG -AG AG AG -AG AG
1633763 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1633791 GACACGTCAC
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
1 1 0.02
2 52 0.91
3 4 0.07
ACGTcount: A:0.44, C:0.06, G:0.46, T:0.03
Consensus pattern (2 bp):
AG
Found at i:1637887 original size:6 final size:6
Alignment explanation
Indices: 1637852--1637908 Score: 51
Period size: 6 Copynumber: 9.5 Consensus size: 6
1637842 AGACCAAGGA
* * * * * *
1637852 GCTGTT GCTGCT GATGGT GGTGTT GCTGTT GTTGTT GCTCTT GCTGTT
1 GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT GCTGTT
*
1637900 GCTTTT GCT
1 GCTGTT GCT
1637909 TTATAACTTG
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.02, C:0.16, G:0.33, T:0.49
Consensus pattern (6 bp):
GCTGTT
Found at i:1638185 original size:12 final size:12
Alignment explanation
Indices: 1638168--1638206 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
1638158 TAAGCTAAGA
1638168 AGAGAAAGAGAG
1 AGAGAAAGAGAG
1638180 AGAGAAACTGAGAG
1 AGAGAAA--GAGAG
*
1638194 GGAGAAAGAGAG
1 AGAGAAAGAGAG
1638206 A
1 A
1638207 AACTTGAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 12 0.52
14 11 0.48
ACGTcount: A:0.54, C:0.03, G:0.41, T:0.03
Consensus pattern (12 bp):
AGAGAAAGAGAG
Found at i:1654870 original size:2 final size:2
Alignment explanation
Indices: 1654863--1654907 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1654853 ATAATTTCAT
1654863 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1654905 TA T
1 TA T
1654908 TCACACAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1658434 original size:19 final size:20
Alignment explanation
Indices: 1658402--1658439 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
1658392 TTCCTCGGGA
1658402 TTTTCTTTTCCCTC-CTTCG
1 TTTTCTTTTCCCTCTCTTCG
1658421 TTTTCTTTAT-CCTCTCTTC
1 TTTTCTTT-TCCCTCTCTTC
1658440 CATTTTTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.03, C:0.34, G:0.03, T:0.61
Consensus pattern (20 bp):
TTTTCTTTTCCCTCTCTTCG
Found at i:1666294 original size:14 final size:13
Alignment explanation
Indices: 1666273--1666308 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
1666263 ATATTAATTG
1666273 TCATATTATCATAA
1 TCATATTATCA-AA
*
1666287 TTATATTATCAAA
1 TCATATTATCAAA
1666300 TCATATTAT
1 TCATATTAT
1666309 GTGTCATGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (13 bp):
TCATATTATCAAA
Found at i:1672836 original size:13 final size:13
Alignment explanation
Indices: 1672818--1672842 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1672808 AAAAAGTAAA
1672818 ATAATATAAAATT
1 ATAATATAAAATT
1672831 ATAATATAAAAT
1 ATAATATAAAAT
1672843 GTAAGAATAT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
ATAATATAAAATT
Found at i:1691632 original size:18 final size:18
Alignment explanation
Indices: 1691609--1691655 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
1691599 TATTCACGAC
*
1691609 CACGATCCCGAGCTCGAT
1 CACGATCACGAGCTCGAT
*
1691627 CACGATCACGTGCTCGAT
1 CACGATCACGAGCTCGAT
1691645 CACGATCACGA
1 CACGATCACGA
1691656 CCACGGTCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.26, C:0.36, G:0.21, T:0.17
Consensus pattern (18 bp):
CACGATCACGAGCTCGAT
Found at i:1694058 original size:278 final size:272
Alignment explanation
Indices: 1693521--1694070 Score: 888
Period size: 278 Copynumber: 2.0 Consensus size: 272
1693511 ACATCTTTGG
* *
1693521 AATTGGATTGTAAAAGTATTGGGAATTGCGAAATAATCAGCCCTTACCAGGTATACCTTTATAGG
1 AATTGGATTGTAAAAGTATTGGGAATTGAGAAATAATCAGCCCTTACCAGGGATACCTTTATAGG
* *
1693586 ATGATTCTTAATGGTACAACAATACCTAAAGAGTGGAAAATCACCTATATCTGGAGATGGTTTCT
66 ATGATTCTTAATGGTACAACAATACCTAAAGAGTGGAAAATCACCTATATCTGGAGACGATTTCT
* *
1693651 ACATCCTACCATATTAAAGCAACTTATCAAGGGGTCCATTGAAACAAACCCATACACCCTTACCA
131 ACATCCTACCATATTAAAGCAACTTATCAAGGGGTCAACTGAAACAAACCCATACACCCTTACCA
* *
1693716 GAAAATAGGCTGTGATACCTGTTATTTTTTTTCAACTTGATCAGACTCCAAGTACAATATATTAC
196 GAAAATAGGCTGTGATACCTGTTATTATTTTTCAACTTGAACAGACTCCAAGTACAATATATTAC
1693781 AGAACAGGCAGA
261 AGAACAGGCAGA
*
1693793 AATTGGATTGTAAAAGTATTGGGGATTGAGAAATAGAGTAATCAGCCCCTTACCAGGGATACCTT
1 AATTGGATTGTAAAAGTATTGGGAATTGAG--A-A-A-TAATCAG-CCCTTACCAGGGATACCTT
* *
1693858 TATAGGATGATTCTTAATGGTACAACAATACCTAAAGAGTGGAAGATCACCTATGTCTGGAGACG
60 TATAGGATGATTCTTAATGGTACAACAATACCTAAAGAGTGGAAAATCACCTATATCTGGAGACG
*
1693923 ATTTCTACATCCTACCATATTAAAGCAACTTATCAAGGGGTCAACTGAAACAAACCCATTCGA-C
125 ATTTCTACATCCTACCATATTAAAGCAACTTATCAAGGGGTCAACTGAAACAAACCCATAC-ACC
* *
1693987 CTTACCAGTAAATAGGCTGTGATACCTGTT-TTCATTTTTCAACTTGAACAGACTCCAAGTACGA
189 CTTACCAGAAAATAGGCTGTGATACCTGTTATT-ATTTTTCAACTTGAACAGACTCCAAGTACAA
1694051 TATATTACAGAACAGGCAGA
253 TATATTACAGAACAGGCAGA
1694071 TGCTCAGCAT
Statistics
Matches: 256, Mismatches: 14, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
272 28 0.11
274 1 0.00
275 1 0.00
276 1 0.00
277 9 0.04
278 215 0.84
279 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (272 bp):
AATTGGATTGTAAAAGTATTGGGAATTGAGAAATAATCAGCCCTTACCAGGGATACCTTTATAGG
ATGATTCTTAATGGTACAACAATACCTAAAGAGTGGAAAATCACCTATATCTGGAGACGATTTCT
ACATCCTACCATATTAAAGCAACTTATCAAGGGGTCAACTGAAACAAACCCATACACCCTTACCA
GAAAATAGGCTGTGATACCTGTTATTATTTTTCAACTTGAACAGACTCCAAGTACAATATATTAC
AGAACAGGCAGA
Found at i:1703677 original size:24 final size:24
Alignment explanation
Indices: 1703650--1703724 Score: 141
Period size: 24 Copynumber: 3.1 Consensus size: 24
1703640 CACTCTCCAA
1703650 ATCTGCCATGACCCAAGAATCACT
1 ATCTGCCATGACCCAAGAATCACT
1703674 ATCTGCCATGACCCAAGAATCACT
1 ATCTGCCATGACCCAAGAATCACT
*
1703698 ATCTGCCATAACCCAAGAATCACT
1 ATCTGCCATGACCCAAGAATCACT
1703722 ATC
1 ATC
1703725 CGAATCAGCC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.35, C:0.33, G:0.11, T:0.21
Consensus pattern (24 bp):
ATCTGCCATGACCCAAGAATCACT
Done.