Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2
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: 5794061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 68655 characters in sequence are not A, C, G, or T
File 8 of 38
Found at i:1202901 original size:20 final size:19
Alignment explanation
Indices: 1202847--1202901 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
1202837 AAAACCCTTA
*
1202847 AAAGTATCGATACACAATTC
1 AAAGTATCGATACA-TATTC
1202867 AAAGTATCGATACATATTGC
1 AAAGTATCGATACATATT-C
*
1202887 AATGTATCGATACAT
1 AAAGTATCGATACAT
1202902 GAAAAAGATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 3 0.09
20 29 0.91
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (19 bp):
AAAGTATCGATACATATTC
Found at i:1202996 original size:20 final size:20
Alignment explanation
Indices: 1202953--1203004 Score: 88
Period size: 19 Copynumber: 2.6 Consensus size: 20
1202943 GTAGCCAAAC
*
1202953 TTGTATCGATACACAAAATA
1 TTGTATCGATACACAAAAAA
1202973 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
1202992 TTGTATCGATACA
1 TTGTATCGATACA
1203005 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:1203505 original size:34 final size:35
Alignment explanation
Indices: 1203442--1203508 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1203432 CTAAGTGATT
1203442 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
1203478 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
1203509 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:1204627 original size:21 final size:21
Alignment explanation
Indices: 1204601--1204642 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1204591 AATCAACCGT
* *
1204601 TCAAGATGATGATGAAGATGA
1 TCAAGAGGATGATGAAAATGA
*
1204622 TCAAGAGGTTGATGAAAATGA
1 TCAAGAGGATGATGAAAATGA
1204643 AGAAATGGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.05, G:0.29, T:0.24
Consensus pattern (21 bp):
TCAAGAGGATGATGAAAATGA
Found at i:1205204 original size:84 final size:84
Alignment explanation
Indices: 1205031--1205195 Score: 210
Period size: 84 Copynumber: 2.0 Consensus size: 84
1205021 ACTCAAAGAA
* * * *
1205031 GAAAATAAATCAATAAGTGTAGAGAATGATATTCTTGAAAAGAAATTAAGTGAATTAGAGAAGAA
1 GAAAATAAATCAATAAGTGTAGAAAATGATATTCTTAAAAAGAAAATAAATGAATTAGAGAAGAA
*
1205096 TATGAAAGAGTTGCAAAAT
66 TAAGAAAGAGTTGCAAAAT
* * *
1205115 GAAAATAAATCAATGAGTTTAGAAAAT-A-ATTCTTTTAAAAAGAAAATAAATGAATTAGAGGAG
1 GAAAATAAATCAATAAGTGTAGAAAATGATATTC--TTAAAAAGAAAATAAATGAATTAGAGAAG
1205178 AA-AAGAAATGAGTTGCAA
64 AATAAGAAA-GAGTTGCAA
1205196 GTGGAAAATG
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
82 4 0.06
83 6 0.09
84 60 0.86
ACGTcount: A:0.53, C:0.04, G:0.19, T:0.25
Consensus pattern (84 bp):
GAAAATAAATCAATAAGTGTAGAAAATGATATTCTTAAAAAGAAAATAAATGAATTAGAGAAGAA
TAAGAAAGAGTTGCAAAAT
Found at i:1206518 original size:13 final size:13
Alignment explanation
Indices: 1206500--1206524 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1206490 TCTTCCAGAT
1206500 TGTATCGATACAA
1 TGTATCGATACAA
1206513 TGTATCGATACA
1 TGTATCGATACA
1206525 TTGCTTCAGT
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:1207380 original size:46 final size:46
Alignment explanation
Indices: 1207318--1207469 Score: 286
Period size: 46 Copynumber: 3.3 Consensus size: 46
1207308 TTGATATAAC
* *
1207318 ATTAAGGGGGAGAGATTATTGTTTATTTGTTTAAGGGTGACAACAT
1 ATTAAGGGGGAGAGATTATTGTTTATTGGTTTAAGGGTGACAACGT
1207364 ATTAAGGGGGAGAGATTATTGTTTATTGGTTTAAGGGTGACAACGT
1 ATTAAGGGGGAGAGATTATTGTTTATTGGTTTAAGGGTGACAACGT
1207410 ATTAAGGGGGAGAGATTATTGTTTATTGGTTTAAGGGTGACAACGT
1 ATTAAGGGGGAGAGATTATTGTTTATTGGTTTAAGGGTGACAACGT
1207456 ATTAAGGGGGAGAG
1 ATTAAGGGGGAGAG
1207470 TTTGTATAAA
Statistics
Matches: 104, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 104 1.00
ACGTcount: A:0.30, C:0.04, G:0.33, T:0.34
Consensus pattern (46 bp):
ATTAAGGGGGAGAGATTATTGTTTATTGGTTTAAGGGTGACAACGT
Found at i:1208640 original size:19 final size:18
Alignment explanation
Indices: 1208616--1208679 Score: 66
Period size: 20 Copynumber: 3.7 Consensus size: 18
1208606 TAGCCAAACT
1208616 TGTATCGATACACAAAATA
1 TGTATCGATACACAAAA-A
1208635 TGTATCGAT--AC---AA
1 TGTATCGATACACAAAAA
1208648 TGTATCGATACACAAAAAA
1 TGTATCGATACAC-AAAAA
1208667 TTGTATCGATACA
1 -TGTATCGATACA
1208680 TTGGCTTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
15 2 0.05
17 2 0.05
19 11 0.29
20 12 0.32
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (18 bp):
TGTATCGATACACAAAAA
Found at i:1208652 original size:13 final size:13
Alignment explanation
Indices: 1208634--1208659 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1208624 TACACAAAAT
1208634 ATGTATCGATACA
1 ATGTATCGATACA
1208647 ATGTATCGATACA
1 ATGTATCGATACA
1208660 CAAAAAATTG
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:1208657 original size:32 final size:33
Alignment explanation
Indices: 1208616--1208679 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 33
1208606 TAGCCAAACT
*
1208616 TGTATCGATACACAAAATA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1208648 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1208680 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 18 0.60
33 12 0.40
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1209180 original size:34 final size:35
Alignment explanation
Indices: 1209117--1209183 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1209107 CTAAGTGATT
1209117 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
1209153 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
1209184 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:1211923 original size:79 final size:78
Alignment explanation
Indices: 1211792--1212403 Score: 300
Period size: 79 Copynumber: 7.8 Consensus size: 78
1211782 CTGGGGCTGA
* * * *
1211792 AGTATCCCCGATTATGAAAAATTAGTGTTCTGAAAATAAAATCGGGGTTGGAGTATCTCCTCGGA
1 AGTATCCCTGATTATGAAAAATTGGTATTTTGAAAATAAAATCGGGGTTGGAGTATC-CCTCGGA
1211857 AATAACAGGGTTGG
65 AATAACAGGGTTGG
*
1211871 AGTATCCCTGATTAT-AGAAAATTGGTATTTTGAAAATAAAATCGGGGTTGGAGTATCCTCTCGA
1 AGTATCCCTGATTATGA-AAAATTGGTATTTTGAAAATAAAATCGGGGTTGGAGTATCC-CTCGG
*
1211935 AAATAA-TGAGGTTGG
64 AAATAACAG-GGTTGG
* * * **
1211950 AGTAT-CCTCGATTATGGAAAA-T-CTATTCTTTAGAAAT-AAGGCTGGGGTTGGAGTATCCC-C
1 AGTATCCCT-GATTATGAAAAATTGGTATT-TTGA-AAATAAAATC-GGGGTTGGAGTATCCCTC
* **
1212010 GCGAAAGTAACGGGGTCAG
62 G-GAAA-TAACAGGGTTGG
* * * *** ** * * * *
1212029 AGTAT-CCTCGATTGTGAGACATCAATATTTT-AGAAATAAAGCCGAGGTTGAATTATCCCCTCA
1 AGTATCCCT-GATTATGAAAAATTGGTATTTTGA-AAATAAAATCGGGGTTGGAGTAT-CCCTCG
*
1212092 GAAATAACGGGGTTGG
63 GAAATAACAGGGTTGG
*** ** * *
1212108 AGTATCCCT-A--ATGAAATAACAGGGTTAGAGTATCCCCGATTATGAAAAATTGGTGTTTTGGA
1 AGTATCCCTGATTATG-AA-AA-A---TT-G-GTAT-TTTGAAAAT--AAAATCGG-G-GTTGGA
* **
1212170 --A---AT---AAA-ATTAGGGTTGG
53 GTATCCCTCGGAAATAACAGGGTTGG
* * * *
1212187 AGTATCTCC-GATTGTGAAAAATTGGTGTTTT-AGAAATAAAATCGGGCTTGGAGTATCTCCTCA
1 AGTATC-CCTGATTATGAAAAATTGGTATTTTGA-AAATAAAATCGGGGTTGGAGTATC-CCTCG
* *
1212250 GAAATAACGGGGTTAG
63 GAAATAACAGGGTTGG
* * * ** *
1212266 AGTATCCCTGATTGTGAAAAATTAGTGTTTTGGGAATAAAATCGAGGTTGGAGTATCCCCTCGGA
1 AGTATCCCTGATTATGAAAAATTGGTATTTTGAAAATAAAATCGGGGTTGGAGTAT-CCCTCGGA
1212331 AATAA-AGGGATTGG
65 AATAACAGGG-TTGG
* * * *
1212345 AGTATCCCTGATTATGAAAAATTGATGTTTTGAAAATAAAACCAGGGTTGGAGTATCCC
1 AGTATCCCTGATTATGAAAAATTGGTATTTTGAAAATAAAATCGGGGTTGGAGTATCCC
1212404 CGAGATGAAA
Statistics
Matches: 404, Mismatches: 79, Indels: 101
0.69 0.14 0.17
Matches are distributed among these distances:
69 5 0.01
70 1 0.00
71 8 0.02
72 1 0.00
73 2 0.00
74 3 0.01
75 2 0.00
76 4 0.01
77 7 0.02
78 30 0.07
79 288 0.71
80 26 0.06
81 7 0.02
82 3 0.01
83 1 0.00
84 3 0.01
85 2 0.00
86 1 0.00
87 5 0.01
88 1 0.00
89 4 0.01
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (78 bp):
AGTATCCCTGATTATGAAAAATTGGTATTTTGAAAATAAAATCGGGGTTGGAGTATCCCTCGGAA
ATAACAGGGTTGG
Found at i:1212113 original size:28 final size:29
Alignment explanation
Indices: 1212082--1212144 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
1212072 GAGGTTGAAT
* * *
1212082 TATCCCCTCA-GAAATAACGGGGTTGGAG
1 TATCCCCTAATGAAATAACAGGGTTAGAG
1212110 TAT-CCCTAATGAAATAACAGGGTTAGAG
1 TATCCCCTAATGAAATAACAGGGTTAGAG
1212138 TATCCCC
1 TATCCCC
1212145 GATTATGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 5 0.17
28 22 0.73
29 3 0.10
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (29 bp):
TATCCCCTAATGAAATAACAGGGTTAGAG
Found at i:1212244 original size:51 final size:51
Alignment explanation
Indices: 1212128--1212246 Score: 177
Period size: 51 Copynumber: 2.3 Consensus size: 51
1212118 ATGAAATAAC
* * *
1212128 AGGGTTAGAGTATCCCCGATTATGAAAAATTGGTGTTTTGGAAATAAAATT
1 AGGGTTGGAGTATCTCCGATTATGAAAAATTGGTGTTTTAGAAATAAAATT
*
1212179 AGGGTTGGAGTATCTCCGATTGTGAAAAATTGGTGTTTTAGAAATAAAA-T
1 AGGGTTGGAGTATCTCCGATTATGAAAAATTGGTGTTTTAGAAATAAAATT
*
1212229 CGGGCTTGGAGTATCTCC
1 AGGG-TTGGAGTATCTCC
1212247 TCAGAAATAA
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
50 4 0.06
51 58 0.94
ACGTcount: A:0.31, C:0.10, G:0.26, T:0.33
Consensus pattern (51 bp):
AGGGTTGGAGTATCTCCGATTATGAAAAATTGGTGTTTTAGAAATAAAATT
Found at i:1214785 original size:20 final size:20
Alignment explanation
Indices: 1214760--1214842 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
1214750 AAACCCAGAT
1214760 TGTATCGATACAATGAACAA
1 TGTATCGATACAATGAACAA
*
1214780 TGTATCGATACATCTGGGTAAAACCCAGA
1 TGTATCGATACA-AT--G---AA--CA-A
1214809 ATGTATCGATACAATGAACAA
1 -TGTATCGATACAATGAACAA
1214830 TGTATCGATACAA
1 TGTATCGATACAA
1214843 ATTGTGCAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 20
0.70 0.03 0.27
Matches are distributed among these distances:
20 25 0.49
21 2 0.04
22 2 0.04
23 1 0.02
24 2 0.04
26 2 0.04
27 1 0.02
28 2 0.04
29 2 0.04
30 12 0.24
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.25
Consensus pattern (20 bp):
TGTATCGATACAATGAACAA
Found at i:1214824 original size:50 final size:49
Alignment explanation
Indices: 1214738--1214841 Score: 181
Period size: 50 Copynumber: 2.1 Consensus size: 49
1214728 GTATCGATAC
*
1214738 ATACATCTAGGTAAACCCAGATTGTATCGATACAATGAACAATGTATCG
1 ATACATCTAGGTAAACCCAGAATGTATCGATACAATGAACAATGTATCG
*
1214787 ATACATCTGGGTAAAACCCAGAATGTATCGATACAATGAACAATGTATCG
1 ATACATCTAGGT-AAACCCAGAATGTATCGATACAATGAACAATGTATCG
1214837 ATACA
1 ATACA
1214842 AATTGTGCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
49 11 0.21
50 41 0.79
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.25
Consensus pattern (49 bp):
ATACATCTAGGTAAACCCAGAATGTATCGATACAATGAACAATGTATCG
Found at i:1217727 original size:13 final size:13
Alignment explanation
Indices: 1217709--1217733 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1217699 TACATAAGTT
1217709 TTGTATCGATACG
1 TTGTATCGATACG
1217722 TTGTATCGATAC
1 TTGTATCGATAC
1217734 AAAGTACCCC
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:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACG
Found at i:1217806 original size:19 final size:20
Alignment explanation
Indices: 1217768--1217813 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
1217758 GAAATATATT
*
1217768 GATACATTAATGAATGTATC
1 GATACATTAATCAATGTATC
*
1217788 GATACATT-ATCATTGTATC
1 GATACATTAATCAATGTATC
1217807 GATACAT
1 GATACAT
1217814 CTGGGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (20 bp):
GATACATTAATCAATGTATC
Found at i:1219321 original size:10 final size:11
Alignment explanation
Indices: 1219297--1219329 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1219287 AATAATAACG
1219297 ATTTTTCTAGA
1 ATTTTTCTAGA
*
1219308 ATTTTT-TAGT
1 ATTTTTCTAGA
1219318 ATTTTTCTAGA
1 ATTTTTCTAGA
1219329 A
1 A
1219330 AATTGTGTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.27, C:0.06, G:0.09, T:0.58
Consensus pattern (11 bp):
ATTTTTCTAGA
Found at i:1221039 original size:19 final size:20
Alignment explanation
Indices: 1220994--1221044 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
1220984 CTGCCACTTT
* *
1220994 CATGTATTGATACAATTGAG
1 CATGTATCGATACAATTGAA
*
1221014 TATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
1221033 CATGTATCGATA
1 CATGTATCGATA
1221045 AAAAGCGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:1229715 original size:13 final size:13
Alignment explanation
Indices: 1229697--1229721 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1229687 CAATTCTTCT
1229697 TGTATCGATACAA
1 TGTATCGATACAA
1229710 TGTATCGATACA
1 TGTATCGATACA
1229722 TTGTCCCATG
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:1229823 original size:19 final size:20
Alignment explanation
Indices: 1229770--1229823 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 20
1229760 CTACCACTTT
*
1229770 CATGTATCGATACAATTGAG
1 CATGTATCGATACAATTGAA
* *
1229790 TATGCATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
*
1229809 CATGTATCAATACAA
1 CATGTATCGATACAA
1229824 AGCGTAATGT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.28
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:1234562 original size:2 final size:2
Alignment explanation
Indices: 1234555--1234580 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1234545 AGGTGGTCTA
1234555 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
1234581 GCGTAACCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1239261 original size:5 final size:5
Alignment explanation
Indices: 1239251--1239311 Score: 50
Period size: 5 Copynumber: 11.0 Consensus size: 5
1239241 ACTAGTTTAA
* *
1239251 AAAAT AAAAT AAAAT AAAAT CCAAAATT AAAAG AAAATT AAAAGA AAAAT
1 AAAAT AAAAT AAAAT AAAAT --AAAA-T AAAAT AAAA-T AAAA-T AAAAT
1239301 AAAATT AAAAT
1 AAAA-T AAAAT
1239312 TGATAATCAT
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
5 24 0.52
6 17 0.37
7 4 0.09
8 1 0.02
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:1239310 original size:11 final size:11
Alignment explanation
Indices: 1239250--1239312 Score: 56
Period size: 11 Copynumber: 5.5 Consensus size: 11
1239240 AACTAGTTTA
*
1239250 AAAAATAAAAT
1 AAAATTAAAAT
1239261 AAAA-TAAAAT
1 AAAATTAAAAT
*
1239271 CCAAAATTAAAAG
1 --AAAATTAAAAT
*
1239284 AAAATTAAAAG
1 AAAATTAAAAT
*
1239295 AAAAATAAAATT
1 AAAATTAAAA-T
1239307 AAAATT
1 AAAATT
1239313 GATAATCATA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
10 6 0.14
11 24 0.55
12 9 0.20
13 5 0.11
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.21
Consensus pattern (11 bp):
AAAATTAAAAT
Found at i:1239310 original size:23 final size:23
Alignment explanation
Indices: 1239250--1239312 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
1239240 AACTAGTTTA
1239250 AAAAATAAAATAAAA-TAAAATCC
1 AAAAATAAAATAAAATTAAAA-CC
* * *
1239273 AAAATTAAAAGAAAATTAAAA-G
1 AAAAATAAAATAAAATTAAAACC
1239295 AAAAATAAAATTAAAATT
1 AAAAATAAAA-TAAAATT
1239313 GATAATCATA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
22 9 0.27
23 19 0.58
24 5 0.15
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.21
Consensus pattern (23 bp):
AAAAATAAAATAAAATTAAAACC
Found at i:1241322 original size:20 final size:20
Alignment explanation
Indices: 1241291--1241347 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
1241281 GTCAAAACCC
*
1241291 TGAAAAGTATCGATACACAT
1 TGAAATGTATCGATACACAT
* *
1241311 TTAAATGTATCGATACAGAT
1 TGAAATGTATCGATACACAT
* *
1241331 TGCATTGTATCGATACA
1 TGAAATGTATCGATACA
1241348 TTGTATCGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (20 bp):
TGAAATGTATCGATACACAT
Found at i:1241351 original size:13 final size:13
Alignment explanation
Indices: 1241333--1241394 Score: 64
Period size: 13 Copynumber: 5.2 Consensus size: 13
1241323 ATACAGATTG
1241333 CATTGTATCGATA
1 CATTGTATCGATA
1241346 CATTGTATCGATA
1 CATTGTATCGATA
*
1241359 CA--G-AT---TG
1 CATTGTATCGATA
1241366 CATTGTATCGATA
1 CATTGTATCGATA
*
1241379 CATTGTATTGATA
1 CATTGTATCGATA
1241392 CAT
1 CAT
1241395 GACCAAATGT
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
7 3 0.08
9 1 0.03
10 4 0.10
11 1 0.03
13 31 0.77
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.39
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:1241358 original size:33 final size:33
Alignment explanation
Indices: 1241316--1241393 Score: 147
Period size: 33 Copynumber: 2.4 Consensus size: 33
1241306 CACATTTAAA
1241316 TGTATCGATACAGATTGCATTGTATCGATACAT
1 TGTATCGATACAGATTGCATTGTATCGATACAT
1241349 TGTATCGATACAGATTGCATTGTATCGATACAT
1 TGTATCGATACAGATTGCATTGTATCGATACAT
*
1241382 TGTATTGATACA
1 TGTATCGATACA
1241394 TGACCAAATG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (33 bp):
TGTATCGATACAGATTGCATTGTATCGATACAT
Found at i:1241371 original size:20 final size:20
Alignment explanation
Indices: 1241297--1241380 Score: 83
Period size: 20 Copynumber: 4.5 Consensus size: 20
1241287 ACCCTGAAAA
* ** *
1241297 GTATCGATACACATTTAAAT
1 GTATCGATACAGATTGCATT
1241317 GTATCGATACAGATTGCATT
1 GTATCGATACAGATTGCATT
1241337 GTATCGAT----A---CATT
1 GTATCGATACAGATTGCATT
1241350 GTATCGATACAGATTGCATT
1 GTATCGATACAGATTGCATT
1241370 GTATCGATACA
1 GTATCGATACA
1241381 TTGTATTGAT
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
13 12 0.23
16 1 0.02
17 1 0.02
20 39 0.74
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (20 bp):
GTATCGATACAGATTGCATT
Found at i:1241406 original size:33 final size:32
Alignment explanation
Indices: 1241316--1241412 Score: 106
Period size: 33 Copynumber: 2.9 Consensus size: 32
1241306 CACATTTAAA
* *
1241316 TGTATCGATACAGATTGCATTGTATCGATACAT
1 TGTATCGATACAGA-TCCAATGTATCGATACAT
* *
1241349 TGTATCGATACAGATTGCATTGTATCGATACAT
1 TGTATCGATACAGA-TCCAATGTATCGATACAT
*
1241382 TGTATTGATACATGA-CCAAATGTATCGATAC
1 TGTATCGATACA-GATCC-AATGTATCGATAC
1241413 CTGAAAAGAA
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
32 1 0.02
33 56 0.95
34 2 0.03
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAGATCCAATGTATCGATACAT
Found at i:1241411 original size:20 final size:21
Alignment explanation
Indices: 1241382--1241434 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
1241372 ATCGATACAT
* **
1241382 TGTATTGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
*
1241402 TGTATCGATACCTGAAAAGAA
1 TGTATCGATACATGAAAAGAA
1241423 TGTATCGATACA
1 TGTATCGATACA
1241435 GGTCATTGGC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGAAAAGAA
Found at i:1241504 original size:13 final size:13
Alignment explanation
Indices: 1241486--1241510 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1241476 ACACACCATA
1241486 TGTATCGATACAT
1 TGTATCGATACAT
1241499 TGTATCGATACA
1 TGTATCGATACA
1241511 CCCTTAATGT
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):
TGTATCGATACAT
Found at i:1241507 original size:32 final size:32
Alignment explanation
Indices: 1241466--1241532 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 32
1241456 GTAGCCAAAT
1241466 TTGTATCGATACACACCAT-ATGTATCGATACA
1 TTGTATCGATACAC-CCATAATGTATCGATACA
*
1241498 TTGTATCGATACACCCTTAATGTATCGATACA
1 TTGTATCGATACACCCATAATGTATCGATACA
1241530 TTG
1 TTG
1241533 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
31 3 0.09
32 30 0.91
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.34
Consensus pattern (32 bp):
TTGTATCGATACACCCATAATGTATCGATACA
Found at i:1250167 original size:20 final size:20
Alignment explanation
Indices: 1250136--1250192 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
1250126 GTCAAAACCC
*
1250136 TGAAAAGTATCGATACACAT
1 TGAAATGTATCGATACACAT
* *
1250156 TTAAATGTATCGATACAGAT
1 TGAAATGTATCGATACACAT
* *
1250176 TGCATTGTATCGATACA
1 TGAAATGTATCGATACA
1250193 TTGTATCGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (20 bp):
TGAAATGTATCGATACACAT
Found at i:1250196 original size:13 final size:13
Alignment explanation
Indices: 1250178--1250206 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1250168 ATACAGATTG
1250178 CATTGTATCGATA
1 CATTGTATCGATA
1250191 CATTGTATCGATA
1 CATTGTATCGATA
1250204 CAT
1 CAT
1250207 GACCAAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:1250219 original size:20 final size:21
Alignment explanation
Indices: 1250194--1250246 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
1250184 ATCGATACAT
**
1250194 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
*
1250214 TGTATCGATACCTGAAAAGAA
1 TGTATCGATACATGAAAAGAA
1250235 TGTATCGATACA
1 TGTATCGATACA
1250247 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (21 bp):
TGTATCGATACATGAAAAGAA
Found at i:1250316 original size:13 final size:13
Alignment explanation
Indices: 1250298--1250324 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1250288 ACACACCATA
1250298 TGTATCGATACAT
1 TGTATCGATACAT
1250311 TGTATCGATACAT
1 TGTATCGATACAT
1250324 T
1 T
1250325 CTAAAATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1254165 original size:32 final size:30
Alignment explanation
Indices: 1254129--1254187 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
1254119 GAAATCAAAT
1254129 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
1254161 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
1254188 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:1254473 original size:21 final size:19
Alignment explanation
Indices: 1254447--1254496 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
1254437 TACAAGCCAA
*
1254447 TGTATCGATATAATTTTTTTG
1 TGTATCGATA-AA-TATTTTG
* *
1254468 TGTATCGCTACATATTTTG
1 TGTATCGATAAATATTTTG
1254487 TGTATCGATA
1 TGTATCGATA
1254497 CAAGTTTGGC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 15 0.60
20 1 0.04
21 9 0.36
ACGTcount: A:0.24, C:0.10, G:0.16, T:0.50
Consensus pattern (19 bp):
TGTATCGATAAATATTTTG
Found at i:1254603 original size:20 final size:20
Alignment explanation
Indices: 1254550--1254605 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
1254540 ACATCTTTTT
*
1254550 CATGTATCGATACATTGCAA
1 CATGTATCGATACTTTGCAA
1254570 CATGTATCGATACTTTG-AA
1 CATGTATCGATACTTTGCAA
*
1254589 CTGTGTATCGATACTTT
1 C-ATGTATCGATACTTT
1254606 TAAGGGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 3 0.09
20 30 0.91
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (20 bp):
CATGTATCGATACTTTGCAA
Found at i:1258089 original size:20 final size:20
Alignment explanation
Indices: 1258063--1258113 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
1258053 TAACGTTAGT
1258063 AATAAGATTAATTATGTAGC
1 AATAAGATTAATTATGTAGC
* *
1258083 TATAAGATTAATTATTTAGC
1 AATAAGATTAATTATGTAGC
*
1258103 AATGAGATTAA
1 AATAAGATTAA
1258114 AATCGGTGGT
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:0.45, C:0.04, G:0.14, T:0.37
Consensus pattern (20 bp):
AATAAGATTAATTATGTAGC
Found at i:1259956 original size:21 final size:22
Alignment explanation
Indices: 1259915--1259961 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
1259905 ATTCAGATAA
*
1259915 AAAATTATATAAAAGTTAAATT
1 AAAATTATATAAAAGTAAAATT
1259937 AAAA-TATAATAAAA-TAAAATT
1 AAAATTAT-ATAAAAGTAAAATT
1259958 AAAA
1 AAAA
1259962 ATATTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (22 bp):
AAAATTATATAAAAGTAAAATT
Found at i:1259962 original size:22 final size:24
Alignment explanation
Indices: 1259914--1259965 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 24
1259904 AATTCAGATA
*
1259914 AAAAAT-TATATAAAAGTTAAATT
1 AAAAATATATATAAAAGTAAAATT
1259937 -AAAATATA-ATAAAA-TAAAATT
1 AAAAATATATATAAAAGTAAAATT
1259958 AAAAATAT
1 AAAAATAT
1259966 TTATTTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 6 0.23
22 18 0.69
23 2 0.08
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (24 bp):
AAAAATATATATAAAAGTAAAATT
Found at i:1261880 original size:17 final size:18
Alignment explanation
Indices: 1261860--1261893 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1261850 AAATTTTGAA
1261860 AAATGAA-AAAAAAAAGG
1 AAATGAAGAAAAAAAAGG
*
1261877 AAATGAAGAAAAGAAAG
1 AAATGAAGAAAAAAAAG
1261894 TAAAGGAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.06
Consensus pattern (18 bp):
AAATGAAGAAAAAAAAGG
Found at i:1264685 original size:16 final size:16
Alignment explanation
Indices: 1264648--1264699 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
1264638 AAAGGATTTT
1264648 TTTTAGTTTTTTAAAA
1 TTTTAGTTTTTTAAAA
1264664 TGTTTA-TTTTTATAAAA
1 T-TTTAGTTTTT-TAAAA
* *
1264681 TTTTAAATTTTTTGAAA
1 TTTT-AGTTTTTTAAAA
1264698 TT
1 TT
1264700 GTCATTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
16 9 0.29
17 17 0.55
18 5 0.16
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.62
Consensus pattern (16 bp):
TTTTAGTTTTTTAAAA
Found at i:1266335 original size:21 final size:21
Alignment explanation
Indices: 1266311--1266350 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1266301 AAAAAAATTT
1266311 AAAA-TCAATTTAAAATATATA
1 AAAATTCAATTT-AAATATATA
1266332 AAAATTCAATTTAAATATA
1 AAAATTCAATTTAAATATA
1266351 AAATCATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAATTCAATTTAAATATATA
Found at i:1267270 original size:13 final size:13
Alignment explanation
Indices: 1267252--1267277 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1267242 CAATTTTTTG
1267252 TGTATCGATACAT
1 TGTATCGATACAT
1267265 TGTATCGATACAT
1 TGTATCGATACAT
1267278 ACTTTGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1267289 original size:32 final size:33
Alignment explanation
Indices: 1267232--1267295 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1267222 TACAAGCCAA
**
1267232 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
1267265 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
1267296 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:1269853 original size:13 final size:12
Alignment explanation
Indices: 1269835--1269872 Score: 58
Period size: 13 Copynumber: 3.0 Consensus size: 12
1269825 ATAATCCCCC
1269835 TGTATCGATACA
1 TGTATCGATACA
1269847 GTGTATCGATACCA
1 -TGTATCGATA-CA
1269861 TGTATCGATACA
1 TGTATCGATACA
1269873 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 2 0.08
13 20 0.83
14 2 0.08
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (12 bp):
TGTATCGATACA
Found at i:1271962 original size:15 final size:15
Alignment explanation
Indices: 1271939--1271974 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
1271929 CATCAAATTC
*
1271939 ATTTGGAGCTTCTTCA
1 ATTT-GAGCTTCCTCA
1271955 ATTTGAGCTTCCTCA
1 ATTTGAGCTTCCTCA
1271970 ATTTG
1 ATTTG
1271975 GATATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.44
Consensus pattern (15 bp):
ATTTGAGCTTCCTCA
Found at i:1276045 original size:20 final size:20
Alignment explanation
Indices: 1276020--1276071 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
1276010 TACAAGCCAA
**
1276020 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATACTTTG
1276040 TGTATCGATAC-ATACTTTG
1 TGTATCGATACAATACTTTG
1276059 TGTATCGATACAA
1 TGTATCGATACAA
1276072 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.42
Consensus pattern (20 bp):
TGTATCGATACAATACTTTG
Found at i:1276931 original size:28 final size:28
Alignment explanation
Indices: 1276861--1276989 Score: 127
Period size: 27 Copynumber: 4.7 Consensus size: 28
1276851 CCAAATGTGT
* * *
1276861 CAAAGTGCTTGTGCAAAAGCACCTGTGC
1 CAAAGTGCCTGTGCCAAAGCACCTATGC
**
1276889 CAAAGTGTTTGTGCCAAAGCACCTATGC
1 CAAAGTGCCTGTGCCAAAGCACCTATGC
* * *
1276917 CAAAGTGCATGTGCC-AGGTACCTATGC
1 CAAAGTGCCTGTGCCAAAGCACCTATGC
** * *
1276944 CAAAGCACCTGTGCC-AGGTACCTATGC
1 CAAAGTGCCTGTGCCAAAGCACCTATGC
*
1276971 CAAAGTACCTGTGCCAAAG
1 CAAAGTGCCTGTGCCAAAG
1276990 AGTATTATGG
Statistics
Matches: 88, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
27 48 0.55
28 40 0.45
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21
Consensus pattern (28 bp):
CAAAGTGCCTGTGCCAAAGCACCTATGC
Found at i:1276947 original size:27 final size:27
Alignment explanation
Indices: 1276909--1276986 Score: 129
Period size: 27 Copynumber: 2.9 Consensus size: 27
1276899 GTGCCAAAGC
* *
1276909 ACCTATGCCAAAGTGCATGTGCCAGGT
1 ACCTATGCCAAAGTACCTGTGCCAGGT
*
1276936 ACCTATGCCAAAGCACCTGTGCCAGGT
1 ACCTATGCCAAAGTACCTGTGCCAGGT
1276963 ACCTATGCCAAAGTACCTGTGCCA
1 ACCTATGCCAAAGTACCTGTGCCA
1276987 AAGAGTATTA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.27, C:0.31, G:0.22, T:0.21
Consensus pattern (27 bp):
ACCTATGCCAAAGTACCTGTGCCAGGT
Found at i:1276958 original size:14 final size:14
Alignment explanation
Indices: 1276856--1276989 Score: 101
Period size: 14 Copynumber: 9.7 Consensus size: 14
1276846 ACATCCCAAA
* * *
1276856 TGTGTCAAAGTGCT
1 TGTGCCAAAGTACC
* *
1276870 TGTGCAAAAGCACC
1 TGTGCCAAAGTACC
***
1276884 TGTGCCAAAGTGTT
1 TGTGCCAAAGTACC
*
1276898 TGTGCCAAAGCACC
1 TGTGCCAAAGTACC
* * *
1276912 TATGCCAAAGTGCA
1 TGTGCCAAAGTACC
*
1276926 TGTGCC-AGGTACC
1 TGTGCCAAAGTACC
* *
1276939 TATGCCAAAGCACC
1 TGTGCCAAAGTACC
*
1276953 TGTGCC-AGGTACC
1 TGTGCCAAAGTACC
*
1276966 TATGCCAAAGTACC
1 TGTGCCAAAGTACC
1276980 TGTGCCAAAG
1 TGTGCCAAAG
1276990 AGTATTATGG
Statistics
Matches: 87, Mismatches: 31, Indels: 4
0.71 0.25 0.03
Matches are distributed among these distances:
13 19 0.22
14 68 0.78
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (14 bp):
TGTGCCAAAGTACC
Found at i:1277702 original size:23 final size:23
Alignment explanation
Indices: 1277647--1277702 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
1277637 CACGAGATAA
1277647 TATCTGTGAGATATTATTTACAT
1 TATCTGTGAGATATTATTTACAT
*
1277670 TATCTATGAGATATTATTTACAT
1 TATCTGTGAGATATTATTTACAT
*
1277693 TATTTGTGAG
1 TATCTGTGAG
1277703 GTAATAGTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.30, C:0.07, G:0.14, T:0.48
Consensus pattern (23 bp):
TATCTGTGAGATATTATTTACAT
Found at i:1278066 original size:18 final size:21
Alignment explanation
Indices: 1278024--1278067 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
1278014 TTTAAATATT
1278024 AAATAGATAAAATATAACATA
1 AAATAGATAAAATATAACATA
1278045 AAAT-GATAAAATA-AA-ATA
1 AAATAGATAAAATATAACATA
1278063 AAATA
1 AAATA
1278068 TTTTTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 7 0.32
19 2 0.09
20 9 0.41
21 4 0.18
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (21 bp):
AAATAGATAAAATATAACATA
Found at i:1278335 original size:2 final size:2
Alignment explanation
Indices: 1278328--1278374 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
1278318 TTATTAAGAG
* *
1278328 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1278370 TA TA T
1 TA TA T
1278375 GTTGCTCGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:1281102 original size:24 final size:23
Alignment explanation
Indices: 1281059--1281151 Score: 82
Period size: 24 Copynumber: 4.0 Consensus size: 23
1281049 TAGCACAACA
* * *
1281059 TTTGACATGACTCTTTGAACATC
1 TTTGGCATGACTCCTAGAACATC
* *
1281082 TTTTGGCACGACTCCTAGAACAAC
1 -TTTGGCATGACTCCTAGAACATC
*
1281106 CTTGGCATGACTCCT-GAAACATCC
1 TTTGGCATGACTCCTAG-AACAT-C
1281130 TTT-GCGATGACTCCTAGAACAT
1 TTTGGC-ATGACTCCTAGAACAT
1281152 AGTTTAGATC
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
22 1 0.02
23 19 0.34
24 35 0.62
25 1 0.02
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (23 bp):
TTTGGCATGACTCCTAGAACATC
Found at i:1281117 original size:23 final size:23
Alignment explanation
Indices: 1281084--1281150 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
1281074 TGAACATCTT
*
1281084 TTGGCACGACTCCTAGAACAACC
1 TTGGCATGACTCCTAGAACAACC
*
1281107 TTGGCATGACTCCT-GAAACATCC
1 TTGGCATGACTCCTAG-AACAACC
*
1281130 TTTGCGATGACTCCTAGAACA
1 TTGGC-ATGACTCCTAGAACA
1281151 TAGTTTAGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
22 1 0.03
23 23 0.61
24 13 0.34
25 1 0.03
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (23 bp):
TTGGCATGACTCCTAGAACAACC
Found at i:1282376 original size:117 final size:118
Alignment explanation
Indices: 1282007--1282475 Score: 586
Period size: 117 Copynumber: 4.0 Consensus size: 118
1281997 AAGAATGTGC
* * * * *** * ** *
1282007 CCAAAGAGAACTATCTACTTTGATTAGGGAGATCAAATCTCAACCTAAAACAAAGTAAATTATTC
1 CCAAAGGGAACTATCCAC-TTCATTAAGGAGATTGTATCTCAACCTTAAATGAAGCAAATTATTC
* * ** * *
1282072 AACCCTTTTTTAAATAAGTGACTTAGGCCAACGTATAAGTGATTATAGCTGCGG
65 AACCCTTTTTCAAATAAATGACTTAGGCCAATATATGAGCGATTATAGCTGCGG
*
1282126 CCAAAGGGAACTATCCACTTCATTAAGGAAATTGTATCTCAA-CTTCAAATGAAGCAAATTATTC
1 CCAAAGGGAACTATCCACTTCATTAAGGAGATTGTATCTCAACCTT-AAATGAAGCAAATTATTC
* *
1282190 AACCCCTTTTTTTCTAATAAATGACTTAGGCCAATATATGAGCGATCATAGCTGCGG
65 AA-CCC--TTTTTCAAATAAATGACTTAGGCCAATATATGAGCGATTATAGCTGCGG
* * * *
1282247 CCAAAGGAAACTATCCATTTCATT-AGAGAGATTGTATCTCAACCTTAAATGAAGCAGATTATTT
1 CCAAAGGGAACTATCCACTTCATTAAG-GAGATTGTATCTCAACCTTAAATGAAGCAAATTATTC
*
1282311 AA-CCTTTTTCAAATAAATGACTTAGGCCAATATATGAGCGATTATAGCTGTGG
65 AACCCTTTTTCAAATAAATGACTTAGGCCAATATATGAGCGATTATAGCTGCGG
** * *
1282364 CCAAAGGGAACTATCCACTTCATTAAGGAGATTGTATCTCAACCTTAAATGAAATAGATTATTTA
1 CCAAAGGGAACTATCCACTTCATTAAGGAGATTGTATCTCAACCTTAAATGAAGCAAATTATTCA
*
1282429 A-CCTTTTTCGAATAAATGACTTAGGCCAATATATGAGCGATTATAGC
66 ACCCTTTTTCAAATAAATGACTTAGGCCAATATATGAGCGATTATAGC
1282476 AACGGCCTGT
Statistics
Matches: 310, Mismatches: 33, Indels: 16
0.86 0.09 0.04
Matches are distributed among these distances:
117 152 0.49
118 37 0.12
119 21 0.07
120 2 0.01
121 95 0.31
122 3 0.01
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (118 bp):
CCAAAGGGAACTATCCACTTCATTAAGGAGATTGTATCTCAACCTTAAATGAAGCAAATTATTCA
ACCCTTTTTCAAATAAATGACTTAGGCCAATATATGAGCGATTATAGCTGCGG
Found at i:1292689 original size:3 final size:3
Alignment explanation
Indices: 1292681--1292709 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1292671 CTTACAAAAC
1292681 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1292710 CTATTTCAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1293569 original size:14 final size:15
Alignment explanation
Indices: 1293532--1293569 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1293522 TTTCTTAAGT
1293532 GAAGGAGAGTTGGAA
1 GAAGGAGAGTTGGAA
*
1293547 GAAGGAGAG-TGGGA
1 GAAGGAGAGTTGGAA
*
1293561 GACGGAGAG
1 GAAGGAGAG
1293570 ATAATAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.37, C:0.03, G:0.53, T:0.08
Consensus pattern (15 bp):
GAAGGAGAGTTGGAA
Found at i:1294919 original size:17 final size:18
Alignment explanation
Indices: 1294897--1294930 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1294887 ATCATCGATT
1294897 AGAAGAA-GAAAGAAAAG
1 AGAAGAATGAAAGAAAAG
*
1294914 AGAAGAATTAAAGAAAA
1 AGAAGAATGAAAGAAAA
1294931 AAAAAGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.71, C:0.00, G:0.24, T:0.06
Consensus pattern (18 bp):
AGAAGAATGAAAGAAAAG
Found at i:1296554 original size:5 final size:5
Alignment explanation
Indices: 1296544--1296568 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1296534 ACTTCGGCTA
1296544 TGCTG TGCTG TGCTG TGCTG TGCTG
1 TGCTG TGCTG TGCTG TGCTG TGCTG
1296569 CGGCTACGTT
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:0.00, C:0.20, G:0.40, T:0.40
Consensus pattern (5 bp):
TGCTG
Found at i:1296876 original size:3 final size:3
Alignment explanation
Indices: 1296861--1296901 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
1296851 TGGTACCATA
*
1296861 ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1296902 GTCCATATGC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1297100 original size:45 final size:45
Alignment explanation
Indices: 1297050--1297138 Score: 110
Period size: 44 Copynumber: 2.0 Consensus size: 45
1297040 TGTTTTTTTA
* *
1297050 ATAATTATTTTTTTAAATAA-ATAATATTAATAT-TATTTTTATATT
1 ATAATTA-TATTTTAAATAATAT-ATATTAATATAAATTTTTATATT
* *
1297095 ATAATTATATTTTAAATATTATATATTTATATAAATTTTTATAT
1 ATAATTATATTTTAAATAATATATATTAATATAAATTTTTATAT
1297139 ATTAATAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
44 19 0.50
45 19 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (45 bp):
ATAATTATATTTTAAATAATATATATTAATATAAATTTTTATATT
Found at i:1297176 original size:20 final size:18
Alignment explanation
Indices: 1297107--1297189 Score: 58
Period size: 19 Copynumber: 4.9 Consensus size: 18
1297097 AATTATATTT
*
1297107 TAAATATTATATATTTATA
1 TAAATTTTATATA-TTATA
1297126 TAAATTTTTATATATTA-A
1 TAAA-TTTTATATATTATA
*
1297144 T-AA--TT-CATATTATA
1 TAAATTTTATATATTATA
1297158 TAAATTTTAATATATT-TA
1 TAAATTTT-ATATATTATA
1297176 T--ATTTT-TATATTAT
1 TAAATTTTATATATTAT
1297190 TTAATTATTT
Statistics
Matches: 53, Mismatches: 3, Indels: 20
0.70 0.04 0.26
Matches are distributed among these distances:
13 6 0.11
14 10 0.19
15 3 0.06
16 5 0.09
17 4 0.08
18 5 0.09
19 12 0.23
20 8 0.15
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (18 bp):
TAAATTTTATATATTATA
Found at i:1297196 original size:8 final size:9
Alignment explanation
Indices: 1297083--1297204 Score: 50
Period size: 8 Copynumber: 14.3 Consensus size: 9
1297073 ATATTAATAT
1297083 TATT-TTTA
1 TATTATTTA
1297091 TATTATAATTA
1 TATTAT--TTA
*
1297102 TATT-TTAAA
1 TATTATT-TA
*
1297111 TATTATATA
1 TATTATTTA
*
1297120 T-TTATATA
1 TATTATTTA
*
1297128 AATT-TTTA
1 TATTATTTA
1297136 TA-TA-TTA
1 TATTATTTA
* *
1297143 -ATAATTCA
1 TATTATTTA
*
1297151 TATTATATA
1 TATTATTTA
* *
1297160 AATT-TTAA
1 TATTATTTA
1297168 TA-TATTTA
1 TATTATTTA
1297176 TATT-TTTA
1 TATTATTTA
1297184 TATTATTTA
1 TATTATTTA
1297193 -ATTATTTCA
1 TATTATTT-A
1297202 TAT
1 TAT
1297205 GAAAGATCTG
Statistics
Matches: 83, Mismatches: 16, Indels: 28
0.65 0.13 0.22
Matches are distributed among these distances:
6 1 0.01
7 6 0.07
8 41 0.49
9 24 0.29
10 4 0.05
11 7 0.08
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (9 bp):
TATTATTTA
Found at i:1298111 original size:11 final size:11
Alignment explanation
Indices: 1298062--1298117 Score: 55
Period size: 11 Copynumber: 5.2 Consensus size: 11
1298052 ATACAAACTT
1298062 AACATATATATA
1 AACATA-ATATA
1298074 AA-A-AATA-A
1 AACATAATATA
* *
1298082 AACATAACATG
1 AACATAATATA
1298093 AACAATAATATA
1 AAC-ATAATATA
1298105 AACATAATATA
1 AACATAATATA
1298116 AA
1 AA
1298118 TACATGAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
8 3 0.08
9 4 0.11
10 4 0.11
11 14 0.39
12 11 0.31
ACGTcount: A:0.66, C:0.09, G:0.02, T:0.23
Consensus pattern (11 bp):
AACATAATATA
Found at i:1298344 original size:27 final size:28
Alignment explanation
Indices: 1298308--1298365 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
1298298 CAATAAAACG
1298308 AATTATTAATATGTAAAAAT-TTATAAAA
1 AATTATTAATATGTAAAAATCTTA-AAAA
* *
1298336 AATTA-TAATATTTAAAACTCTTAAAAA
1 AATTATTAATATGTAAAAATCTTAAAAA
1298363 AAT
1 AAT
1298366 AATGTAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 19 0.70
28 8 0.30
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (28 bp):
AATTATTAATATGTAAAAATCTTAAAAA
Found at i:1298403 original size:17 final size:17
Alignment explanation
Indices: 1298381--1298422 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
1298371 AAACACAAAA
1298381 TTTTTTTATCTTTCTTT
1 TTTTTTTATCTTTCTTT
*
1298398 TTTTTTTGTCTTTCTTT
1 TTTTTTTATCTTTCTTT
1298415 TCTTTTTT
1 T-TTTTTT
1298423 TCTCTCTCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 17 0.74
18 6 0.26
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.83
Consensus pattern (17 bp):
TTTTTTTATCTTTCTTT
Found at i:1298434 original size:20 final size:19
Alignment explanation
Indices: 1298381--1298438 Score: 59
Period size: 18 Copynumber: 3.1 Consensus size: 19
1298371 AAACACAAAA
* *
1298381 TTTTTTTATCTTTCTTTT-
1 TTTTTTTCTCTTCCTTTTC
1298399 TTTTTTGTCT-TT-CTTTTC
1 TTTTTT-TCTCTTCCTTTTC
1298417 TTTTTTTCTCTCTCCTTTTC
1 TTTTTTTCTCT-TCCTTTTC
1298437 TT
1 TT
1298439 CCTTCTTTCT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
17 8 0.24
18 15 0.44
19 3 0.09
20 8 0.24
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.78
Consensus pattern (19 bp):
TTTTTTTCTCTTCCTTTTC
Found at i:1298925 original size:14 final size:15
Alignment explanation
Indices: 1298887--1298926 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
1298877 AAAAAATAAC
*
1298887 ATAAACATGATATTT
1 ATAAACATAATATTT
1298902 ATAAA-A-AATATTT
1 ATAAACATAATATTT
1298915 -TAAACATAATAT
1 ATAAACATAATAT
1298927 AAAAATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
12 4 0.18
13 7 0.32
14 6 0.27
15 5 0.23
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (15 bp):
ATAAACATAATATTT
Found at i:1299009 original size:15 final size:15
Alignment explanation
Indices: 1298985--1299033 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
1298975 ATAAAATAAA
*
1298985 ATAAATTATTAATAT
1 ATAAAATATTAATAT
*
1299000 ATAAAATATTTATAT
1 ATAAAATATTAATAT
1299015 A-AAAATA-TAATATT
1 ATAAAATATTAATA-T
1299029 ATAAA
1 ATAAA
1299034 TAAAAAACAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 4 0.14
14 8 0.28
15 17 0.59
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAAAATATTAATAT
Found at i:1299048 original size:22 final size:20
Alignment explanation
Indices: 1299003--1299049 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
1298993 TTAATATATA
* *
1299003 AAATATTTATATAAAAATAT
1 AAATATTTAAATAAAAACAT
1299023 -AATATTATAAATAAAAAACAT
1 AAATATT-TAAAT-AAAAACAT
1299044 AAATAT
1 AAATAT
1299050 AAATATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 6 0.27
20 4 0.18
21 7 0.32
22 5 0.23
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
AAATATTTAAATAAAAACAT
Found at i:1299053 original size:6 final size:6
Alignment explanation
Indices: 1298949--1299068 Score: 50
Period size: 6 Copynumber: 19.2 Consensus size: 6
1298939 TAGATAACAC
* * *
1298949 AAATAT -AA-AT ACATAT AAAAAT ATATAT AAA-AT AAA-AT AAATTATT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAA-TA-T
* * * *
1298995 AATATAT AAAATATTT ATATAA AAATAT AATATTAT AAATAAA AAACAT
1 AA-ATAT -AAATA--T AAATAT AAATAT AA-A-TAT AAAT-AT AAATAT
* *
1299044 AAATAT AAATAT ATATAT ATATAT A
1 AAATAT AAATAT AAATAT AAATAT A
1299069 TTTTCTCTTC
Statistics
Matches: 87, Mismatches: 15, Indels: 24
0.69 0.12 0.19
Matches are distributed among these distances:
4 2 0.02
5 13 0.15
6 43 0.49
7 11 0.13
8 16 0.18
9 2 0.02
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (6 bp):
AAATAT
Found at i:1300269 original size:15 final size:14
Alignment explanation
Indices: 1300246--1300275 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1300236 TTTACAGGTG
1300246 TAAAATTATAATTT
1 TAAAATTATAATTT
1300260 TAAAATTTATAATTT
1 TAAAA-TTATAATTT
1300275 T
1 T
1300276 TTTTTTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TAAAATTATAATTT
Found at i:1300646 original size:2 final size:2
Alignment explanation
Indices: 1300641--1300675 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1300631 TTTATTTTGT
*
1300641 TA TA TA TA TA TA TA TA TA TA TA TC TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1300676 TTTACCTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1302436 original size:3 final size:3
Alignment explanation
Indices: 1302428--1302478 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
1302418 ATTAAAACAC
1302428 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1302476 AAT
1 AAT
1302479 TAGGAATTGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1310657 original size:17 final size:17
Alignment explanation
Indices: 1310635--1310690 Score: 57
Period size: 16 Copynumber: 3.4 Consensus size: 17
1310625 ACGTCGATAA
1310635 AAAATTATTATTATTTT
1 AAAATTATTATTATTTT
1310652 AAAATTTATT-TTA-TTT
1 AAAA-TTATTATTATTTT
*
1310668 AATA-TATTATT-TTTAT
1 AAAATTATTATTATTT-T
1310684 AAAATTA
1 AAAATTA
1310691 AAAAAATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
14 4 0.12
15 4 0.12
16 10 0.31
17 9 0.28
18 5 0.16
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
AAAATTATTATTATTTT
Found at i:1310660 original size:18 final size:17
Alignment explanation
Indices: 1310634--1310680 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
1310624 TACGTCGATA
1310634 AAAAATTATTATTATTTT
1 AAAAATTATT-TTATTTT
*
1310652 AAAATTTATTTTA-TTT
1 AAAAATTATTTTATTTT
*
1310668 AATATATTATTTT
1 AA-AAATTATTTT
1310681 TATAAAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 5 0.20
17 11 0.44
18 9 0.36
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
AAAAATTATTTTATTTT
Found at i:1310701 original size:30 final size:32
Alignment explanation
Indices: 1310667--1310730 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 32
1310657 TTATTTTATT
*
1310667 TAATATA-TTATTTTTATAAAATTAAAAA-AA
1 TAATATAGATATTTTTATAAAATTAAAAATAA
1310697 TAATATAGATATTTTTATAAAATTAAAAATAA
1 TAATATAGATATTTTTATAAAATTAAAAATAA
1310729 TA
1 TA
1310731 TGTTTTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 7 0.23
31 20 0.65
32 4 0.13
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (32 bp):
TAATATAGATATTTTTATAAAATTAAAAATAA
Found at i:1317922 original size:11 final size:11
Alignment explanation
Indices: 1317902--1317947 Score: 62
Period size: 10 Copynumber: 4.5 Consensus size: 11
1317892 TTCATTAGGT
1317902 GAAA-AAAAAA
1 GAAAGAAAAAA
*
1317912 GAGAGAAAAAA
1 GAAAGAAAAAA
1317923 GAAAG-AAAAA
1 GAAAGAAAAAA
1317933 GAAAGAAAAAA
1 GAAAGAAAAAA
1317944 -AAAG
1 GAAAG
1317948 CTAAACCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 17 0.53
11 15 0.47
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (11 bp):
GAAAGAAAAAA
Found at i:1317926 original size:21 final size:21
Alignment explanation
Indices: 1317902--1317943 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1317892 TTCATTAGGT
*
1317902 GAAAAAAAAAGAGAGAAAAAA
1 GAAAAAAAAAGAAAGAAAAAA
*
1317923 GAAAGAAAAAGAAAGAAAAAA
1 GAAAAAAAAAGAAAGAAAAAA
1317944 AAAGCTAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (21 bp):
GAAAAAAAAAGAAAGAAAAAA
Found at i:1318946 original size:20 final size:19
Alignment explanation
Indices: 1318916--1318971 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
1318906 CCCCATCACT
1318916 ATTTGTATCGATACATG-GCA
1 ATTT-TATCGATACATGAG-A
*
1318936 CATTTTATCGATGCATGAAGA
1 -ATTTTATCGATACATG-AGA
1318957 ATTTTATCGATACAT
1 ATTTTATCGATACAT
1318972 TGTCCCAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 25 0.81
21 5 0.16
22 1 0.03
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (19 bp):
ATTTTATCGATACATGAGA
Found at i:1327560 original size:78 final size:79
Alignment explanation
Indices: 1327256--1327600 Score: 369
Period size: 78 Copynumber: 4.4 Consensus size: 79
1327246 TATTTTGGCG
* * * *
1327256 ATAAAGAT-GAGGTTGGAGTATCCCCTCAGAAATAACAGGGTTGAAGTATCCCCGATTATGGAAA
1 ATAAA-ATCGAGGTTAGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAA
* *
1327320 ATCGATGTTCTGAAA
65 ATCGGTGTTTTGAAA
* * * * *
1327335 ATAAAATCGGGGTTAGAGTATCCCCTCAAAAATAACGGGATTGGA-TATCCCTGATTGTGAAAAA
1 ATAAAATCGAGGTTAGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAA
*
1327399 TCAGTGTTTT-ATAA
66 TCGGTGTTTTGA-AA
* * * * *
1327413 ATAAAATCGAGGTTGGAGCATCCCCTCAGAAATAACGGGGTTAGAGTATCTCCGATTATGAAAAT
1 ATAAAATCGAGGTTAGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAA
*
1327478 TTGGTGTTTTGAAA
66 TCGGTGTTTTGAAA
* * * *
1327492 ATAAAATTGAGGTTAGAGTATCCCTTTA-AAATAACGGGGTTGGAGTATCCCCAATTATGAAAAA
1 ATAAAATCGAGGTTAGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAA
* * *
1327556 TTGGTATTTTGGAA
66 TCGGTGTTTTGAAA
* * *
1327570 ATAAAACCG-GGATTGGAGTATTCCCTC-GAAA
1 ATAAAATCGAGG-TTAGAGTATCCCCTCAGAAA
1327601 GTAAAAACAT
Statistics
Matches: 219, Mismatches: 41, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
77 3 0.01
78 131 0.60
79 84 0.38
80 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (79 bp):
ATAAAATCGAGGTTAGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAA
TCGGTGTTTTGAAA
Found at i:1327572 original size:157 final size:157
Alignment explanation
Indices: 1327246--1327600 Score: 416
Period size: 157 Copynumber: 2.3 Consensus size: 157
1327236 AAAAATTTAA
**
1327246 TATTTTGGCGATAAAGAT-GAGGTTGGAGTATCCCCTCAGAAATAACAGGGTTGAAGTATCCCCG
1 TATTTTGGAAATAAA-ATCGAGGTTGGAGTATCCCCTCAGAAATAACAGGGTTGAAGTATCCCCG
*
1327310 ATTATGGAAAATCGATGTTCTGAAAATAAAATCGGGGTTAGAGTATCCCCTCAAAAATAACGGGA
65 ATTATGGAAAATCGATGTTCTGAAAATAAAATCGAGGTTAGAGTATCCCCTCAAAAATAACGGGA
** *
1327375 TTGGATATCCCTGATTGTGAAAAATCAG
130 TTGGATATCCCCAATTATGAAAAATCAG
* ** * * *
1327403 TGTTTTATAAATAAAATCGAGGTTGGAGCATCCCCTCAGAAATAACGGGGTT-AGAGTATCTCCG
1 TATTTTGGAAATAAAATCGAGGTTGGAGTATCCCCTCAGAAATAACAGGGTTGA-AGTATCCCCG
* * * * **
1327467 ATTAT-GAAAATTTGGTGTTTTGAAAATAAAATTGAGGTTAGAGTAT-CCCTTTAAAATAACGGG
65 ATTATGGAAAA-TCGATGTTCTGAAAATAAAATCGAGGTTAGAGTATCCCCTCAAAAATAACGGG
* **
1327530 GTTGGAGTATCCCCAATTATGAAAAATTGG
129 ATTGGA-TATCCCCAATTATGAAAAATCAG
* *
1327560 TATTTTGGAAATAAAACCG-GGATTGGAGTATTCCCTC-GAAA
1 TATTTTGGAAATAAAATCGAGG-TTGGAGTATCCCCTCAGAAA
1327601 GTAAAAACAT
Statistics
Matches: 166, Mismatches: 27, Indels: 11
0.81 0.13 0.05
Matches are distributed among these distances:
156 34 0.20
157 132 0.80
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (157 bp):
TATTTTGGAAATAAAATCGAGGTTGGAGTATCCCCTCAGAAATAACAGGGTTGAAGTATCCCCGA
TTATGGAAAATCGATGTTCTGAAAATAAAATCGAGGTTAGAGTATCCCCTCAAAAATAACGGGAT
TGGATATCCCCAATTATGAAAAATCAG
Found at i:1330534 original size:30 final size:33
Alignment explanation
Indices: 1330498--1330570 Score: 89
Period size: 34 Copynumber: 2.3 Consensus size: 33
1330488 AGGGGAAAGA
* *
1330498 AAAGGAAAA-G-GT-GGCTTGCTCTTTGAGGAC
1 AAAGGAAAAGGAGTAGGCCTGCTCTTCGAGGAC
*
1330528 AAAGGAAAAGGAGTACGTCCTGCTCTTCGAGGAC
1 AAAGGAAAAGGAGTA-GGCCTGCTCTTCGAGGAC
1330562 AAAGGAAAA
1 AAAGGAAAA
1330571 TGAGGAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 9 0.25
31 1 0.03
32 2 0.06
34 24 0.67
ACGTcount: A:0.37, C:0.15, G:0.30, T:0.18
Consensus pattern (33 bp):
AAAGGAAAAGGAGTAGGCCTGCTCTTCGAGGAC
Found at i:1330859 original size:45 final size:45
Alignment explanation
Indices: 1330647--1330920 Score: 188
Period size: 45 Copynumber: 6.4 Consensus size: 45
1330637 CAAGGAGAAA
* * *
1330647 GCGTCCTGCTCTTTGAGGACAAAAG-GAAAAGAAGGAAATGAAA-T
1 GCGTCCTGCTCTTTGAGGATAAAAGAGGAAAGAAGAAAAT-AAAGT
* * *
1330691 ACGTCTTGCTCTTTGAGGAT--AA-AGG--AGAA-AAAAAAAAG-
1 GCGTCCTGCTCTTTGAGGATAAAAGAGGAAAGAAGAAAATAAAGT
* * * *
1330729 GCATCCCGCTGTTTGAGGACT--AAG-GGAAAAGAAGAAAATAAGGT
1 GCGTCCTGCTCTTTGAGGA-TAAAAGAGG-AAAGAAGAAAATAAAGT
* * ** *
1330773 GTGCCCTATTCTTTGAGG--ACAA-AGGAAA-AATG-AAATAAAGT
1 GCGTCCTGCTCTTTGAGGATAAAAGAGGAAAGAA-GAAAATAAAGT
*
1330814 GTGTCCTGCTCTTTGAGGATAAAAGAGGAAAGAAGAAAATAAAGT
1 GCGTCCTGCTCTTTGAGGATAAAAGAGGAAAGAAGAAAATAAAGT
* * *
1330859 GCGTCCTGCTCTTTAAAGACAAAAGAGGAAAGAAGAAAATGAAA-T
1 GCGTCCTGCTCTTTGAGGATAAAAGAGGAAAGAAGAAAAT-AAAGT
* *
1330904 GTGTCCTGCTCCTTGAG
1 GCGTCCTGCTCTTTGAG
1330921 ACCTCTATAA
Statistics
Matches: 178, Mismatches: 33, Indels: 37
0.72 0.13 0.15
Matches are distributed among these distances:
38 17 0.10
39 8 0.04
40 4 0.02
41 25 0.14
42 11 0.06
43 14 0.08
44 35 0.20
45 61 0.34
46 3 0.02
ACGTcount: A:0.40, C:0.13, G:0.26, T:0.21
Consensus pattern (45 bp):
GCGTCCTGCTCTTTGAGGATAAAAGAGGAAAGAAGAAAATAAAGT
Found at i:1331461 original size:178 final size:180
Alignment explanation
Indices: 1331162--1331623 Score: 585
Period size: 178 Copynumber: 2.6 Consensus size: 180
1331152 ATATTTTTAT
* * * ** * *
1331162 TATTCTTATGGTTGCTCGTAAAGGTATAGAAATATTTAAAACTTTTTGTATCTTTTTGGATTTCC
1 TATTCTTATGGTTGTTTGTAAGGGTATAGAAATATTTAAAACTTTTCATATCTTTTCGGATTTAC
* * *
1331227 TTTAAGGTATGAAATAAAATTTTCAAAAATAAAAAATTATAAAATAAAT-AA-AAT-AATAAATA
66 TTTAAGGTACGAAATAGAATTTTTAAAAATAAAAAATTATAAAATAAATAAATAATAAATAAATA
* * **
1331289 TTATTTTATCACTAAATAAAAATCATTATCTTAAATTTTCAAGATTTTTGC
131 TTATATTATCACTAAAT-AAAATCATTATCTTAAATTTTCAAGATTTCTAA
* *
1331340 TATTCTTATGGTTGTTTGTAAGGGCATAGAAATATTTAAAACTTTTCATATCTTTCCGGATTTAC
1 TATTCTTATGGTTGTTTGTAAGGGTATAGAAATATTTAAAACTTTTCATATCTTTTCGGATTTAC
* *
1331405 TTTAAAGTACGAAATAGAATTTTTAAAAATAAAAAATTATAAAATGAATAAAATAATAAATAAAT
66 TTTAAGGTACGAAATAGAATTTTTAAAAATAAAAAATTATAAAATAAAT-AAATAATAAATAAAT
* * * **
1331470 ATTATATTATCACTAAATAAAATTATTATTTTAATTTTTTGAGATTTCTAA
130 ATTATATTATCACTAAATAAAATCATTATCTTAAATTTTCAAGATTTCTAA
* *
1331521 TATTCTTATGGTT-TTTCATAAGGGTATAAAAATATTTAAAACTTTTCATATCTTTTCGG-TTCT
1 TATTCTTATGGTTGTTT-GTAAGGGTATAGAAATATTTAAAACTTTTCATATCTTTTCGGATT-T
* * * *
1331584 TCATTAAGGTACGAAAT-GAATTTTTAGAAATTAAAAATTA
64 ACTTTAAGGTACGAAATAGAATTTTTAAAAATAAAAAATTA
1331624 AATAAAAATT
Statistics
Matches: 246, Mismatches: 32, Indels: 10
0.85 0.11 0.03
Matches are distributed among these distances:
178 100 0.41
180 28 0.11
181 94 0.38
182 24 0.10
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (180 bp):
TATTCTTATGGTTGTTTGTAAGGGTATAGAAATATTTAAAACTTTTCATATCTTTTCGGATTTAC
TTTAAGGTACGAAATAGAATTTTTAAAAATAAAAAATTATAAAATAAATAAATAATAAATAAATA
TTATATTATCACTAAATAAAATCATTATCTTAAATTTTCAAGATTTCTAA
Found at i:1337477 original size:310 final size:306
Alignment explanation
Indices: 1337130--1337756 Score: 814
Period size: 310 Copynumber: 2.0 Consensus size: 306
1337120 GTGCATTTAT
* * * *
1337130 GATAGGTTCATTATTTATGATTATTTTTGAGTCTTTTAGGGATATC-AAGATATTTTCATGTTGA
1 GATAGGTTCATTATTTATGATTATTTTTGAATCTTTTAAGGATACCGAA-ATACTTTCATGTTGA
* * * * *
1337194 AAGTATAACCTAAGGGTATTTTAGTAATTTTTGTATAACCAAGT-CTTATGAAGTCACCAAGATT
65 AAGTATAACCTAAGGGTATTTTAGTAATTTTTCTAAAACCAAGTGC-GAAGAAGTCACCAAGATG
* * *
1337258 CTTTTATGCCAAAGGTGCATAGTTAAGATAGGTTTGCCTTTTTATGATCATTTTCGAGTCTTTTA
129 CTTTTATGCCAAAGGTG--T-G--AAGATAGGTTTACCTTTCTATGATCATTTTCGAGTCATTTA
* * * * * *
1337323 AGGTTACTAGGATGCTTCCATGTCGAAGATATA-CCTAAAGGTATTTTGGTAATTTTGTATTGAA
189 AGGTTACCAGGATACTTCCATGGCAAAGATATACCCCAAAGGTATTTTGGTAATTTTGCATT-AA
* * *
1337387 A-CCAAGTCTTATGTGATTACTTGGATACTTTCATGTTAAAGGTACACATTAGG
253 AGCCAAGTCCTATGTGATTACTTGAATACTTTCATGTCAAAGGTACACATTAGG
* * *
1337440 GATAGGTTTATTATTTATGATTATTTTTGAATCTTTTAAGGTTACCGAAATACTTTCATTTTGAA
1 GATAGGTTCATTATTTATGATTATTTTTGAATCTTTTAAGGATACCGAAATACTTTCATGTTGAA
* * * *
1337505 GGTATAATCTAAGGGTATTTTGGTAATTTTTCTAAAACTAAGTGCGAAGAAGTCACCAAGATGCT
66 AGTATAACCTAAGGGTATTTTAGTAATTTTTCTAAAACCAAGTGCGAAGAAGTCACCAAGATGCT
* ** * *
1337570 TTTATGCCAAAGGTGTGCATTTAGGTTTACCTTTCTATGATCATTTTTGAGTCATTTATGGTTAC
131 TTTATGCCAAAGGTGTGAAGATAGGTTTACCTTTCTATGATCATTTTCGAGTCATTTAAGGTTAC
* ** *
1337635 CATGATACTTTTATGGCAAATATATACCCCAAAGGTATTTTGGTAATTTTGCATTAAAGCCAAGT
196 CAGGATACTTCCATGGCAAAGATATACCCCAAAGGTATTTTGGTAATTTTGCATTAAAGCCAAGT
1337700 CCTATGTGATTACTTGAATACTTTCATGTCAAAGGTACACATTAGG
261 CCTATGTGATTACTTGAATACTTTCATGTCAAAGGTACACATTAGG
1337746 GATA-GTTCATT
1 GATAGGTTCATT
1337757 GTTTCAAACT
Statistics
Matches: 275, Mismatches: 38, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
305 67 0.24
306 79 0.29
307 1 0.00
308 1 0.00
310 124 0.45
311 3 0.01
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.40
Consensus pattern (306 bp):
GATAGGTTCATTATTTATGATTATTTTTGAATCTTTTAAGGATACCGAAATACTTTCATGTTGAA
AGTATAACCTAAGGGTATTTTAGTAATTTTTCTAAAACCAAGTGCGAAGAAGTCACCAAGATGCT
TTTATGCCAAAGGTGTGAAGATAGGTTTACCTTTCTATGATCATTTTCGAGTCATTTAAGGTTAC
CAGGATACTTCCATGGCAAAGATATACCCCAAAGGTATTTTGGTAATTTTGCATTAAAGCCAAGT
CCTATGTGATTACTTGAATACTTTCATGTCAAAGGTACACATTAGG
Found at i:1337594 original size:155 final size:153
Alignment explanation
Indices: 1336944--1337594 Score: 557
Period size: 155 Copynumber: 4.2 Consensus size: 153
1336934 GTAGTTAACG
* *
1336944 AGATGCTTTTATGCCAAAGTTGTGCATTTAGGATAGGTTTACCTTTTTATGATTA-TTTTCAAGT
1 AGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTTA--TTTTTATGATTATTTTTGAA-T
* * * *
1337008 CTTTTTAAAGTCT-CCAAGATACTTTCATGTTGAAGGTATAACTTATGAGTATTTTAGTAATTTT
63 C-TTTTAAGGT-TACCAAGATACTTTCATGTTGAAGGTATAACCTAAGGGTATTTTAGTAATTTT
* * * * *
1337072 TTTAGATCGAA-TTTGATGTAGTCACCA
126 TTTAAAACCAAGTCTGATGAAGTCACCA
** * * *
1337099 AGATGCTTTTATGTAAAAGGTGTGCATTTATGATAGGTTCATTATTTATGATTATTTTTGAGTCT
1 AGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTTATT-TTTATGATTATTTTTGAATCT
* * * * * *
1337164 TTTAGGGATATCAAGATATTTTCATGTTGAAAGTATAACCTAAGGGTATTTTAGTAATTTTTGTA
65 TTTAAGGTTACCAAGATACTTTCATGTTGAAGGTATAACCTAAGGGTATTTTAGTAATTTTTTTA
* *
1337229 TAACCAAGTCTTATGAAGTCACCA
130 AAACCAAGTCTGATGAAGTCACCA
* * * * * *
1337253 AGATTCTTTTATGCCAAA-G-GTGCATAGTTAAGATAGGTTTGCCTTTTTATGATCATTTTCGAG
1 AGATGCTTTTATGCCAAAGGTGTGCAT--TTAGGATAGGTTT--ATTTTTATGATTATTTTTGAA
* * * * * * * *
1337316 TCTTTTAAGGTTACTAGGATGCTTCCATGTCGAAGATAT-ACCTAAAGGTATTTTGGTAATTTTG
62 TCTTTTAAGGTTACCAAGATACTTTCATGTTGAAGGTATAACCTAAGGGTATTTTAGTAATTTT-
* * * * **
1337380 TATTGAAACCAAGTCTTATG-TGATTACTT
126 T-TTAAAACCAAGTCTGATGAAG-TCACCA
* * * ** ***
1337409 GGATACTTTCATGTTAAAGGTACACA-TTAGGGATAGGTTTATTATTTATGATTATTTTTGAATC
1 AGATGCTTTTATGCCAAAGGTGTGCATTTA-GGATAGGTTTATT-TTTATGATTATTTTTGAATC
* * * *
1337473 TTTTAAGGTTACCGAA-ATACTTTCATTTTGAAGGTATAATCTAAGGGTATTTTGGTAATTTTTC
64 TTTTAAGGTTACC-AAGATACTTTCATGTTGAAGGTATAACCTAAGGGTATTTTAGTAATTTTTT
* *
1337537 TAAAACTAAGTGC-GAAGAAGTCACCA
128 TAAAACCAAGT-CTGATGAAGTCACCA
1337563 AGATGCTTTTATGCCAAAGGTGTGCATTTAGG
1 AGATGCTTTTATGCCAAAGGTGTGCATTTAGG
1337595 TTTACCTTTC
Statistics
Matches: 386, Mismatches: 90, Indels: 41
0.75 0.17 0.08
Matches are distributed among these distances:
152 7 0.02
153 61 0.16
154 109 0.28
155 141 0.37
156 65 0.17
157 1 0.00
158 2 0.01
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.41
Consensus pattern (153 bp):
AGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTTATTTTTATGATTATTTTTGAATCTT
TTAAGGTTACCAAGATACTTTCATGTTGAAGGTATAACCTAAGGGTATTTTAGTAATTTTTTTAA
AACCAAGTCTGATGAAGTCACCA
Found at i:1341932 original size:13 final size:13
Alignment explanation
Indices: 1341914--1341939 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1341904 CAATTTTTTG
1341914 TGTATCGATACAT
1 TGTATCGATACAT
1341927 TGTATCGATACAT
1 TGTATCGATACAT
1341940 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1342678 original size:21 final size:21
Alignment explanation
Indices: 1342637--1342680 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1342627 CTCCCCTTTA
* *
1342637 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
1342658 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
1342679 TC
1 TC
1342681 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:1346592 original size:15 final size:15
Alignment explanation
Indices: 1346572--1346602 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1346562 ATTTCGTTTG
*
1346572 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1346587 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1346602 G
1 G
1346603 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1348451 original size:21 final size:21
Alignment explanation
Indices: 1348406--1348454 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1348396 AAGTTTTCAT
1348406 TTTTC-TTAGCTAACTCATTA
1 TTTTCATTAGCTAACTCATTA
*
1348426 TTTTCATTAGCTAACTTCTTTA
1 TTTTCATTAGCTAAC-TCATTA
1348448 -TTTCATT
1 TTTTCATT
1348455 TTGCAAATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 5 0.19
21 16 0.62
22 5 0.19
ACGTcount: A:0.22, C:0.18, G:0.04, T:0.55
Consensus pattern (21 bp):
TTTTCATTAGCTAACTCATTA
Found at i:1350683 original size:13 final size:13
Alignment explanation
Indices: 1350665--1350690 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1350655 CAATTTTTTG
1350665 TGTATCGATACAT
1 TGTATCGATACAT
1350678 TGTATCGATACAT
1 TGTATCGATACAT
1350691 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1351100 original size:20 final size:20
Alignment explanation
Indices: 1351072--1351111 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1351062 AGATCCTAAC
*
1351072 AAACTTCACTTGATTCGATT
1 AAACGTCACTTGATTCGATT
*
1351092 AAACGTCACTTGATTTGATT
1 AAACGTCACTTGATTCGATT
1351112 TTTTTTAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.40
Consensus pattern (20 bp):
AAACGTCACTTGATTCGATT
Found at i:1351987 original size:20 final size:20
Alignment explanation
Indices: 1351942--1351996 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
1351932 TTCTACAATT
*
1351942 TGTATTGATACAATTAGTGCA
1 TGTATTGATAC-ATAAGTGCA
*
1351963 CGTATTGATACATAAGTG-A
1 TGTATTGATACATAAGTGCA
*
1351982 GTGTATCGATACATA
1 -TGTATTGATACATA
1351997 TCTCAAATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 1 0.03
20 18 0.62
21 10 0.34
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.35
Consensus pattern (20 bp):
TGTATTGATACATAAGTGCA
Found at i:1360156 original size:24 final size:24
Alignment explanation
Indices: 1360110--1360160 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1360100 TTGGACATGA
** *
1360110 TCTCTAATGAAATAATGTTTAATC
1 TCTCTAATGAAATAACATATAATC
*
1360134 TCTCTAATGAAATGACATATAATC
1 TCTCTAATGAAATAACATATAATC
1360158 TCT
1 TCT
1360161 ACGTGCTTAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (24 bp):
TCTCTAATGAAATAACATATAATC
Found at i:1368096 original size:2 final size:2
Alignment explanation
Indices: 1368089--1368117 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1368079 TGCCTCATTG
1368089 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
1368118 ATTAAAAGGG
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:1370890 original size:21 final size:21
Alignment explanation
Indices: 1370864--1370939 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
1370854 CTGCCAAGAA
*
1370864 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1370885 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
*
1370905 ATGTATCGATACATCATTTTC
1 ATGTATCGATACATCTTTTTC
1370926 ATGTATCGATACAT
1 ATGTATCGATACAT
1370940 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1370910 original size:20 final size:20
Alignment explanation
Indices: 1370885--1370957 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
1370875 CATCTTTTTT
1370885 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
*
1370905 ATGTATCGATACA-T-CATTTTC
1 ATGTATCGATACATTGCA---AC
1370926 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1370946 ATGTATCGATAC
1 ATGTATCGATAC
1370958 TTTGAATTGT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
18 2 0.04
19 1 0.02
20 26 0.57
21 14 0.30
22 1 0.02
23 2 0.04
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1370930 original size:41 final size:41
Alignment explanation
Indices: 1370864--1370957 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
1370854 CTGCCAAGAA
* *
1370864 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCATTTTCATGTATCGATACATTGCAAC
1370905 ATGTATCGATACATCATTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCATTTTCATGTATCGATACATTGCAAC
1370946 ATGTATCGATAC
1 ATGTATCGATAC
1370958 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACATCATTTTCATGTATCGATACATTGCAAC
Found at i:1373431 original size:13 final size:13
Alignment explanation
Indices: 1373413--1373450 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1373403 ATAATCACCC
1373413 TGTATCGATACAG
1 TGTATCGATACAG
*
1373426 TGTATCGATACAT
1 TGTATCGATACAG
1373439 TGTATCGATACA
1 TGTATCGATACA
1373451 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1373464 original size:20 final size:20
Alignment explanation
Indices: 1373439--1373515 Score: 66
Period size: 20 Copynumber: 3.6 Consensus size: 20
1373429 ATCGATACAT
1373439 TGTATCGATACAAAGAAAAA
1 TGTATCGATACAAAGAAAAA
* *
1373459 TGTATCGATACATAGAATTTCCAGA
1 TGTATCGATACAAAGAA-----AAA
*
1373484 TGTATCGATACACAA-AAACA
1 TGTATCGATACA-AAGAAAAA
1373504 TGTATCGATACA
1 TGTATCGATACA
1373516 TTTTGGACAT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
20 30 0.64
25 16 0.34
26 1 0.02
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.26
Consensus pattern (20 bp):
TGTATCGATACAAAGAAAAA
Found at i:1377387 original size:21 final size:21
Alignment explanation
Indices: 1377358--1377402 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1377348 AAGTTTTCAT
*
1377358 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1377378 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1377400 TTT
1 TTT
1377403 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1379631 original size:13 final size:13
Alignment explanation
Indices: 1379613--1379638 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1379603 CAATTTTTTG
1379613 TGTATCGATACAT
1 TGTATCGATACAT
1379626 TGTATCGATACAT
1 TGTATCGATACAT
1379639 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1379703 original size:21 final size:21
Alignment explanation
Indices: 1379677--1379752 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
1379667 CTGCCAAGAA
*
1379677 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1379698 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
*
1379718 ATGTATCGATACATCATTTTC
1 ATGTATCGATACATCTTTTTC
1379739 ATGTATCGATACAT
1 ATGTATCGATACAT
1379753 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1379723 original size:20 final size:20
Alignment explanation
Indices: 1379698--1379770 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
1379688 CATCTTTTTT
1379698 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
*
1379718 ATGTATCGATACA-T-CATTTTC
1 ATGTATCGATACATTGCA---AC
1379739 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1379759 ATGTATCGATAC
1 ATGTATCGATAC
1379771 TTTGAATTGT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
18 2 0.04
19 1 0.02
20 26 0.57
21 14 0.30
22 1 0.02
23 2 0.04
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1379743 original size:41 final size:41
Alignment explanation
Indices: 1379677--1379770 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
1379667 CTGCCAAGAA
* *
1379677 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCATTTTCATGTATCGATACATTGCAAC
1379718 ATGTATCGATACATCATTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCATTTTCATGTATCGATACATTGCAAC
1379759 ATGTATCGATAC
1 ATGTATCGATAC
1379771 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACATCATTTTCATGTATCGATACATTGCAAC
Found at i:1384566 original size:21 final size:21
Alignment explanation
Indices: 1384533--1384573 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1384523 TCATCTAAAC
1384533 AGCTCATGTCCATGCATTTTG
1 AGCTCATGTCCATGCATTTTG
1384554 AGCT-ATGTACCATGCATTTT
1 AGCTCATGT-CCATGCATTTT
1384574 AATATGTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (21 bp):
AGCTCATGTCCATGCATTTTG
Found at i:1387857 original size:13 final size:13
Alignment explanation
Indices: 1387839--1387865 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1387829 AATAGAATCA
1387839 AAATTTAAATTTT
1 AAATTTAAATTTT
1387852 AAATTTAAATTTT
1 AAATTTAAATTTT
1387865 A
1 A
1387866 GATGACATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AAATTTAAATTTT
Found at i:1392681 original size:20 final size:21
Alignment explanation
Indices: 1392639--1392689 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
1392629 TTCAACAATT
* *
1392639 TGTATTGATACACCAAGTTAA
1 TGTATCGATACACCAAGTGAA
*
1392660 TGTATCGATACA-TAAGTGAA
1 TGTATCGATACACCAAGTGAA
1392680 TGTATCGATA
1 TGTATCGATA
1392690 TTGGACCTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (21 bp):
TGTATCGATACACCAAGTGAA
Found at i:1394486 original size:21 final size:20
Alignment explanation
Indices: 1394453--1394491 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1394443 CAACTGTTGC
*
1394453 ATATTAAAAAATTATTTTAAA
1 ATATCAAAAAATT-TTTTAAA
*
1394474 ATATCAAACAATTTTTTA
1 ATATCAAAAAATTTTTTA
1394492 TGAATTTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (20 bp):
ATATCAAAAAATTTTTTAAA
Found at i:1399173 original size:52 final size:52
Alignment explanation
Indices: 1399103--1399244 Score: 225
Period size: 52 Copynumber: 2.7 Consensus size: 52
1399093 GAAAATTTAT
*
1399103 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
1399155 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
1399207 CTGCATGTATCGATACA--AAGATCAATGTATCGATACAT
1 CTGCATGTATCGATACATTTA-AT-AATGTATCGATACAT
1399245 AAGTCGAATC
Statistics
Matches: 84, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
51 2 0.02
52 82 0.98
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:1402238 original size:13 final size:13
Alignment explanation
Indices: 1402220--1402244 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1402210 AAATAGAATC
1402220 AAAATTTAAATTA
1 AAAATTTAAATTA
1402233 AAAATTTAAATT
1 AAAATTTAAATT
1402245 TTTATGACAC
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATTTAAATTA
Found at i:1402754 original size:26 final size:28
Alignment explanation
Indices: 1402718--1402783 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 28
1402708 ATTTTAATAA
*
1402718 TATAATAATATATGCA-CT-AAAAAAGT
1 TATAATAATATATGCATCTAAAAAAAAT
1402744 TATAATAATAT-T--ATCTAAAAAAAAT
1 TATAATAATATATGCATCTAAAAAAAAT
1402769 T-TAATAATATATGCA
1 TATAATAATATATGCA
1402784 ATTGGATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
23 1 0.03
24 11 0.32
25 10 0.29
26 11 0.32
27 1 0.03
ACGTcount: A:0.55, C:0.06, G:0.05, T:0.35
Consensus pattern (28 bp):
TATAATAATATATGCATCTAAAAAAAAT
Found at i:1404861 original size:16 final size:17
Alignment explanation
Indices: 1404832--1404865 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
1404822 TAGGTTCAGA
1404832 TTAAATTATTTTTAAAT
1 TTAAATTATTTTTAAAT
1404849 TTAAATT-TTTTTAAAT
1 TTAAATTATTTTTAAAT
1404865 T
1 T
1404866 ATTTCGAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTAAATTATTTTTAAAT
Done.