Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168492.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_9, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 25814696
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 122000 characters in sequence are not A, C, G, or T
File 6 of 126
Found at i:1417969 original size:48 final size:48
Alignment explanation
Indices: 1417898--1417994 Score: 140
Period size: 48 Copynumber: 2.0 Consensus size: 48
1417888 CCCATATGTA
*
1417898 TCCATACATCATACCTATATGGACCCTCTTAATCTCCTCTAATCCACT
1 TCCATACATCATACCTATATGGACCCTCTCAATCTCCTCTAATCCACT
* * * * *
1417946 TCCATGCATCATACTTATGTGGACCCTCTCAGTCTCCTCTAGTCCACT
1 TCCATACATCATACCTATATGGACCCTCTCAATCTCCTCTAATCCACT
1417994 T
1 T
1417995 ATAAACATTC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.23, C:0.35, G:0.08, T:0.34
Consensus pattern (48 bp):
TCCATACATCATACCTATATGGACCCTCTCAATCTCCTCTAATCCACT
Found at i:1418225 original size:52 final size:52
Alignment explanation
Indices: 1418139--1418238 Score: 148
Period size: 52 Copynumber: 1.9 Consensus size: 52
1418129 AGTATAAAAG
**
1418139 CTTGCCTATTAAGAATCCTTTTTCTCTTGGAATTCTTATTCTACAAGTCAAA
1 CTTGCCTATTAAGAATCCTTTTTCTCTTAAAATTCTTATTCTACAAGTCAAA
* *
1418191 CTTGTCTATTAAGAAT-CTCTTTTCTCTTAAAATTCTTTTTCTACAAGT
1 CTTGCCTATTAAGAATCCT-TTTTCTCTTAAAATTCTTATTCTACAAGT
1418239 TTTTTTGTCT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.05
52 41 0.95
ACGTcount: A:0.26, C:0.20, G:0.08, T:0.46
Consensus pattern (52 bp):
CTTGCCTATTAAGAATCCTTTTTCTCTTAAAATTCTTATTCTACAAGTCAAA
Found at i:1418686 original size:17 final size:16
Alignment explanation
Indices: 1418648--1418690 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
1418638 ACTTTCATAG
**
1418648 ATTTTTATATAACTTC
1 ATTTTTATATAAAATC
1418664 ATTTTTATATAAAATC
1 ATTTTTATATAAAATC
1418680 ATGTTTTATAT
1 AT-TTTTATAT
1418691 TTGAATTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (16 bp):
ATTTTTATATAAAATC
Found at i:1419823 original size:16 final size:16
Alignment explanation
Indices: 1419804--1419845 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1419794 ACGTTCATAG
**
1419804 ATTTTTATATAACTTC
1 ATTTTTATATAAAATC
1419820 ATTTTTATATAAAATC
1 ATTTTTATATAAAATC
*
1419836 ATGTTTATAT
1 ATTTTTATAT
1419846 TTGAATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (16 bp):
ATTTTTATATAAAATC
Found at i:1419997 original size:16 final size:16
Alignment explanation
Indices: 1419969--1420007 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
1419959 GCTTCTTTAA
*
1419969 ATTTTTTGTAA-TTTT
1 ATTTTTTCTAATTTTT
1419984 ATTTTTTCTAAATTTTT
1 ATTTTTTCT-AATTTTT
1420001 ATTTTTT
1 ATTTTTT
1420008 ATTTATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.38
16 2 0.10
17 11 0.52
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (16 bp):
ATTTTTTCTAATTTTT
Found at i:1424638 original size:43 final size:43
Alignment explanation
Indices: 1424588--1424672 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 43
1424578 ATTAAAAATC
* * *
1424588 AAATCTAAATCATCATAAAAAATTTTAGTCGTATTTTTCTTTT
1 AAATCTAAATCATCATAAAAAAATTTAATCGCATTTTTCTTTT
1424631 AAATCTAAATCATCATAAAAAAATTTAATCGCATTTTTCTTT
1 AAATCTAAATCATCATAAAAAAATTTAATCGCATTTTTCTTT
1424673 CTCTTTTTCT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.44
Consensus pattern (43 bp):
AAATCTAAATCATCATAAAAAAATTTAATCGCATTTTTCTTTT
Found at i:1427762 original size:15 final size:16
Alignment explanation
Indices: 1427744--1427778 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1427734 TTATGTTTTT
1427744 TTTTTCTTTTCT-TTC
1 TTTTTCTTTTCTCTTC
*
1427759 TTTTTCTTTTTTCTTC
1 TTTTTCTTTTCTCTTC
1427775 TTTT
1 TTTT
1427779 GTATTTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTCTTTTCTCTTC
Found at i:1427879 original size:15 final size:16
Alignment explanation
Indices: 1427855--1427896 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
1427845 TTTTTTCTCT
1427855 GTTA-ATATTTATAT-
1 GTTATATATTTATATA
1427869 G-TATTATATTTATATA
1 GTTA-TATATTTATATA
1427885 GTTATATATTTA
1 GTTATATATTTA
1427897 CTATTATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 2 0.08
14 1 0.04
15 10 0.42
16 9 0.38
17 2 0.08
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (16 bp):
GTTATATATTTATATA
Found at i:1427904 original size:28 final size:27
Alignment explanation
Indices: 1427870--1427922 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
1427860 TATTTATATG
*
1427870 TATTATATT-TATATAGTTATATATTTAC
1 TATTATATTATA-ATAATTAT-TATTTAC
1427898 TATTATATTATAATAATTATTATTT
1 TATTATATTATAATAATTATTATTT
1427923 TTTTCTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 5 0.22
28 16 0.70
29 2 0.09
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (27 bp):
TATTATATTATAATAATTATTATTTAC
Found at i:1428397 original size:26 final size:24
Alignment explanation
Indices: 1428359--1428408 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
1428349 GATCGAAAAT
1428359 AATTTTTTAGAAATTTTTGGCGAAA
1 AATTTTTTAGAAATTTTTGG-GAAA
*
1428384 AATTTTTCTGGAAATTTTTGGGAAA
1 AATTTTT-TAGAAATTTTTGGGAAA
1428409 TTTCCAGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.34, C:0.04, G:0.18, T:0.44
Consensus pattern (24 bp):
AATTTTTTAGAAATTTTTGGGAAA
Found at i:1429013 original size:16 final size:16
Alignment explanation
Indices: 1428953--1429028 Score: 64
Period size: 16 Copynumber: 4.4 Consensus size: 16
1428943 TTATTTAATA
1428953 TTTTTTATCTTTATCTTAT
1 TTTTTTAT-TTT-T-TTAT
1428972 TTTTATT-TTTGTTTTACT
1 TTTT-TTATTT-TTTTA-T
1428990 TTTCTTTATTTTTTTAT
1 TTT-TTTATTTTTTTAT
* *
1429007 TTTTTTATTATTCTAT
1 TTTTTTATTTTTTTAT
1429023 TTTTTT
1 TTTTTT
1429029 TAAATAAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
16 17 0.34
17 7 0.14
18 14 0.28
19 10 0.20
20 2 0.04
ACGTcount: A:0.13, C:0.07, G:0.01, T:0.79
Consensus pattern (16 bp):
TTTTTTATTTTTTTAT
Found at i:1429380 original size:59 final size:60
Alignment explanation
Indices: 1429035--1429497 Score: 489
Period size: 58 Copynumber: 8.0 Consensus size: 60
1429025 TTTTTAAATA
* * *
1429035 AAAATCAAAATTTTCAAAAAAAAAATATTTTT-AGGGAAAAGTTGAAAGTATCAATTTTCCTTA
1 AAAATCAAAGTTTTC---AAAAAAATATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTTCTTT
** * *
1429098 AAAAT--AAGTTTTCAAAAAAAGGTTTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTTG
1 AAAATCAAAGTTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTT
* * *
1429156 AAAATCAAAATTTTC-GAAAAATATTTTT-AGAAAAAGTTGAAAGTATCAATTTTTC-TT
1 AAAATCAAAGTTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTT
* ** *
1429213 AAAGAT-AAA-TTTTC-CAAAAAGGTTTTCGAGGAAAAGTTGAAAGTATCAATTTTTCTTT
1 AAA-ATCAAAGTTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTT
* * *
1429271 AAAATCAAAGTTTTCAAAAAAAAAATTTTCGAGAAAAAGTTGAAAGTATCAATTTTTCTTT
1 AAAATCAAAGTTTTC-AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTT
* *
1429332 AAAATCAAAGTTTTCAAAAAAATATTTTTG-GGAGAAGTTGAAAGTATCAATTTTTCTTA
1 AAAATCAAAGTTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTT
* * * *
1429391 AAAAT-AAA-TTTT-----TAA-ATTTTTGAGAAAAAGTTGAAAGTATCAA-TTTTCCTC
1 AAAATCAAAGTTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTT
* * * *
1429442 GAAATTAAAG-TTTCAAAAGAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTC
1 AAAATCAAAGTTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTC
1429498 CTGCACAAAA
Statistics
Matches: 344, Mismatches: 36, Indels: 44
0.81 0.08 0.10
Matches are distributed among these distances:
51 17 0.05
52 26 0.08
56 14 0.04
57 41 0.12
58 107 0.31
59 52 0.15
60 20 0.06
61 62 0.18
63 5 0.01
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.36
Consensus pattern (60 bp):
AAAATCAAAGTTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTT
Found at i:1433573 original size:10 final size:10
Alignment explanation
Indices: 1433558--1433594 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
1433548 AGAAGATGAG
1433558 GAAAAAAAAA
1 GAAAAAAAAA
1433568 G-AAAAAAAA
1 GAAAAAAAAA
*
1433577 GAAAAAAAGA
1 GAAAAAAAAA
1433587 GAAAAAAA
1 GAAAAAAA
1433595 TGGAAAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:1433574 original size:9 final size:9
Alignment explanation
Indices: 1433560--1433594 Score: 61
Period size: 9 Copynumber: 3.8 Consensus size: 9
1433550 AAGATGAGGA
1433560 AAAAAAAAG
1 AAAAAAAAG
1433569 AAAAAAAAG
1 AAAAAAAAG
1433578 AAAAAAAGAG
1 AAAAAAA-AG
1433588 AAAAAAA
1 AAAAAAA
1433595 TGGAAAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 16 0.64
10 9 0.36
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:1433600 original size:10 final size:9
Alignment explanation
Indices: 1433560--1433602 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
1433550 AAGATGAGGA
*
1433560 AAAAAAAAG
1 AAAAAAAGG
*
1433569 AAAAAAAAG
1 AAAAAAAGG
1433578 AAAAAAAGAG
1 AAAAAAAG-G
1433588 AAAAAAATGG
1 AAAAAAA-GG
1433598 AAAAA
1 AAAAA
1433603 TGAGAAAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
9 16 0.52
10 14 0.45
11 1 0.03
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (9 bp):
AAAAAAAGG
Found at i:1433601 original size:19 final size:19
Alignment explanation
Indices: 1433558--1433623 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
1433548 AGAAGATGAG
*
1433558 GAAAAAAAAAGAAAAAAAA
1 GAAAAAAAGAGAAAAAAAA
*
1433577 GAAAAAAAGAGAAAAAAAT
1 GAAAAAAAGAGAAAAAAAA
* * **
1433596 GGAAAAATGAGAAAATGAA
1 GAAAAAAAGAGAAAAAAAA
1433615 -AAAAAAAGA
1 GAAAAAAAGA
1433624 TTCAAATTGA
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
18 7 0.18
19 31 0.82
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.05
Consensus pattern (19 bp):
GAAAAAAAGAGAAAAAAAA
Found at i:1434959 original size:42 final size:40
Alignment explanation
Indices: 1434910--1435125 Score: 198
Period size: 41 Copynumber: 5.5 Consensus size: 40
1434900 AGTTCGCGTT
1434910 GCCTCTGTTTAGAGGGAGCAATTTA-TTTTCAAAATCGTTGAG
1 GCCTCTGTTTAGA-GGAGCAATTTACTTTTCAAAATCG-TG-G
* ** *
1434952 GCGTCTGTTTAGAGGAGC--TTT--TGAT--AAAT-G-GT
1 GCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAATCGTGG
* * *
1434984 GCCTCTGTTTAGAGGAACAATTTATTTTTCAAAGTCGTGG
1 GCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAATCGTGG
* * *
1435024 TGCCTCTGTTTAGAGGAGCAATTTACTTTCCCAAAGTCATGG
1 -GCCTCTGTTTAGAGGAGCAATTTACTTT-TCAAAATCGTGG
*
1435066 TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAATCGTTGA
1 -GCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAATCG-TGG
*
1435108 GCCTCTGTTTATAGGAGC
1 GCCTCTGTTTAGAGGAGC
1435126 TTTGATAAAA
Statistics
Matches: 144, Mismatches: 19, Indels: 23
0.77 0.10 0.12
Matches are distributed among these distances:
32 16 0.11
33 1 0.01
34 3 0.02
35 1 0.01
36 6 0.04
38 5 0.03
39 4 0.03
40 1 0.01
41 54 0.38
42 53 0.37
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (40 bp):
GCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAATCGTGG
Found at i:1435037 original size:41 final size:41
Alignment explanation
Indices: 1434980--1435125 Score: 202
Period size: 41 Copynumber: 3.5 Consensus size: 41
1434970 TTTTGATAAA
*
1434980 TGGTGCCTCTGTTTAGAGGAACAATTTATTTTTCAAAGTCG
1 TGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCG
** *
1435021 TGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCCAAAGTCA
1 TGGTGCCTCTGTTTAGAGGAGCAATTTA-TTTTTCAAAGTCG
* *
1435063 TGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAATCG
1 TGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCG
* * *
1435104 TTGAGCCTCTGTTTATAGGAGC
1 TGGTGCCTCTGTTTAGAGGAGC
1435126 TTTGATAAAA
Statistics
Matches: 92, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
41 54 0.59
42 38 0.41
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (41 bp):
TGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCG
Found at i:1435156 original size:12 final size:12
Alignment explanation
Indices: 1435139--1435176 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
1435129 GATAAAAAAC
1435139 AAAAAAATAC-A
1 AAAAAAATACAA
*
1435150 AAAAAAA-ACAT
1 AAAAAAATACAA
1435161 AAAAAAATACAA
1 AAAAAAATACAA
1435173 AAAA
1 AAAA
1435177 CAAAAAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 2 0.09
11 14 0.61
12 7 0.30
ACGTcount: A:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (12 bp):
AAAAAAATACAA
Found at i:1435164 original size:22 final size:20
Alignment explanation
Indices: 1435132--1435176 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 20
1435122 GAGCTTTGAT
1435132 AAAAAACAAAAAAATACAAA
1 AAAAAACAAAAAAATACAAA
1435152 AAAAAACATAAAAAAATACAAA
1 AAAAAAC--AAAAAAATACAAA
1435174 AAA
1 AAA
1435177 CAAAAAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 7 0.30
22 16 0.70
ACGTcount: A:0.84, C:0.09, G:0.00, T:0.07
Consensus pattern (20 bp):
AAAAAACAAAAAAATACAAA
Found at i:1435184 original size:10 final size:10
Alignment explanation
Indices: 1435132--1435176 Score: 63
Period size: 10 Copynumber: 4.3 Consensus size: 10
1435122 GAGCTTTGAT
1435132 AAAAAACAAA
1 AAAAAACAAA
*
1435142 AAAATACAAA
1 AAAAAACAAA
1435152 AAAAAACATAA
1 AAAAAACA-AA
1435163 AAAAATACAAA
1 AAAAA-ACAAA
1435174 AAA
1 AAA
1435177 CAAAAAAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
10 16 0.52
11 12 0.39
12 3 0.10
ACGTcount: A:0.84, C:0.09, G:0.00, T:0.07
Consensus pattern (10 bp):
AAAAAACAAA
Found at i:1435316 original size:20 final size:21
Alignment explanation
Indices: 1435277--1435316 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1435267 GTTGTAGACA
1435277 CCCAATTGGGTCCAGGCCCAG
1 CCCAATTGGGTCCAGGCCCAG
*
1435298 CCCAATTGGG-CCTGGCCCA
1 CCCAATTGGGTCCAGGCCCA
1435317 AATGGGTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.17, C:0.40, G:0.28, T:0.15
Consensus pattern (21 bp):
CCCAATTGGGTCCAGGCCCAG
Found at i:1435373 original size:15 final size:16
Alignment explanation
Indices: 1435355--1435389 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1435345 TTATGTTTTT
1435355 TTTTTCTTTTCT-TTC
1 TTTTTCTTTTCTCTTC
*
1435370 TTTTTCTTTTTTCTTC
1 TTTTTCTTTTCTCTTC
1435386 TTTT
1 TTTT
1435390 GTATTTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTCTTTTCTCTTC
Found at i:1435990 original size:26 final size:25
Alignment explanation
Indices: 1435959--1436009 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
1435949 GATCGAAAAT
1435959 AATTTTTTT-AGAAATTTTTGGCGAAA
1 AATTTTTTTGA-AAATTTTTGG-GAAA
1435985 AATTTTTTTGAAAATTTTTGGGAAA
1 AATTTTTTTGAAAATTTTTGGGAAA
1436010 TTTCCAGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 4 0.17
26 19 0.79
27 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.47
Consensus pattern (25 bp):
AATTTTTTTGAAAATTTTTGGGAAA
Found at i:1436537 original size:21 final size:22
Alignment explanation
Indices: 1436507--1436653 Score: 108
Period size: 21 Copynumber: 6.6 Consensus size: 22
1436497 CCGCTCCAGA
1436507 TTTT-TTTTTTA-ATTTAATTT
1 TTTTATTTTTTATATTTAATTT
1436527 TTTTATTTTTTA-ATTTAATTT
1 TTTTATTTTTTATATTTAATTT
* *
1436548 TTTTATTTATTAGA-TTAGATTT
1 TTTTATTTTTTATATTTA-ATTT
* *
1436570 ATTTAATATTTTTTATCTTTATCTTAT
1 -TTT--TATTTTTTATATTTA-ATT-T
* *
1436597 TTTTA-TTTTTGT-TTTACTTT
1 TTTTATTTTTTATATTTAATTT
* *
1436617 TCTTTATTTTTTATTTTTTATTT
1 T-TTTATTTTTTATATTTAATTT
1436640 TTTTATTATTTTAT
1 TTTTATT-TTTTAT
1436654 TTTTTTAAAA
Statistics
Matches: 105, Mismatches: 10, Indels: 21
0.77 0.07 0.15
Matches are distributed among these distances:
20 6 0.06
21 37 0.35
22 21 0.20
23 22 0.21
24 2 0.02
25 8 0.08
26 8 0.08
27 1 0.01
ACGTcount: A:0.20, C:0.03, G:0.02, T:0.75
Consensus pattern (22 bp):
TTTTATTTTTTATATTTAATTT
Found at i:1436611 original size:11 final size:10
Alignment explanation
Indices: 1436596--1436657 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 10
1436586 CTTTATCTTA
1436596 TTTTTATTTT
1 TTTTTATTTT
1436606 TGTTTTACTTTT
1 T-TTTTA-TTTT
*
1436618 CTTTATTTTTTAT
1 -TTT-TTATTT-T
1436631 TTTTTATTTT
1 TTTTTATTTT
1436641 TTTATTATTTT
1 TTT-TTATTTT
1436652 ATTTTT
1 -TTTTT
1436658 TTAAAATAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
10 5 0.12
11 19 0.44
12 15 0.35
13 4 0.09
ACGTcount: A:0.13, C:0.03, G:0.02, T:0.82
Consensus pattern (10 bp):
TTTTTATTTT
Found at i:1436628 original size:23 final size:21
Alignment explanation
Indices: 1436510--1436656 Score: 89
Period size: 22 Copynumber: 6.6 Consensus size: 21
1436500 CTCCAGATTT
*
1436510 TTTTTTTAATTTAATTTTTTTA
1 TTTTTTT-ATTTTATTTTTTTA
* *
1436532 TTTTTTAATTTAATTTTTTTA
1 TTTTTTTATTTTATTTTTTTA
** ** *
1436553 TTTATTAGATTAGATTTATTTAA
1 TTT-TTTTATTTTATTT-TTTTA
1436576 TATTTTTTATCTTTATCTTATTTT-
1 T-TTTTTTAT-TTTAT-TT-TTTTA
* *
1436600 TATTTTTGTTTTACTTTTCTTTA
1 TTTTTTTATTTTA-TTTT-TTTA
*
1436623 TTTTTTATTTTTTATTTTTTTA
1 TTTTTT-TATTTTATTTTTTTA
*
1436645 TTATTTTATTTT
1 TTTTTTTATTTT
1436657 TTTAAAATAA
Statistics
Matches: 99, Mismatches: 17, Indels: 19
0.73 0.13 0.14
Matches are distributed among these distances:
21 23 0.23
22 33 0.33
23 25 0.25
24 12 0.12
25 6 0.06
ACGTcount: A:0.20, C:0.03, G:0.02, T:0.75
Consensus pattern (21 bp):
TTTTTTTATTTTATTTTTTTA
Found at i:1436631 original size:7 final size:7
Alignment explanation
Indices: 1436619--1436658 Score: 62
Period size: 7 Copynumber: 5.4 Consensus size: 7
1436609 TTTACTTTTC
1436619 TTTATTT
1 TTTATTT
1436626 TTTATTT
1 TTTATTT
1436633 TTTATTTT
1 TTTA-TTT
1436641 TTTATTAT
1 TTTATT-T
1436649 TTTATTT
1 TTTATTT
1436656 TTT
1 TTT
1436659 TAAAATAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 17 0.55
8 14 0.45
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTATTT
Found at i:1436633 original size:6 final size:6
Alignment explanation
Indices: 1436579--1436657 Score: 51
Period size: 6 Copynumber: 13.8 Consensus size: 6
1436569 TATTTAATAT
* * * * * *
1436579 TTTTTA TCTTTA -TCTTA TTTTTA TTTTT- GTTTTA CTTTTC TTTAT-
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
*
1436624 TTTTTA TTTTTTA TTTTT- TTATTA -TTTTA TTTTT
1 TTTTTA -TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
1436658 TTAAAATAAA
Statistics
Matches: 55, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
5 19 0.35
6 30 0.55
7 6 0.11
ACGTcount: A:0.14, C:0.05, G:0.01, T:0.80
Consensus pattern (6 bp):
TTTTTA
Found at i:1436659 original size:16 final size:15
Alignment explanation
Indices: 1436576--1436660 Score: 73
Period size: 16 Copynumber: 5.1 Consensus size: 15
1436566 ATTTATTTAA
1436576 TATTTTTTATCTTTATCT
1 TATTTTTTAT-TTT-T-T
*
1436594 TATTTTTATTTTTGTTT
1 TATTTTT-TATTT-TTT
1436611 TACTTTTCTT-TATTTTT
1 TA-TTTT-TTAT-TTTTT
1436628 TATTTTTTATTTTTT
1 TATTTTTTATTTTTT
1436643 TATTATTTTATTTTTT
1 TATT-TTTTATTTTTT
1436659 TA
1 TA
1436661 AAATAAAAAT
Statistics
Matches: 59, Mismatches: 1, Indels: 16
0.78 0.01 0.21
Matches are distributed among these distances:
15 11 0.19
16 18 0.31
17 9 0.15
18 17 0.29
19 4 0.07
ACGTcount: A:0.15, C:0.05, G:0.01, T:0.79
Consensus pattern (15 bp):
TATTTTTTATTTTTT
Found at i:1436864 original size:58 final size:58
Alignment explanation
Indices: 1436685--1437070 Score: 436
Period size: 58 Copynumber: 6.7 Consensus size: 58
1436675 ATTTCCAAAA
* *
1436685 AAAAAATATTTTT-AGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAGTTTTC
1 AAAAAAGATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCTTTAAAATAAAGTTTTC
*
1436742 AAAAAAAGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCC-TTAAAGATAAA-TTTTC
1 -AAAAAA-GATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTTAAA-ATAAAGTTTTC
* * * *
1436801 CAAAAAGGTTTTCGAGGAAAAGTTGAAAGTATTAATTTTCCTTTAAAATCAAAGTTTTC
1 AAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTTAAAAT-AAAGTTTTC
* * *
1436860 AAAAAAAAGATTTTCGAGGAAAAATTGAAAGTATAAATTTTCCTTTAAAATCAAAGTTTTC
1 --AAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTTAAAAT-AAAGTTTTC
* * *
1436921 AAAAAATATTTTTG-GGAGAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA-TTTT-
1 AAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTTAAAATAAAGTTTTC
* ** *
1436976 ---TAA-ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAG-TTTC
1 AAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTTAAAATAAAGTTTTC
* *
1437029 AAAAGAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCC
1 AAAA-AAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCC
1437071 CTGCACAAGA
Statistics
Matches: 288, Mismatches: 23, Indels: 34
0.83 0.07 0.10
Matches are distributed among these distances:
51 7 0.02
52 38 0.13
56 4 0.01
57 40 0.14
58 86 0.30
59 55 0.19
60 3 0.01
61 55 0.19
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.35
Consensus pattern (58 bp):
AAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTTAAAATAAAGTTTTC
Found at i:1436899 original size:118 final size:118
Alignment explanation
Indices: 1436685--1437070 Score: 404
Period size: 110 Copynumber: 3.3 Consensus size: 118
1436675 ATTTCCAAAA
* *
1436685 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAGTTTTCAAAAAAA
1 AAAAAAGA-TTTTCGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAGTTTTCAAAAAAA
* * * * *
1436749 GGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCC-TTAAAGAT-AAA-TTTTC
65 AGATTTTCGAGGAAAAATTGAAAGTATAAATTTTCCTTTAAA-ATCAAAGTTTTC
* * * *
1436801 CAAAAAGGTTTTCGAGGAAAAGTTGAAAGTATTAATTTTCCTTTAAAATCAAAGTTTTCAAAAAA
1 AAAAAAGATTTTCG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAAGTTTTCAAAAAA
1436866 AAGATTTTCGAGGAAAAATTGAAAGTATAAATTTTCCTTTAAAATCAAAGTTTTC
64 AAGATTTTCGAGGAAAAATTGAAAGTATAAATTTTCCTTTAAAATCAAAGTTTTC
* * * *
1436921 AAAAAATATTTTTGGGAGAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA-TTTT------TAA
1 AAAAAAGATTTTCGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAGTTTTCAAAAAAAA
* * * ** *
1436979 -ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCC-TCGAAATTAAAG-TTTC
66 GATTTTCGAGGAAAAATTGAAAGTATAAATTTTCCTTTAAAATCAAAGTTTTC
* * *
1437029 AAAAGAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCC
1 AAAA-AAGATTTTCG-GGAAAAGTTGAAAGTATCAATTTTCC
1437071 CTGCACAAGA
Statistics
Matches: 235, Mismatches: 27, Indels: 22
0.83 0.10 0.08
Matches are distributed among these distances:
108 8 0.03
109 19 0.08
110 55 0.23
111 2 0.01
115 5 0.02
116 37 0.16
117 4 0.02
118 51 0.22
119 39 0.17
120 15 0.06
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.35
Consensus pattern (118 bp):
AAAAAAGATTTTCGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAGTTTTCAAAAAAAA
GATTTTCGAGGAAAAATTGAAAGTATAAATTTTCCTTTAAAATCAAAGTTTTC
Found at i:1437067 original size:27 final size:27
Alignment explanation
Indices: 1436978--1437068 Score: 71
Period size: 27 Copynumber: 3.2 Consensus size: 27
1436968 TAAATTTTTA
*
1436978 AATTTTTGAGGAAAAGTTGAAAGTATC
1 AATTTTTGAGAAAAAGTTGAAAGTATC
* *
1437005 AATTTTCCTCGA-AATTAAAGTTTCAAAAGAAT-
1 AATTTT--T-GAGAA--AAAG-TT-GAAAGTATC
1437037 -ATTTTTGAGAAAAAGTTGAAAGTATC
1 AATTTTTGAGAAAAAGTTGAAAGTATC
1437063 AATTTT
1 AATTTT
1437069 CCCTGCACAA
Statistics
Matches: 49, Mismatches: 5, Indels: 20
0.66 0.07 0.27
Matches are distributed among these distances:
25 6 0.12
26 2 0.04
27 15 0.31
28 2 0.04
29 5 0.10
30 2 0.04
31 9 0.18
32 2 0.04
33 6 0.12
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.36
Consensus pattern (27 bp):
AATTTTTGAGAAAAAGTTGAAAGTATC
Found at i:1442782 original size:20 final size:20
Alignment explanation
Indices: 1442745--1442783 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1442735 TTTTTGTAGT
* *
1442745 TTTTTTTTTCTATATTTTCA
1 TTTTTATTTATATATTTTCA
*
1442765 TTTTTATTTATATTTTTTC
1 TTTTTATTTATATATTTTC
1442784 TCTTTTCTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTTATTTATATATTTTCA
Found at i:1446880 original size:21 final size:21
Alignment explanation
Indices: 1446840--1446881 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1446830 TTATTTTTTG
** *
1446840 TATTAAAAATAATTATAAATA
1 TATTAAAAATAACGAAAAATA
1446861 TATTAAAAATAACGAAAAATA
1 TATTAAAAATAACGAAAAATA
1446882 ACTTATCCTA
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:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (21 bp):
TATTAAAAATAACGAAAAATA
Found at i:1456753 original size:2 final size:2
Alignment explanation
Indices: 1456746--1456772 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1456736 GCTTGTAAAC
1456746 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1456773 GGATGGTAAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1456952 original size:18 final size:19
Alignment explanation
Indices: 1456904--1456954 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1456894 TGACGCGAAA
1456904 TTAATA-AAATATTATTTT
1 TTAATATAAATATTATTTT
1456922 TTAAATATAAAATATTA-TTT
1 TT-AATAT-AAATATTATTTT
1456942 TTAATATAAATAT
1 TTAATATAAATAT
1456955 AAAATTAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 8 0.27
19 9 0.30
20 5 0.17
21 8 0.27
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTAATATAAATATTATTTT
Found at i:1456959 original size:25 final size:21
Alignment explanation
Indices: 1456907--1456951 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
1456897 CGCGAAATTA
1456907 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTTAAAT
1456928 ATAAAATATTA-TTTTT-AAT
1 ATAAAATATTATTTTTTAAAT
1456947 ATAAA
1 ATAAA
1456952 TATAAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 8 0.33
20 5 0.21
21 11 0.46
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATAAAATATTATTTTTTAAAT
Found at i:1457183 original size:2 final size:2
Alignment explanation
Indices: 1457176--1457230 Score: 74
Period size: 2 Copynumber: 27.5 Consensus size: 2
1457166 ACCTTCATTT
* * * *
1457176 TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA GA TA AA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1457218 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
1457231 CATGGATCAA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1458473 original size:24 final size:25
Alignment explanation
Indices: 1458445--1458492 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
1458435 ATTTTTATTT
1458445 ATTTATTTAATT-TTTTAAAAATTA
1 ATTTATTTAATTATTTTAAAAATTA
* *
1458469 ATTTATTTTATTATTTTTAAAATT
1 ATTTATTTAATTATTTTAAAAATT
1458493 TAAATTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
ATTTATTTAATTATTTTAAAAATTA
Found at i:1458606 original size:14 final size:15
Alignment explanation
Indices: 1458578--1458610 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1458568 AATTTGATAA
*
1458578 AAATGTATTTTAATT
1 AAATGTATTTAAATT
1458593 AAATG-ATTTAAATT
1 AAATGTATTTAAATT
1458607 AAAT
1 AAAT
1458611 TTGTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (15 bp):
AAATGTATTTAAATT
Found at i:1469531 original size:32 final size:32
Alignment explanation
Indices: 1469458--1469532 Score: 98
Period size: 32 Copynumber: 2.4 Consensus size: 32
1469448 CAAATGAAAT
* * *
1469458 CAAATGAAATC-CACGTGCGTTAATATTTTAT
1 CAAATGAAATCAAACGTGCATTAATATTTTAC
* *
1469489 TAAATAAAATCAAACGTGCATTAATATTTTAC
1 CAAATGAAATCAAACGTGCATTAATATTTTAC
1469521 CAAATGAAATCA
1 CAAATGAAATCA
1469533 CATTTAATGA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 9 0.25
32 27 0.75
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.32
Consensus pattern (32 bp):
CAAATGAAATCAAACGTGCATTAATATTTTAC
Found at i:1470742 original size:263 final size:269
Alignment explanation
Indices: 1470267--1470758 Score: 782
Period size: 263 Copynumber: 1.8 Consensus size: 269
1470257 ACTCAAATGA
* * *
1470267 ATACTATATTTAATTAAATATAAATGTATCGAATAATTAATTAGAAAATCAATTATTTTATAATT
1 ATACTATATTTAATCAAATATAAATATATCAAATAATTAATTAGAAAATCAATTATTTTATAATT
1470332 GTAATTGTAGTATTTATTAATTTATTAATTATATATTGATTGATTTAATTTGTCAAATTAAGAAA
66 GTAATTGTAGTA-TTATTAA-TTATTAATTATATATTGATTGATTTAATTTGTCAAATTAAGAAA
1470397 ATTTTTAAAATTTTAATACTTTTAATATGAATTGAATTGAGAATAATTTAAAATAAATAATAAAA
129 ATTTTTAAAATTTTAATACTTTTAATATGAATTGAATTGAGAATAATTTAAAATAAATAATAAAA
* * *
1470462 ACATAAACATTATCAATTTAGTTTTTTGAATTATATTTGCTTTATATATTTACATATGAAATACA
194 ACATAAACATGATCAATTTAATTTTTTAAATTATATTTGCTTTATATATTTACATATGAAATACA
1470527 TCAATTACTTG
259 TCAATTACTTG
* *
1470538 ATACTATATTTAATCAAATATAAATATATCAAATAATTGATTAGAGAATCAATTATTTTATAATT
1 ATACTATATTTAATCAAATATAAATATATCAAATAATTAATTAGAAAATCAATTATTTTATAATT
1470603 GTAATTGTAGTA-T-TT-A-T-TTAATTATATATTGATTGATTTAATTTGTCAAATTAAGAAAA-
66 GTAATTGTAGTATTATTAATTATTAATTATATATTGATTGATTTAATTTGTCAAATTAAGAAAAT
* * * *
1470662 TTTTAAAATTTTAATATTTTTAATATGAATTGAATTGAGAGTGATTTAAAGGT-AATAATAAAAA
131 TTTTAAAATTTTAATACTTTTAATATGAATTGAATTGAGAATAATTTAAA-ATAAATAATAAAAA
* *
1470726 TATAAATATGATCAATTTAATTTTTTAAATTAT
195 CATAAACATGATCAATTTAATTTTTTAAATTAT
1470759 TTTTAAATTA
Statistics
Matches: 206, Mismatches: 14, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
263 86 0.42
264 43 0.21
265 1 0.00
267 1 0.00
268 2 0.01
269 1 0.00
271 72 0.35
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (269 bp):
ATACTATATTTAATCAAATATAAATATATCAAATAATTAATTAGAAAATCAATTATTTTATAATT
GTAATTGTAGTATTATTAATTATTAATTATATATTGATTGATTTAATTTGTCAAATTAAGAAAAT
TTTTAAAATTTTAATACTTTTAATATGAATTGAATTGAGAATAATTTAAAATAAATAATAAAAAC
ATAAACATGATCAATTTAATTTTTTAAATTATATTTGCTTTATATATTTACATATGAAATACATC
AATTACTTG
Found at i:1471068 original size:18 final size:18
Alignment explanation
Indices: 1471042--1471081 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1471032 TTTAAAATTA
**
1471042 AATTAAATTATTTTTATT
1 AATTAAATTAAATTTATT
*
1471060 AATTGAATTAAATTTATT
1 AATTAAATTAAATTTATT
1471078 AATT
1 AATT
1471082 TTAAAAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (18 bp):
AATTAAATTAAATTTATT
Found at i:1471160 original size:16 final size:16
Alignment explanation
Indices: 1471103--1471163 Score: 53
Period size: 16 Copynumber: 4.1 Consensus size: 16
1471093 ATCGATCAAA
1471103 TTAAATTAAATTAT-T
1 TTAAATTAAATTATAT
*
1471118 TATTAATTAAA-TATA-
1 T-TAAATTAAATTATAT
*
1471133 -T-AA-TAAAATATAT
1 TTAAATTAAATTATAT
1471146 TTAAATTAAATTATAT
1 TTAAATTAAATTATAT
1471162 TT
1 TT
1471164 TAAACGTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
11 4 0.11
12 6 0.16
13 1 0.03
14 1 0.03
15 6 0.16
16 19 0.51
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTAAATTAAATTATAT
Found at i:1472670 original size:85 final size:84
Alignment explanation
Indices: 1472570--1472737 Score: 255
Period size: 85 Copynumber: 2.0 Consensus size: 84
1472560 AAAAGCTTTT
* * * * *
1472570 TATGGAGCTTTGGGATAATAATGACAGCTAACAGAGGCCAAGAAAAATTGAATCTTTCAAACTGT
1 TATGAAGCTTTGGGATAACAATGACAGCTAAAAGAGGCCAAGAAAAATCGAATCTTTCAAACTGC
*
1472635 AATTCATTTGTTGCAAATG
66 AATTCACTTGTTGCAAATG
*
1472654 TATGAAGCTTTTGGGATAACAATGACAGCTAAAAGAGGCTAAGAAAAATCGAATCTTTCAAACTG
1 TATGAAGC-TTTGGGATAACAATGACAGCTAAAAGAGGCCAAGAAAAATCGAATCTTTCAAACTG
*
1472719 CAATTCACTTGTTTCAAAT
65 CAATTCACTTGTTGCAAAT
1472738 TTTTTCTGTT
Statistics
Matches: 75, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
84 7 0.09
85 68 0.91
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.29
Consensus pattern (84 bp):
TATGAAGCTTTGGGATAACAATGACAGCTAAAAGAGGCCAAGAAAAATCGAATCTTTCAAACTGC
AATTCACTTGTTGCAAATG
Found at i:1476270 original size:18 final size:20
Alignment explanation
Indices: 1476236--1476277 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
1476226 ATAGAATTGA
*
1476236 TTTATATATATTTTTAA-TT
1 TTTACATATATTTTTAAGTT
1476255 TTTACATATA-TTTTAAGTT
1 TTTACATATATTTTTAAGTT
1476274 TTTA
1 TTTA
1476278 TATAATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (20 bp):
TTTACATATATTTTTAAGTT
Found at i:1476280 original size:17 final size:17
Alignment explanation
Indices: 1476235--1476281 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
1476225 AATAGAATTG
*
1476235 ATTTATATATATTTTTA
1 ATTTTTATATATTTTTA
*
1476252 ATTTTTACATATATTTTA
1 ATTTTTATATAT-TTTTA
1476270 AGTTTTTATATA
1 A-TTTTTATATA
1476282 ATAAAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 10 0.40
18 6 0.24
19 9 0.36
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (17 bp):
ATTTTTATATATTTTTA
Found at i:1476317 original size:10 final size:10
Alignment explanation
Indices: 1476297--1476347 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
1476287 AAAATAATTT
1476297 TATATTAAAA
1 TATATTAAAA
* *
1476307 TTTATTTAAA
1 TATATTAAAA
1476317 TATATTAAAA
1 TATATTAAAA
1476327 TAATATATAAAA
1 T-ATAT-TAAAA
*
1476339 -ATTTTAAAA
1 TATATTAAAA
1476348 ATTAATAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
9 5 0.15
10 20 0.59
11 4 0.12
12 5 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
TATATTAAAA
Found at i:1477366 original size:166 final size:166
Alignment explanation
Indices: 1477074--1477391 Score: 557
Period size: 166 Copynumber: 1.9 Consensus size: 166
1477064 ATTTTTTTTC
1477074 TTGAGATTGTTTCAAATGGAGTATAAATCGGAATTTTACATTGCTTGATAGTGGTTAGTGTAGTT
1 TTGAGATTGTTTCAAATGGAGTATAAATCGGAATTTTACATTGCTTGATAGTGGTTAGTGTAGTT
*
1477139 GGGTTTCTTCTTAAAAGATCAAATCAGTTCTAGGTATTGAAGCTTTTCAGGGTTGGATTTGTAAG
66 GGGTTTCTTCTTAAAAGATCAAATCAGTTCTAGGTATTGAAGCTTTTCAGGGTTCGATTTGTAAG
1477204 TTGGCTTCTTCCTTAAATGTTAGGGTTTTTTTGGGG
131 TTGGCTTCTTCCTTAAATGTTAGGGTTTTTTTGGGG
* * * * *
1477240 TTGAGATTGTTTCAAATTGGATTATAAATTGGACTTTTACATTGCTTGATATTGGTTATTGTAGT
1 TTGAGATTGTTTCAAA-TGGAGTATAAATCGGAATTTTACATTGCTTGATAGTGGTTAGTGTAGT
*
1477305 TGGGTTTCTTCTTAAAAGATCAAAT-AGTTCTGGGTATTGAAGCTTTTCAGGGTTCGATTTGTAA
65 TGGGTTTCTTCTTAAAAGATCAAATCAGTTCTAGGTATTGAAGCTTTTCAGGGTTCGATTTGTAA
1477369 GTTGGCTTCTTCCTTAAATGTTA
130 GTTGGCTTCTTCCTTAAATGTTA
1477392 ATGATTTTTG
Statistics
Matches: 144, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
166 76 0.53
167 68 0.47
ACGTcount: A:0.24, C:0.09, G:0.23, T:0.43
Consensus pattern (166 bp):
TTGAGATTGTTTCAAATGGAGTATAAATCGGAATTTTACATTGCTTGATAGTGGTTAGTGTAGTT
GGGTTTCTTCTTAAAAGATCAAATCAGTTCTAGGTATTGAAGCTTTTCAGGGTTCGATTTGTAAG
TTGGCTTCTTCCTTAAATGTTAGGGTTTTTTTGGGG
Found at i:1480631 original size:18 final size:18
Alignment explanation
Indices: 1480608--1480674 Score: 53
Period size: 18 Copynumber: 3.4 Consensus size: 18
1480598 TTTGCAGAAG
1480608 TCTTTATACAGTATGTTT
1 TCTTTATACAGTATGTTT
** *
1480626 TCTTTATATGTGTCTGAATTCT
1 TCTTTATA-CAGTATG--TT-T
*
1480648 GTCTTTATACAATATGTTT
1 -TCTTTATACAGTATGTTT
1480667 TCTTTATA
1 TCTTTATA
1480675 TGTTGTACAT
Statistics
Matches: 37, Mismatches: 7, Indels: 10
0.69 0.13 0.19
Matches are distributed among these distances:
18 16 0.43
19 5 0.14
20 2 0.05
21 2 0.05
22 4 0.11
23 8 0.22
ACGTcount: A:0.22, C:0.12, G:0.10, T:0.55
Consensus pattern (18 bp):
TCTTTATACAGTATGTTT
Found at i:1482585 original size:35 final size:35
Alignment explanation
Indices: 1482546--1482613 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
1482536 AGTTTCAAGC
*
1482546 AGGTATGATGTCATTTATTACATAAGAAACTAAGT
1 AGGTATGATGTCATTTATTACACAAGAAACTAAGT
*
1482581 AGGTATGATGTCATTTATTGCACAAGAAACTAA
1 AGGTATGATGTCATTTATTACACAAGAAACTAA
1482614 TTGTTTCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.32
Consensus pattern (35 bp):
AGGTATGATGTCATTTATTACACAAGAAACTAAGT
Found at i:1483240 original size:12 final size:12
Alignment explanation
Indices: 1483210--1483261 Score: 56
Period size: 12 Copynumber: 4.5 Consensus size: 12
1483200 TTTTATATCT
1483210 AATTT-TATTAA
1 AATTTATATTAA
1483221 AA--TATATTAA
1 AATTTATATTAA
1483231 AATTTATATTAA
1 AATTTATATTAA
* *
1483243 AATAATATATAAA
1 AAT-TTATATTAA
1483256 AATTTA
1 AATTTA
1483262 AAATTAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
9 1 0.03
10 8 0.24
11 2 0.06
12 13 0.38
13 10 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
AATTTATATTAA
Found at i:1483257 original size:25 final size:22
Alignment explanation
Indices: 1483210--1483261 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 22
1483200 TTTTATATCT
1483210 AATTT-TATTAAAATATATTAA
1 AATTTATATTAAAATATATTAA
1483231 AATTTATATTAAAATAATATATAAA
1 AATTTATATTAAAAT-ATAT-T-AA
1483256 AATTTA
1 AATTTA
1483262 AAATTAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.19
22 9 0.33
23 4 0.15
24 1 0.04
25 8 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
AATTTATATTAAAATATATTAA
Found at i:1490149 original size:17 final size:17
Alignment explanation
Indices: 1490122--1490262 Score: 61
Period size: 19 Copynumber: 8.4 Consensus size: 17
1490112 AAATATAAAA
1490122 AATTATTATATTAAATAT
1 AATT-TTATATTAAATAT
1490140 ATATTTATATATTAAATAT
1 A-ATTT-TATATTAAATAT
1490159 AATTTT-T-TT-AAT-T
1 AATTTTATATTAAATAT
* **
1490172 --TTTATAAATTTTTATAT
1 AATTT-TATA-TTAAATAT
*
1490189 AATTTT-TATTAAAATTTT
1 AATTTTATATT-AAA-TAT
1490207 AA-TTTATA-TAAA-A-
1 AATTTTATATTAAATAT
*
1490220 AATTATTATATTAAATTT
1 AATT-TTATATTAAATAT
*
1490238 ATATTTATACATTAAATAT
1 A-ATTT-TATATTAAATAT
1490257 AATTTT
1 AATTTT
1490263 TTAAATTTTT
Statistics
Matches: 93, Mismatches: 10, Indels: 41
0.65 0.07 0.28
Matches are distributed among these distances:
11 3 0.03
12 1 0.01
13 3 0.03
14 4 0.04
15 9 0.10
16 12 0.13
17 9 0.10
18 19 0.20
19 33 0.35
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (17 bp):
AATTTTATATTAAATAT
Found at i:1490152 original size:19 final size:18
Alignment explanation
Indices: 1490128--1490163 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
1490118 AAAAAATTAT
1490128 TATATTAAATATATATTTA
1 TATATTAAATATA-ATTTA
1490147 TATATTAAATATAATTT
1 TATATTAAATATAATTT
1490164 TTTTAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TATATTAAATATAATTTA
Found at i:1490170 original size:9 final size:10
Alignment explanation
Indices: 1490158--1490200 Score: 61
Period size: 10 Copynumber: 4.3 Consensus size: 10
1490148 ATATTAAATA
1490158 TAATTTTT-T
1 TAATTTTTAT
1490167 TAATTTTTAT
1 TAATTTTTAT
*
1490177 AAATTTTTAT
1 TAATTTTTAT
1490187 ATAATTTTTAT
1 -TAATTTTTAT
1490198 TAA
1 TAA
1490201 AATTTTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
9 8 0.27
10 13 0.43
11 9 0.30
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TAATTTTTAT
Found at i:1490193 original size:21 final size:21
Alignment explanation
Indices: 1490159--1490207 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1490149 TATTAAATAT
1490159 AATTTTT-TTAATTTTTA-TA
1 AATTTTTATTAATTTTTATTA
1490178 AATTTTTATATAATTTTTATTA
1 AATTTTTAT-TAATTTTTATTA
*
1490200 AAATTTTA
1 AATTTTTA
1490208 ATTTATATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 7 0.27
20 1 0.04
21 9 0.35
22 9 0.35
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
AATTTTTATTAATTTTTATTA
Found at i:1490204 original size:12 final size:11
Alignment explanation
Indices: 1490168--1490206 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
1490158 TAATTTTTTT
1490168 AATTTTTAT-A
1 AATTTTTATAA
*
1490178 AATTTTTATAT
1 AATTTTTATAA
1490189 AATTTTTATTAA
1 AATTTTTA-TAA
1490201 AATTTT
1 AATTTT
1490207 AATTTATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 9 0.36
11 8 0.32
12 8 0.32
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
AATTTTTATAA
Found at i:1490206 original size:11 final size:10
Alignment explanation
Indices: 1490159--1490207 Score: 55
Period size: 11 Copynumber: 4.8 Consensus size: 10
1490149 TATTAAATAT
*
1490159 AATTTTT-TT
1 AATTTTTATA
1490168 AATTTTTATA
1 AATTTTTATA
1490178 AATTTTTATA
1 AATTTTTATA
1490188 TAATTTTTATTA
1 -AATTTTTA-TA
*
1490200 AAATTTTA
1 AATTTTTA
1490208 ATTTATATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 7 0.20
10 11 0.31
11 15 0.43
12 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
AATTTTTATA
Found at i:1490270 original size:98 final size:98
Alignment explanation
Indices: 1490114--1490311 Score: 360
Period size: 98 Copynumber: 2.0 Consensus size: 98
1490104 TGTGTATAAA
* *
1490114 ATATAAAAAATTATTATATTAAATATATATTTATATATTAAATATAATTTTTTTAATTTTTATAA
1 ATATAAAAAATTATTATATTAAATATATATTTATACATTAAATATAATTTTTTAAATTTTTATAA
*
1490179 ATTTTTATATAATTTTTATTAAAATTTTAATTT
66 ATTTATATATAATTTTTATTAAAATTTTAATTT
*
1490212 ATATAAAAAATTATTATATTAAATTTATATTTATACATTAAATATAATTTTTTAAATTTTTATAA
1 ATATAAAAAATTATTATATTAAATATATATTTATACATTAAATATAATTTTTTAAATTTTTATAA
1490277 ATTTATATATAATTTTTATTAAAATTTTAATTT
66 ATTTATATATAATTTTTATTAAAATTTTAATTT
1490310 AT
1 AT
1490312 GTTATTTTTA
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 96 1.00
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (98 bp):
ATATAAAAAATTATTATATTAAATATATATTTATACATTAAATATAATTTTTTAAATTTTTATAA
ATTTATATATAATTTTTATTAAAATTTTAATTT
Found at i:1490277 original size:10 final size:10
Alignment explanation
Indices: 1490257--1490305 Score: 55
Period size: 11 Copynumber: 4.8 Consensus size: 10
1490247 CATTAAATAT
1490257 AATTTTT-TA
1 AATTTTTATA
1490266 AATTTTTATA
1 AATTTTTATA
*
1490276 AATTTATATA
1 AATTTTTATA
1490286 TAATTTTTATTA
1 -AATTTTTA-TA
*
1490298 AAATTTTA
1 AATTTTTA
1490306 ATTTATGTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 7 0.21
10 11 0.32
11 14 0.41
12 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
AATTTTTATA
Found at i:1490302 original size:33 final size:33
Alignment explanation
Indices: 1490155--1490304 Score: 115
Period size: 30 Copynumber: 4.7 Consensus size: 33
1490145 TATATATTAA
*
1490155 ATATAATTTTT-TT--AATTTTTATAAATTTTT
1 ATATAATTTTTATTAAAATTTTTATAAATTTAT
1490185 ATATAATTTTTATTAAAA--TTT-T-AATTTAT
1 ATATAATTTTTATTAAAATTTTTATAAATTTAT
* * * *
1490214 ATAAAAAATTATTATATTAAATTTATATTTATACA-TTAA
1 AT--ATAATT-TT-TATTAAA---ATTTTTATAAATTTAT
1490253 ATATAA-TTTT-TT-AAATTTTTATAAATTTAT
1 ATATAATTTTTATTAAAATTTTTATAAATTTAT
1490283 ATATAATTTTTATTAAAATTTT
1 ATATAATTTTTATTAAAATTTT
1490305 AATTTATGTT
Statistics
Matches: 94, Mismatches: 8, Indels: 33
0.70 0.06 0.24
Matches are distributed among these distances:
29 17 0.18
30 21 0.22
31 14 0.15
32 6 0.06
33 18 0.19
34 1 0.01
35 2 0.02
36 2 0.02
37 3 0.03
38 3 0.03
39 6 0.06
40 1 0.01
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (33 bp):
ATATAATTTTTATTAAAATTTTTATAAATTTAT
Found at i:1490424 original size:22 final size:22
Alignment explanation
Indices: 1490398--1490445 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
1490388 ATAAAATTTT
*
1490398 AAATTTTAATTTAATTTAAATC
1 AAATTTTAATATAATTTAAATC
* * *
1490420 AAATTTTTATATGATTTAATTC
1 AAATTTTAATATAATTTAAATC
1490442 AAAT
1 AAAT
1490446 AAAATTTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (22 bp):
AAATTTTAATATAATTTAAATC
Found at i:1490439 original size:27 final size:26
Alignment explanation
Indices: 1490406--1490481 Score: 91
Period size: 27 Copynumber: 2.9 Consensus size: 26
1490396 TTAAATTTTA
1490406 ATTTAATTTAAATCAAATTTTTATATG
1 ATTTAATTTAAATCAAATTTTTAT-TG
* *
1490433 ATTTAATTCAAAT-AAAATTTTATTG
1 ATTTAATTTAAATCAAATTTTTATTG
* *
1490458 ATTTAATTTGATTCATAATTTTTA
1 ATTTAATTTAAATCA-AATTTTTA
1490482 AATTATTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
25 12 0.29
26 10 0.24
27 19 0.46
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (26 bp):
ATTTAATTTAAATCAAATTTTTATTG
Found at i:1490508 original size:46 final size:45
Alignment explanation
Indices: 1490450--1490543 Score: 102
Period size: 46 Copynumber: 2.1 Consensus size: 45
1490440 TCAAATAAAA
* * ** *
1490450 TTTTATTGATTTAATTTGATTCATAATTTTTAAATTATT-TTTTTAT
1 TTTTATTGATTTAAATAGA-T-ATAAAATTTAAATAATTATTTTTAT
1490496 TTTTATAT-ATTTAAATAGATATAAAATTTAAATAATTATTTTTAT
1 TTTTAT-TGATTTAAATAGATATAAAATTTAAATAATTATTTTTAT
1490541 TTT
1 TTT
1490544 ATAAAAATTA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
44 14 0.34
45 11 0.27
46 15 0.37
47 1 0.02
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (45 bp):
TTTTATTGATTTAAATAGATATAAAATTTAAATAATTATTTTTAT
Found at i:1490555 original size:45 final size:44
Alignment explanation
Indices: 1490478--1490566 Score: 108
Period size: 45 Copynumber: 2.0 Consensus size: 44
1490468 ATTCATAATT
* * * * *
1490478 TTTAAATTATTTTTTTATTTTTATATATTTAAATAGATATAAAA
1 TTTAAATAATTTTTTTATTTTTATAAAATTAAAAAAATATAAAA
1490522 TTTAAATAATTATTTTTA-TTTTATAAAAATTAAAAAAATATAAAA
1 TTTAAATAATT-TTTTTATTTTTAT-AAAATTAAAAAAATATAAAA
1490567 ACTAACAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
44 16 0.42
45 22 0.58
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (44 bp):
TTTAAATAATTTTTTTATTTTTATAAAATTAAAAAAATATAAAA
Found at i:1492937 original size:2 final size:2
Alignment explanation
Indices: 1492930--1492961 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1492920 TATGTTATTT
1492930 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
1492962 AAGATTATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1493778 original size:42 final size:42
Alignment explanation
Indices: 1493684--1493779 Score: 108
Period size: 42 Copynumber: 2.3 Consensus size: 42
1493674 TTTTAATTGT
* *
1493684 ATATAAATATAATATTTTTATTAAGTTAATATCTTAAATTAAA
1 ATATAAA-ATAATAATTTTATTAAGTTAATATCCTAAATTAAA
*
1493727 ATATTAAATAATAATTTTATTAA-TATAATATACCTAAATATAAA
1 ATATAAAATAATAATTTTATTAAGT-TAATAT-CCTAAAT-TAAA
1493771 A-A-AAAATAA
1 ATATAAAATAA
1493780 ATTATAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
41 1 0.02
42 27 0.59
43 13 0.28
44 5 0.11
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (42 bp):
ATATAAAATAATAATTTTATTAAGTTAATATCCTAAATTAAA
Found at i:1495740 original size:11 final size:11
Alignment explanation
Indices: 1495710--1495752 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
1495700 AGATGATTTA
*
1495710 AAATACAATAT
1 AAATATAATAT
1495721 GATAATATAATAT
1 -A-AATATAATAT
1495734 AAATATAATAT
1 AAATATAATAT
*
1495745 AAAAATAA
1 AAATATAA
1495753 AAATAATATG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 17 0.61
12 2 0.07
13 9 0.32
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AAATATAATAT
Found at i:1495884 original size:8 final size:8
Alignment explanation
Indices: 1495859--1495894 Score: 54
Period size: 8 Copynumber: 4.2 Consensus size: 8
1495849 TATAATTTTT
1495859 ATATATAA
1 ATATATAA
1495867 TATGATATAA
1 -AT-ATATAA
1495877 ATATATAA
1 ATATATAA
1495885 ATATATAA
1 ATATATAA
1495893 AT
1 AT
1495895 TATCTATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 16 0.62
9 4 0.15
10 6 0.23
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (8 bp):
ATATATAA
Found at i:1497626 original size:27 final size:26
Alignment explanation
Indices: 1497596--1497655 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
1497586 ATACAAAATG
1497596 ATATTATTTAAT-TTAATCTTATTTATA
1 ATATTATTTAATCTT-ATCTTA-TTATA
* *
1497623 ATATAATTTAATCTTATTTTATTATA
1 ATATTATTTAATCTTATCTTATTATA
*
1497649 ATCTTAT
1 ATATTAT
1497656 ATTTCAAACA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 10 0.36
27 16 0.57
28 2 0.07
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (26 bp):
ATATTATTTAATCTTATCTTATTATA
Found at i:1497629 original size:22 final size:21
Alignment explanation
Indices: 1497604--1497650 Score: 76
Period size: 22 Copynumber: 2.2 Consensus size: 21
1497594 TGATATTATT
1497604 TAATTTAATCTTATTTATAATA
1 TAATTTAATCTTATTT-TAATA
*
1497626 TAATTTAATCTTATTTTATTA
1 TAATTTAATCTTATTTTAATA
1497647 TAAT
1 TAAT
1497651 CTTATATTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (21 bp):
TAATTTAATCTTATTTTAATA
Found at i:1508110 original size:19 final size:19
Alignment explanation
Indices: 1508074--1508111 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1508064 CGAACTCGAT
*
1508074 AAATTATATTTTTATAAAA
1 AAATTATATATTTATAAAA
1508093 AAATTATATAATTT-TAAAA
1 AAATTATAT-ATTTATAAAA
1508112 TTAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AAATTATATATTTATAAAA
Found at i:1508560 original size:29 final size:28
Alignment explanation
Indices: 1508507--1508571 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 28
1508497 ATATATTTAT
*
1508507 ATTTTTATCAATATAAATTATAATAAATA
1 ATTTTTAT-AATAAAAATTATAATAAATA
*
1508536 ATTTTTAT-ATAAAAATATATAAATATATA
1 ATTTTTATAATAAAAAT-TAT-AATAAATA
*
1508565 AATTTTA
1 ATTTTTA
1508572 ATATTTTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 7 0.23
28 3 0.10
29 21 0.68
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (28 bp):
ATTTTTATAATAAAAATTATAATAAATA
Found at i:1516841 original size:59 final size:60
Alignment explanation
Indices: 1516769--1516889 Score: 174
Period size: 62 Copynumber: 2.0 Consensus size: 60
1516759 GAAGTTCAAC
* *
1516769 GTAATATTCAACAT-A-AATTGAACTTATTCTGTGTAAATGAAGTGTTTATGCAAACCTAA
1 GTAATATTCAACATAATAATTGAACTTATTCTGTGT-AATAAAGTATTTATGCAAACCTAA
*
1516828 GTAATATTCAACATAATCTAATTGAACTTTTTCTGTGTAATAAAGTATTTATGCAAACCTAA
1 GTAATATTCAACATAA--TAATTGAACTTATTCTGTGTAATAAAGTATTTATGCAAACCTAA
1516890 AAAATTATAC
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
59 14 0.25
60 1 0.02
62 22 0.40
63 18 0.33
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (60 bp):
GTAATATTCAACATAATAATTGAACTTATTCTGTGTAATAAAGTATTTATGCAAACCTAA
Found at i:1547074 original size:2 final size:2
Alignment explanation
Indices: 1547067--1547109 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1547057 CCATAGTTTC
1547067 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1547109 A
1 A
1547110 CATACATTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1550132 original size:2 final size:2
Alignment explanation
Indices: 1550125--1550173 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1550115 TTTTGGAAAT
1550125 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
1550167 TC TC TC T
1 TC TC TC T
1550174 TTATAGTGAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1550333 original size:28 final size:28
Alignment explanation
Indices: 1550299--1550354 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
1550289 CCTCAAAAAA
*
1550299 AAAAAAAATAAATGTGGACACAATTTGTCC
1 AAAAAAAAT--ATGTGGACACAAATTGTCC
*
1550329 AAAAAAAATATGTGGGCACAAATTGT
1 AAAAAAAATATGTGGACACAAATTGT
1550355 ACACCAGAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 15 0.62
30 9 0.38
ACGTcount: A:0.50, C:0.11, G:0.16, T:0.23
Consensus pattern (28 bp):
AAAAAAAATATGTGGACACAAATTGTCC
Found at i:1551106 original size:20 final size:21
Alignment explanation
Indices: 1551078--1551116 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1551068 TTGACAATAA
1551078 AAATAAAGT-TTAAATTTTAT
1 AAATAAAGTATTAAATTTTAT
* *
1551098 AAATGAAGTATTTAATTTT
1 AAATAAAGTATTAAATTTT
1551117 TATTAATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (21 bp):
AAATAAAGTATTAAATTTTAT
Found at i:1552426 original size:10 final size:10
Alignment explanation
Indices: 1552411--1552443 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1552401 TAAGTTTAAT
1552411 TTTTTATATA
1 TTTTTATATA
1552421 TTTTTATATA
1 TTTTTATATA
*
1552431 -TTTTATTTA
1 TTTTTATATA
1552440 TTTT
1 TTTT
1552444 AATTAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTTATATA
Found at i:1552638 original size:12 final size:12
Alignment explanation
Indices: 1552618--1552651 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1552608 ATTTTAAACT
1552618 TCAAATTTAAAA
1 TCAAATTTAAAA
* *
1552630 TCGAATTTAAAC
1 TCAAATTTAAAA
1552642 TCAAATTTAA
1 TCAAATTTAA
1552652 TATTATATCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.35
Consensus pattern (12 bp):
TCAAATTTAAAA
Found at i:1552895 original size:19 final size:19
Alignment explanation
Indices: 1552871--1552908 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1552861 ATTGTTTTAT
1552871 CAGCCATGAAAATAAGAAA
1 CAGCCATGAAAATAAGAAA
*
1552890 CAGCCATGAAAATATGAAA
1 CAGCCATGAAAATAAGAAA
1552909 GAGACCATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.16, G:0.16, T:0.13
Consensus pattern (19 bp):
CAGCCATGAAAATAAGAAA
Found at i:1553633 original size:18 final size:20
Alignment explanation
Indices: 1553584--1553636 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 20
1553574 AAATTAATAA
*
1553584 ATTATTAAAAAATAAATTAT
1 ATTATTAAATAATAAATTAT
*
1553604 TTTATTTCAAATAAT-AATT-T
1 ATTA-TT-AAATAATAAATTAT
1553624 ATTATTAAATAAT
1 ATTATTAAATAAT
1553637 TAAAAATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 7 0.25
19 2 0.07
20 7 0.25
21 6 0.21
22 6 0.21
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTATTAAATAATAAATTAT
Found at i:1554152 original size:21 final size:21
Alignment explanation
Indices: 1554128--1554174 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
1554118 TCTAAAATTA
1554128 ATAAAATATTATTTGTTAAAT
1 ATAAAATATTATTTGTTAAAT
*
1554149 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTGTTAAAT
1554170 ATAAA
1 ATAAA
1554175 TATAAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
ATAAAATATTATTTGTTAAAT
Found at i:1554695 original size:10 final size:10
Alignment explanation
Indices: 1554662--1554709 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
1554652 TTTTTAAAAT
*
1554662 TTTTTATTTA
1 TTTTTATATA
*
1554672 ATTTTATAATTA
1 TTTTTAT-A-TA
1554684 TTTTTATATA
1 TTTTTATATA
1554694 TTTTTATATA
1 TTTTTATATA
*
1554704 TATTTA
1 TTTTTA
1554710 ATTTTATATT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 23 0.72
11 1 0.03
12 8 0.25
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTTATATA
Found at i:1554717 original size:12 final size:12
Alignment explanation
Indices: 1554659--1554721 Score: 56
Period size: 12 Copynumber: 5.1 Consensus size: 12
1554649 TAATTTTTAA
*
1554659 AATTTTTTATTT
1 AATTTTATATTT
*
1554671 AATTTTATAATT
1 AATTTTATATTT
*
1554683 ATTTTTATATATT
1 AATTTTATAT-TT
*
1554696 -TTTATATATATTT
1 AATT-T-TATATTT
1554709 AATTTTATATTT
1 AATTTTATATTT
1554721 A
1 A
1554722 TATTAAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
12 29 0.69
13 6 0.14
14 7 0.17
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
AATTTTATATTT
Found at i:1555788 original size:21 final size:20
Alignment explanation
Indices: 1555764--1555806 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1555754 TTTTGATATA
*
1555764 AATTATTAAAAATTAAATTTT
1 AATTATT-AAAATTAAAATTT
*
1555785 AATTATTAGAATTAAAATTT
1 AATTATTAAAATTAAAATTT
1555805 AA
1 AA
1555807 CATTTTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
AATTATTAAAATTAAAATTT
Found at i:1556024 original size:16 final size:16
Alignment explanation
Indices: 1555977--1556029 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
1555967 AAAATATAAT
*
1555977 ATTTAATTCGATTTAA
1 ATTTAATTTGATTTAA
* **
1555993 ATTGAATTTTTTTTAA
1 ATTTAATTTGATTTAA
*
1556009 ATTTAATTTGAATTAA
1 ATTTAATTTGATTTAA
1556025 ATTTA
1 ATTTA
1556030 TATATTAAAT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.55
Consensus pattern (16 bp):
ATTTAATTTGATTTAA
Found at i:1556038 original size:13 final size:13
Alignment explanation
Indices: 1556020--1556051 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
1556010 TTTAATTTGA
1556020 ATTAAATTTATAT
1 ATTAAATTTATAT
1556033 ATTAAA--TATAT
1 ATTAAATTTATAT
1556044 ATTAAATT
1 ATTAAATT
1556052 AAAATCGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 4
0.81 0.00 0.19
Matches are distributed among these distances:
11 11 0.65
13 6 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATTAAATTTATAT
Found at i:1556137 original size:17 final size:19
Alignment explanation
Indices: 1556095--1556137 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1556085 TTAAATTAAA
*
1556095 TTATATATTTTTATTAATT
1 TTATATATTTTTATGAATT
1556114 TTATATATTTTT-TGAATT
1 TTATATATTTTTATGAATT
1556132 TT-TATA
1 TTATATA
1556138 AAATAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 4 0.17
18 7 0.30
19 12 0.52
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TTATATATTTTTATGAATT
Found at i:1556197 original size:22 final size:21
Alignment explanation
Indices: 1556162--1556208 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 21
1556152 TTTTATACTC
*
1556162 AAATTTATTTAAAT-ATATTA
1 AAATTTATTTAAATAATATAA
1556182 AAATTTATATTAAAATAATATAA
1 AAATTTAT-TT-AAATAATATAA
1556205 AAAT
1 AAAT
1556209 AAAAATCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 8 0.35
21 2 0.09
22 4 0.17
23 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AAATTTATTTAAATAATATAA
Found at i:1560131 original size:40 final size:40
Alignment explanation
Indices: 1560076--1560156 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
1560066 GATGCTTGAG
1560076 ACTACAAAATTATCCTTGAAAGCTAGAGGTGAATATTTTT
1 ACTACAAAATTATCCTTGAAAGCTAGAGGTGAATATTTTT
*
1560116 ACTACAAAATTATCCTTGAAAGCTGGAGGTGAATATTTTT
1 ACTACAAAATTATCCTTGAAAGCTAGAGGTGAATATTTTT
1560156 A
1 A
1560157 AGGTCTGGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (40 bp):
ACTACAAAATTATCCTTGAAAGCTAGAGGTGAATATTTTT
Found at i:1566634 original size:3 final size:3
Alignment explanation
Indices: 1566628--1566653 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1566618 TGAAACAACA
1566628 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
1566654 AAAGAGGCGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:1567460 original size:7 final size:7
Alignment explanation
Indices: 1567448--1567473 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1567438 GTGTGAAAAT
1567448 AAAATAA
1 AAAATAA
1567455 AAAATAA
1 AAAATAA
1567462 AAAATAA
1 AAAATAA
1567469 AAAAT
1 AAAAT
1567474 TTTAATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAATAA
Found at i:1567793 original size:28 final size:28
Alignment explanation
Indices: 1567739--1567796 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
1567729 AAATAGTAAT
* *
1567739 AAAAATTATAGTAATTATGATTGAAAAA
1 AAAAATTATAGTAATTATAATTAAAAAA
* * *
1567767 AAAAATTATTGTAGTTGTAATTAAAAAA
1 AAAAATTATAGTAATTATAATTAAAAAA
1567795 AA
1 AA
1567797 TATTTAATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (28 bp):
AAAAATTATAGTAATTATAATTAAAAAA
Found at i:1570682 original size:24 final size:24
Alignment explanation
Indices: 1570655--1570710 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
1570645 GAGTAAAAAA
*
1570655 GAAGATGAAAACGAGGAA-ACGAGT
1 GAAGAAGAAAACGAGGAAGAC-AGT
* *
1570679 GAAGAAGAAGAGGAGGAAGACAGT
1 GAAGAAGAAAACGAGGAAGACAGT
1570703 GAAGAAGA
1 GAAGAAGA
1570711 GGAGAACGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 26 0.93
25 2 0.07
ACGTcount: A:0.52, C:0.05, G:0.38, T:0.05
Consensus pattern (24 bp):
GAAGAAGAAAACGAGGAAGACAGT
Found at i:1575339 original size:10 final size:10
Alignment explanation
Indices: 1575314--1575348 Score: 61
Period size: 10 Copynumber: 3.4 Consensus size: 10
1575304 TTTTAATTGA
1575314 TATATATATAT
1 TATATATAT-T
1575325 TATATATATT
1 TATATATATT
1575335 TATATATATT
1 TATATATATT
1575345 TATA
1 TATA
1575349 CTAGACTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 15 0.62
11 9 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
TATATATATT
Found at i:1576007 original size:28 final size:28
Alignment explanation
Indices: 1575960--1576030 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 28
1575950 AAATAATAAC
*
1575960 TTTATTGATTTAATATAATAAATTAAT-TT
1 TTTATTGA-ATAA-ATAATAAATTAATATT
*
1575989 TATTATAT-AATAAATAATATATTAATATT
1 T-TTAT-TGAATAAATAATAAATTAATATT
1576018 TTTATTGAATAAA
1 TTTATTGAATAAA
1576031 ATTTAAGATT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
27 1 0.03
28 22 0.61
29 7 0.19
30 5 0.14
31 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
TTTATTGAATAAATAATAAATTAATATT
Found at i:1576206 original size:21 final size:21
Alignment explanation
Indices: 1576180--1576225 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1576170 CAACTGATTT
* *
1576180 TAATTTTACAATTATAGTAAC
1 TAATTTCACAATTATAATAAC
*
1576201 TAATTTCACTATTATAATAAC
1 TAATTTCACAATTATAATAAC
1576222 TAAT
1 TAAT
1576226 CTAATTTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.43
Consensus pattern (21 bp):
TAATTTCACAATTATAATAAC
Found at i:1589091 original size:24 final size:25
Alignment explanation
Indices: 1589052--1589115 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 25
1589042 TATATAAAAA
1589052 AATTA-TGTT-TAA-TTTATAT-AT
1 AATTATTGTTATAATTTTATATCAT
*
1589073 AATTATTGTTATAATTTTAAATCAT
1 AATTATTGTTATAATTTTATATCAT
*
1589098 -ATTATTTTTAT-ATTTTAT
1 AATTATTGTTATAATTTTAT
1589116 TTTTATATCG
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
21 5 0.14
22 4 0.11
23 9 0.25
24 16 0.44
25 2 0.06
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (25 bp):
AATTATTGTTATAATTTTATATCAT
Found at i:1589117 original size:13 final size:13
Alignment explanation
Indices: 1589099--1589123 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1589089 TTAAATCATA
1589099 TTATTTTTATATT
1 TTATTTTTATATT
1589112 TTATTTTTATAT
1 TTATTTTTATAT
1589124 CGTATTCGTA
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:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTATTTTTATATT
Found at i:1591666 original size:19 final size:19
Alignment explanation
Indices: 1591642--1591686 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
1591632 TTGTTTCATC
1591642 AGCCATGAAAATAAGAAAG
1 AGCCATGAAAATAAGAAAG
**
1591661 AGCCATGAAAATGTGAAAG
1 AGCCATGAAAATAAGAAAG
1591680 AGACCAT
1 AG-CCAT
1591687 TGTTTCATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.51, C:0.13, G:0.22, T:0.13
Consensus pattern (19 bp):
AGCCATGAAAATAAGAAAG
Found at i:1593231 original size:18 final size:20
Alignment explanation
Indices: 1593200--1593250 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
1593190 ATCTAAAATT
1593200 AATA-AAATATTATT-TGTTA
1 AATATAAATA-TATTATGTTA
* *
1593219 AATATAAA-ATATTATTTTT
1 AATATAAATATATTATGTTA
1593238 AATATAAATATAT
1 AATATAAATATAT
1593251 ATAAAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 4 0.15
19 16 0.59
20 7 0.26
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
AATATAAATATATTATGTTA
Found at i:1593250 original size:20 final size:21
Alignment explanation
Indices: 1593201--1593250 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
1593191 TCTAAAATTA
1593201 ATAAAATATTATTTGTTAAAT
1 ATAAAATATTATTTGTTAAAT
1593222 ATAAAATATTATTT-TT-AAT
1 ATAAAATATTATTTGTTAAAT
1593241 ATAAATATAT
1 ATAAA-ATAT
1593251 ATAAAATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.29
20 6 0.21
21 14 0.50
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
ATAAAATATTATTTGTTAAAT
Found at i:1593758 original size:21 final size:20
Alignment explanation
Indices: 1593731--1593781 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
1593721 ATATATATAA
1593731 ATAATTTTTTAAATAATTTAT
1 ATAATTTTTT-AATAATTTAT
* * *
1593752 TTAATTTTATAATTATTTAT
1 ATAATTTTTTAATAATTTAT
1593772 ATATATTTTT
1 ATA-ATTTTT
1593782 ATATATATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
ATAATTTTTTAATAATTTAT
Found at i:1593782 original size:12 final size:12
Alignment explanation
Indices: 1593767--1593791 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1593757 TTTATAATTA
1593767 TTTATATATATT
1 TTTATATATATT
1593779 TTTATATATATT
1 TTTATATATATT
1593791 T
1 T
1593792 AATTTTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTATATATATT
Found at i:1593783 original size:16 final size:17
Alignment explanation
Indices: 1593764--1593807 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
1593754 AATTTTATAA
1593764 TTATTTATATAT-ATTT
1 TTATTTATATATAATTT
* *
1593780 TTATATATATTTAATTT
1 TTATTTATATATAATTT
1593797 TATATTTATAT
1 T-TATTTATAT
1593808 TAAAAATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 10 0.43
17 5 0.22
18 8 0.35
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTATTTATATATAATTT
Found at i:1594875 original size:21 final size:21
Alignment explanation
Indices: 1594851--1594894 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1594841 TTTGATAATA
1594851 AATTATTAAAAATT-AAAATTT
1 AATTATT-AAAATTAAAAATTT
*
1594872 AATTATTAGAATTAAAAATTT
1 AATTATTAAAATTAAAAATTT
1594893 AA
1 AA
1594895 CATTTTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
AATTATTAAAATTAAAAATTT
Found at i:1594912 original size:27 final size:26
Alignment explanation
Indices: 1594846--1594912 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 26
1594836 TATTTTTTGA
*
1594846 TAATAAATT-ATTAAAAATTAAAATT
1 TAATTAATTGATTAAAAATTAAAATT
*
1594871 TAATT-ATTAGAATTAAAAATTTAACATT
1 TAATTAATT-G-ATTAAAAA-TTAAAATT
*
1594899 TTATTAATTGATTA
1 TAATTAATTGATTA
1594913 TACGATATTG
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
24 3 0.09
25 4 0.12
27 12 0.35
28 12 0.35
29 3 0.09
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (26 bp):
TAATTAATTGATTAAAAATTAAAATT
Found at i:1595398 original size:31 final size:31
Alignment explanation
Indices: 1595363--1595434 Score: 144
Period size: 31 Copynumber: 2.3 Consensus size: 31
1595353 TCAGATCTTA
1595363 TAAAAATTTAATTTAAATTTAAATAAAATTT
1 TAAAAATTTAATTTAAATTTAAATAAAATTT
1595394 TAAAAATTTAATTTAAATTTAAATAAAATTT
1 TAAAAATTTAATTTAAATTTAAATAAAATTT
1595425 TAAAAATTTA
1 TAAAAATTTA
1595435 TAATTTATGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
TAAAAATTTAATTTAAATTTAAATAAAATTT
Found at i:1595422 original size:11 final size:11
Alignment explanation
Indices: 1595365--1595424 Score: 61
Period size: 11 Copynumber: 5.6 Consensus size: 11
1595355 AGATCTTATA
*
1595365 AAAATTTAATT
1 AAAATTTAAAT
*
1595376 TAAATTTAAAT
1 AAAATTTAAAT
*
1595387 AAAATTT-TA-
1 AAAATTTAAAT
*
1595396 AAAATTTAATT
1 AAAATTTAAAT
*
1595407 TAAATTTAAAT
1 AAAATTTAAAT
1595418 AAAATTT
1 AAAATTT
1595425 TAAAAATTTA
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
9 7 0.18
10 1 0.03
11 30 0.79
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
AAAATTTAAAT
Found at i:1599249 original size:40 final size:40
Alignment explanation
Indices: 1599194--1599274 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
1599184 GATGCTTGAG
1599194 ACTACAAAATTATCCTTGAAAGCTAGAGGTGAATATTTTT
1 ACTACAAAATTATCCTTGAAAGCTAGAGGTGAATATTTTT
*
1599234 ACTACAAAATTATCCTTGAAAGCTGGAGGTGAATATTTTT
1 ACTACAAAATTATCCTTGAAAGCTAGAGGTGAATATTTTT
1599274 A
1 A
1599275 AGGTCTGGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (40 bp):
ACTACAAAATTATCCTTGAAAGCTAGAGGTGAATATTTTT
Found at i:1607372 original size:106 final size:106
Alignment explanation
Indices: 1607157--1607355 Score: 301
Period size: 106 Copynumber: 1.9 Consensus size: 106
1607147 TTAATTTATC
* *
1607157 TTTTTATTAGTCTATTATTGCTAATTGTTATAAAAACTAACATACTTTTTCTGATGATAGGTATC
1 TTTTTATTAGTCTATTATTGCTAATTGTTATAAAAACTAACATACTTTTTCTAATGATAGCTATC
* *
1607222 ATTTTACTAAATATATTATTCACTCCATCAGACATGATTTT
66 ATTTCACTAAATATACTATTCACTCCATCAGACATGATTTT
* * *
1607263 TTTTTATTAGTCTATTTTTGCTAATTGTTAT-AGAACTTAACATGCTTTTTCTAATGATAGCTAT
1 TTTTTATTAGTCTATTATTGCTAATTGTTATAAAAAC-TAACATACTTTTTCTAATGATAGCTAT
* *
1607327 TATTTCACTAAATATACTATTTACTCCAT
65 CATTTCACTAAATATACTATTCACTCCAT
1607356 GTAAGATTTT
Statistics
Matches: 83, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
105 4 0.05
106 79 0.95
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.48
Consensus pattern (106 bp):
TTTTTATTAGTCTATTATTGCTAATTGTTATAAAAACTAACATACTTTTTCTAATGATAGCTATC
ATTTCACTAAATATACTATTCACTCCATCAGACATGATTTT
Found at i:1607846 original size:17 final size:17
Alignment explanation
Indices: 1607803--1607846 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
1607793 AACTAAATAG
* *
1607803 ATAAAATTATTATTTAA
1 ATAAAATTATGAATTAA
* *
1607820 ATATATTTATGAATTAA
1 ATAAAATTATGAATTAA
1607837 ATAAAATTAT
1 ATAAAATTAT
1607847 ATAACTTGAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
ATAAAATTATGAATTAA
Found at i:1608875 original size:20 final size:21
Alignment explanation
Indices: 1608823--1608877 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
1608813 TTAATTAAAA
*
1608823 ATTTTAATTTTATTATTTGAT
1 ATTTTAATTATATTATTTGAT
1608844 ATTTTAATTATATTATTT-AT
1 ATTTTAATTATATTATTTGAT
1608864 ATTTTACA-TATATT
1 ATTTTA-ATTATATT
1608878 TTGAACATGA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (21 bp):
ATTTTAATTATATTATTTGAT
Found at i:1612604 original size:24 final size:24
Alignment explanation
Indices: 1612533--1612620 Score: 72
Period size: 24 Copynumber: 3.5 Consensus size: 24
1612523 TGAGGAAGGT
*
1612533 AGTGAAGCAGAAGAGGAGGAAA-G
1 AGTGAAGAAGAAGAGGAGGAAACG
* *
1612556 AGTAAAAAAGAAGATGAAAACGAGGAAACG
1 AGTGAAGAAGAAGA-G-----GAGGAAACG
1612586 AGTGAAGAAGAAGAGGAGGAAGAC-
1 AGTGAAGAAGAAGAGGAGGAA-ACG
1612610 AGTGAAGAAGA
1 AGTGAAGAAGA
1612621 GGAGAACGAC
Statistics
Matches: 52, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
23 11 0.21
24 18 0.35
25 2 0.04
29 8 0.15
30 13 0.25
ACGTcount: A:0.53, C:0.05, G:0.36, T:0.06
Consensus pattern (24 bp):
AGTGAAGAAGAAGAGGAGGAAACG
Found at i:1617872 original size:21 final size:21
Alignment explanation
Indices: 1617831--1617873 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1617821 TATTGATTTA
*
1617831 ATATAATAAATTAATTTTATT
1 ATATAATAAATTAATTATATT
1617852 ATATAATAAA-TAATATATATT
1 ATATAATAAATTAAT-TATATT
1617873 A
1 A
1617874 ATATTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATATAATAAATTAATTATATT
Found at i:1617890 original size:30 final size:27
Alignment explanation
Indices: 1617819--1617891 Score: 67
Period size: 30 Copynumber: 2.5 Consensus size: 27
1617809 AAATAATAAC
*
1617819 TTTATTGATTTAATATAATAAATTAATTT
1 TTTATTGA-ATAA-ATAATAAATTAATTT
1617848 TATTATAT-AATAAATAATATATATTAATATT
1 T-TTAT-TGAATAAATAATA-A-ATTAAT-TT
1617879 TTTATTGAATAAA
1 TTTATTGAATAAA
1617892 ATTTAAGATT
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
28 6 0.16
29 6 0.16
30 21 0.57
31 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.51
Consensus pattern (27 bp):
TTTATTGAATAAATAATAAATTAATTT
Found at i:1618067 original size:21 final size:21
Alignment explanation
Indices: 1618042--1618089 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
1618032 CAACTGATTT
*
1618042 TAATTTTACCATTACAGTAAC
1 TAATTTTACCATTACAATAAC
* *
1618063 TAATTTTACTATTATAATAAC
1 TAATTTTACCATTACAATAAC
1618084 TAATTT
1 TAATTT
1618090 AATTTTCATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.46
Consensus pattern (21 bp):
TAATTTTACCATTACAATAAC
Done.