Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 63 of 125
Found at i:19310190 original size:7 final size:7
Alignment explanation
Indices: 19310180--19310204 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
19310170 AACCCTAATT
19310180 TCCATCA
1 TCCATCA
19310187 TCCATCA
1 TCCATCA
19310194 TCCATCA
1 TCCATCA
19310201 TCCA
1 TCCA
19310205 CCAACCACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.44, G:0.00, T:0.28
Consensus pattern (7 bp):
TCCATCA
Found at i:19316268 original size:16 final size:16
Alignment explanation
Indices: 19316210--19316290 Score: 58
Period size: 16 Copynumber: 4.9 Consensus size: 16
19316200 CATCACTCTT
*
19316210 ACTTTCTTTTTCCTCTC
1 ACTTTCTTTTT-CTTTC
* *
19316227 ACTCTCTTTTTGTTTC
1 ACTTTCTTTTTCTTTC
19316243 AGC-TTC-TTTTCTTTC
1 A-CTTTCTTTTTCTTTC
* *
19316258 ATTTTCTTTTTCATTC
1 ACTTTCTTTTTCTTTC
19316274 ACAATTTCTTGTTTCTT
1 AC--TTTCTT-TTTCTT
19316291 CCTCTCCAAC
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
15 12 0.24
16 15 0.31
17 11 0.22
18 6 0.12
19 5 0.10
ACGTcount: A:0.10, C:0.25, G:0.04, T:0.62
Consensus pattern (16 bp):
ACTTTCTTTTTCTTTC
Found at i:19316443 original size:21 final size:20
Alignment explanation
Indices: 19316383--19316440 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
19316373 TCTCTTTCAA
19316383 TTTATTTTT-ATCTCATTTCT
1 TTTATTTTTCA-CTCATTTCT
* * *
19316403 TTT-TTCTTCTCTCAAATTCT
1 TTTATTTTTCACTC-ATTTCT
19316423 TTTATTTTTCACTCATTT
1 TTTATTTTTCACTCATTT
19316441 TCTCTCATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
19 7 0.24
20 14 0.48
21 8 0.28
ACGTcount: A:0.16, C:0.19, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTATTTTTCACTCATTTCT
Found at i:19320000 original size:21 final size:22
Alignment explanation
Indices: 19319976--19320017 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
19319966 ATCAAAAAGA
19319976 AAAAGAAAAATGAGT-AGAAAC
1 AAAAGAAAAATGAGTAAGAAAC
**
19319997 AAAAGAAGCATGAGTAAGAAA
1 AAAAGAAAAATGAGTAAGAAA
19320018 GCATGTGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.64, C:0.05, G:0.21, T:0.10
Consensus pattern (22 bp):
AAAAGAAAAATGAGTAAGAAAC
Found at i:19334589 original size:25 final size:25
Alignment explanation
Indices: 19334550--19334726 Score: 147
Period size: 25 Copynumber: 7.0 Consensus size: 25
19334540 ATTTAGCTTA
* *
19334550 TACGAGCCCAGACAGATTTACGCTCT
1 TACGAG-CCAAACAGAATTACGCTCT
*
19334576 TATGAGCCAAACAGAATTACGCTCT
1 TACGAGCCAAACAGAATTACGCTCT
* * * *
19334601 TACGAGCCAGACAAAAATTTCACTCT
1 TACGAGCCAAAC-AGAATTACGCTCT
* * * *
19334627 TACGAGCCAGACAAAATTACACTTT
1 TACGAGCCAAACAGAATTACGCTCT
* * * *
19334652 TACAAGCCAGATAGAAATTTCGCTCT
1 TACGAGCCAAACAG-AATTACGCTCT
* *
19334678 CACGAGCCAAACAGAATTTCGCTCT
1 TACGAGCCAAACAGAATTACGCTCT
* * *
19334703 CACGAGCCAAATAGAATTTCGCTC
1 TACGAGCCAAACAGAATTACGCTC
19334727 GTAAATTACG
Statistics
Matches: 128, Mismatches: 21, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
25 83 0.65
26 45 0.35
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.23
Consensus pattern (25 bp):
TACGAGCCAAACAGAATTACGCTCT
Found at i:19334605 original size:51 final size:49
Alignment explanation
Indices: 19334550--19334726 Score: 165
Period size: 51 Copynumber: 3.5 Consensus size: 49
19334540 ATTTAGCTTA
*
19334550 TACGAGCCCAGACAGATTTACGCTCTTATGAGCCAAACAGAATTACGCTCT
1 TACGAG-CCAGACAGATTT-CGCTCTTACGAGCCAAACAGAATTACGCTCT
* * * * * *
19334601 TACGAGCCAGACAAAAATTTCACTCTTACGAGCCAGACAAAATTACACTTT
1 TACGAGCCAGAC--AGATTTCGCTCTTACGAGCCAAACAGAATTACGCTCT
* * * *
19334652 TACAAGCCAGATAGAAATTTCGCTCTCACGAGCCAAACAGAATTTCGCTCT
1 TACGAGCCAGACAG--ATTTCGCTCTTACGAGCCAAACAGAATTACGCTCT
* * *
19334703 CACGAGCCAAATAGAATTTCGCTC
1 TACGAGCCAGACAG-ATTTCGCTC
19334727 GTAAATTACG
Statistics
Matches: 102, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
49 1 0.01
50 16 0.16
51 80 0.78
52 5 0.05
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.23
Consensus pattern (49 bp):
TACGAGCCAGACAGATTTCGCTCTTACGAGCCAAACAGAATTACGCTCT
Found at i:19340898 original size:28 final size:28
Alignment explanation
Indices: 19340855--19340914 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
19340845 ACATCTACCG
*
19340855 AAACAAGTCATGCTTCTACTGATACTAA
1 AAACAAGTCATACTTCTACTGATACTAA
19340883 AAACAAGTCATACTTCTACTGATACTAA
1 AAACAAGTCATACTTCTACTGATACTAA
19340911 AAAC
1 AAAC
19340915 TTCTACCGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.27
Consensus pattern (28 bp):
AAACAAGTCATACTTCTACTGATACTAA
Found at i:19341610 original size:25 final size:25
Alignment explanation
Indices: 19341582--19341751 Score: 144
Period size: 25 Copynumber: 6.7 Consensus size: 25
19341572 CCAGACATAT
19341582 TTACGCTCTTACGAGCCAAACAGAA
1 TTACGCTCTTACGAGCCAAACAGAA
19341607 TTACGCTCTTACGAGCCAAACAGAAA
1 TTACGCTCTTACGAGCCAAACAG-AA
*** * * *
19341633 TTATAATCTTAAGAGCTAGAGA-AAAA
1 TTACGCTCTTACGAGCCA-A-ACAGAA
* * * *
19341659 TTTCGCTCTTATGAGCTAAATAGAA
1 TTACGCTCTTACGAGCCAAACAGAA
* ** *
19341684 TTACACTCTTTTGAGCCACACAGAA
1 TTACGCTCTTACGAGCCAAACAGAA
* * * *
19341709 TTACGCTCTTACGAGCTAGATAAAA
1 TTACGCTCTTACGAGCCAAACAGAA
19341734 TTACGCTCTTACGAGCCA
1 TTACGCTCTTACGAGCCA
19341752 GAATTCAAAA
Statistics
Matches: 115, Mismatches: 26, Indels: 8
0.77 0.17 0.05
Matches are distributed among these distances:
24 1 0.01
25 81 0.70
26 30 0.26
27 2 0.02
28 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.26
Consensus pattern (25 bp):
TTACGCTCTTACGAGCCAAACAGAA
Found at i:19345735 original size:18 final size:18
Alignment explanation
Indices: 19345709--19345743 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19345699 TAGAAAAGCG
*
19345709 AAAGATTTTTAAGGTTTC
1 AAAGATTTTTAAAGTTTC
*
19345727 AAAGGTTTTTAAAGTTT
1 AAAGATTTTTAAAGTTT
19345744 TAAAATGTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.03, G:0.17, T:0.46
Consensus pattern (18 bp):
AAAGATTTTTAAAGTTTC
Found at i:19346933 original size:24 final size:23
Alignment explanation
Indices: 19346891--19346968 Score: 93
Period size: 24 Copynumber: 3.3 Consensus size: 23
19346881 TTTAGCCCAC
*
19346891 ACGAGCCCAAATGGGTAGCTCTT
1 ACGAGCCCAAATGGTTAGCTCTT
*
19346914 ATGAGCCCAAAATGGTTAGCTCTT
1 ACGAGCCC-AAATGGTTAGCTCTT
* * *
19346938 ACGAGCCCGGAATTGTTAGTTCTT
1 ACGAGCCC-AAATGGTTAGCTCTT
19346962 ACGAGCC
1 ACGAGCC
19346969 TAGACAGAGT
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 7 0.15
24 40 0.85
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (23 bp):
ACGAGCCCAAATGGTTAGCTCTT
Found at i:19361325 original size:48 final size:48
Alignment explanation
Indices: 19361268--19361410 Score: 223
Period size: 48 Copynumber: 3.0 Consensus size: 48
19361258 GATATAGATG
* *
19361268 TATTAAAGCAAAACATTAAATAAAGATGCATTTAACAAACAAAACACA
1 TATTGAAGCAAAACATTAAACAAAGATGCATTTAACAAACAAAACACA
*
19361316 TATTGAAGCAAATCATTAAACAAAGATGCATTTAACAAACAAAACACA
1 TATTGAAGCAAAACATTAAACAAAGATGCATTTAACAAACAAAACACA
* * *
19361364 TAATGATGCAGAACATTAAACAAAGATGCATTTAACCAAACAAAACA
1 TATTGAAGCAAAACATTAAACAAAGATGCATTTAA-CAAACAAAACA
19361411 TATAATTAAA
Statistics
Matches: 87, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
48 76 0.87
49 11 0.13
ACGTcount: A:0.55, C:0.16, G:0.08, T:0.20
Consensus pattern (48 bp):
TATTGAAGCAAAACATTAAACAAAGATGCATTTAACAAACAAAACACA
Found at i:19363917 original size:15 final size:16
Alignment explanation
Indices: 19363897--19363930 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
19363887 CAGAAATTGA
19363897 TTTTTTTAACTC-AAT
1 TTTTTTTAACTCGAAT
*
19363912 TTTTTTTAATTCGAAT
1 TTTTTTTAACTCGAAT
19363928 TTT
1 TTT
19363931 CCCTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.24, C:0.09, G:0.03, T:0.65
Consensus pattern (16 bp):
TTTTTTTAACTCGAAT
Found at i:19363951 original size:23 final size:21
Alignment explanation
Indices: 19363912--19363960 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
19363902 TTAACTCAAT
19363912 TTTTTTTAATTCGAATTTTCCC
1 TTTTTTTAATTCGAATTTT-CC
**
19363934 TTTTTTTAATTTTTAATTTTCC
1 TTTTTTTAA-TTCGAATTTTCC
19363956 TTTTT
1 TTTTT
19363961 ATCATAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.16, C:0.12, G:0.02, T:0.69
Consensus pattern (21 bp):
TTTTTTTAATTCGAATTTTCC
Found at i:19365260 original size:75 final size:75
Alignment explanation
Indices: 19365100--19365263 Score: 190
Period size: 75 Copynumber: 2.2 Consensus size: 75
19365090 ATTCAATATG
* * * *
19365100 AAAATCACATAATGCATGTATTAAATGATGCTAATGTATTAATGTAAAGCATTAAGTAAATACGC
1 AAAA-CACATAATGCAAGTATTAAAAGATGCTAATGTATTAATGTAAAGCATTAAATAAAGACGC
*
19365165 ATTCAATAAAC
65 ATTCAACAAAC
* *
19365176 AAGAA-ACATAATGCAAGTTTTAAAAGAT-TTAGATGTATTAATGCTAAA-CATTAAATAAAGAC
1 AA-AACACATAATGCAAGTATTAAAAGATGCTA-ATGTATTAATG-TAAAGCATTAAATAAAGAC
* *
19365238 GCATTTAACAGAC
63 GCATTCAACAAAC
19365251 AAAACACATAATG
1 AAAACACATAATG
19365264 AAGCAAATCA
Statistics
Matches: 75, Mismatches: 9, Indels: 9
0.81 0.10 0.10
Matches are distributed among these distances:
74 4 0.05
75 63 0.84
76 6 0.08
77 2 0.03
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (75 bp):
AAAACACATAATGCAAGTATTAAAAGATGCTAATGTATTAATGTAAAGCATTAAATAAAGACGCA
TTCAACAAAC
Found at i:19365276 original size:48 final size:47
Alignment explanation
Indices: 19365222--19365357 Score: 148
Period size: 48 Copynumber: 2.8 Consensus size: 47
19365212 ATTAATGCTA
* *
19365222 AACATTAAATAAAGACGCATTTAACAGACAAAACACATAATGAAGCA-
1 AACATTAAACAAAGA-GCATTTAACAAACAAAACACATAATGAAGCAG
* ** * *
19365269 AATCATTAAACAAATATTATTTTAACAAACAAAACAGATAATGATGCAG
1 AA-CATTAAACAAAGAGCA-TTTAACAAACAAAACACATAATGAAGCAG
* *
19365318 AACATTAAACAAAGATGCATTTAATAAAAAAAACACATAA
1 AACATTAAACAAAGA-GCATTTAACAAACAAAACACATAA
19365358 CTAAAAACTG
Statistics
Matches: 72, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
47 3 0.04
48 66 0.92
49 3 0.04
ACGTcount: A:0.57, C:0.14, G:0.08, T:0.21
Consensus pattern (47 bp):
AACATTAAACAAAGAGCATTTAACAAACAAAACACATAATGAAGCAG
Found at i:19366805 original size:19 final size:18
Alignment explanation
Indices: 19366750--19366845 Score: 86
Period size: 19 Copynumber: 5.1 Consensus size: 18
19366740 CAGTAATTTT
*
19366750 CTCTTACGAGCCAGTGTCG
1 CTCTTACGAGCCA-TATCG
* * *
19366769 CTTTTATGAGCTAGTATCG
1 CTCTTACGAGCCA-TATCG
*
19366788 CTCTTACAAGCCTATATCG
1 CTCTTACGAGCC-ATATCG
19366807 CTCTTACGAGCCAATAT-G
1 CTCTTACGAGCC-ATATCG
*
19366825 CCCTTACGAGCCAGTATCG
1 CTCTTACGAGCCA-TATCG
19366844 CT
1 CT
19366846 ATTCCTTCCA
Statistics
Matches: 62, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
17 1 0.02
18 15 0.24
19 45 0.73
20 1 0.02
ACGTcount: A:0.22, C:0.29, G:0.19, T:0.30
Consensus pattern (18 bp):
CTCTTACGAGCCATATCG
Found at i:19370508 original size:17 final size:17
Alignment explanation
Indices: 19370487--19370533 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
19370477 GAAATCTAAC
19370487 GACAATGAAAATGC-GA
1 GACAATGAAAATGCAGA
19370503 GAACAA-GTAAAATGCAGA
1 G-ACAATG-AAAATGCAGA
*
19370521 GACAATAAAAATG
1 GACAATGAAAATG
19370534 TAATGACAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 2 0.08
17 21 0.81
18 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.21, T:0.13
Consensus pattern (17 bp):
GACAATGAAAATGCAGA
Found at i:19370956 original size:9 final size:9
Alignment explanation
Indices: 19370942--19370976 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
19370932 AGGCAACGTC
19370942 TTCTTCTTT
1 TTCTTCTTT
*
19370951 TTCTTCCTT
1 TTCTTCTTT
*
19370960 CTCTTCTTT
1 TTCTTCTTT
19370969 TTCTTCTT
1 TTCTTCTT
19370977 CTTGTCTTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (9 bp):
TTCTTCTTT
Found at i:19370993 original size:18 final size:17
Alignment explanation
Indices: 19370943--19370993 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 17
19370933 GGCAACGTCT
19370943 TCTTCTTTTTCTTCCTTC
1 TCTTCTTTTTCTT-CTTC
19370961 TCTTCTTTTTCTTCTTC
1 TCTTCTTTTTCTTCTTC
19370978 T-TGTCTTTCTTCTTCT
1 TCT-TCTTT-TTCTTCT
19370994 GCCTCAATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.03
17 10 0.32
18 20 0.65
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.69
Consensus pattern (17 bp):
TCTTCTTTTTCTTCTTC
Found at i:19379255 original size:18 final size:19
Alignment explanation
Indices: 19379232--19379277 Score: 78
Period size: 18 Copynumber: 2.5 Consensus size: 19
19379222 AACATAACAT
19379232 CTTCAACATCT-CTTTTTG
1 CTTCAACATCTACTTTTTG
19379250 CTTCAACAT-TACTTTTTG
1 CTTCAACATCTACTTTTTG
19379268 CTTCAACATC
1 CTTCAACATC
19379278 CAACTCTGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 1 0.04
18 25 0.96
ACGTcount: A:0.22, C:0.28, G:0.04, T:0.46
Consensus pattern (19 bp):
CTTCAACATCTACTTTTTG
Found at i:19385977 original size:5 final size:5
Alignment explanation
Indices: 19385967--19385991 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
19385957 CTTTGTTCAT
19385967 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
19385992 GCACGTTGCT
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:19396681 original size:13 final size:13
Alignment explanation
Indices: 19396663--19396687 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19396653 CCCTTTATAT
19396663 CATTTTTAGCATG
1 CATTTTTAGCATG
19396676 CATTTTTAGCAT
1 CATTTTTAGCAT
19396688 TTCATACTTA
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:0.12, T:0.48
Consensus pattern (13 bp):
CATTTTTAGCATG
Found at i:19415715 original size:158 final size:160
Alignment explanation
Indices: 19415421--19415742 Score: 549
Period size: 158 Copynumber: 2.0 Consensus size: 160
19415411 GTTACTTCCC
*
19415421 AGGAACAAGAGTATAGTAATGCAACGACATCCCTCAGTCACATAAAAAAAATAAAAGAAGAAAAA
1 AGGAACAAGAGTATAGTAAAGCAACGACATCCCTCAGTCAC----AAAAAATAAAAGAAGAAAAA
*
19415486 AATATACATGTACATATTACTGTATAATAAATGTTGTTTTGGGAGAAAGAATTTAAGATTTAAAG
62 AATATACATGTACATATTACTGTATAATAAATGCTGTTTTGGGAGAAAGAATTTAAGATTTAAAG
* *
19415551 TATGATGTTAGCATTGATGAAGTTGAAATTTTAA
127 TATGATGCTAGCATTGATGAAATTGAAATTTTAA
19415585 AGGAACAAGAGTATAGTAAAGCAACGACATCCCTCAGTCAC-AAAAA-AAAAGAAGAAAAAAATA
1 AGGAACAAGAGTATAGTAAAGCAACGACATCCCTCAGTCACAAAAAATAAAAGAAGAAAAAAATA
19415648 TACATGTACATATTACTGTATAATAAATGCTGTTTTGGGAGAAAGAATTTAAGATTTAAAGTATG
66 TACATGTACATATTACTGTATAATAAATGCTGTTTTGGGAGAAAGAATTTAAGATTTAAAGTATG
*
19415713 ATGCTAGCATTGATGAAATTGCAATTTTAA
131 ATGCTAGCATTGATGAAATTGAAATTTTAA
19415743 TTATTCATAC
Statistics
Matches: 153, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
158 108 0.71
159 5 0.03
164 40 0.26
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.28
Consensus pattern (160 bp):
AGGAACAAGAGTATAGTAAAGCAACGACATCCCTCAGTCACAAAAAATAAAAGAAGAAAAAAATA
TACATGTACATATTACTGTATAATAAATGCTGTTTTGGGAGAAAGAATTTAAGATTTAAAGTATG
ATGCTAGCATTGATGAAATTGAAATTTTAA
Found at i:19417594 original size:20 final size:19
Alignment explanation
Indices: 19417570--19417617 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
19417560 TTTTTGACCC
* *
19417570 AAATTAATTATTTTCTCTA
1 AAATTAATTAATTACTCTA
* *
19417589 ATAATTATTTAATTACTTTA
1 A-AATTAATTAATTACTCTA
19417609 AAATTAATT
1 AAATTAATT
19417618 TTTCAAAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (19 bp):
AAATTAATTAATTACTCTA
Found at i:19423070 original size:27 final size:26
Alignment explanation
Indices: 19423006--19423075 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 26
19422996 TTATCTTTAC
*
19423006 AGAGTTTTCCACAAAGGCGGTTCTTA
1 AGAGTTTTCCACAAAGGCGATTCTTA
*** *
19423032 AGAGTGCACCACAAAGGC-ATTCCTTTT
1 AGAGTTTTCCACAAAGGCGATT-C-TTA
19423059 AGAGTTTTCCACAAAGG
1 AGAGTTTTCCACAAAGG
19423076 TAGTTTCTTT
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
25 2 0.06
26 16 0.47
27 16 0.47
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.27
Consensus pattern (26 bp):
AGAGTTTTCCACAAAGGCGATTCTTA
Found at i:19423086 original size:27 final size:26
Alignment explanation
Indices: 19423006--19423090 Score: 73
Period size: 27 Copynumber: 3.2 Consensus size: 26
19422996 TTATCTTTAC
* * *
19423006 AGAGTTTTCCACAAAGGCGGTTCTTA
1 AGAGTTTTCCACAAAGGAGTTTCTTT
*** *
19423032 AGAGTGCACCACAAAGGCA-TTCCTTTT
1 AGAGTTTTCCACAAAGG-AGTTTC-TTT
19423059 AGAGTTTTCCACAAAGGTAGTTTCTTT
1 AGAGTTTTCCACAAAGG-AGTTTCTTT
19423086 AGAGT
1 AGAGT
19423091 GCGCCATAAA
Statistics
Matches: 44, Mismatches: 12, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
26 16 0.36
27 25 0.57
28 3 0.07
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (26 bp):
AGAGTTTTCCACAAAGGAGTTTCTTT
Found at i:19426711 original size:31 final size:31
Alignment explanation
Indices: 19426676--19426736 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
19426666 TTTCATTTTG
* *
19426676 TCACTCAATTTTTCGAAATTAAATATTTTAA
1 TCACTCAACTTTTCAAAATTAAATATTTTAA
*
19426707 TCACTTAACTTTTCAAAATTAAATATTTTA
1 TCACTCAACTTTTCAAAATTAAATATTTTA
19426737 GTTATTATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.39, C:0.13, G:0.02, T:0.46
Consensus pattern (31 bp):
TCACTCAACTTTTCAAAATTAAATATTTTAA
Found at i:19427277 original size:13 final size:13
Alignment explanation
Indices: 19427259--19427284 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19427249 AAAGAAAATC
19427259 AAAAATTAATTTT
1 AAAAATTAATTTT
19427272 AAAAATTAATTTT
1 AAAAATTAATTTT
19427285 TTTAAATAAT
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAAAATTAATTTT
Found at i:19429032 original size:17 final size:17
Alignment explanation
Indices: 19428998--19429059 Score: 65
Period size: 18 Copynumber: 3.7 Consensus size: 17
19428988 CATATTATAT
*
19428998 TTTATTTTTTTTTAAATA
1 TTTATTTTATTTT-AATA
19429016 TTTATTTTATTTTAATA
1 TTTATTTTATTTTAATA
* *
19429033 TTTA-ATAATTTT-ATA
1 TTTATTTTATTTTAATA
*
19429048 TTTTTTTTATTT
1 TTTATTTTATTT
19429060 ATTAATAATT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
15 6 0.16
16 11 0.30
17 8 0.22
18 12 0.32
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTATTTTATTTTAATA
Found at i:19429049 original size:28 final size:30
Alignment explanation
Indices: 19429018--19429087 Score: 85
Period size: 28 Copynumber: 2.4 Consensus size: 30
19429008 TTTAAATATT
19429018 TATTTTATTTTAATAT-TTAATAA-TTTTA
1 TATTTTATTTTAATATATTAATAATTTTTA
*
19429046 TATTTT-TTTT-ATTTATTAATAATTTTTA
1 TATTTTATTTTAATATATTAATAATTTTTA
*
19429074 TATAGTTATTTTAA
1 TAT-TTTATTTTAA
19429088 AATTATTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
26 3 0.09
27 11 0.31
28 14 0.40
29 2 0.06
30 4 0.11
31 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (30 bp):
TATTTTATTTTAATATATTAATAATTTTTA
Found at i:19429123 original size:14 final size:15
Alignment explanation
Indices: 19429106--19429138 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
19429096 TAATCTTCAC
19429106 ATTTAGTAT-TGTAT
1 ATTTAGTATATGTAT
*
19429120 ATTTAGTATATGTTT
1 ATTTAGTATATGTAT
19429135 ATTT
1 ATTT
19429139 TTTAATGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (15 bp):
ATTTAGTATATGTAT
Found at i:19430913 original size:2 final size:2
Alignment explanation
Indices: 19430906--19430937 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
19430896 TTTATTATTC
19430906 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
19430938 TTGTAATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19438194 original size:5 final size:5
Alignment explanation
Indices: 19438184--19438213 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
19438174 AAAGACTTGG
19438184 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
19438214 AAATATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:19439507 original size:18 final size:17
Alignment explanation
Indices: 19439476--19439519 Score: 63
Period size: 16 Copynumber: 2.5 Consensus size: 17
19439466 ATGCCTTTCT
19439476 TTTTTATTTTTCATTTA
1 TTTTTATTTTTCATTTA
19439493 -TTTTATTTATCTCATTTA
1 TTTTTATTT-T-TCATTTA
19439511 TTTTTATTT
1 TTTTTATTT
19439520 CATGCTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.33
17 1 0.04
18 7 0.29
19 8 0.33
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTTATTTTTCATTTA
Found at i:19439545 original size:17 final size:17
Alignment explanation
Indices: 19439477--19439557 Score: 57
Period size: 17 Copynumber: 5.1 Consensus size: 17
19439467 TGCCTTTCTT
*
19439477 TTTTATTTTTCATTT-A
1 TTTTATTTTTTATTTCA
*
19439493 TTTTA---TTTATCTCA
1 TTTTATTTTTTATTTCA
19439507 -TTTA-TTTTTATTTCA
1 TTTTATTTTTTATTTCA
** *
19439522 TGCTATTTTTTATTTTA
1 TTTTATTTTTTATTTCA
*
19439539 TTTTATTTTATTTTTTCA
1 TTTTATTTT-TTATTTCA
19439557 T
1 T
19439558 GATTGTGGAT
Statistics
Matches: 49, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
13 9 0.18
14 1 0.02
15 8 0.16
16 7 0.14
17 17 0.35
18 7 0.14
ACGTcount: A:0.19, C:0.07, G:0.01, T:0.73
Consensus pattern (17 bp):
TTTTATTTTTTATTTCA
Found at i:19439550 original size:22 final size:22
Alignment explanation
Indices: 19439477--19439554 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 22
19439467 TGCCTTTCTT
*
19439477 TTTTATTTTTCA-TTTATTTTA
1 TTTTATTTTTTATTTTATTTTA
* *
19439498 -TTTATCTCATTTATTTTTATTTCA
1 TTTTAT-T-TTTTA-TTTTATTTTA
**
19439522 TGCTATTTTTTATTTTATTTTA
1 TTTTATTTTTTATTTTATTTTA
19439544 TTTTATTTTTT
1 TTTTATTTTTT
19439555 CATGATTGTG
Statistics
Matches: 43, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
20 5 0.12
21 1 0.02
22 21 0.49
23 4 0.09
24 9 0.21
25 3 0.07
ACGTcount: A:0.18, C:0.06, G:0.01, T:0.74
Consensus pattern (22 bp):
TTTTATTTTTTATTTTATTTTA
Found at i:19439612 original size:3 final size:3
Alignment explanation
Indices: 19439604--19439644 Score: 66
Period size: 3 Copynumber: 13.7 Consensus size: 3
19439594 ATTGATTAAC
19439604 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TT
19439645 TGCTTAATTG
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:19440265 original size:109 final size:109
Alignment explanation
Indices: 19440074--19440278 Score: 320
Period size: 109 Copynumber: 1.9 Consensus size: 109
19440064 TAATTTTATT
* * * *
19440074 TTATTTTTGAGAATTCGAGAAATTGTGCCATAACGTATTAGGTATGATTTTTCTTTGAACCTAAA
1 TTATTTTAGAGAAATCGAGAAATTGTGCCATAACGTATTAGGTATAATTTTTCCTTGAACCTAAA
*
19440139 TAATTGAGTATCCTATTTAAAATCGATAAATACTCAATGTTCTG
66 TAATTGAATATCCTATTTAAAATCGATAAATACTCAATGTTCTG
* * * *
19440183 TTATTTTAGGGAAATCGAGAAATTGTGCCCTAACGTGTTGGGTATAATTTTTCCTTGAACCTAAA
1 TTATTTTAGAGAAATCGAGAAATTGTGCCATAACGTATTAGGTATAATTTTTCCTTGAACCTAAA
*
19440248 TAATTGAATATCCTATTTAAAATTGATAAAT
66 TAATTGAATATCCTATTTAAAATCGATAAAT
19440279 GTTCTTTGTT
Statistics
Matches: 86, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
109 86 1.00
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.40
Consensus pattern (109 bp):
TTATTTTAGAGAAATCGAGAAATTGTGCCATAACGTATTAGGTATAATTTTTCCTTGAACCTAAA
TAATTGAATATCCTATTTAAAATCGATAAATACTCAATGTTCTG
Found at i:19449693 original size:28 final size:28
Alignment explanation
Indices: 19449652--19449706 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
19449642 GATATCTGAT
*
19449652 TTACTCCCTATTGACCCAAAGTTCATGC
1 TTACTCCCTATTGACCCAAAGGTCATGC
* *
19449680 TTACTCTCTGTTGACCCAAAGGTCATG
1 TTACTCCCTATTGACCCAAAGGTCATG
19449707 ATGCTCATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.33
Consensus pattern (28 bp):
TTACTCCCTATTGACCCAAAGGTCATGC
Found at i:19452927 original size:42 final size:42
Alignment explanation
Indices: 19452879--19453713 Score: 891
Period size: 42 Copynumber: 20.4 Consensus size: 42
19452869 ACAAAGCTAC
* * *
19452879 CATCCAATCTCTTACCTCTATCATGGTGCAGATTGAAGACAT
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACAT
*
19452921 CATCCAATCTCTTACCCCGGTCATGGGGCAGATTGAAG---T
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACAT
* * *** *
19452960 CATCCTATCTCTTACCCCGACCATGAAACAAATTGAAG-C--
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACAT
* *
19452999 CATCCAATCTCTTACCCCGATCATGGTGCAAATTGAAGACAT
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACAT
* * * * *
19453041 CATATCTAATCTCTTACCCCGATCATGTGGTAGATTGAAGCCAC
1 C--ATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACAT
* * *
19453085 CATCCAATCTCTTACCCCGA-CGATAGGCCAGATTAAAG-C--
1 CATCCAATCTCTTACCCCGATC-ATGGGGCAGATTGAAGACAT
* *
19453124 CATCCAATCTCTTACCCTGATCATGGGGCATATTGAAGACAT
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACAT
* *
19453166 CATCCAATCTCTTA-CCCGACCATGGGGCATATTGAAGACAT
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACAT
* * * *
19453207 CATCCAATCCCTTA-CCCGACCATGGGGCAAATTGAAAACAT
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACAT
* *
19453248 CATCCAATCTCTTACCCCGATCATGGGGTAGATTGAAAACAT
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACAT
* * * *
19453290 -ATCCAATCTCTTAACTCTACCATGGGGCAGATTGAAG---T
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACAT
* **
19453328 CATCCAATCTCTTACCCTGATCATAAGGCAGATTG-A-AC-T
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACAT
*
19453367 CATCTAATCTCTTACCCCGATCATGGGGCAGATTGAAGACAT
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACAT
* ** *
19453409 CATCCAATCTCTTACCTCGATCATGGGATAGATTAAAGACAT
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACAT
* ** *
19453451 CATCCAATCTCTTACCCCGACCATGATGCAGATTG-A-AC-C
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACAT
*
19453490 CATCCAATCTCTTACCCTGATCATGGGGCAGATTGAA-AGC--
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGA-CAT
* *
19453530 CATCCAATCTCTTACCCTGATCATGGGGCAGATTAAAGACAT
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACAT
*
19453572 CATTCAATCTCTTACCCCGATCATGGGGCAGATTGAA-AGC--
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGA-CAT
*
19453612 CATCCAATCTCTTACCCCGATCATTGGGCAGATTGAAGACAT
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACAT
* * * * *
19453654 CATTCAATCTCTTACCCCAACCATGGGGTAGATTGAA-ACCAC
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGA-CAT
* *
19453696 CACCCAATCTTTTACCCC
1 CATCCAATCTCTTACCCC
19453714 TAATCAAGAG
Statistics
Matches: 673, Mismatches: 92, Indels: 56
0.82 0.11 0.07
Matches are distributed among these distances:
38 2 0.00
39 186 0.28
40 81 0.12
41 117 0.17
42 252 0.37
44 35 0.05
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (42 bp):
CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACAT
Found at i:19453691 original size:82 final size:83
Alignment explanation
Indices: 19452879--19453713 Score: 888
Period size: 82 Copynumber: 10.2 Consensus size: 83
19452869 ACAAAGCTAC
* * * *
19452879 CATCCAATCTCTTACCTCTATCATGGTGCAGATTGAAGACATCATCCAATCTCTTACCCCGGTCA
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTACCCCGATCA
*
19452944 TGGGGCAGATTG-AAG-T
66 TGGGGCAGATTGAAAGCA
* * *** *
19452960 CATCCTATCTCTTACCCCGACCATGAAACAAATTGAAG-C--CATCCAATCTCTTACCCCGATCA
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTACCCCGATCA
* *
19453022 TGGTGCAAATTG-AAGACA
66 TGGGGCAGATTGAAAG-CA
* * * * *
19453040 TCATATCTAATCTCTTACCCCGATCATGTGGTAGATTGAAGCCACCATCCAATCTCTTACCCCGA
1 -C--ATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTACCCCGA
* *
19453105 -CGATAGGCCAGATT-AAAGC-
63 TC-ATGGGGCAGATTGAAAGCA
* * *
19453124 CATCCAATCTCTTACCCTGATCATGGGGCATATTGAAGACATCATCCAATCTCTTA-CCCGACCA
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTACCCCGATCA
*
19453188 TGGGGCATATTG-AAGACA
66 TGGGGCAGATTGAAAG-CA
* * * *
19453206 TCATCCAATCCCTTA-CCCGACCATGGGGCAAATTGAAAACATCATCCAATCTCTTACCCCGATC
1 -CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTACCCCGATC
* *
19453270 ATGGGGTAGATTGAAAACA
65 ATGGGGCAGATTGAAAGCA
* * * * * *
19453289 TATCCAATCTCTTAACTCTACCATGGGGCAGATTGAAG---TCATCCAATCTCTTACCCTGATCA
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTACCCCGATCA
** *
19453351 TAAGGCAGATTG-AA-CT
66 TGGGGCAGATTGAAAGCA
* *
19453367 CATCTAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTACCTCGATCA
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTACCCCGATCA
**
19453432 TGGGATAGATT-AAAGACA
66 TGGGGCAGATTGAAAG-CA
* ** * *
19453450 TCATCCAATCTCTTACCCCGACCATGATGCAGATTG-A-AC-CCATCCAATCTCTTACCCTGATC
1 -CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTACCCCGATC
19453512 ATGGGGCAGATTGAAAGC-
65 ATGGGGCAGATTGAAAGCA
* * *
19453530 CATCCAATCTCTTACCCTGATCATGGGGCAGATTAAAGACATCATTCAATCTCTTACCCCGATCA
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTACCCCGATCA
19453595 TGGGGCAGATTGAAAGC-
66 TGGGGCAGATTGAAAGCA
* * * *
19453612 CATCCAATCTCTTACCCCGATCATTGGGCAGATTGAAGACATCATTCAATCTCTTACCCCAACCA
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTACCCCGATCA
* *
19453677 TGGGGTAGATTGAAACCA
66 TGGGGCAGATTGAAAGCA
* *
19453695 CCACCCAATCTTTTACCCC
1 -CATCCAATCTCTTACCCC
19453714 TAATCAAGAG
Statistics
Matches: 630, Mismatches: 93, Indels: 59
0.81 0.12 0.08
Matches are distributed among these distances:
78 68 0.11
79 32 0.05
80 51 0.08
81 145 0.23
82 168 0.27
83 83 0.13
84 50 0.08
85 2 0.00
86 31 0.05
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (83 bp):
CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTACCCCGATCA
TGGGGCAGATTGAAAGCA
Found at i:19453823 original size:46 final size:45
Alignment explanation
Indices: 19453637--19453828 Score: 169
Period size: 45 Copynumber: 4.3 Consensus size: 45
19453627 CCCGATCATT
* * * * *
19453637 GGGCAGATTGAAGACA-TCATTCAATCTCTTACCCC-AA-CCA-TG
1 GGGCAGATTGAAGCCACT-ATCCAATCTTTTACCCCTAATCAAGAG
* * * *
19453679 GGGTAGATTGAAACCACCACCCAATCTTTTACCCCTAATCAAGAG
1 GGGCAGATTGAAGCCACTATCCAATCTTTTACCCCTAATCAAGAG
* * * ** *
19453724 AGACAGATTAAAGAAACTATCCAATTTTTTACCCCTAATCAAGA-
1 GGGCAGATTGAAGCCACTATCCAATCTTTTACCCCTAATCAAGAG
* *
19453768 GGGCAAGATTGAAGCCACTATCTAATCTTTTACACCTACATCAAGAG
1 GGGC-AGATTGAAGCCACTATCCAATCTTTTACCCCTA-ATCAAGAG
19453815 GGGCAGATTGAAGC
1 GGGCAGATTGAAGC
19453829 TACCATCTCA
Statistics
Matches: 116, Mismatches: 27, Indels: 10
0.76 0.18 0.07
Matches are distributed among these distances:
42 27 0.23
43 2 0.02
44 4 0.03
45 62 0.53
46 17 0.15
47 4 0.03
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (45 bp):
GGGCAGATTGAAGCCACTATCCAATCTTTTACCCCTAATCAAGAG
Found at i:19455015 original size:34 final size:34
Alignment explanation
Indices: 19454973--19455042 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
19454963 TCCTTTACCC
* *
19454973 TTTTATTTATTTGT-TTTATGTC-TTTCTTTTTAT
1 TTTTATTTATTT-TATTTATCTCATTTATTTTTAT
19455006 TTTTCATTTATTTTATTTATCTCATTTATTTTTAT
1 TTTT-ATTTATTTTATTTATCTCATTTATTTTTAT
19455041 TT
1 TT
19455043 CATGCTATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 5 0.16
34 15 0.47
35 12 0.38
ACGTcount: A:0.16, C:0.07, G:0.03, T:0.74
Consensus pattern (34 bp):
TTTTATTTATTTTATTTATCTCATTTATTTTTAT
Found at i:19455032 original size:18 final size:17
Alignment explanation
Indices: 19454999--19455042 Score: 63
Period size: 16 Copynumber: 2.5 Consensus size: 17
19454989 TATGTCTTTC
19454999 TTTTTATTTTTCATTTA
1 TTTTTATTTTTCATTTA
19455016 -TTTTATTTATCTCATTTA
1 TTTTTATTT-T-TCATTTA
19455034 TTTTTATTT
1 TTTTTATTT
19455043 CATGCTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.33
17 1 0.04
18 7 0.29
19 8 0.33
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTTATTTTTCATTTA
Found at i:19455133 original size:3 final size:3
Alignment explanation
Indices: 19455125--19455165 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
19455115 ATTAATTAAC
*
19455125 TTA TTA TTA GTA TTA TTA TTA TTA TTA TTA TTTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TT
19455166 TACTTAATTG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:19477026 original size:15 final size:16
Alignment explanation
Indices: 19476999--19477028 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
19476989 ATTTTATTTT
19476999 AATAATAAATTTTAAA
1 AATAATAAATTTTAAA
19477015 AATAAT-AATTTTAA
1 AATAATAAATTTTAA
19477029 TTAATATTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATAATAAATTTTAAA
Found at i:19477034 original size:16 final size:16
Alignment explanation
Indices: 19476987--19477034 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
19476977 ATTTAAATTT
*
19476987 TAATTTTATTTTAATAA
1 TAATTTTA-ATTAATAA
*
19477004 TAAATTTTAA-AAATAA
1 T-AATTTTAATTAATAA
19477020 TAATTTTAATTAATA
1 TAATTTTAATTAATA
19477035 TTCTTTATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 8 0.31
16 10 0.38
17 1 0.04
18 7 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TAATTTTAATTAATAA
Found at i:19477217 original size:15 final size:15
Alignment explanation
Indices: 19477156--19477221 Score: 53
Period size: 15 Copynumber: 4.1 Consensus size: 15
19477146 ATTATTCAAA
19477156 ATATTCAAT-ATAAAT
1 ATATT-AATAATAAAT
*
19477171 ATTTTAATAATGAATAT
1 ATATTAATAAT-AA-AT
* *
19477188 TTATTATAATTATAAAT
1 ATA-T-TAATAATAAAT
19477205 ATATTAATAATAAAT
1 ATATTAATAATAAAT
19477220 AT
1 AT
19477222 TTTGTAGTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
14 3 0.08
15 18 0.45
16 3 0.08
17 7 0.17
18 3 0.08
19 6 0.15
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (15 bp):
ATATTAATAATAAAT
Found at i:19477721 original size:14 final size:13
Alignment explanation
Indices: 19477690--19477723 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
19477680 AATAAGTCAT
19477690 TTTTCAAAAATCA
1 TTTTCAAAAATCA
*
19477703 TTTTCTAAAAATTA
1 TTTTC-AAAAATCA
19477717 TTTTCAA
1 TTTTCAA
19477724 TGAAACAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (13 bp):
TTTTCAAAAATCA
Found at i:19478506 original size:34 final size:34
Alignment explanation
Indices: 19478443--19478507 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
19478433 AAGGATCAAA
* * **
19478443 TTTTTTTTCAGCTTTTGAGGGGTTTAAAAAAGTT
1 TTTTTTTTCAACTTTTAAGGGGTCCAAAAAAGTT
19478477 TTTTTTTTCAACTTTTAAGGGGTCCAAAAAA
1 TTTTTTTTCAACTTTTAAGGGGTCCAAAAAA
19478508 AATTTACCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.28, C:0.09, G:0.17, T:0.46
Consensus pattern (34 bp):
TTTTTTTTCAACTTTTAAGGGGTCCAAAAAAGTT
Found at i:19478554 original size:31 final size:30
Alignment explanation
Indices: 19478485--19478556 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
19478475 TTTTTTTTTT
*
19478485 CAACTTTTAAGGGGTCCAAAAAAAATTTAC
1 CAACTTTTAAGGAGTCCAAAAAAAATTTAC
* * *
19478515 CAATTTTTAAGGAG-CCTAAAAAAATTTTCTC
1 CAACTTTTAAGGAGTCC-AAAAAAAATTT-AC
19478546 CAACTTTTAAG
1 CAACTTTTAAG
19478557 AGGTTCAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 2 0.06
30 22 0.63
31 11 0.31
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (30 bp):
CAACTTTTAAGGAGTCCAAAAAAAATTTAC
Found at i:19478991 original size:21 final size:21
Alignment explanation
Indices: 19478961--19479003 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
19478951 ACAAACAATA
* *
19478961 TAATGGTTTTGCCTTTTAACT
1 TAATGATTTTGACTTTTAACT
19478982 TAATGATTTTGACTTTTAACT
1 TAATGATTTTGACTTTTAACT
19479003 T
1 T
19479004 TAGAAAAGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.53
Consensus pattern (21 bp):
TAATGATTTTGACTTTTAACT
Found at i:19482502 original size:24 final size:24
Alignment explanation
Indices: 19482466--19482511 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
19482456 ATTCTAAGTT
*
19482466 ATTTTTAATTTTTTATAAGTAAACC
1 ATTTTTAATTTTTCATAA-TAAACC
*
19482491 ATTTTTTA-TTTTCATAATAAA
1 ATTTTTAATTTTTCATAATAAA
19482512 ATAAAGTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 8 0.42
25 7 0.37
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (24 bp):
ATTTTTAATTTTTCATAATAAACC
Found at i:19482743 original size:16 final size:17
Alignment explanation
Indices: 19482714--19482746 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
19482704 AAATCATTTT
*
19482714 AATTAATTTTTTCTATA
1 AATTAATTTATTCTATA
19482731 AATT-ATTTATTCTATA
1 AATTAATTTATTCTATA
19482747 CGAAACAGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (17 bp):
AATTAATTTATTCTATA
Found at i:19483048 original size:17 final size:18
Alignment explanation
Indices: 19483021--19483055 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
19483011 TTTAATATAG
19483021 TTTTAAGTTTTTATATTT
1 TTTTAAGTTTTTATATTT
*
19483039 TTTTAA-TTTTTTTATTT
1 TTTTAAGTTTTTATATTT
19483056 AAAAAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (18 bp):
TTTTAAGTTTTTATATTT
Found at i:19489254 original size:18 final size:18
Alignment explanation
Indices: 19489231--19489265 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
19489221 GAGTTAAATG
*
19489231 AATCGAGTTGTTCGAGTT
1 AATCGAGTTATTCGAGTT
19489249 AATCGAGTTATTCGAGT
1 AATCGAGTTATTCGAGT
19489266 CAGCTCGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.37
Consensus pattern (18 bp):
AATCGAGTTATTCGAGTT
Found at i:19493185 original size:63 final size:61
Alignment explanation
Indices: 19493075--19493237 Score: 230
Period size: 63 Copynumber: 2.7 Consensus size: 61
19493065 TTCTTATTAT
19493075 TTTTATTTATTTATTTATTATTTTTATGAACATAAATAAAT--A-TAAAATAATATTAATTTTA
1 TTTTA-TTATTTATTTATTA-TTTTATGAA-ATAAATAAATAAATTAAAATAATATTAATTTTA
*
19493136 TTTTATTATTTATTTATTATTTTATGAATATAAATAAATAAATGTAAAATAATATTAATTTTG
1 TTTTATTATTTATTTATTATTTTATGAA-ATAAATAAATAAAT-TAAAATAATATTAATTTTA
19493199 TTTTATTATTTATTTATTA--TTAT-AAATAAATAAATAAAT
1 TTTTATTATTTATTTATTATTTTATGAAATAAATAAATAAAT
19493238 AAATAACAAA
Statistics
Matches: 96, Mismatches: 2, Indels: 10
0.89 0.02 0.09
Matches are distributed among these distances:
59 33 0.34
60 16 0.17
61 10 0.10
63 37 0.39
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (61 bp):
TTTTATTATTTATTTATTATTTTATGAAATAAATAAATAAATTAAAATAATATTAATTTTA
Found at i:19493208 original size:59 final size:60
Alignment explanation
Indices: 19493080--19493237 Score: 195
Period size: 59 Copynumber: 2.6 Consensus size: 60
19493070 ATTATTTTTA
*
19493080 TTTATTTATTTATTATTTTTATGAACATAAATAAAT--A-TAAAATAATATTAATTTTATTT
1 TTTATTTATTTATTA-TTTTATGAA-ATAAATAAATAAATTAAAATAATATTAATTTTATGT
19493139 TATTATTTATTTATTATTTTATGAATATAAATAAATAAATGTAAAATAATATTAA-TTT-TGT
1 T-TTATTTATTTATTATTTTATGAA-ATAAATAAATAAAT-TAAAATAATATTAATTTTATGT
19493200 TTTA-TTATTTATTTATTATTAT-AAATAAATAAATAAAT
1 TTTATTTATTTA-TTATT-TTATGAAATAAATAAATAAAT
19493238 AAATAACAAA
Statistics
Matches: 90, Mismatches: 2, Indels: 14
0.85 0.02 0.13
Matches are distributed among these distances:
59 41 0.46
60 24 0.27
61 8 0.09
62 3 0.03
63 14 0.16
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (60 bp):
TTTATTTATTTATTATTTTATGAAATAAATAAATAAATTAAAATAATATTAATTTTATGT
Found at i:19498231 original size:6 final size:6
Alignment explanation
Indices: 19498217--19498259 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
19498207 AAGAAATTTC
*
19498217 AAAAA- AAAAAG AAAAAAG AAAAAAG ACAAAG AAAAAG AAAAAG
1 AAAAAG AAAAAG -AAAAAG -AAAAAG AAAAAG AAAAAG AAAAAG
19498260 GGGAGGTCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
5 5 0.15
6 16 0.47
7 13 0.38
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:19498233 original size:7 final size:7
Alignment explanation
Indices: 19498217--19498258 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
19498207 AAGAAATTTC
19498217 AAAA-AA
1 AAAAGAA
19498223 AAAAGAA
1 AAAAGAA
19498230 AAAAGAA
1 AAAAGAA
19498237 AAAAG-A
1 AAAAGAA
*
19498243 CAAAG-A
1 AAAAGAA
19498249 AAAAGAA
1 AAAAGAA
19498256 AAA
1 AAA
19498259 GGGGAGGTCG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
6 14 0.44
7 18 0.56
ACGTcount: A:0.86, C:0.02, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:19499242 original size:50 final size:50
Alignment explanation
Indices: 19499179--19499324 Score: 204
Period size: 50 Copynumber: 2.9 Consensus size: 50
19499169 ATCTTTTACC
*
19499179 CCTAAAGCGGTGGAGGTGCAGATTGAAACTGCAATGGTAAATCTCATACA
1 CCTAAAGCTGTGGAGGTGCAGATTGAAACTGCAATGGTAAATCTCATACA
*
19499229 CCTAAAGCTGTGGAGGTGCAGATTGAAACCGCAAT-GTCAAATCTCATACA
1 CCTAAAGCTGTGGAGGTGCAGATTGAAACTGCAATGGT-AAATCTCATACA
* * * * * *
19499279 CCTAAAGCTGTAGAGGGGCAGAATGAAGCTGTAATGGCAAATCTCA
1 CCTAAAGCTGTGGAGGTGCAGATTGAAACTGCAATGGTAAATCTCA
19499325 GTCATTTAAA
Statistics
Matches: 85, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
49 2 0.02
50 82 0.96
51 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.21
Consensus pattern (50 bp):
CCTAAAGCTGTGGAGGTGCAGATTGAAACTGCAATGGTAAATCTCATACA
Found at i:19499335 original size:50 final size:50
Alignment explanation
Indices: 19499179--19499355 Score: 203
Period size: 50 Copynumber: 3.5 Consensus size: 50
19499169 ATCTTTTACC
* * *
19499179 CCTAAAGCGGTGGAGGTGCAGATTGAAACTGCAATGGTAAATCTCATACA
1 CCTAAAGCTGTAGAGGTGCAGATTGAAACTGCAATGGCAAATCTCATACA
* * *
19499229 CCTAAAGCTGTGGAGGTGCAGATTGAAACCGCAATGTCAAATCTCATACA
1 CCTAAAGCTGTAGAGGTGCAGATTGAAACTGCAATGGCAAATCTCATACA
* * * *
19499279 CCTAAAGCTGTAGAGGGGCAGAATGAAGCTGTAATGGCAAATCTCAGT-CA
1 CCTAAAGCTGTAGAGGTGCAGATTGAAACTGCAATGGCAAATCTCA-TACA
** * * *
19499329 TTTAAAGCTATAGAGGAGAAGATTGAA
1 CCTAAAGCTGTAGAGGTGCAGATTGAA
19499356 GTCATAAGGA
Statistics
Matches: 109, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
50 108 0.99
51 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (50 bp):
CCTAAAGCTGTAGAGGTGCAGATTGAAACTGCAATGGCAAATCTCATACA
Found at i:19499550 original size:80 final size:80
Alignment explanation
Indices: 19499413--19500783 Score: 2244
Period size: 80 Copynumber: 17.1 Consensus size: 80
19499403 TACAACCTCT
* * * *
19499413 AATCTTTTACCCTCACAAGAGGGCAAGATTGAAAACCATCAGATCTTTTACCCCGATCATGGGGC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
*
19499478 AAATTGAAGAAATCC
66 AGATTGAAGAAATCC
*
19499493 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCTCGATCATGGGGC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
* *
19499558 AAATTGAAGAAATCT
66 AGATTGAAGAAATCC
19499573 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
19499638 AGATTGAAGAAATCC
66 AGATTGAAGAAATCC
* *
19499653 AATCTTTTACCCTAATCAGAGGGCAAGATTGAAGATCATCCGATCTTTTACCCCGATCATGGGGC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
19499718 AGATTGAAGAAATCC
66 AGATTGAAGAAATCC
19499733 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
*
19499798 AGATTGAAAAAATCC
66 AGATTGAAGAAATCC
19499813 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
19499878 AGATTGAAGAAATCC
66 AGATTGAAGAAATCC
* * * * * *
19499893 AATCTTTTACCCTAACTAGAGGGCAAAATTGAATACCATTCGATCTTTTACCCCGATCATGAGGT
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
*
19499958 AAATTGAAGAAATCC
66 AGATTGAAGAAATCC
*
19499973 AATCTTTTGCCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
*
19500038 AGATTGAAGAAATCA
66 AGATTGAAGAAATCC
* *
19500053 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTCTACCCCGATCATGGGGA
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
* *
19500118 AAATTAAAGAAATCC
66 AGATTGAAGAAATCC
* *
19500133 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATTCGATCTTCTACCCCGATCATGGGGC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
* *
19500198 AAATTAAAGAAATCC
66 AGATTGAAGAAATCC
** *
19500213 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATTTGATCTTCTACCCCGATCATGGGGC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
* *
19500278 AAATTAAAGAAATCC
66 AGATTGAAGAAATCC
* *
19500293 AATCGTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGAC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
*
19500358 AGATTGAAAAAATCC
66 AGATTGAAGAAATCC
*
19500373 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCTCGATCATGGGGC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
*
19500438 AGATTGAAAAAATCC
66 AGATTGAAGAAATCC
* *
19500453 AATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACCATCCGATCTTCTACCCCGATCATGGGGC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
19500518 AGATTGAAGAAATCC
66 AGATTGAAGAAATCC
* *
19500533 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAAACCATCCGATCTTTTACCTCGATCATGGGGC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
19500598 AGATTGAAGAAATCC
66 AGATTGAAGAAATCC
* * *
19500613 AATCTTTTACCTTAACTAGAGGGCAAGATTGAAGACCATCTGATCTTTTACCCCGATCATGGGGC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
19500678 AGATTGAAGAAATCC
66 AGATTGAAGAAATCC
* * * * *
19500693 AATCTTTTACCCTAACCAAAGGGC-AGATTGAAGACCATCAGATCTCTTACCTCGACCATGGGGC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
*
19500757 A-AGTTGAA-ACAATCT
66 AGA-TTGAAGA-AATCC
19500772 AATCTTTTACCC
1 AATCTTTTACCC
19500784 CTAAAGTTAT
Statistics
Matches: 1217, Mismatches: 72, Indels: 5
0.94 0.06 0.00
Matches are distributed among these distances:
78 2 0.00
79 58 0.05
80 1157 0.95
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.25
Consensus pattern (80 bp):
AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
AGATTGAAGAAATCC
Found at i:19505633 original size:21 final size:21
Alignment explanation
Indices: 19505607--19505659 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
19505597 GATTTTATAA
19505607 TTGGACATTTTTGTAATGTAT
1 TTGGACATTTTTGTAATGTAT
19505628 TTGGACATTTTTGTAATGTAT
1 TTGGACATTTTTGTAATGTAT
19505649 TTGGACATTTT
1 TTGGACATTTT
19505660 AAATTTAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.23, C:0.06, G:0.19, T:0.53
Consensus pattern (21 bp):
TTGGACATTTTTGTAATGTAT
Found at i:19505707 original size:16 final size:16
Alignment explanation
Indices: 19505686--19505739 Score: 72
Period size: 16 Copynumber: 3.3 Consensus size: 16
19505676 TTAAAACCAT
*
19505686 TTTAAATTTAACTAAA
1 TTTAAATTTAAATAAA
* *
19505702 TTTAAATTCAAAAAAA
1 TTTAAATTTAAATAAA
19505718 TTTTAAATTTAAATAAA
1 -TTTAAATTTAAATAAA
19505735 TTTAA
1 TTTAA
19505740 TATAAATTCA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
16 18 0.56
17 14 0.44
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:19505735 original size:17 final size:17
Alignment explanation
Indices: 19505684--19505737 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
19505674 GTTTAAAACC
*
19505684 ATTTTAAATTTAACTAA
1 ATTTTAAATTTAAATAA
* *
19505701 A-TTTAAATTCAAAAAA
1 ATTTTAAATTTAAATAA
19505717 ATTTTAAATTTAAATAA
1 ATTTTAAATTTAAATAA
19505734 ATTT
1 ATTT
19505738 AATATAAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
16 13 0.42
17 18 0.58
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTTTAAATTTAAATAA
Found at i:19505874 original size:19 final size:21
Alignment explanation
Indices: 19505850--19505897 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 21
19505840 CAACAAAAAT
19505850 AATAACAAAACA-A-TAAT-AA
1 AATAACAAAA-ATAGTAATAAA
19505869 AATAACAAAAATAGTAATAAA
1 AATAACAAAAATAGTAATAAA
19505890 AATAACAA
1 AATAACAA
19505898 TAAAAATAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 1 0.04
19 11 0.42
20 4 0.15
21 10 0.38
ACGTcount: A:0.73, C:0.08, G:0.02, T:0.17
Consensus pattern (21 bp):
AATAACAAAAATAGTAATAAA
Found at i:19505924 original size:15 final size:12
Alignment explanation
Indices: 19505814--19505950 Score: 113
Period size: 12 Copynumber: 11.8 Consensus size: 12
19505804 TATATATATA
*
19505814 AACAATCAAAAT
1 AACAATAAAAAT
*
19505826 AACAATAAAAAC
1 AACAATAAAAAT
*
19505838 AACAACAAAAAT
1 AACAATAAAAAT
*
19505850 ---AATAACAA-
1 AACAATAAAAAT
*
19505858 AACAATAATAA-
1 AACAATAAAAAT
* *
19505869 AATAACAAAAAT
1 AACAATAAAAAT
**
19505881 AGTAATAAAAAT
1 AACAATAAAAAT
19505893 AACAATAAAAAT
1 AACAATAAAAAT
19505905 AACAATAAAAAT
1 AACAATAAAAAT
** *
19505917 AGTAACAAAAAT
1 AACAATAAAAAT
*
19505929 AACAATAAAAAC
1 AACAATAAAAAT
*
19505941 AACACTAAAA
1 AACAATAAAA
19505951 TAATAAAAAA
Statistics
Matches: 99, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
9 6 0.06
11 15 0.15
12 78 0.79
ACGTcount: A:0.72, C:0.12, G:0.01, T:0.15
Consensus pattern (12 bp):
AACAATAAAAAT
Found at i:19506000 original size:22 final size:22
Alignment explanation
Indices: 19505975--19506041 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
19505965 ATTAAAAAGT
19505975 AAAAAAAAAAATCAAAACAACA
1 AAAAAAAAAAATCAAAACAACA
* ** * **
19505997 AAAAATAGCAATCAAAATAGTA
1 AAAAAAAAAAATCAAAACAACA
* *
19506019 AAAAAATAACATCAAAACAACA
1 AAAAAAAAAAATCAAAACAACA
19506041 A
1 A
19506042 TATAATTTTT
Statistics
Matches: 31, Mismatches: 14, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.73, C:0.13, G:0.03, T:0.10
Consensus pattern (22 bp):
AAAAAAAAAAATCAAAACAACA
Found at i:19507521 original size:8 final size:8
Alignment explanation
Indices: 19507488--19507569 Score: 50
Period size: 8 Copynumber: 10.5 Consensus size: 8
19507478 AATATTTATC
19507488 TTTATA-T
1 TTTATATT
19507495 TTT-TATT
1 TTTATATT
*
19507502 TTTAAAGTTT
1 TTTATA--TT
19507512 TTTATATT
1 TTTATATT
*
19507520 TTTAAATT
1 TTTATATT
*
19507528 TCTTAAAATT
1 T-TT-ATATT
19507538 TTTATA--
1 TTTATATT
*
19507544 -ATATATT
1 TTTATATT
19507551 TTTATATT
1 TTTATATT
19507559 TTTA-ATT
1 TTTATATT
19507566 TTTA
1 TTTA
19507570 AATATAAATT
Statistics
Matches: 60, Mismatches: 6, Indels: 18
0.71 0.07 0.21
Matches are distributed among these distances:
5 4 0.07
6 2 0.03
7 14 0.23
8 23 0.38
9 4 0.07
10 13 0.22
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (8 bp):
TTTATATT
Found at i:19508747 original size:169 final size:169
Alignment explanation
Indices: 19508468--19508807 Score: 680
Period size: 169 Copynumber: 2.0 Consensus size: 169
19508458 ACGACCAAAA
19508468 CAAAAAATTATTAATAATTAAATAAACTACTAGTGTAATTTGATCTCGTATAAAAGATGTAAAAA
1 CAAAAAATTATTAATAATTAAATAAACTACTAGTGTAATTTGATCTCGTATAAAAGATGTAAAAA
19508533 ACTGGAGATGAAGTTTTTTTATTAATTTAATGATTAAATTACACTAAAAAAGTGGTTGAGACCAT
66 ACTGGAGATGAAGTTTTTTTATTAATTTAATGATTAAATTACACTAAAAAAGTGGTTGAGACCAT
19508598 TTAATTAACGAATTTGTCGTCTTCTTTCTTTTTCAACTT
131 TTAATTAACGAATTTGTCGTCTTCTTTCTTTTTCAACTT
19508637 CAAAAAATTATTAATAATTAAATAAACTACTAGTGTAATTTGATCTCGTATAAAAGATGTAAAAA
1 CAAAAAATTATTAATAATTAAATAAACTACTAGTGTAATTTGATCTCGTATAAAAGATGTAAAAA
19508702 ACTGGAGATGAAGTTTTTTTATTAATTTAATGATTAAATTACACTAAAAAAGTGGTTGAGACCAT
66 ACTGGAGATGAAGTTTTTTTATTAATTTAATGATTAAATTACACTAAAAAAGTGGTTGAGACCAT
19508767 TTAATTAACGAATTTGTCGTCTTCTTTCTTTTTCAACTT
131 TTAATTAACGAATTTGTCGTCTTCTTTCTTTTTCAACTT
19508806 CA
1 CA
19508808 TTTTTCAAAT
Statistics
Matches: 171, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
169 171 1.00
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (169 bp):
CAAAAAATTATTAATAATTAAATAAACTACTAGTGTAATTTGATCTCGTATAAAAGATGTAAAAA
ACTGGAGATGAAGTTTTTTTATTAATTTAATGATTAAATTACACTAAAAAAGTGGTTGAGACCAT
TTAATTAACGAATTTGTCGTCTTCTTTCTTTTTCAACTT
Found at i:19509070 original size:12 final size:12
Alignment explanation
Indices: 19509053--19509077 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19509043 ATTTCTAATT
19509053 GGAATTGGAATA
1 GGAATTGGAATA
19509065 GGAATTGGAATA
1 GGAATTGGAATA
19509077 G
1 G
19509078 AAGGAAGTTG
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:0.40, C:0.00, G:0.36, T:0.24
Consensus pattern (12 bp):
GGAATTGGAATA
Found at i:19510025 original size:14 final size:14
Alignment explanation
Indices: 19510006--19510032 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19509996 AATTTTCACC
19510006 ATTTGTTTGTTACT
1 ATTTGTTTGTTACT
19510020 ATTTGTTTGTTAC
1 ATTTGTTTGTTAC
19510033 AAAATGATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.07, G:0.15, T:0.63
Consensus pattern (14 bp):
ATTTGTTTGTTACT
Found at i:19522264 original size:25 final size:25
Alignment explanation
Indices: 19522236--19522348 Score: 104
Period size: 25 Copynumber: 4.5 Consensus size: 25
19522226 TCTGATTCTA
*
19522236 GCTCGTAAGAGCATAATACTGTTTG
1 GCTCGTAAGAGCATAATTCTGTTTG
* *
19522261 GCTCGTAAGAGCATAATTTTGTCTG
1 GCTCGTAAGAGCATAATTCTGTTTG
* * *
19522286 GCTCGTAAGGGCGTAATTCTATTTG
1 GCTCGTAAGAGCATAATTCTGTTTG
* *
19522311 GCTCATGAA-AGCA-ATATTCTGTCTGG
1 GCTCGT-AAGAGCATA-ATTCTGT-TTG
*
19522337 GCTCGTATGAGC
1 GCTCGTAAGAGC
19522349 CAAATTTCTA
Statistics
Matches: 69, Mismatches: 15, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
24 1 0.01
25 56 0.81
26 12 0.17
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.33
Consensus pattern (25 bp):
GCTCGTAAGAGCATAATTCTGTTTG
Found at i:19522334 original size:50 final size:51
Alignment explanation
Indices: 19522236--19522348 Score: 124
Period size: 50 Copynumber: 2.2 Consensus size: 51
19522226 TCTGATTCTA
* * *
19522236 GCTCGTAAGAGCATAATACTGTTTGGCTCGTAAGAGCATAATTTTGTCT-G
1 GCTCGTAAGAGCATAATACTATTTGGCTCATAAGAGCATAATTCTGTCTGG
* * *
19522286 GCTCGTAAGGGCGTAATTCTATTTGGCTCATGAA-AGCA-ATATTCTGTCTGG
1 GCTCGTAAGAGCATAATACTATTTGGCTCAT-AAGAGCATA-ATTCTGTCTGG
*
19522337 GCTCGTATGAGC
1 GCTCGTAAGAGC
19522349 CAAATTTCTA
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
49 1 0.02
50 38 0.73
51 13 0.25
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.33
Consensus pattern (51 bp):
GCTCGTAAGAGCATAATACTATTTGGCTCATAAGAGCATAATTCTGTCTGG
Found at i:19523452 original size:21 final size:21
Alignment explanation
Indices: 19523395--19523452 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
19523385 GGAGTTTTTA
* * *
19523395 GTATCAGTAGAAGTATGACTT
1 GTATCGGTAGAAGTCTCACTT
*
19523416 GTATCGGTAGATGTCTCACTT
1 GTATCGGTAGAAGTCTCACTT
19523437 GTATCGGTAGAAGTCT
1 GTATCGGTAGAAGTCT
19523453 GTACTGTTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (21 bp):
GTATCGGTAGAAGTCTCACTT
Found at i:19532060 original size:13 final size:13
Alignment explanation
Indices: 19532039--19532072 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
19532029 TAAATAATAT
19532039 AATAATAATCCTA
1 AATAATAATCCTA
*
19532052 AATATTAATCCTA
1 AATAATAATCCTA
*
19532065 AAAAATAA
1 AATAATAA
19532073 AGTTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:19533794 original size:177 final size:177
Alignment explanation
Indices: 19533498--19533852 Score: 595
Period size: 177 Copynumber: 2.0 Consensus size: 177
19533488 AATCCTAGAT
* * *
19533498 TGCGAAGCAGATAAGGGGGTGCCCATTATCTTGGGGCGACCATTTCTAGCAACGGTACGCACACT
1 TGCGAAGCAGATAAGGAGGTGCCCATTATCTTAGGGCGACCATTTCTAGCAACGGGACGCACACT
19533563 TATCGATGTATTCAAAGGAGAACTTATCATGTAACATAATGATGAACATGTGACCTT-TAGCGTG
66 TATCGATGTATTCAAAGGAGAACTTATCATGTAACATAATGATGAACATGTGACCTTCT-GCGTG
* *
19533627 TTTGAGGCATCCCCGTCTAGATCTAAAGAGCAATGTAATCACATTGAC
130 TTTGAGGCATCCCCGTCCAAATCTAAAGAGCAATGTAATCACATTGAC
* * *
19533675 TGCGAAGTAGATAAGGAGGTGCCCATTATCTTAGGGTGACCATTTTTAGCAACGGGACGCACACT
1 TGCGAAGCAGATAAGGAGGTGCCCATTATCTTAGGGCGACCATTTCTAGCAACGGGACGCACACT
* *
19533740 TATCGATGTATTCAAAGGAGAACTTATCATGTAACATAATGATGAGCATGTGACCTTCTGTGTGT
66 TATCGATGTATTCAAAGGAGAACTTATCATGTAACATAATGATGAACATGTGACCTTCTGCGTGT
*
19533805 TTGAGGCATCCCCGTCCAAATCTAAAGAGCAATGTCATCACATTGAC
131 TTGAGGCATCCCCGTCCAAATCTAAAGAGCAATGTAATCACATTGAC
19533852 T
1 T
19533853 TGTTGGACGA
Statistics
Matches: 166, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
177 165 0.99
178 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (177 bp):
TGCGAAGCAGATAAGGAGGTGCCCATTATCTTAGGGCGACCATTTCTAGCAACGGGACGCACACT
TATCGATGTATTCAAAGGAGAACTTATCATGTAACATAATGATGAACATGTGACCTTCTGCGTGT
TTGAGGCATCCCCGTCCAAATCTAAAGAGCAATGTAATCACATTGAC
Found at i:19540427 original size:18 final size:17
Alignment explanation
Indices: 19540383--19540427 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
19540373 CAGATGAAGG
*
19540383 AGAAG-GAAGAAGAAGA
1 AGAAGAGAAGAAAAAGA
19540399 A-AAG-GAAGAAAAAGA
1 AGAAGAGAAGAAAAAGA
19540414 AGAAGAGAATGAAA
1 AGAAGAGAA-GAAA
19540428 TGAAGGAACC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 14 0.56
16 4 0.16
17 3 0.12
18 4 0.16
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (17 bp):
AGAAGAGAAGAAAAAGA
Found at i:19541524 original size:18 final size:18
Alignment explanation
Indices: 19541486--19541535 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
19541476 TCAATCACTT
*
19541486 GAAAAAGAAACAAAATGA
1 GAAAAAGAAAGAAAATGA
19541504 GAAAAAGAAAGAAAA-GAA
1 GAAAAAGAAAGAAAATG-A
*
19541522 GAAGAAG-AAGAAAA
1 GAAAAAGAAAGAAAA
19541536 AATTTATTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 8 0.28
18 21 0.72
ACGTcount: A:0.74, C:0.02, G:0.22, T:0.02
Consensus pattern (18 bp):
GAAAAAGAAAGAAAATGA
Found at i:19547856 original size:36 final size:36
Alignment explanation
Indices: 19547814--19547949 Score: 200
Period size: 36 Copynumber: 3.8 Consensus size: 36
19547804 TGGTAACAAG
*
19547814 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAACAGAGAGTAAAATGAGCAT
* * *
19547850 CATGACCTTTGGGTGAATAAAGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAACAGAGAGTAAAATGAGCAT
* * * *
19547886 CATGATCTTTGGGTTAACAGGGAGTGAAATGAGCAT
1 CATGACCTTTGGGTCAACAGAGAGTAAAATGAGCAT
19547922 CATGACCTTTGGGTCAACAGAGAGTAAA
1 CATGACCTTTGGGTCAACAGAGAGTAAA
19547950 TCGGATATCG
Statistics
Matches: 86, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 86 1.00
ACGTcount: A:0.35, C:0.14, G:0.27, T:0.24
Consensus pattern (36 bp):
CATGACCTTTGGGTCAACAGAGAGTAAAATGAGCAT
Found at i:19548609 original size:21 final size:21
Alignment explanation
Indices: 19548578--19548632 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
19548568 GGAGTTTTTA
* * *
19548578 GTATTGGTAGAAGCATGATTT
1 GTATCGGTAGAAGCATCACTT
* *
19548599 GTTTCGGTAGAAGCTTCACTT
1 GTATCGGTAGAAGCATCACTT
19548620 GTATCGGTAGAAG
1 GTATCGGTAGAAG
19548633 TCTGCACTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.25, C:0.11, G:0.29, T:0.35
Consensus pattern (21 bp):
GTATCGGTAGAAGCATCACTT
Found at i:19552303 original size:21 final size:20
Alignment explanation
Indices: 19552275--19552322 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
19552265 CATCTCTAAA
19552275 TAATATTTA-ATTTTTTACTT
1 TAATATTTAGATTTTTTA-TT
*
19552295 TAATGATTTAGCTTTTTTATT
1 TAAT-ATTTAGATTTTTTATT
19552316 T-ATATTT
1 TAATATTT
19552323 TTTAATAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 4 0.16
20 6 0.24
21 8 0.32
22 7 0.28
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (20 bp):
TAATATTTAGATTTTTTATT
Found at i:19553234 original size:13 final size:13
Alignment explanation
Indices: 19553213--19553315 Score: 84
Period size: 13 Copynumber: 7.9 Consensus size: 13
19553203 TAAACCAAAT
19553213 TTTTTAAAAGTAC
1 TTTTTAAAAGTAC
*
19553226 -TTTTAAAAATCAC
1 TTTTTAAAAGT-AC
* *
19553239 TTTTTCAGAGTAC
1 TTTTTAAAAGTAC
*
19553252 TTTTTAAAAGTGC
1 TTTTTAAAAGTAC
* * *
19553265 TTTTCAAAATTAT
1 TTTTTAAAAGTAC
* *
19553278 TTTTTCAGAGTAC
1 TTTTTAAAAGTAC
*
19553291 TTTTTAAAAGCA-
1 TTTTTAAAAGTAC
19553303 TTTTTCAAAAGTA
1 TTTTT-AAAAGTA
19553316 ATGCTAAACT
Statistics
Matches: 67, Mismatches: 20, Indels: 6
0.72 0.22 0.06
Matches are distributed among these distances:
12 14 0.21
13 46 0.69
14 7 0.10
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.46
Consensus pattern (13 bp):
TTTTTAAAAGTAC
Found at i:19553308 original size:39 final size:39
Alignment explanation
Indices: 19553213--19553312 Score: 146
Period size: 39 Copynumber: 2.6 Consensus size: 39
19553203 TAAACCAAAT
*
19553213 TTTTTAAAAGTACTTTTAAAAATCACTTTTTCAGAGTAC
1 TTTTTAAAAGTACTTTTCAAAATCACTTTTTCAGAGTAC
* * *
19553252 TTTTTAAAAGTGCTTTTCAAAATTATTTTTTCAGAGTAC
1 TTTTTAAAAGTACTTTTCAAAATCACTTTTTCAGAGTAC
* *
19553291 TTTTTAAAAGCATTTTTCAAAA
1 TTTTTAAAAGTACTTTTCAAAA
19553313 GTAATGCTAA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.35, C:0.11, G:0.08, T:0.46
Consensus pattern (39 bp):
TTTTTAAAAGTACTTTTCAAAATCACTTTTTCAGAGTAC
Found at i:19556280 original size:22 final size:21
Alignment explanation
Indices: 19556251--19556319 Score: 86
Period size: 21 Copynumber: 3.3 Consensus size: 21
19556241 CTCACAAAGA
* *
19556251 AAAAAGA-AAGTGAGTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
* *
19556271 AAAAAGAGAAGCAACTTGAAC
1 AAAAAGAGAAGTAACTTGGAC
*
19556292 AAAAAGAGAAGTAACTTTGAC
1 AAAAAGAGAAGTAACTTGGAC
19556313 AAAAAGA
1 AAAAAGA
19556320 AACAAAGTGA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
20 7 0.17
21 34 0.83
ACGTcount: A:0.57, C:0.09, G:0.22, T:0.13
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTGGAC
Found at i:19563771 original size:29 final size:29
Alignment explanation
Indices: 19563734--19563790 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
19563724 TCTCAATTAA
* *
19563734 TTGGGTGACCAATTTAAACAAATCCATAG
1 TTGGATGACCAATTTAAAAAAATCCATAG
*
19563763 TTGGATGACCAATTTAAAAAAATTCATA
1 TTGGATGACCAATTTAAAAAAATCCATA
19563791 ATTAAATGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (29 bp):
TTGGATGACCAATTTAAAAAAATCCATAG
Found at i:19563799 original size:29 final size:29
Alignment explanation
Indices: 19563739--19563800 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
19563729 ATTAATTGGG
* * **
19563739 TGACCAATTTAAACAAATCCATAGTTGGA
1 TGACCAATTTAAAAAAATCCATAATTAAA
*
19563768 TGACCAATTTAAAAAAATTCATAATTAAA
1 TGACCAATTTAAAAAAATCCATAATTAAA
19563797 TGAC
1 TGAC
19563801 TAGAAAAGAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.47, C:0.15, G:0.10, T:0.29
Consensus pattern (29 bp):
TGACCAATTTAAAAAAATCCATAATTAAA
Found at i:19564126 original size:22 final size:23
Alignment explanation
Indices: 19564087--19564131 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
19564077 TTTTAAAATA
19564087 TAAATATCAATTATAAAAATATT
1 TAAATATCAATTATAAAAATATT
19564110 TAAATATCAA-TATAAAAATATT
1 TAAATATCAATTATAAAAATATT
19564132 CATTTTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (23 bp):
TAAATATCAATTATAAAAATATT
Found at i:19565871 original size:19 final size:19
Alignment explanation
Indices: 19565844--19565885 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
19565834 AAATATATTA
*
19565844 TATAAACTATTTTAAAAAT
1 TATAAACTAATTTAAAAAT
*
19565863 TATATACTAATTTAAAAA-
1 TATAAACTAATTTAAAAAT
19565881 TATAA
1 TATAA
19565886 CAAAATCCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (19 bp):
TATAAACTAATTTAAAAAT
Found at i:19567473 original size:12 final size:12
Alignment explanation
Indices: 19567451--19567489 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
19567441 TTTATTTAGC
19567451 ATTTAAT-TTTT
1 ATTTAATGTTTT
19567462 ATTTAATGTTTT
1 ATTTAATGTTTT
*
19567474 ATTTATTGTATTT
1 ATTTAATGT-TTT
19567487 ATT
1 ATT
19567490 ATATTCATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 7 0.28
12 12 0.48
13 6 0.24
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (12 bp):
ATTTAATGTTTT
Found at i:19567695 original size:16 final size:17
Alignment explanation
Indices: 19567674--19567715 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
19567664 TTGTATTTCC
*
19567674 TATATTTATGATT-ATT
1 TATATTTATAATTAATT
*
19567690 TATATTTTTAATTAATT
1 TATATTTATAATTAATT
*
19567707 GATATTTAT
1 TATATTTAT
19567716 TGCTATTATT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (17 bp):
TATATTTATAATTAATT
Found at i:19577990 original size:21 final size:20
Alignment explanation
Indices: 19577966--19578004 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
19577956 TTGATTGATG
*
19577966 TTTGCCATTTCTTTACCAAAA
1 TTTGCCATTT-TTGACCAAAA
*
19577987 TTTGCTATTTTTGACCAA
1 TTTGCCATTTTTGACCAA
19578005 TGTTTGATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.26, C:0.21, G:0.08, T:0.46
Consensus pattern (20 bp):
TTTGCCATTTTTGACCAAAA
Found at i:19578010 original size:20 final size:21
Alignment explanation
Indices: 19577963--19578010 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
19577953 CTTTTGATTG
*
19577963 ATGTTTGCCATTTCTTTACCA
1 ATGTTTGCCATTTCTTGACCA
** *
19577984 AAATTTGCTATTT-TTGACCA
1 ATGTTTGCCATTTCTTGACCA
19578004 ATGTTTG
1 ATGTTTG
19578011 ATATATTTGG
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.23, C:0.17, G:0.12, T:0.48
Consensus pattern (21 bp):
ATGTTTGCCATTTCTTGACCA
Found at i:19578855 original size:6 final size:6
Alignment explanation
Indices: 19578830--19578874 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
19578820 ACAATTCATA
* * *
19578830 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
19578875 ATTTTGCTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.22, C:0.31, G:0.00, T:0.47
Consensus pattern (6 bp):
TCACTT
Found at i:19585761 original size:22 final size:22
Alignment explanation
Indices: 19585709--19585756 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
19585699 CCATGATTAT
*
19585709 ATTATTATTTTATTTATTACTA
1 ATTACTATTTTATTTATTACTA
* *
19585731 TTTACTATTTTATTGTATTATTA
1 ATTACTATTTTATT-TATTACTA
19585754 ATT
1 ATT
19585757 GTATTCATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (22 bp):
ATTACTATTTTATTTATTACTA
Found at i:19588064 original size:18 final size:19
Alignment explanation
Indices: 19588029--19588063 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
19588019 CGTCAGCAAA
19588029 AAAAATTTAAAGTTAAAAC
1 AAAAATTTAAAGTTAAAAC
19588048 AAAAA-TTAAA-TTAAAA
1 AAAAATTTAAAGTTAAAA
19588064 AAACAAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 5 0.31
19 5 0.31
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (19 bp):
AAAAATTTAAAGTTAAAAC
Found at i:19588585 original size:25 final size:22
Alignment explanation
Indices: 19588533--19588581 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
19588523 TGTTTAATCA
* *
19588533 TGTTTAATCGATGTTGTTGTTT
1 TGTTTAATCGATATCGTTGTTT
19588555 TGTTTAATCGATATCGTTGTTT
1 TGTTTAATCGATATCGTTGTTT
19588577 TGTTT
1 TGTTT
19588582 TTTATTCCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.14, C:0.06, G:0.20, T:0.59
Consensus pattern (22 bp):
TGTTTAATCGATATCGTTGTTT
Found at i:19588831 original size:22 final size:22
Alignment explanation
Indices: 19588792--19588836 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
19588782 TGTTTAATAA
**
19588792 TGTTTAATCGATTTTGCTATTT
1 TGTTTAATCGATGCTGCTATTT
*
19588814 TGTTTAATCGATGCTGCTGTTT
1 TGTTTAATCGATGCTGCTATTT
19588836 T
1 T
19588837 ACCGAGAGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.16, C:0.11, G:0.18, T:0.56
Consensus pattern (22 bp):
TGTTTAATCGATGCTGCTATTT
Found at i:19589739 original size:42 final size:42
Alignment explanation
Indices: 19589680--19589765 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
19589670 CTTGAAATTC
19589680 TGCTTGTCTGTTGATGGTTTACCCTTGCAGTCCTACTGCAAT
1 TGCTTGTCTGTTGATGGTTTACCCTTGCAGTCCTACTGCAAT
* *
19589722 TGCTTGTCTGTTGATGGTTTACCCTTGCCGTCCTATTGCAAT
1 TGCTTGTCTGTTGATGGTTTACCCTTGCAGTCCTACTGCAAT
19589764 TG
1 TG
19589766 GAGATTGATG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.42
Consensus pattern (42 bp):
TGCTTGTCTGTTGATGGTTTACCCTTGCAGTCCTACTGCAAT
Found at i:19590609 original size:158 final size:155
Alignment explanation
Indices: 19590357--19590659 Score: 455
Period size: 158 Copynumber: 1.9 Consensus size: 155
19590347 AAATGGCATC
* * *
19590357 CTTTTTTGGCTTCTAGTTCTCATACTCGTACCAAATTGAGAACAACAATCAAAACCCAAATTAGA
1 CTTTTTTGGCTTCTAGTTCTCATACTCGTACCAAATTAAGAACAAAAATAAAAACCCAAATTAGA
* *
19590422 TTTAAATAATTTGGAATTGACAATGAGAAAGTGTTTACGATATACCTGTGATCCAGTTGTGTTAG
66 TTTAAATAATTTGGAATTGACAATGAGAAAATGTTTACGATATACCAGTGATCCAGTTGTGTTAG
19590487 GCTGAATGCATGGTGTTTTGTCGTT
131 GCTGAATGCATGGTGTTTTGTCGTT
* * * * *
19590512 CTTTTCTTGGGTTGTAGTTCTCGTACTCGTACCAGATTAAGACACAAAAAATAAAAACCGAAATT
1 CTTTT-TTGGCTTCTAGTTCTCATACTCGTACCAAATTAAGA-AC-AAAAATAAAAACCCAAATT
* *
19590577 AGA-TTATTATAATTTGGAATTGACAATGAGAAAATGTTTACGATATACCAGTGATCTAGTTGTG
63 AGATTTA-AATAATTTGGAATTGACAATGAGAAAATGTTTACGATATACCAGTGATCCAGTTGTG
19590641 TTAGGCTGAATGCATGGTG
127 TTAGGCTGAATGCATGGTG
19590660 GTGTTCAATT
Statistics
Matches: 132, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
155 5 0.04
156 31 0.23
157 5 0.04
158 91 0.69
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.34
Consensus pattern (155 bp):
CTTTTTTGGCTTCTAGTTCTCATACTCGTACCAAATTAAGAACAAAAATAAAAACCCAAATTAGA
TTTAAATAATTTGGAATTGACAATGAGAAAATGTTTACGATATACCAGTGATCCAGTTGTGTTAG
GCTGAATGCATGGTGTTTTGTCGTT
Found at i:19590819 original size:21 final size:21
Alignment explanation
Indices: 19590793--19590833 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
19590783 TTGAGTCAAA
* *
19590793 CATTTTCAAATATGTTAAAAC
1 CATTTTCAAACAAGTTAAAAC
19590814 CATTTTCAAACAAGTTAAAA
1 CATTTTCAAACAAGTTAAAA
19590834 TTGCTCCAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.34
Consensus pattern (21 bp):
CATTTTCAAACAAGTTAAAAC
Found at i:19593892 original size:21 final size:21
Alignment explanation
Indices: 19593866--19593907 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
19593856 TTGAGTCAAA
*
19593866 CATTTTCAAATATGTTAAAAC
1 CATTTTCAAATAAGTTAAAAC
19593887 CATTTTCAAATAAGTTAAAAC
1 CATTTTCAAATAAGTTAAAAC
19593908 TGCTTCAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (21 bp):
CATTTTCAAATAAGTTAAAAC
Found at i:19594917 original size:36 final size:36
Alignment explanation
Indices: 19594865--19594955 Score: 164
Period size: 36 Copynumber: 2.5 Consensus size: 36
19594855 GAGACCCTGC
*
19594865 AATTTAAATTAGAAAACATAAGTAAGTCTACTGTCA
1 AATTTAAATTAAAAAACATAAGTAAGTCTACTGTCA
*
19594901 AATTTAAATTAAAAAACATAAGTAAGTCTATTGTCA
1 AATTTAAATTAAAAAACATAAGTAAGTCTACTGTCA
19594937 AATTTAAATTAAAAAACAT
1 AATTTAAATTAAAAAACAT
19594956 CTCATATGCT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 53 1.00
ACGTcount: A:0.52, C:0.09, G:0.08, T:0.32
Consensus pattern (36 bp):
AATTTAAATTAAAAAACATAAGTAAGTCTACTGTCA
Found at i:19595201 original size:2 final size:2
Alignment explanation
Indices: 19595194--19595222 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19595184 CAACCAAAGA
19595194 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
19595223 ACTTTAAAGG
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:19597365 original size:63 final size:63
Alignment explanation
Indices: 19597284--19597417 Score: 180
Period size: 63 Copynumber: 2.1 Consensus size: 63
19597274 ACCTCACCCT
* * *
19597284 AACCCTCAACACCTTCACTAATAGCATCCA-TACCCGAACCCTCACCACCTCCCTCACCCTTAA
1 AACCCTCAACACCCTCACTAACAGCA-CCATTACCCGAACCCTCACCACCTCCCTCACCCTCAA
* * * *
19597347 AACCCTTAGCACCCTCACTAACAGCACCATTACCCGAATCCTCACCACCTCGCTCACCCTCAA
1 AACCCTCAACACCCTCACTAACAGCACCATTACCCGAACCCTCACCACCTCCCTCACCCTCAA
*
19597410 CACCCTCA
1 AACCCTCA
19597418 CCCTTACCCG
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
62 3 0.05
63 58 0.95
ACGTcount: A:0.29, C:0.49, G:0.04, T:0.18
Consensus pattern (63 bp):
AACCCTCAACACCCTCACTAACAGCACCATTACCCGAACCCTCACCACCTCCCTCACCCTCAA
Found at i:19597466 original size:30 final size:30
Alignment explanation
Indices: 19597431--19597493 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
19597421 TTACCCGAAT
* *
19597431 CCTCACCACCCTTACT-GTCATTATCCAAAC
1 CCTCACCACCCTTACTACT-ATCATCCAAAC
19597461 CCTCACCACCCTTACTACTATCATCCAAAC
1 CCTCACCACCCTTACTACTATCATCCAAAC
19597491 CCT
1 CCT
19597494 TACCCTCACC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 29 0.97
31 1 0.03
ACGTcount: A:0.27, C:0.46, G:0.02, T:0.25
Consensus pattern (30 bp):
CCTCACCACCCTTACTACTATCATCCAAAC
Found at i:19597509 original size:9 final size:9
Alignment explanation
Indices: 19597495--19597542 Score: 62
Period size: 9 Copynumber: 5.3 Consensus size: 9
19597485 CCAAACCCTT
19597495 ACCCTCACC
1 ACCCTCACC
19597504 ACCCTCACC
1 ACCCTCACC
*
19597513 A-CCTCCCGC
1 ACCCTCAC-C
*
19597522 ACCCTCAAC
1 ACCCTCACC
19597531 ACCCTCACC
1 ACCCTCACC
19597540 ACC
1 ACC
19597543 TTTTTTACCA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
8 5 0.15
9 24 0.73
10 4 0.12
ACGTcount: A:0.23, C:0.65, G:0.02, T:0.10
Consensus pattern (9 bp):
ACCCTCACC
Found at i:19607451 original size:3 final size:3
Alignment explanation
Indices: 19607443--19607495 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
19607433 AAATACTTAG
19607443 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
19607491 A-A AGA
1 AGA AGA
19607496 GTTTTGGGTT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:19612478 original size:6 final size:6
Alignment explanation
Indices: 19612467--19612516 Score: 72
Period size: 6 Copynumber: 9.0 Consensus size: 6
19612457 TCTTACCACC
19612467 TCTTTT TCTTTT TCTTTT TC--TT TCTTTT TCTTTT TC--TT TCTTTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT
19612511 TCTTTT
1 TCTTTT
19612517 CTCTCGCGCT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
4 8 0.20
6 32 0.80
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TCTTTT
Found at i:19612490 original size:16 final size:16
Alignment explanation
Indices: 19612471--19612516 Score: 92
Period size: 16 Copynumber: 2.9 Consensus size: 16
19612461 ACCACCTCTT
19612471 TTTCTTTTTCTTTTTC
1 TTTCTTTTTCTTTTTC
19612487 TTTCTTTTTCTTTTTC
1 TTTCTTTTTCTTTTTC
19612503 TTTCTTTTTCTTTT
1 TTTCTTTTTCTTTT
19612517 CTCTCGCGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTCTTTTTCTTTTTC
Found at i:19612492 original size:22 final size:22
Alignment explanation
Indices: 19612467--19612516 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
19612457 TCTTACCACC
19612467 TCTTTTTCTTTTTCTTTTTCTT
1 TCTTTTTCTTTTTCTTTTTCTT
19612489 TCTTTTTCTTTTTCTTTCTT-TT
1 TCTTTTTCTTTTTCTTT-TTCTT
19612511 TCTTTT
1 TCTTTT
19612517 CTCTCGCGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 25 0.93
23 2 0.07
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (22 bp):
TCTTTTTCTTTTTCTTTTTCTT
Found at i:19616746 original size:55 final size:55
Alignment explanation
Indices: 19616661--19616797 Score: 175
Period size: 55 Copynumber: 2.5 Consensus size: 55
19616651 TTCCTCAGAG
* * * * * *
19616661 TTAGCCATGAAGGTGTCTTTTAACAGAGATAGCCAGAAATACTTTCTTTAACATAA
1 TTAGCCATGAAGG-CTCCTTTAACAGAGATAGCCAGAAAGACTTCCCTTAACAAAA
* * *
19616717 TTAGCCACGAAGGCTCCTTTAATAGAGATAGCCAGAAAGGCTTCCCTTAACAAAA
1 TTAGCCATGAAGGCTCCTTTAACAGAGATAGCCAGAAAGACTTCCCTTAACAAAA
*
19616772 TTAGCCATGAAGACTCCTTTAACAGA
1 TTAGCCATGAAGGCTCCTTTAACAGA
19616798 ATCAACTAGA
Statistics
Matches: 69, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
55 57 0.83
56 12 0.17
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (55 bp):
TTAGCCATGAAGGCTCCTTTAACAGAGATAGCCAGAAAGACTTCCCTTAACAAAA
Found at i:19616748 original size:27 final size:26
Alignment explanation
Indices: 19616706--19616795 Score: 83
Period size: 27 Copynumber: 3.3 Consensus size: 26
19616696 GAAATACTTT
*
19616706 CTTTAACATAATTAGCCACGAAGGCTC
1 CTTTAACAAAATTAGCCA-GAAGGCTC
* *
19616733 CTTTAATAGAGA-TAGCCAGAAAGGCTTC
1 CTTTAACA-AAATTAGCCAG-AAGGC-TC
* *
19616761 CCTTAACAAAATTAGCCATGAAGACTC
1 CTTTAACAAAATTAGCCA-GAAGGCTC
19616788 CTTTAACA
1 CTTTAACA
19616796 GAATCAACTA
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
26 1 0.02
27 29 0.58
28 19 0.38
29 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (26 bp):
CTTTAACAAAATTAGCCAGAAGGCTC
Found at i:19616809 original size:55 final size:55
Alignment explanation
Indices: 19616679--19616811 Score: 151
Period size: 55 Copynumber: 2.4 Consensus size: 55
19616669 GAAGGTGTCT
* ** * * * *
19616679 TTTAACAGAGATAGCCAGAAATACTTTCTTTAACATAATTAGCCACGAAGGCTCC
1 TTTAACAGAGATAACCAGAAAGGCTTCCCTTAACAAAATTAGCCACGAAGACTCC
* * *
19616734 TTTAATAGAGATAGCCAGAAAGGCTTCCCTTAACAAAATTAGCCATGAAGACTCC
1 TTTAACAGAGATAACCAGAAAGGCTTCCCTTAACAAAATTAGCCACGAAGACTCC
*
19616789 TTTAACAGA-ATCAACTAGAAAGG
1 TTTAACAGAGAT-AACCAGAAAGG
19616812 TTTTTTTACA
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
54 2 0.03
55 64 0.97
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (55 bp):
TTTAACAGAGATAACCAGAAAGGCTTCCCTTAACAAAATTAGCCACGAAGACTCC
Found at i:19619271 original size:20 final size:21
Alignment explanation
Indices: 19619243--19619285 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
19619233 CACAATTAAA
*
19619243 TAATTTTAAATTCTAAAA-AT
1 TAATATTAAATTCTAAAATAT
* *
19619263 TAATATTAATTTTTAAAATAT
1 TAATATTAAATTCTAAAATAT
19619284 TA
1 TA
19619286 TCAATAATAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
TAATATTAAATTCTAAAATAT
Found at i:19619517 original size:10 final size:10
Alignment explanation
Indices: 19619502--19619534 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
19619492 GTAACTGAAT
19619502 TTAATTGTAA
1 TTAATTGTAA
19619512 TTAATTGTAA
1 TTAATTGTAA
*
19619522 TTATTTGTAA
1 TTAATTGTAA
19619532 TTA
1 TTA
19619535 CATATATGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (10 bp):
TTAATTGTAA
Found at i:19622726 original size:14 final size:14
Alignment explanation
Indices: 19622709--19622739 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
19622699 TGTATTTATA
19622709 CATATATATATACC
1 CATATATATATACC
19622723 CATATATATATACC
1 CATATATATATACC
19622737 CAT
1 CAT
19622740 TAAGGGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (14 bp):
CATATATATATACC
Found at i:19628506 original size:26 final size:25
Alignment explanation
Indices: 19628446--19628530 Score: 109
Period size: 26 Copynumber: 3.3 Consensus size: 25
19628436 CGTGCCTAGA
19628446 CAGTATATCGCTCTTACGAGCC-TAT
1 CAGTATATCGCTCTTACGAGCCAT-T
*
19628471 CAGAATATCGCTCTTACGAGCCAGTT
1 CAGTATATCGCTCTTACGAGCCA-TT
*
19628497 CAGTATATCGCTCTTTCGAGCCAATT
1 CAGTATATCGCTCTTACGAGCC-ATT
*
19628523 TAGTATAT
1 CAGTATAT
19628531 TTGTCAAGTC
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
25 21 0.40
26 30 0.57
27 2 0.04
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (25 bp):
CAGTATATCGCTCTTACGAGCCATT
Found at i:19631955 original size:222 final size:222
Alignment explanation
Indices: 19631569--19632009 Score: 828
Period size: 222 Copynumber: 2.0 Consensus size: 222
19631559 CGAAAGTCAT
* *
19631569 AGGCTTCAATACTTGTTCTAAGCCTAACTCCATCTTGTGTAGACATTCTCTTATTCGATGCTCTA
1 AGGCTTCAATACTTGTTCTAAGCCTAAATCCATCTTGTGCAGACATTCTCTTATTCGATGCTCTA
19631634 GAGATCCACAATGAAAACAACCCCAATCTTGGATTTACACTCTCTTGCATGAAATTTTCCACAAT
66 GAGATCCACAATGAAAACAACCCCAATCTTGGATTTACACTCTCTTGCATGAAATTTTCCACAAT
19631699 TCTTACAAAGAAGGATATCTATATTTCGAACACTTCCAACACTAGCCACGGAAGTAGCTTGTGAC
131 TCTTACAAAGAAGGATATCTATATTTCGAACACTTCCAACACTAGCCACGGAAGTAGCTTGTGAC
19631764 TTCAAAGAAAACTGATTAAATGTGCAC
196 TTCAAAGAAAACTGATTAAATGTGCAC
*
19631791 AGGCTTCGATACTTGTTCTAAGCCTAAATCCATCTTGTGCAGACATTCTCTTATTCGATGCTCTA
1 AGGCTTCAATACTTGTTCTAAGCCTAAATCCATCTTGTGCAGACATTCTCTTATTCGATGCTCTA
19631856 GAGATCCACAATGAAAACAACCCCAATCTTGGATTTACACTCTCTTGCATGAAATTTTCCACAAT
66 GAGATCCACAATGAAAACAACCCCAATCTTGGATTTACACTCTCTTGCATGAAATTTTCCACAAT
* * *
19631921 TCTTACAAAGAGGGATGTCTGTATTTCGAACACTTCCAACACTAGCCACGGAAGTAGCTTGTGAC
131 TCTTACAAAGAAGGATATCTATATTTCGAACACTTCCAACACTAGCCACGGAAGTAGCTTGTGAC
19631986 TTCAAAGAAAACTGATTAAATGTG
196 TTCAAAGAAAACTGATTAAATGTG
19632010 TTTCTTCTCA
Statistics
Matches: 213, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
222 213 1.00
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (222 bp):
AGGCTTCAATACTTGTTCTAAGCCTAAATCCATCTTGTGCAGACATTCTCTTATTCGATGCTCTA
GAGATCCACAATGAAAACAACCCCAATCTTGGATTTACACTCTCTTGCATGAAATTTTCCACAAT
TCTTACAAAGAAGGATATCTATATTTCGAACACTTCCAACACTAGCCACGGAAGTAGCTTGTGAC
TTCAAAGAAAACTGATTAAATGTGCAC
Done.