Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 11 of 185
Found at i:3136726 original size:3 final size:3
Alignment explanation
Indices: 3136718--3136749 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3136708 CAATTTCTAG
3136718 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3136750 CCCATAATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3138510 original size:39 final size:39
Alignment explanation
Indices: 3138467--3138545 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
3138457 ATTATCGAGT
3138467 TAATACCATTTTACGTTGATGTATTGCATATACAAACAA
1 TAATACCATTTTACGTTGATGTATTGCATATACAAACAA
*
3138506 TAATACCATTTTACGTTGATTTATTGCATATACAAACAA
1 TAATACCATTTTACGTTGATGTATTGCATATACAAACAA
3138545 T
1 T
3138546 TATATTAATC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (39 bp):
TAATACCATTTTACGTTGATGTATTGCATATACAAACAA
Found at i:3139856 original size:33 final size:33
Alignment explanation
Indices: 3139810--3139965 Score: 92
Period size: 33 Copynumber: 4.6 Consensus size: 33
3139800 CATATAAAGG
**
3139810 GGTTGCTGTGTGCTGATTCCCCTGTTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCTGTTCATTGGT
* * *
3139843 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGGAAGGG
1 GGTTGCTAAGTGCTGATTCC-CC---TGTT-CAT-T----GGT
*
3139886 GGTTGCTAAGTGCTGATTCCCCCG---A--GG-
1 GGTTGCTAAGTGCTGATTCCCCTGTTCATTGGT
**
3139913 GGTTGCTAAGTGCTGATTCCCCT-ACCTATTGGT
1 GGTTGCTAAGTGCTGATTCCCCTGTTC-ATTGGT
3139946 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
3139966 ACCGTATTTT
Statistics
Matches: 98, Mismatches: 8, Indels: 34
0.70 0.06 0.24
Matches are distributed among these distances:
27 22 0.22
28 2 0.02
30 1 0.01
32 2 0.02
33 38 0.39
34 2 0.02
35 1 0.01
37 3 0.03
38 2 0.02
39 1 0.01
42 2 0.02
43 22 0.22
ACGTcount: A:0.15, C:0.21, G:0.29, T:0.35
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCTGTTCATTGGT
Found at i:3139935 original size:103 final size:103
Alignment explanation
Indices: 3139807--3140173 Score: 544
Period size: 103 Copynumber: 3.6 Consensus size: 103
3139797 TTGCATATAA
** *
3139807 AGGGGTTGCTGTGTGCTGATTCCCCTG-TTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
1 AGGGGTTGCTAAGTGCTGATTCCCC-GATCCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
3139871 TTAAATGTGGAAGGGGGTTGCTAAGTGCTGATTCCCCCG
65 TTAAATGTGGAAGGGGGTTGCTAAGTGCTGATTCCCCCG
*
3139910 AGGGGTTGCTAAGTGCTGATTCCCCTA-CCTATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATCC-ATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
*
3139974 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCCG
65 TTAAATGTGGAAGGGGGTTGCTAAGTGCTGATTCCCCCG
* * *
3140013 AGGGGTTGCTAAGTGCTGATTCCCCGACCCATTTGGTGGTTGCTAAGTGCTGATTCCACCGCATC
1 AGGGGTTGCTAAGTGCTGATTCCCCGATCCA-TTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
* *
3140078 TGAAATGT-GAAGGGGGTTGCTAAGTGCTGATTCCCCCA
65 TTAAATGTGGAAGGGGGTTGCTAAGTGCTGATTCCCCCG
** * * *
3140116 AGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGG-TGCTAAGTGCGGAATCCACC
1 AGGGGTTGCTAAGTGCTGATTCCCCGATCCATTGGTGGTTGCTAAGTGCTGATTCCACC
3140174 AACAACGGTT
Statistics
Matches: 243, Mismatches: 17, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
101 18 0.07
102 8 0.03
103 177 0.73
104 40 0.16
ACGTcount: A:0.18, C:0.21, G:0.30, T:0.31
Consensus pattern (103 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATCCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATTT
TAAATGTGGAAGGGGGTTGCTAAGTGCTGATTCCCCCG
Found at i:3141576 original size:19 final size:19
Alignment explanation
Indices: 3141552--3141589 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3141542 CAAGTGTGTA
3141552 TCTACTTTAGTGGTTAAGT
1 TCTACTTTAGTGGTTAAGT
3141571 TCTACTTTAGTGGTTAAGT
1 TCTACTTTAGTGGTTAAGT
3141590 GTTTTTGGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.11, G:0.21, T:0.47
Consensus pattern (19 bp):
TCTACTTTAGTGGTTAAGT
Found at i:3166932 original size:18 final size:19
Alignment explanation
Indices: 3166900--3166935 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
3166890 TACTTTACTC
3166900 TTTATTTTATTGTTTATTG
1 TTTATTTTATTGTTTATTG
3166919 TTTATTTT-TTGTTTATT
1 TTTATTTTATTGTTTATT
3166936 TTTTTTTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.14, C:0.00, G:0.08, T:0.78
Consensus pattern (19 bp):
TTTATTTTATTGTTTATTG
Found at i:3169380 original size:26 final size:26
Alignment explanation
Indices: 3169350--3169473 Score: 176
Period size: 26 Copynumber: 4.7 Consensus size: 26
3169340 TTCCTTATTT
* *
3169350 GCCACAAAGGCATTCTTTCATATTAT
1 GCCACAAAGGCTTTCTTTCATATTAC
3169376 GCCACAAAGGCTTTCTTTCATATTAC
1 GCCACAAAGGCTTTCTTTCATATTAC
**
3169402 ATCACAAAGGCTTTCTTTCATATTAC
1 GCCACAAAGGCTTTCTTTCATATTAC
*
3169428 GCCACAAAGGATTTTCTTTCATATTAC
1 GCCACAAAGG-CTTTCTTTCATATTAC
* *
3169455 GTCATAAAGGCTTTCTTTC
1 GCCACAAAGGCTTTCTTTC
3169474 TTCATATTAC
Statistics
Matches: 87, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
26 64 0.74
27 23 0.26
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.37
Consensus pattern (26 bp):
GCCACAAAGGCTTTCTTTCATATTAC
Found at i:3170134 original size:20 final size:19
Alignment explanation
Indices: 3170091--3170134 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
3170081 CCGTCACACC
*
3170091 AAAATTTAATTAATTTTTT
1 AAAATTTAATAAATTTTTT
3170110 AAAATTTAA-AAATATTTTT
1 AAAATTTAATAAAT-TTTTT
3170129 ATAAAT
1 A-AAAT
3170135 GTTACACTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 15 0.68
20 4 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AAAATTTAATAAATTTTTT
Found at i:3176414 original size:6 final size:6
Alignment explanation
Indices: 3176361--3176410 Score: 91
Period size: 6 Copynumber: 8.3 Consensus size: 6
3176351 GAGTGAGTAT
*
3176361 TGGGTA TGGGTA TGGGTA TGGGTA TGGGTA TGGGTA TGGGTA TGAGTA
1 TGGGTA TGGGTA TGGGTA TGGGTA TGGGTA TGGGTA TGGGTA TGGGTA
3176409 TG
1 TG
3176411 AGTACGAGTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.18, C:0.00, G:0.48, T:0.34
Consensus pattern (6 bp):
TGGGTA
Found at i:3177171 original size:28 final size:27
Alignment explanation
Indices: 3177136--3177193 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 27
3177126 AGGTTCTGAA
3177136 TAAAAAGAAATATGTTTT-GTTGAAATAG
1 TAAAAAGAAATAT-TTTTAGTTG-AATAG
3177164 TAAAAAGAAATATTTTTAGTTGAATAG
1 TAAAAAGAAATATTTTTAGTTGAATAG
3177191 TAA
1 TAA
3177194 GATTGCTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
27 12 0.41
28 17 0.59
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (27 bp):
TAAAAAGAAATATTTTTAGTTGAATAG
Found at i:3177590 original size:16 final size:16
Alignment explanation
Indices: 3177569--3177602 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
3177559 AAGGACATCT
3177569 TTCGGTTTACCTCTGA
1 TTCGGTTTACCTCTGA
3177585 TTCGGTTTACCTCTGA
1 TTCGGTTTACCTCTGA
3177601 TT
1 TT
3177603 ATTACATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.47
Consensus pattern (16 bp):
TTCGGTTTACCTCTGA
Found at i:3180727 original size:4 final size:4
Alignment explanation
Indices: 3180718--3180751 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
3180708 ACAAAGGTGC
3180718 TTTA TTTA TTTA TTTA TTTA TTTA TTT- TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
3180752 CAAAATAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (4 bp):
TTTA
Found at i:3182885 original size:3 final size:3
Alignment explanation
Indices: 3182863--3183056 Score: 86
Period size: 3 Copynumber: 65.0 Consensus size: 3
3182853 AAATGGAAAT
* * * * *
3182863 ATA ATG ATA AGA ACA ATA ATA ATA ATA TTA ATA TTA ATAA ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA
* * * * * * * * *
3182908 AAA ATA ACA ACA TTA GTA ATA ATT CTA ATG ATA ATA CTA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* ** * * * * *
3182956 GTA AGG GTA ATA ATA ATA ATA TTA TTA ATA ATA CTA CTA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * ** * *
3183004 ATC GTA ATC ATA A-A CTA ATT AGC TTA ATA ATA ATA AAA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3183051 ATA ATA
1 ATA ATA
3183057 GGACTAAATT
Statistics
Matches: 136, Mismatches: 52, Indels: 6
0.70 0.27 0.03
Matches are distributed among these distances:
2 3 0.02
3 130 0.96
4 3 0.02
ACGTcount: A:0.57, C:0.06, G:0.05, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3184087 original size:2 final size:2
Alignment explanation
Indices: 3184082--3184111 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3184072 TCATTATTAT
3184082 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
3184112 TATATATGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:3185015 original size:38 final size:37
Alignment explanation
Indices: 3184946--3185018 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 37
3184936 TTTTCATAAT
* *
3184946 TTCACTTTTTCACTTTTAATCACTATTCAATTCAAAA
1 TTCACTTTTCCACTTTTAATCAATATTCAATTCAAAA
3184983 TTCACTTTTCCA-TTTTCAAGTCAATATTCAATTCAA
1 TTCACTTTTCCACTTTT-AA-TCAATATTCAATTCAA
3185019 TTCCACACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 4 0.12
37 13 0.41
38 15 0.47
ACGTcount: A:0.32, C:0.22, G:0.01, T:0.45
Consensus pattern (37 bp):
TTCACTTTTCCACTTTTAATCAATATTCAATTCAAAA
Found at i:3185049 original size:23 final size:22
Alignment explanation
Indices: 3185006--3185049 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
3184996 TTTCAAGTCA
3185006 ATATTCAATTCAATTCCACACAT
1 ATATTCAATTCAATT-CACACAT
3185029 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
3185050 TTAATCGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACAT
Found at i:3185174 original size:23 final size:23
Alignment explanation
Indices: 3185148--3185246 Score: 171
Period size: 23 Copynumber: 4.3 Consensus size: 23
3185138 ATAAGTGCCA
3185148 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
3185171 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
3185194 CACTGATATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
3185217 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
3185240 CACTGAT
1 CACTGAT
3185247 CAATAACACT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:3185215 original size:46 final size:46
Alignment explanation
Indices: 3185148--3185246 Score: 189
Period size: 46 Copynumber: 2.2 Consensus size: 46
3185138 ATAAGTGCCA
*
3185148 CACTGATATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTAC
3185194 CACTGATATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTAC
3185240 CACTGAT
1 CACTGAT
3185247 CAATAACACT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 52 1.00
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.20
Consensus pattern (46 bp):
CACTGATATGTAGCCAAAGCTACCACTGAAATGTAGCCGAAGCTAC
Found at i:3188609 original size:14 final size:14
Alignment explanation
Indices: 3188590--3188621 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
3188580 TAAATATATA
3188590 TTTTTTATTTTTAT
1 TTTTTTATTTTTAT
3188604 TTTTTTATTTTTAT
1 TTTTTTATTTTTAT
3188618 TTTT
1 TTTT
3188622 AAAATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTTTATTTTTAT
Found at i:3194398 original size:25 final size:25
Alignment explanation
Indices: 3194353--3194400 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
3194343 AAAAAATTAA
* *
3194353 TTTATTTTTAATTATTTAAATATTT
1 TTTATTTTGAATTATTCAAATATTT
3194378 TTTATTTTGAACTTA-TCAAATAT
1 TTTATTTTGAA-TTATTCAAATAT
3194401 GGTAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 17 0.85
26 3 0.15
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.60
Consensus pattern (25 bp):
TTTATTTTGAATTATTCAAATATTT
Found at i:3200558 original size:20 final size:18
Alignment explanation
Indices: 3200533--3200584 Score: 50
Period size: 20 Copynumber: 2.8 Consensus size: 18
3200523 CAATAAATGC
3200533 ATAAAAAATTATAAAAAT
1 ATAAAAAATTATAAAAAT
** *
3200551 AATCAAAATTTTACAAAAAT
1 -AT-AAAAAATTATAAAAAT
*
3200571 ATAAAAAATAATAA
1 ATAAAAAATTATAA
3200585 GCGTAATTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 3
0.71 0.20 0.09
Matches are distributed among these distances:
18 8 0.32
19 4 0.16
20 13 0.52
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (18 bp):
ATAAAAAATTATAAAAAT
Found at i:3200738 original size:20 final size:21
Alignment explanation
Indices: 3200687--3200741 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 21
3200677 TTCTTTACAA
*
3200687 TTTT-TTATAATTTTTGTGAT
1 TTTTATTATAATTTTTCTGAT
* *
3200707 TTCTA-TAAAATTTTTCT-AT
1 TTTTATTATAATTTTTCTGAT
3200726 TTTTATTATAATTTTT
1 TTTTATTATAATTTTT
3200742 AAATATTTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.67
Consensus pattern (21 bp):
TTTTATTATAATTTTTCTGAT
Found at i:3200759 original size:10 final size:9
Alignment explanation
Indices: 3200667--3200804 Score: 51
Period size: 10 Copynumber: 13.8 Consensus size: 9
3200657 TTTGAATTTT
3200667 TTTTTATAAA
1 TTTTTAT-AA
*
3200677 TTCTTTACAA
1 TT-TTTATAA
3200687 TTTTTTATAA
1 -TTTTTATAA
* *
3200697 TTTTTGTGA
1 TTTTTATAA
*
3200706 TTTCTATAAAA
1 TTT-T-TATAA
* *
3200717 TTTTTCTATT
1 TTTTTATA-A
3200727 TTTATTATAA
1 TTT-TTATAA
*
3200737 TTTTTAAATA
1 TTTTTATA-A
3200747 TTTTCTATAA
1 TTTT-TATAA
3200757 TTTTTTATAAAA
1 -TTTTTAT--AA
* *
3200769 TTTTAATAT
1 TTTTTATAA
3200778 TTTTCTATAA
1 TTTT-TATAA
* *
3200788 CTTTTATCGA
1 TTTTTAT-AA
3200798 TTTTTAT
1 TTTTTAT
3200805 TTCTTTTATC
Statistics
Matches: 94, Mismatches: 21, Indels: 26
0.67 0.15 0.18
Matches are distributed among these distances:
9 24 0.26
10 40 0.43
11 28 0.30
12 2 0.02
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:3200782 original size:31 final size:31
Alignment explanation
Indices: 3200712--3200792 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 31
3200702 GTGATTTCTA
**
3200712 TAAA-ATTTTTCTAT--TTTTATTATAATTTT
1 TAAATATTTTTCTATAATTTT-TTATAAAATT
3200741 TAAATAT-TTTCTATAATTTTTTATAAAATT
1 TAAATATTTTTCTATAATTTTTTATAAAATT
* *
3200771 TTAATATTTTTCTATAACTTTT
1 TAAATATTTTTCTATAATTTTT
3200793 ATCGATTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
29 11 0.25
30 16 0.36
31 17 0.39
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (31 bp):
TAAATATTTTTCTATAATTTTTTATAAAATT
Found at i:3205373 original size:32 final size:31
Alignment explanation
Indices: 3205331--3205393 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 31
3205321 TTGAATTTAA
* *
3205331 TAAAATAAAACAAA-ACATTAAATTAAATATT
1 TAAAATAAAACAAATA-ATAAAATCAAATATT
3205362 TAAAAGTAAAACAAATAATAAAATCAAATATT
1 TAAAA-TAAAACAAATAATAAAATCAAATATT
3205394 CATATCCTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 5 0.18
32 22 0.79
33 1 0.04
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (31 bp):
TAAAATAAAACAAATAATAAAATCAAATATT
Found at i:3214395 original size:29 final size:29
Alignment explanation
Indices: 3214268--3214433 Score: 136
Period size: 29 Copynumber: 5.6 Consensus size: 29
3214258 GTCATTAGGG
* *
3214268 TTTATCAGACACTATGTACAGGTGATTATA
1 TTTATCAGGCACTATGTACCGGTG-TTATA
* * * **
3214298 TTTATTAGGTACTATGAACCGGTGGCCATA
1 TTTATCAGGCACTATGTACCGGT-GTTATA
* * * * *
3214328 -TTATCAAGTACTTTGTATCGGTGTTCATG
1 TTTATCAGGCACTATGTACCGGTGTT-ATA
*
3214357 TTGTATCAGGCACTATGTGCCGGTGTTATA
1 TT-TATCAGGCACTATGTACCGGTGTTATA
* *
3214387 TTTATCAGGCACTATGTGCCAGTGTTATA
1 TTTATCAGGCACTATGTACCGGTGTTATA
**
3214416 TTTATCAGATACTATGTA
1 TTTATCAGGCACTATGTA
3214434 TAGGTGGTGG
Statistics
Matches: 107, Mismatches: 25, Indels: 9
0.76 0.18 0.06
Matches are distributed among these distances:
28 1 0.01
29 60 0.56
30 26 0.24
31 20 0.19
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (29 bp):
TTTATCAGGCACTATGTACCGGTGTTATA
Found at i:3214422 original size:89 final size:90
Alignment explanation
Indices: 3214270--3214439 Score: 193
Period size: 89 Copynumber: 1.9 Consensus size: 90
3214260 CATTAGGGTT
* * *
3214270 TATCAGACACTATGTACAGGTGATTATATTTATTAGGTACTATGAACCGGTGGCCATATTATCA-
1 TATCAGACACTATGTACAGGTGATTATATTTATCAGGCACTATGAACCAGTGGCCATATTATCAG
* *
3214334 AGTACTTTGTATCGGTGTTCATGTTG
66 A-TACTATGTATAGGTGTTCATGTTG
* * * ** **
3214360 TATCAGGCACTATGTGCCGGTG-TTATATTTATCAGGCACTATGTGCCAGT-GTTATATTTATCA
1 TATCAGACACTATGTACAGGTGATTATATTTATCAGGCACTATGAACCAGTGGCCATA-TTATCA
3214423 GATACTATGTATAGGTG
65 GATACTATGTATAGGTG
3214440 GTGGATATCA
Statistics
Matches: 66, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
88 4 0.06
89 42 0.64
90 20 0.30
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.38
Consensus pattern (90 bp):
TATCAGACACTATGTACAGGTGATTATATTTATCAGGCACTATGAACCAGTGGCCATATTATCAG
ATACTATGTATAGGTGTTCATGTTG
Found at i:3216509 original size:51 final size:51
Alignment explanation
Indices: 3216382--3216564 Score: 194
Period size: 51 Copynumber: 3.6 Consensus size: 51
3216372 AAAGTGATGG
* * *
3216382 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGA-ATGATAGGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATA-GTTATGA
* * * * *
3216433 TGCA--TGTCTAGTACTATGTGTAGGCTACTATGCGTACCGGATAGTTTTGA
1 T-CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTTATGA
* * *
3216483 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGTAAT-A
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTTATGA
* *
3216533 GTCACATGTGTAGTACTATGTGCAGGGTACTA
1 -TCACGTGTGTAGTACTATGTGCAGGCTACTA
3216565 TATGAACTGA
Statistics
Matches: 109, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
49 2 0.02
50 38 0.35
51 67 0.61
52 2 0.02
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.32
Consensus pattern (51 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTTATGA
Found at i:3216626 original size:45 final size:45
Alignment explanation
Indices: 3216575--3216663 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
3216565 TATGAACTGA
* *
3216575 ACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCCACCGG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCGG
*
3216620 ACATCATTGATTAATGAGGTGGTTGCTATGTGCTGAATCCACCG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCG
3216664 AGTATCTGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.33
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCGG
Found at i:3220150 original size:6 final size:6
Alignment explanation
Indices: 3220126--3220206 Score: 72
Period size: 6 Copynumber: 13.0 Consensus size: 6
3220116 CAAGTCGTTG
* * * * * *
3220126 CCTCCA CTTCCA CCACCT CCTCCT CCTCCA CCACCA CCTCCT CCTCCA
1 CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA
*
3220174 CCTCCA CCTCCA CCACTACCA CCTCCA CTTCCA
1 CCTCCA CCTCCA -C-CT-CCA CCTCCA CCTCCA
3220207 TATCCGGACC
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
6 52 0.85
7 3 0.05
8 3 0.05
9 3 0.05
ACGTcount: A:0.17, C:0.63, G:0.00, T:0.20
Consensus pattern (6 bp):
CCTCCA
Found at i:3220155 original size:18 final size:18
Alignment explanation
Indices: 3220134--3220184 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
3220124 TGCCTCCACT
*
3220134 TCCACCACCTCCTCCTCC
1 TCCACCACCACCTCCTCC
3220152 TCCACCACCACCTCCTCC
1 TCCACCACCACCTCCTCC
*
3220170 TCCACCTCCACCTCC
1 TCCACCACCACCTCC
3220185 ACCACTACCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.14, C:0.67, G:0.00, T:0.20
Consensus pattern (18 bp):
TCCACCACCACCTCCTCC
Found at i:3220195 original size:15 final size:15
Alignment explanation
Indices: 3220150--3220201 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
3220140 ACCTCCTCCT
* *
3220150 CCTCCACCACCACCT
1 CCTCCACCACTACCA
*
3220165 CCTCCTCCACCT-CCA
1 CCTCCACCA-CTACCA
3220180 CCTCCACCACTACCA
1 CCTCCACCACTACCA
3220195 CCTCCAC
1 CCTCCAC
3220202 TTCCATATCC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 2 0.06
15 28 0.90
16 1 0.03
ACGTcount: A:0.19, C:0.65, G:0.00, T:0.15
Consensus pattern (15 bp):
CCTCCACCACTACCA
Found at i:3220246 original size:3 final size:3
Alignment explanation
Indices: 3220240--3220297 Score: 53
Period size: 3 Copynumber: 19.3 Consensus size: 3
3220230 TCCTCCATTG
* * * * * *
3220240 CCA CCA CCA CCT CCA CCA CCT CTA CCA CCA CCA CCT CCT CCA CCA CCT
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA
*
3220288 CCA CCT CCA C
1 CCA CCA CCA C
3220298 TTCCATATCC
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.22, C:0.66, G:0.00, T:0.12
Consensus pattern (3 bp):
CCA
Found at i:3220257 original size:9 final size:9
Alignment explanation
Indices: 3220243--3220292 Score: 73
Period size: 9 Copynumber: 5.6 Consensus size: 9
3220233 TCCATTGCCA
3220243 CCACCACCT
1 CCACCACCT
3220252 CCACCACCT
1 CCACCACCT
* *
3220261 CTACCACCA
1 CCACCACCT
*
3220270 CCACCTCCT
1 CCACCACCT
3220279 CCACCACCT
1 CCACCACCT
3220288 CCACC
1 CCACC
3220293 TCCACTTCCA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.22, C:0.66, G:0.00, T:0.12
Consensus pattern (9 bp):
CCACCACCT
Found at i:3220257 original size:12 final size:12
Alignment explanation
Indices: 3220240--3220302 Score: 74
Period size: 12 Copynumber: 5.2 Consensus size: 12
3220230 TCCTCCATTG
3220240 CCACCACCACCT
1 CCACCACCACCT
*
3220252 CCACCACC-TCT
1 CCACCACCACCT
3220263 ACCACCACCACCT
1 -CCACCACCACCT
*
3220276 CCTCCACCACCT
1 CCACCACCACCT
* *
3220288 CCACCTCCACTT
1 CCACCACCACCT
3220300 CCA
1 CCA
3220303 TATCCAGATC
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
11 2 0.05
12 39 0.91
13 2 0.05
ACGTcount: A:0.22, C:0.63, G:0.00, T:0.14
Consensus pattern (12 bp):
CCACCACCACCT
Found at i:3220271 original size:114 final size:107
Alignment explanation
Indices: 3220135--3220471 Score: 404
Period size: 114 Copynumber: 3.1 Consensus size: 107
3220125 GCCTCCACTT
* * * *
3220135 CCACCACCTCCTCCTCCT-CCACCACCACCTCCTCCTCCACCTCCACCTCCACCACTACCACCTC
1 CCACCGCCTCCACCACCTACCACCACCACCTCCTCCACCACCTCCACCTCCACCACTACCA--TC
3220199 CACTTCCATATCCGGACCCATATCCTGACCCTCCTCCATTGCCA
64 CACTTCCATATCCGGACCCATATCCTGACCCTCCTCCATTGCCA
*
3220243 CCACCACCTCCACCACCTCTACCACCACCACCTCCTCCACCACCTCCACCTCCACTTC-CATATC
1 CCACCGCCTCCACCA-C-CTACCACCACCACCTCCTCCACCACCTCCACCTCCAC--CAC-TA-C
*
3220307 CAGATCCACTTCCATATCCGGACCCATATCCTGACCCTCCTCTATTGCCA
60 C--ATCCACTTCCATATCCGGACCCATATCCTGACCCTCCTCCATTGCCA
*
3220357 CCACCGCCTCCACCACCTCCACCACCACCACCTCCTCCACCACCTCCACCT---CCACTTCCAT-
1 CCACCGCCTCCACCACCT--ACCACCACCACCTCCTCCACCACCTCCACCTCCACCACTACCATC
* ** *
3220418 -A--TCCAGATCCAAACCCATATCCTGACCCTTCTCCATTGCCA
64 CACTTCCATATCCGGACCCATATCCTGACCCTCCTCCATTGCCA
3220459 CCACCGCCTCCAC
1 CCACCGCCTCCAC
3220472 TTCCATATCC
Statistics
Matches: 206, Mismatches: 11, Indels: 30
0.83 0.04 0.12
Matches are distributed among these distances:
102 48 0.23
104 1 0.00
106 2 0.01
108 15 0.07
109 3 0.01
110 3 0.01
111 34 0.17
112 3 0.01
113 4 0.02
114 92 0.45
116 1 0.00
ACGTcount: A:0.21, C:0.55, G:0.04, T:0.20
Consensus pattern (107 bp):
CCACCGCCTCCACCACCTACCACCACCACCTCCTCCACCACCTCCACCTCCACCACTACCATCCA
CTTCCATATCCGGACCCATATCCTGACCCTCCTCCATTGCCA
Found at i:3220308 original size:18 final size:18
Alignment explanation
Indices: 3220287--3220325 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
3220277 CTCCACCACC
*
3220287 TCCACCTCCACTTCCATA
1 TCCACATCCACTTCCATA
*
3220305 TCCAGATCCACTTCCATA
1 TCCACATCCACTTCCATA
3220323 TCC
1 TCC
3220326 GGACCCATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.23, C:0.46, G:0.03, T:0.28
Consensus pattern (18 bp):
TCCACATCCACTTCCATA
Found at i:3220371 original size:12 final size:12
Alignment explanation
Indices: 3220354--3220416 Score: 72
Period size: 12 Copynumber: 5.2 Consensus size: 12
3220344 TCCTCTATTG
*
3220354 CCACCACCGCCT
1 CCACCACCACCT
* *
3220366 CCACCACCTCCA
1 CCACCACCACCT
3220378 CCACCACCACCT
1 CCACCACCACCT
*
3220390 CCTCCACCACCT
1 CCACCACCACCT
* *
3220402 CCACCTCCACTT
1 CCACCACCACCT
3220414 CCA
1 CCA
3220417 TATCCAGATC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 43 1.00
ACGTcount: A:0.21, C:0.65, G:0.02, T:0.13
Consensus pattern (12 bp):
CCACCACCACCT
Found at i:3220375 original size:9 final size:9
Alignment explanation
Indices: 3220357--3220406 Score: 73
Period size: 9 Copynumber: 5.6 Consensus size: 9
3220347 TCTATTGCCA
*
3220357 CCACCGCCT
1 CCACCACCT
3220366 CCACCACCT
1 CCACCACCT
*
3220375 CCACCACCA
1 CCACCACCT
*
3220384 CCACCTCCT
1 CCACCACCT
3220393 CCACCACCT
1 CCACCACCT
3220402 CCACC
1 CCACC
3220407 TCCACTTCCA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.20, C:0.68, G:0.02, T:0.10
Consensus pattern (9 bp):
CCACCACCT
Found at i:3220384 original size:15 final size:15
Alignment explanation
Indices: 3220354--3220411 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
3220344 TCCTCTATTG
* *
3220354 CCACCACCGCCTCCA
1 CCACCACCTCCACCA
* *
3220369 CCACCTCCACCACCA
1 CCACCACCTCCACCA
*
3220384 CCACCTCCTCCACCA
1 CCACCACCTCCACCA
*
3220399 CCTCCACCTCCAC
1 CCACCACCTCCAC
3220412 TTCCATATCC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.21, C:0.67, G:0.02, T:0.10
Consensus pattern (15 bp):
CCACCACCTCCACCA
Found at i:3220504 original size:3 final size:3
Alignment explanation
Indices: 3220498--3220546 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
3220488 TCCTCCACTG
* * * * *
3220498 CCA CCA CCT CCA CCG CCA CCT CCT CCT CCA CCA CCA CCA CCA CCA CCA
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA
3220546 C
1 C
3220547 TAGCACTACC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.22, C:0.67, G:0.02, T:0.08
Consensus pattern (3 bp):
CCA
Found at i:3220509 original size:15 final size:15
Alignment explanation
Indices: 3220489--3220546 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
3220479 TCCAAACCCT
*
3220489 CCTCCACTGCCACCA
1 CCTCCACCGCCACCA
*
3220504 CCTCCACCGCCACCT
1 CCTCCACCGCCACCA
* *
3220519 CCTCCTCCACCACCA
1 CCTCCACCGCCACCA
* *
3220534 CCACCACCACCAC
1 CCTCCACCGCCAC
3220547 TAGCACTACC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.21, C:0.66, G:0.03, T:0.10
Consensus pattern (15 bp):
CCTCCACCGCCACCA
Found at i:3220581 original size:18 final size:18
Alignment explanation
Indices: 3220560--3220595 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3220550 CACTACCACC
3220560 TCCACTTCCATATCCAGA
1 TCCACTTCCATATCCAGA
*
3220578 TCCACTTCCGTATCCAGA
1 TCCACTTCCATATCCAGA
3220596 CCCTTCTCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.39, G:0.08, T:0.28
Consensus pattern (18 bp):
TCCACTTCCATATCCAGA
Found at i:3220621 original size:9 final size:9
Alignment explanation
Indices: 3220609--3220643 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
3220599 TTCTCCACTG
3220609 CCACCACCT
1 CCACCACCT
*
3220618 CCACCACCA
1 CCACCACCT
*
3220627 CCACCTCCT
1 CCACCACCT
3220636 CCACCACC
1 CCACCACC
3220644 ACTAGAAATA
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:0.23, C:0.69, G:0.00, T:0.09
Consensus pattern (9 bp):
CCACCACCT
Found at i:3220621 original size:15 final size:15
Alignment explanation
Indices: 3220609--3220645 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
3220599 TTCTCCACTG
3220609 CCACCACCTCCACCA
1 CCACCACCTCCACCA
*
3220624 CCACCACCTCCTCCA
1 CCACCACCTCCACCA
3220639 CCACCAC
1 CCACCAC
3220646 TAGAAATACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.24, C:0.68, G:0.00, T:0.08
Consensus pattern (15 bp):
CCACCACCTCCACCA
Found at i:3220630 original size:18 final size:18
Alignment explanation
Indices: 3220609--3220645 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
3220599 TTCTCCACTG
3220609 CCACCACCTCCACCACCA
1 CCACCACCTCCACCACCA
*
3220627 CCACCTCCTCCACCACCA
1 CCACCACCTCCACCACCA
3220645 C
1 C
3220646 TAGAAATACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.68, G:0.00, T:0.08
Consensus pattern (18 bp):
CCACCACCTCCACCACCA
Found at i:3220718 original size:99 final size:99
Alignment explanation
Indices: 3220513--3220704 Score: 249
Period size: 99 Copynumber: 1.9 Consensus size: 99
3220503 ACCTCCACCG
* * * *
3220513 CCACCTCCTCCTCCACCACCACCACCACCACCACTAGCACTACCACCTCCACTTCCATATCCAGA
1 CCACCTCCACCACCACCACCACCACCACCACCACTAGAAATACCACCTCCACTTCCATATCCAGA
* * ****
3220578 TCCACTTCCGTATCCAGACCCTTCTCCACTGCCA
66 CCCACTTCCATATCCAGACCCGAAACCACTGCCA
* * *
3220612 CCACCTCCACCACCACCACCTCCTCCACCACCACTAGAAATACCACCTTCACTTCCATATCCAGA
1 CCACCTCCACCACCACCACCACCACCACCACCACTAGAAATACCACCTCCACTTCCATATCCAGA
* *
3220677 CCCACTTCCATATCCGGATCCGAAACCA
66 CCCACTTCCATATCCAGACCCGAAACCA
3220705 TATCCCGATC
Statistics
Matches: 78, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
99 78 1.00
ACGTcount: A:0.26, C:0.51, G:0.05, T:0.18
Consensus pattern (99 bp):
CCACCTCCACCACCACCACCACCACCACCACCACTAGAAATACCACCTCCACTTCCATATCCAGA
CCCACTTCCATATCCAGACCCGAAACCACTGCCA
Found at i:3220735 original size:3 final size:3
Alignment explanation
Indices: 3220729--3220760 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
3220719 TCCATTGCCG
*
3220729 CCA CCA CCA CCA CCT CCA CCA CCA CCA CCA CC
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CC
3220761 TCCTCTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.28, C:0.69, G:0.00, T:0.03
Consensus pattern (3 bp):
CCA
Found at i:3222338 original size:9 final size:9
Alignment explanation
Indices: 3222324--3222365 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
3222314 AATATTAATT
3222324 TTTTTATAA
1 TTTTTATAA
3222333 TTTTTAT-A
1 TTTTTATAA
3222341 TTTTTAATAA
1 TTTTT-ATAA
* *
3222351 TTTTAATGA
1 TTTTTATAA
3222360 TTTTTA
1 TTTTTA
3222366 ATTCTATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
8 6 0.21
9 17 0.61
10 5 0.18
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (9 bp):
TTTTTATAA
Found at i:3222350 original size:18 final size:19
Alignment explanation
Indices: 3222323--3222367 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
3222313 AAATATTAAT
* *
3222323 TTTTTTATAATTTTTAT-A
1 TTTTTAATAATTTTAATGA
3222341 TTTTTAATAATTTTAATGA
1 TTTTTAATAATTTTAATGA
3222360 TTTTTAAT
1 TTTTTAAT
3222368 TCTATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTTAATAATTTTAATGA
Found at i:3222353 original size:10 final size:10
Alignment explanation
Indices: 3222323--3222367 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
3222313 AAATATTAAT
*
3222323 TTTTTTATAA
1 TTTTTAATAA
3222333 TTTTT-AT-A
1 TTTTTAATAA
3222341 TTTTTAATAA
1 TTTTTAATAA
*
3222351 -TTTTAATGA
1 TTTTTAATAA
3222360 TTTTTAAT
1 TTTTTAAT
3222368 TCTATTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
8 6 0.19
9 12 0.39
10 13 0.42
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:3222925 original size:24 final size:23
Alignment explanation
Indices: 3222898--3222960 Score: 63
Period size: 25 Copynumber: 2.6 Consensus size: 23
3222888 TTAAAAATTT
3222898 TCTTAACAATAATTATAAAAAAAA
1 TCTTAACAATAATTAT-AAAAAAA
* *
3222922 TCTTAGACTAAAAATTATTAAAAAA
1 TCTTA-AC-AATAATTATAAAAAAA
*
3222947 TCTATAAAAATAAT
1 TCT-TAACAATAAT
3222961 AAAATATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
24 10 0.31
25 12 0.38
26 10 0.31
ACGTcount: A:0.59, C:0.08, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTTAACAATAATTATAAAAAAA
Found at i:3223256 original size:19 final size:19
Alignment explanation
Indices: 3223213--3223258 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
3223203 CTACAATTGA
*
3223213 TTTTTTAATGATTTTTTTT
1 TTTTTTAATGATTTTTATT
3223232 TATTTTTAA-GATTTTTAATT
1 T-TTTTTAATGATTTTT-ATT
3223252 TTTTTTA
1 TTTTTTA
3223259 CAATTATTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (19 bp):
TTTTTTAATGATTTTTATT
Found at i:3226516 original size:21 final size:21
Alignment explanation
Indices: 3226475--3226539 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
3226465 CCATTGCCTT
* *
3226475 CACCTCCGCCTCCTCCACCTC
1 CACCTCCACCACCTCCACCTC
*
3226496 CA-CTGCCACCACCTCCTCCTC
1 CACCT-CCACCACCTCCACCTC
* *
3226517 CACCTCTACCACCTCCACTTC
1 CACCTCCACCACCTCCACCTC
3226538 CA
1 CA
3226540 TTCCCACTCC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 2 0.06
21 32 0.89
22 2 0.06
ACGTcount: A:0.15, C:0.62, G:0.03, T:0.20
Consensus pattern (21 bp):
CACCTCCACCACCTCCACCTC
Found at i:3226636 original size:30 final size:30
Alignment explanation
Indices: 3226600--3226658 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
3226590 TCCCGACCCT
3226600 CCTCCA-TGACCACCACCTCCGCCACCACCA
1 CCTCCATTG-CCACCACCTCCGCCACCACCA
* *
3226630 CCTCCATTGCCACCACCTCCTCCTCCACC
1 CCTCCATTGCCACCACCTCCGCCACCACC
3226659 TCTACCTCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 24 0.92
31 2 0.08
ACGTcount: A:0.19, C:0.61, G:0.05, T:0.15
Consensus pattern (30 bp):
CCTCCATTGCCACCACCTCCGCCACCACCA
Found at i:3226641 original size:18 final size:15
Alignment explanation
Indices: 3226608--3226658 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 15
3226598 CTCCTCCATG
3226608 ACCACCACCTCCGCC
1 ACCACCACCTCCGCC
3226623 ACCACCACCTCCATTGCC
1 ACCACCACCTCC---GCC
* *
3226641 ACCACCTCCTCCTCC
1 ACCACCACCTCCGCC
3226656 ACC
1 ACC
3226659 TCTACCTCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
15 17 0.55
18 14 0.45
ACGTcount: A:0.20, C:0.63, G:0.04, T:0.14
Consensus pattern (15 bp):
ACCACCACCTCCGCC
Found at i:3226698 original size:18 final size:18
Alignment explanation
Indices: 3226675--3226714 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
3226665 TCTACCACCT
3226675 CCACTTCCATATCCAGAC
1 CCACTTCCATATCCAGAC
*
3226693 CCACTTCCATATCCCGAC
1 CCACTTCCATATCCAGAC
3226711 CCAC
1 CCAC
3226715 CTCCGTTGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.25, C:0.50, G:0.05, T:0.20
Consensus pattern (18 bp):
CCACTTCCATATCCAGAC
Found at i:3226759 original size:15 final size:15
Alignment explanation
Indices: 3226711--3226760 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
3226701 ATATCCCGAC
**
3226711 CCACCTCCGTTGCCA
1 CCACCTCCACTGCCA
** *
3226726 CCACCTCCACCACCG
1 CCACCTCCACTGCCA
3226741 CCACCTCCACTGCCA
1 CCACCTCCACTGCCA
3226756 CCACC
1 CCACC
3226761 ACCTCCTCCA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.18, C:0.62, G:0.08, T:0.12
Consensus pattern (15 bp):
CCACCTCCACTGCCA
Found at i:3226771 original size:15 final size:15
Alignment explanation
Indices: 3226723--3226774 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
3226713 ACCTCCGTTG
*
3226723 CCACCACCTCCACCA
1 CCACCACCTCCTCCA
*
3226738 CCGCCACCTCCACTGCCA
1 CCACCACCT-C-CT-CCA
3226756 CCACCACCTCCTCCA
1 CCACCACCTCCTCCA
3226771 CCAC
1 CCAC
3226775 TTCCTATCCC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 15 0.48
16 3 0.10
17 2 0.06
18 11 0.35
ACGTcount: A:0.21, C:0.65, G:0.04, T:0.10
Consensus pattern (15 bp):
CCACCACCTCCTCCA
Found at i:3230059 original size:42 final size:42
Alignment explanation
Indices: 3230008--3230422 Score: 575
Period size: 42 Copynumber: 9.9 Consensus size: 42
3229998 GTTTACAAAC
* *
3230008 AAAAACGCCGTTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
*
3230050 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
*
3230092 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
3230134 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
*
3230176 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
3230218 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
*
3230260 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTA-AGG
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGA-A
* * * ****
3230302 GAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTTTTTT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCG-CTTAGAA
** * * * ***
3230345 CTAATCGCCGCTAAAGAACATGTTCTTTAGTGGC-ATT-TTT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
* * *
3230385 ACAAACGCCGCAAAAGAACATGTTCTTTAGTGGCGCTT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTT
3230423 TTATACAAAA
Statistics
Matches: 346, Mismatches: 23, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
40 33 0.10
41 5 0.01
42 277 0.80
43 31 0.09
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
Found at i:3230513 original size:14 final size:14
Alignment explanation
Indices: 3230490--3230523 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
3230480 GCCCTCCTGT
*
3230490 AGCAAAATTTCAAA
1 AGCAACATTTCAAA
3230504 AGCAACATTTCAAA
1 AGCAACATTTCAAA
3230518 AGCAAC
1 AGCAAC
3230524 CAATAGCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.53, C:0.21, G:0.09, T:0.18
Consensus pattern (14 bp):
AGCAACATTTCAAA
Found at i:3230815 original size:21 final size:21
Alignment explanation
Indices: 3230747--3230817 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
3230737 TTTTGCTCTG
* *
3230747 CTCTGCTTCTCTTGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* *
3230768 CTCCGCTTCCCTCGCTGCAGT
1 CTCTGCTTCCCTCGCTGCAGC
* * *
3230789 CGCTGCTTCCCTCGCTTCCGC
1 CTCTGCTTCCCTCGCTGCAGC
3230810 CTCTGCTT
1 CTCTGCTT
3230818 TAAGTTGTAG
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.03, C:0.45, G:0.18, T:0.34
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:3236313 original size:11 final size:9
Alignment explanation
Indices: 3236265--3236757 Score: 76
Period size: 7 Copynumber: 57.0 Consensus size: 9
3236255 AATTGCAATG
3236265 GTAAGTTAT
1 GTAAGTTAT
3236274 GTAAGTTAT
1 GTAAGTTAT
3236283 GTAAGTTAAAT
1 GTAAGTT--AT
3236294 GT-A-TTAT
1 GTAAGTTAT
3236301 GTAAGTTAAAT
1 GTAAGTT--AT
3236312 GTAAG-T-T
1 GTAAGTTAT
3236319 GTAAGTTAT
1 GTAAGTTAT
*
3236328 -TATGTATTAT
1 GTAAG--TTAT
3236338 GTAAG-T-T
1 GTAAGTTAT
3236345 GTAAGTTAAAT
1 GTAAGTT--AT
*
3236356 GT-A-TTGT
1 GTAAGTTAT
3236363 GTAAG-T-T
1 GTAAGTTAT
3236370 GTAAGTTAAAT
1 GTAAGTT--AT
3236381 GT-A-TTAT
1 GTAAGTTAT
3236388 GTAAG-T-T
1 GTAAGTTAT
3236395 GTAAGTTAT
1 GTAAGTTAT
*
3236404 -TATGTATTAT
1 GTAAG--TTAT
3236414 GTAAG-T-T
1 GTAAGTTAT
3236421 GTAAGTTAT
1 GTAAGTTAT
* *
3236430 -TATGTATTGT
1 GTAAG--TTAT
3236440 GTAAG-T-T
1 GTAAGTTAT
*
3236447 GCAAGTTAAAT
1 GTAAGTT--AT
3236458 GT-A-TTAT
1 GTAAGTTAT
3236465 GTAAG-T-T
1 GTAAGTTAT
3236472 GTAAGTTAT
1 GTAAGTTAT
*
3236481 -TATGTATTAT
1 GTAAG--TTAT
3236491 GTAAG-T-T
1 GTAAGTTAT
3236498 GTAAGTTAT
1 GTAAGTTAT
*
3236507 -TATGTATTAT
1 GTAAG--TTAT
3236517 GTAAG-T-T
1 GTAAGTTAT
3236524 GTAAGTTAT
1 GTAAGTTAT
*
3236533 -TATGTATTAT
1 GTAAG--TTAT
3236543 GTAAG-T-T
1 GTAAGTTAT
3236550 GTAAGTTAT
1 GTAAGTTAT
* *
3236559 -TATGTATTGT
1 GTAAG--TTAT
3236569 GTAAG-T-T
1 GTAAGTTAT
3236576 GTAAGTTAT
1 GTAAGTTAT
*
3236585 -TATGTATTAT
1 GTAAG--TTAT
3236595 GTAAG-T-T
1 GTAAGTTAT
3236602 GTAAGTTAT
1 GTAAGTTAT
* *
3236611 -TATGTATTGT
1 GTAAG--TTAT
3236621 GTAAG-T-T
1 GTAAGTTAT
3236628 GTAAGTTAAAT
1 GTAAGTT--AT
3236639 GT-A-TTAT
1 GTAAGTTAT
* *
3236646 GTCAGTCAAAT
1 GTAAGT--TAT
3236657 GT-A-TTAT
1 GTAAGTTAT
3236664 GTAAG-T-T
1 GTAAGTTAT
3236671 GTAAGTTAAAT
1 GTAAGTT--AT
3236682 GT-A-TTAT
1 GTAAGTTAT
3236689 GTAAG-T-T
1 GTAAGTTAT
3236696 GTAAGTTAT
1 GTAAGTTAT
*
3236705 -TATGTATTAT
1 GTAAG--TTAT
*
3236715 GTAAGTAAT
1 GTAAGTTAT
3236724 GTAAGTTAAAT
1 GTAAGTT--AT
3236735 GT-A-TTAT
1 GTAAGTTAT
3236742 GTAAG-T-T
1 GTAAGTTAT
3236749 GTAAGTTAT
1 GTAAGTTAT
3236758 TATGTATTAT
Statistics
Matches: 358, Mismatches: 30, Indels: 192
0.62 0.05 0.33
Matches are distributed among these distances:
7 126 0.35
8 69 0.19
9 54 0.15
10 46 0.13
11 63 0.18
ACGTcount: A:0.33, C:0.01, G:0.20, T:0.46
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:3236340 original size:19 final size:19
Alignment explanation
Indices: 3236279--3236748 Score: 99
Period size: 18 Copynumber: 24.6 Consensus size: 19
3236269 GTTATGTAAG
*
3236279 TTATGTAAGTTA-AATGTA
1 TTATGTAAGTTATTATGTA
*
3236297 TTATGTAAGTTA-AATGTAA
1 TTATGTAAGTTATTATGT-A
*
3236316 GT-TGTAAGTTATTATGTA
1 TTATGTAAGTTATTATGTA
3236334 TTATGTAAGTTGTAAGTTAAATGTA
1 TTATGTAAG-T-T-A-TT--ATGTA
*
3236359 TTGTGTAAGTTGTAAGTTAAATGTA
1 TTATGTAAG-T-T-A-TT--ATGTA
* *
3236384 TTATGTAAGTT-GTAAG--
1 TTATGTAAGTTATTATGTA
*
3236400 TTAT-TATG-TATTATGTAA
1 TTATGTAAGTTATTATGT-A
*
3236418 GT-TGTAAGTTATTATGTA
1 TTATGTAAGTTATTATGTA
*
3236436 TTGTGTAAGTTGCAAGTTAAATGTA
1 TTATGTAAGTT---A-TT--ATGTA
* *
3236461 TTATGTAAGTT-GTAAG--
1 TTATGTAAGTTATTATGTA
*
3236477 TTAT-TATG-TATTATGTAA
1 TTATGTAAGTTATTATGT-A
*
3236495 GT-TGTAAGTTATTATGTA
1 TTATGTAAGTTATTATGTA
* *
3236513 TTATGTAAGTT-GTAAG--
1 TTATGTAAGTTATTATGTA
*
3236529 TTAT-TATG-TATTATGTAA
1 TTATGTAAGTTATTATGT-A
*
3236547 GT-TGTAAGTTATTATGTA
1 TTATGTAAGTTATTATGTA
* * *
3236565 TTGTGTAAGTT-GTAAG--
1 TTATGTAAGTTATTATGTA
*
3236581 TTAT-TATG-TATTATGTAA
1 TTATGTAAGTTATTATGT-A
*
3236599 GT-TGTAAGTTATTATGTA
1 TTATGTAAGTTATTATGTA
*
3236617 TTGTGTAAGTTGTAAGTTAAATGTA
1 TTATGTAAG-T-T-A-TT--ATGTA
* * *
3236642 TTATGTCAGTCA-AATGTA
1 TTATGTAAGTTATTATGTA
3236660 TTATGTAAGTTGTAAGTTAAATGTA
1 TTATGTAAG-T-T-A-TT--ATGTA
* *
3236685 TTATGTAAGTT-GTAAGTTA
1 TTATGTAAGTTATTATG-TA
*
3236704 TTATGT-A-TTATGTAAGTA
1 TTATGTAAGTTAT-TATGTA
*
3236722 --ATGTAAGTTA-AATGTA
1 TTATGTAAGTTATTATGTA
3236738 TTATGTAAGTT
1 TTATGTAAGTT
3236749 GTAAGTTATT
Statistics
Matches: 338, Mismatches: 51, Indels: 126
0.66 0.10 0.24
Matches are distributed among these distances:
14 4 0.01
15 24 0.07
16 23 0.07
17 7 0.02
18 92 0.27
19 87 0.26
20 5 0.01
21 3 0.01
22 4 0.01
23 8 0.02
24 3 0.01
25 78 0.23
ACGTcount: A:0.33, C:0.01, G:0.20, T:0.47
Consensus pattern (19 bp):
TTATGTAAGTTATTATGTA
Found at i:3236344 original size:26 final size:26
Alignment explanation
Indices: 3236310--3236767 Score: 683
Period size: 26 Copynumber: 18.1 Consensus size: 26
3236300 TGTAAGTTAA
3236310 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
*
3236336 ATGTAAGTTGTAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
* *
3236361 GTGTAAGTTGTAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
3236386 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
3236412 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
* * *
3236438 GTGTAAGTTGCAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
3236463 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
3236489 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
3236515 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
3236541 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
*
3236567 GTGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
3236593 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
* *
3236619 GTGTAAGTTGTAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
* *
3236644 ATGTCA---GTCA---A--ATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
*
3236662 ATGTAAGTTGTAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
3236687 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
*
3236713 ATGTAAGTAATGTAAGTTA-AATGTATT
1 ATGTAAGT--TGTAAGTTATTATGTATT
3236740 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
3236766 AT
1 AT
3236768 TTAATAAAAT
Statistics
Matches: 397, Mismatches: 22, Indels: 26
0.89 0.05 0.06
Matches are distributed among these distances:
18 12 0.03
19 1 0.00
21 3 0.01
22 3 0.01
24 1 0.00
25 113 0.28
26 240 0.60
27 15 0.04
28 9 0.02
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.47
Consensus pattern (26 bp):
ATGTAAGTTGTAAGTTATTATGTATT
Found at i:3236859 original size:34 final size:34
Alignment explanation
Indices: 3236821--3236936 Score: 88
Period size: 34 Copynumber: 3.2 Consensus size: 34
3236811 ATTAATAATA
3236821 TTTAATAAAATAAAATTTTATTTTAATAGTCAAT
1 TTTAATAAAATAAAATTTTATTTTAATAGTCAAT
** * * * * * *
3236855 TTTAATATTCCACATATTTTTTTTTATAATTATTAATAAT
1 TTTAATA--AAATAAAATTTTATTT-TAA-TAGT--CAAT
*
3236895 ATTTAATAAAATAACATTTTATTTTAATAGTCAAT
1 -TTTAATAAAATAAAATTTTATTTTAATAGTCAAT
3236930 TTTAATA
1 TTTAATA
3236937 TTCCACATAT
Statistics
Matches: 58, Mismatches: 17, Indels: 14
0.65 0.19 0.16
Matches are distributed among these distances:
34 14 0.24
35 3 0.05
36 10 0.17
37 6 0.10
38 6 0.10
39 9 0.16
40 3 0.05
41 7 0.12
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (34 bp):
TTTAATAAAATAAAATTTTATTTTAATAGTCAAT
Found at i:3236862 original size:41 final size:40
Alignment explanation
Indices: 3236816--3236938 Score: 107
Period size: 41 Copynumber: 3.2 Consensus size: 40
3236806 TAATTATTAA
3236816 TAATATTTAATAAAATAAAATTTTATTTTAATAGTCAATTT
1 TAATATTTAATAAAAT-AAATTTTATTTTAATAGTCAATTT
** * * * * *
3236857 TAATA-TT--CCACAT--ATTTT-TTTTTATAAT-TATTAA
1 TAATATTTAATAAAATAAATTTTATTTTAATAGTCAATT-T
3236891 TAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTT
1 TAATATTTAATAAAATAA-ATTTTATTTTAATAGTCAATTT
3236932 TAATATT
1 TAATATT
3236939 CCACATATTT
Statistics
Matches: 59, Mismatches: 14, Indels: 18
0.65 0.15 0.20
Matches are distributed among these distances:
33 3 0.05
34 13 0.22
35 7 0.12
37 3 0.05
38 3 0.05
40 7 0.12
41 20 0.34
42 3 0.05
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (40 bp):
TAATATTTAATAAAATAAATTTTATTTTAATAGTCAATTT
Found at i:3236883 original size:75 final size:75
Alignment explanation
Indices: 3236804--3236952 Score: 289
Period size: 75 Copynumber: 2.0 Consensus size: 75
3236794 ACATTACTAA
3236804 TATAATTATTAATAATATTTAATAAAATAAAATTTTATTTTAATAGTCAATTTTAATATTCCACA
1 TATAATTATTAATAATATTTAATAAAATAAAATTTTATTTTAATAGTCAATTTTAATATTCCACA
3236869 TATTTTTTTT
66 TATTTTTTTT
*
3236879 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
1 TATAATTATTAATAATATTTAATAAAATAAAATTTTATTTTAATAGTCAATTTTAATATTCCACA
3236944 TATTTTTTT
66 TATTTTTTT
3236953 ATATTTTATT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.41, C:0.06, G:0.01, T:0.52
Consensus pattern (75 bp):
TATAATTATTAATAATATTTAATAAAATAAAATTTTATTTTAATAGTCAATTTTAATATTCCACA
TATTTTTTTT
Found at i:3239849 original size:27 final size:27
Alignment explanation
Indices: 3239817--3239868 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
3239807 TCTTACTTTT
* *
3239817 AAATAATTAATTACCAATTTATTTAAC
1 AAATAAATAATTACCAACTTATTTAAC
*
3239844 AAATAAATAATTACTAACTTATTTA
1 AAATAAATAATTACCAACTTATTTA
3239869 TTTGTTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (27 bp):
AAATAAATAATTACCAACTTATTTAAC
Found at i:3239959 original size:8 final size:10
Alignment explanation
Indices: 3239936--3239972 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
3239926 TAATAACTAT
3239936 ATATATATCC
1 ATATATATCC
*
3239946 ATATATATTC
1 ATATATATCC
3239956 ATATATATCC
1 ATATATATCC
3239966 ATATATA
1 ATATATA
3239973 AGTAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (10 bp):
ATATATATCC
Found at i:3240990 original size:82 final size:82
Alignment explanation
Indices: 3240871--3241047 Score: 336
Period size: 82 Copynumber: 2.2 Consensus size: 82
3240861 GCTACCGGAA
*
3240871 AAAACGCCACTAACTTTTCAATTACAGAAAGAAACGGTGACGTTTTCACAAAATTGTAGACATAT
1 AAAACGCCACTAAATTTTCAATTACAGAAAGAAACGGTGACGTTTTCACAAAATTGTAGACATAT
3240936 TTGCGGCGTTTTACCTT
66 TTGCGGCGTTTTACCTT
3240953 AAAACGCCACTAAATTTTCAATTACAGAAAGAAACGGTGACGTTTTCACAAAATTGTAGACATAT
1 AAAACGCCACTAAATTTTCAATTACAGAAAGAAACGGTGACGTTTTCACAAAATTGTAGACATAT
*
3241018 TTGCGGCGTTTTCCCTT
66 TTGCGGCGTTTTACCTT
3241035 AAAACGCCACTAA
1 AAAACGCCACTAA
3241048 TAGAGTACAC
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 93 1.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (82 bp):
AAAACGCCACTAAATTTTCAATTACAGAAAGAAACGGTGACGTTTTCACAAAATTGTAGACATAT
TTGCGGCGTTTTACCTT
Found at i:3241272 original size:41 final size:41
Alignment explanation
Indices: 3241227--3241380 Score: 186
Period size: 41 Copynumber: 3.8 Consensus size: 41
3241217 AGAACAGAGA
* *
3241227 ATTAGTGGCGCTCAGATAAAAACGCCACTAATAATACGAGC
1 ATTAGCGGCGCTCAGACAAAAACGCCACTAATAATACGAGC
* * *
3241268 ATTAGCGGCGCTAAGACAAAAACGCCGCTAA-AGA-ACAGAGA
1 ATTAGCGGCGCTCAGACAAAAACGCCACTAATA-ATAC-GAGC
* * *
3241309 ATTAGTGGCGCTCAGATAAAAACGCCACTAATGATACGAGC
1 ATTAGCGGCGCTCAGACAAAAACGCCACTAATAATACGAGC
* *
3241350 ATTAGCGGCGCTTAGACAAAAACGCCGCTAA
1 ATTAGCGGCGCTCAGACAAAAACGCCACTAA
3241381 AGGTTTAAAA
Statistics
Matches: 94, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
40 3 0.03
41 89 0.95
42 2 0.02
ACGTcount: A:0.39, C:0.23, G:0.22, T:0.16
Consensus pattern (41 bp):
ATTAGCGGCGCTCAGACAAAAACGCCACTAATAATACGAGC
Found at i:3241324 original size:82 final size:82
Alignment explanation
Indices: 3241187--3241382 Score: 349
Period size: 82 Copynumber: 2.4 Consensus size: 82
3241177 AACACGAACT
*
3241187 TTAGCGGCGCTTAG-CAAAAAATGCCGCTAAAGAACAGAGAATTAGTGGCGCTCAGATAAAAACG
1 TTAGCGGCGCTTAGAC-AAAAACGCCGCTAAAGAACAGAGAATTAGTGGCGCTCAGATAAAAACG
3241251 CCACTAATAATACGAGCA
65 CCACTAATAATACGAGCA
*
3241269 TTAGCGGCGCTAAGACAAAAACGCCGCTAAAGAACAGAGAATTAGTGGCGCTCAGATAAAAACGC
1 TTAGCGGCGCTTAGACAAAAACGCCGCTAAAGAACAGAGAATTAGTGGCGCTCAGATAAAAACGC
*
3241334 CACTAATGATACGAGCA
66 CACTAATAATACGAGCA
3241351 TTAGCGGCGCTTAGACAAAAACGCCGCTAAAG
1 TTAGCGGCGCTTAGACAAAAACGCCGCTAAAG
3241383 GTTTAAAAAA
Statistics
Matches: 109, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
82 108 0.99
83 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.23, T:0.16
Consensus pattern (82 bp):
TTAGCGGCGCTTAGACAAAAACGCCGCTAAAGAACAGAGAATTAGTGGCGCTCAGATAAAAACGC
CACTAATAATACGAGCA
Found at i:3242722 original size:21 final size:21
Alignment explanation
Indices: 3242698--3242775 Score: 77
Period size: 21 Copynumber: 3.7 Consensus size: 21
3242688 CCATTGCCTT
* *
3242698 CACCTCCACCTCCGCCTCCTC
1 CACCTCCACCTCCACCACCTC
3242719 CACCTCCA-CTGCCACCACCTC
1 CACCTCCACCT-CCACCACCTC
* * *
3242740 CTCCTCCACCTCTACCACTTC
1 CACCTCCACCTCCACCACCTC
* *
3242761 CACTTCCACTTCCAC
1 CACCTCCACCTCCAC
3242776 TCCCACTCCC
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
20 2 0.04
21 42 0.91
22 2 0.04
ACGTcount: A:0.15, C:0.60, G:0.03, T:0.22
Consensus pattern (21 bp):
CACCTCCACCTCCACCACCTC
Found at i:3242763 original size:6 final size:6
Alignment explanation
Indices: 3242754--3242791 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
3242744 TCCACCTCTA
* *
3242754 CCACTT CCACTT CCACTT CCACTC CCACTC CCACTT CC
1 CCACTT CCACTT CCACTT CCACTT CCACTT CCACTT CC
3242792 GTATCCGGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.16, C:0.58, G:0.00, T:0.26
Consensus pattern (6 bp):
CCACTT
Found at i:3242841 original size:18 final size:16
Alignment explanation
Indices: 3242820--3242881 Score: 67
Period size: 15 Copynumber: 3.9 Consensus size: 16
3242810 ATATCCTGAC
3242820 CCTCCTCCATGACCACCA
1 CCTCCTCC-T-ACCACCA
*
3242838 CCTCCGCC-ACCACCA
1 CCTCCTCCTACCACCA
*
3242853 CCTCC-ACTACCACCA
1 CCTCCTCCTACCACCA
3242868 CCTCCTCCT-CCACC
1 CCTCCTCCTACCACC
3242882 TCTACCTCTA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
14 1 0.03
15 29 0.74
16 2 0.05
18 7 0.18
ACGTcount: A:0.19, C:0.63, G:0.03, T:0.15
Consensus pattern (16 bp):
CCTCCTCCTACCACCA
Found at i:3242870 original size:132 final size:132
Alignment explanation
Indices: 3242703--3243013 Score: 401
Period size: 132 Copynumber: 2.4 Consensus size: 132
3242693 GCCTTCACCT
* * * *
3242703 CCACCTCCGCCTCCTCCACCTCCACTGCCACCACCTCCTCCTCCACCTCTACCACTTCCACTTCC
1 CCACCTCCGCCACCACCACCTCCACTGCCACCACCTCCTCCTCCACCTCTACCACTACCACCTCC
* * * * * * *
3242768 ACTTCCACT-CCCACTCCCACTTCCGTATCCGGACCCTGATCCATATCCTGACCCTCCTCC-ATG
66 ACTTCCA-TACCCACACCCACTTCCATATCCAGACCCAGACCCATATCCCGACCCACCTCCGATG
3242831 ACCA
130 -CCA
* *
3242835 CCACCTCCGCCACCACCACCTCCACTACCACCACCTCCTCCTCCACCTCTACCTCTACCACCTCC
1 CCACCTCCGCCACCACCACCTCCACTGCCACCACCTCCTCCTCCACCTCTACCACTACCACCTCC
* * * *
3242900 ACTTCCATATCCAGACCCACTTCCATATCCAGATCCAGACCCATATCCCGACCCACCTCCGTTGC
66 ACTTCCATACCCACACCCACTTCCATATCCAGACCCAGACCCATATCCCGACCCACCTCCGATGC
3242965 CA
131 CA
* * * *
3242967 CCACCTCCACCACCGCCACCTCCGCTGCCACCACCACCTCCTCCACC
1 CCACCTCCGCCACCACCACCTCCACTGCCACCACCTCCTCCTCCACC
3243014 ACTTCCTATC
Statistics
Matches: 155, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
131 1 0.01
132 152 0.98
133 2 0.01
ACGTcount: A:0.19, C:0.56, G:0.06, T:0.19
Consensus pattern (132 bp):
CCACCTCCGCCACCACCACCTCCACTGCCACCACCTCCTCCTCCACCTCTACCACTACCACCTCC
ACTTCCATACCCACACCCACTTCCATATCCAGACCCAGACCCATATCCCGACCCACCTCCGATGC
CA
Found at i:3242919 original size:24 final size:24
Alignment explanation
Indices: 3242892--3242942 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
3242882 TCTACCTCTA
*
3242892 CCACCTCCACT-TCCATATCCAGAC
1 CCACCTCCA-TATCCAGATCCAGAC
*
3242916 CCACTTCCATATCCAGATCCAGAC
1 CCACCTCCATATCCAGATCCAGAC
3242940 CCA
1 CCA
3242943 TATCCCGACC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.27, C:0.47, G:0.06, T:0.20
Consensus pattern (24 bp):
CCACCTCCATATCCAGATCCAGAC
Found at i:3242921 original size:18 final size:18
Alignment explanation
Indices: 3242898--3242955 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
3242888 TCTACCACCT
3242898 CCACTTCCATATCCAGAC
1 CCACTTCCATATCCAGAC
*
3242916 CCACTTCCATATCCAGAT
1 CCACTTCCATATCCAGAC
*** *
3242934 CCAGACCCATATCCCGAC
1 CCACTTCCATATCCAGAC
3242952 CCAC
1 CCAC
3242956 CTCCGTTGCC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.28, C:0.47, G:0.07, T:0.19
Consensus pattern (18 bp):
CCACTTCCATATCCAGAC
Found at i:3242986 original size:18 final size:18
Alignment explanation
Indices: 3242963--3243015 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
3242953 CACCTCCGTT
*
3242963 GCCACCACCTCCACCACC
1 GCCACCTCCTCCACCACC
* **
3242981 GCCACCTCCGCTGCCACC
1 GCCACCTCCTCCACCACC
*
3242999 ACCACCTCCTCCACCAC
1 GCCACCTCCTCCACCAC
3243016 TTCCTATCCC
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.19, C:0.64, G:0.08, T:0.09
Consensus pattern (18 bp):
GCCACCTCCTCCACCACC
Found at i:3243000 original size:15 final size:15
Alignment explanation
Indices: 3242952--3243001 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
3242942 ATATCCCGAC
*
3242952 CCACCTCCGTTGCCA
1 CCACCTCCGCTGCCA
* ** *
3242967 CCACCTCCACCACCG
1 CCACCTCCGCTGCCA
3242982 CCACCTCCGCTGCCA
1 CCACCTCCGCTGCCA
3242997 CCACC
1 CCACC
3243002 ACCTCCTCCA
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.16, C:0.62, G:0.10, T:0.12
Consensus pattern (15 bp):
CCACCTCCGCTGCCA
Found at i:3243012 original size:15 final size:15
Alignment explanation
Indices: 3242964--3243015 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
3242954 ACCTCCGTTG
*
3242964 CCACCACCTCCACCA
1 CCACCACCTCCTCCA
*
3242979 CCGCCACCTCCGCTGCCA
1 CCACCACCT-C-CT-CCA
3242997 CCACCACCTCCTCCA
1 CCACCACCTCCTCCA
3243012 CCAC
1 CCAC
3243016 TTCCTATCCC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 15 0.48
16 3 0.10
17 2 0.06
18 11 0.35
ACGTcount: A:0.19, C:0.65, G:0.06, T:0.10
Consensus pattern (15 bp):
CCACCACCTCCTCCA
Found at i:3247823 original size:18 final size:18
Alignment explanation
Indices: 3247796--3247846 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
3247786 TCCACTACTA
*
3247796 CCATAACCTGACCCACTT
1 CCATAACCTGAACCACTT
*
3247814 CCATATCCTGAACCACTT
1 CCATAACCTGAACCACTT
3247832 CCATAACCTGAACCA
1 CCATAACCTGAACCA
3247847 TTGCCTCCAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.31, C:0.41, G:0.06, T:0.22
Consensus pattern (18 bp):
CCATAACCTGAACCACTT
Found at i:3247870 original size:15 final size:15
Alignment explanation
Indices: 3247850--3247905 Score: 76
Period size: 15 Copynumber: 3.5 Consensus size: 15
3247840 TGAACCATTG
3247850 CCTCCACCACCTCCT
1 CCTCCACCACCTCCT
*
3247865 CCTCCACCTCCACCTCCA
1 CCTCCA---CCACCTCCT
3247883 CCTCCACCACCTCCT
1 CCTCCACCACCTCCT
3247898 CCTCCACC
1 CCTCCACC
3247906 TCTACCACCA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
15 22 0.61
18 14 0.39
ACGTcount: A:0.14, C:0.68, G:0.00, T:0.18
Consensus pattern (15 bp):
CCTCCACCACCTCCT
Found at i:3247901 original size:21 final size:21
Alignment explanation
Indices: 3247850--3247919 Score: 86
Period size: 21 Copynumber: 3.3 Consensus size: 21
3247840 TGAACCATTG
* * *
3247850 CCTCCACCACCTCCTCCTCCA
1 CCTCCACCTCCACCTCCACCA
3247871 CCTCCACCTCCACCTCCACCA
1 CCTCCACCTCCACCTCCACCA
* *
3247892 CCTCCTCCTCCACCTCTACCA
1 CCTCCACCTCCACCTCCACCA
*
3247913 CCACCAC
1 CCTCCAC
3247920 TTCCGTATCC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.17, C:0.66, G:0.00, T:0.17
Consensus pattern (21 bp):
CCTCCACCTCCACCTCCACCA
Found at i:3247906 original size:12 final size:12
Alignment explanation
Indices: 3247850--3247907 Score: 68
Period size: 12 Copynumber: 5.1 Consensus size: 12
3247840 TGAACCATTG
*
3247850 CCTCCACCACCT
1 CCTCCTCCACCT
3247862 CCTCCTCCACCT
1 CCTCCTCCACCT
*
3247874 CCACCTCCA---
1 CCTCCTCCACCT
*
3247883 CCTCCACCACCT
1 CCTCCTCCACCT
3247895 CCTCCTCCACCT
1 CCTCCTCCACCT
3247907 C
1 C
3247908 TACCACCACC
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
9 7 0.18
12 31 0.82
ACGTcount: A:0.14, C:0.67, G:0.00, T:0.19
Consensus pattern (12 bp):
CCTCCTCCACCT
Found at i:3247919 original size:6 final size:6
Alignment explanation
Indices: 3247856--3247917 Score: 67
Period size: 6 Copynumber: 10.8 Consensus size: 6
3247846 ATTGCCTCCA
* *
3247856 CCACCT CCTCCT CCACCT CCACCT CCACCT CCA--- CCACCT CCTCCT
1 CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT
* *
3247901 CCACCT CTACCA CCACC
1 CCACCT CCACCT CCACC
3247918 ACTTCCGTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
3 3 0.07
6 43 0.93
ACGTcount: A:0.16, C:0.66, G:0.00, T:0.18
Consensus pattern (6 bp):
CCACCT
Found at i:3248018 original size:18 final size:18
Alignment explanation
Indices: 3247982--3248034 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
3247972 TCCTCCATTG
3247982 CCACCACCTCCACCACCA
1 CCACCACCTCCACCACCA
* * *
3248000 CCACCTCCTCTACCGCCA
1 CCACCACCTCCACCACCA
*
3248018 CCACCACCACCACCACC
1 CCACCACCTCCACCACC
3248035 TCCTATCCCA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.25, C:0.66, G:0.02, T:0.08
Consensus pattern (18 bp):
CCACCACCTCCACCACCA
Found at i:3248029 original size:27 final size:27
Alignment explanation
Indices: 3247985--3248050 Score: 87
Period size: 30 Copynumber: 2.3 Consensus size: 27
3247975 TCCATTGCCA
*
3247985 CCACCTCCACCACCACCACCTCCTCTACC
1 CCACCACCACCACCACCACCT-C-CTACC
*
3248014 GCCACCACCACCACCACCACCTCCTATC
1 -CCACCACCACCACCACCACCTCCTACC
3248042 CCACCACCA
1 CCACCACCA
3248051 GACCCATACC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 9 0.26
28 4 0.12
29 1 0.03
30 20 0.59
ACGTcount: A:0.24, C:0.64, G:0.02, T:0.11
Consensus pattern (27 bp):
CCACCACCACCACCACCACCTCCTACC
Found at i:3248049 original size:15 final size:15
Alignment explanation
Indices: 3247982--3248037 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 15
3247972 TCCTCCATTG
3247982 CCACCACCTCCACCA
1 CCACCACCTCCACCA
* *
3247997 CCACCACCTCCTCTA
1 CCACCACCTCCACCA
* *
3248012 CCGCCACCACCACCA
1 CCACCACCTCCACCA
3248027 CCACCACCTCC
1 CCACCACCTCC
3248038 TATCCCACCA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.23, C:0.66, G:0.02, T:0.09
Consensus pattern (15 bp):
CCACCACCTCCACCA
Found at i:3248050 original size:3 final size:3
Alignment explanation
Indices: 3247982--3248034 Score: 61
Period size: 3 Copynumber: 17.7 Consensus size: 3
3247972 TCCTCCATTG
* * * * *
3247982 CCA CCA CCT CCA CCA CCA CCA CCT CCT CTA CCG CCA CCA CCA CCA CCA
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA
3248030 CCA CC
1 CCA CC
3248035 TCCTATCCCA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.25, C:0.66, G:0.02, T:0.08
Consensus pattern (3 bp):
CCA
Found at i:3248123 original size:6 final size:6
Alignment explanation
Indices: 3248114--3248156 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
3248104 AGAGCTGCCA
* * *
3248114 CCACCT CCACCT CCACCT CCGCCC CCACCA CC-CCT CCACCT CC
1 CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CC
3248157 TCCACTACCA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
5 4 0.13
6 27 0.87
ACGTcount: A:0.14, C:0.72, G:0.02, T:0.12
Consensus pattern (6 bp):
CCACCT
Found at i:3248166 original size:23 final size:23
Alignment explanation
Indices: 3248110--3248166 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
3248100 ATCCAGAGCT
*
3248110 GCCACCACCTCCACCTCCACCTCC
1 GCCACCACCACC-CCTCCACCTCC
*
3248134 GCCCCCACCACCCCTCCACCTCC
1 GCCACCACCACCCCTCCACCTCC
* *
3248157 TCCACTACCA
1 GCCACCACCA
3248167 TAAGCTCCCG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 18 0.64
24 10 0.36
ACGTcount: A:0.18, C:0.67, G:0.04, T:0.12
Consensus pattern (23 bp):
GCCACCACCACCCCTCCACCTCC
Found at i:3248227 original size:12 final size:12
Alignment explanation
Indices: 3248176--3248228 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
3248166 ATAAGCTCCC
3248176 GAACCATATCCT
1 GAACCATATCCT
* *
3248188 GAGCCACT-TCCG
1 GAACCA-TATCCT
*
3248200 GAACCATACCCT
1 GAACCATATCCT
*
3248212 GAACCATATCCA
1 GAACCATATCCT
3248224 GAACC
1 GAACC
3248229 TGAGCCTAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
11 1 0.03
12 30 0.94
13 1 0.03
ACGTcount: A:0.32, C:0.38, G:0.13, T:0.17
Consensus pattern (12 bp):
GAACCATATCCT
Found at i:3248227 original size:24 final size:24
Alignment explanation
Indices: 3248176--3248228 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
3248166 ATAAGCTCCC
* * *
3248176 GAACCATATCCTGAGCCACTTCCG
1 GAACCATACCCTGAACCACTTCCA
3248200 GAACCATACCCTGAACCA-TATCCA
1 GAACCATACCCTGAACCACT-TCCA
3248224 GAACC
1 GAACC
3248229 TGAGCCTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.32, C:0.38, G:0.13, T:0.17
Consensus pattern (24 bp):
GAACCATACCCTGAACCACTTCCA
Found at i:3252327 original size:30 final size:28
Alignment explanation
Indices: 3252273--3252343 Score: 99
Period size: 30 Copynumber: 2.5 Consensus size: 28
3252263 AAAAAATAAT
*
3252273 CAAAATATTATAAATTTTTTTTATTTAC
1 CAAAATATTATAAATTTTTATTATTTAC
3252301 CAAAATATTATAATTATTTTTATTATTTAC
1 CAAAATATTATAA--ATTTTTATTATTTAC
*
3252331 AAAAATA-TATAAA
1 CAAAATATTATAAA
3252344 AAAACCAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
27 1 0.03
28 13 0.33
29 5 0.13
30 20 0.51
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (28 bp):
CAAAATATTATAAATTTTTATTATTTAC
Found at i:3252601 original size:27 final size:29
Alignment explanation
Indices: 3252563--3252633 Score: 94
Period size: 27 Copynumber: 2.6 Consensus size: 29
3252553 AAAAAAAAAG
*
3252563 GAAAGAAG-AAGAAGAGGAAAGGAG-A-A
1 GAAAAAAGAAAGAAGAGGAAAGGAGAAGA
*
3252589 GAAAAAAGAAAGAAAAGGAAAGGAGAAGA
1 GAAAAAAGAAAGAAGAGGAAAGGAGAAGA
*
3252618 GAAAAAAAAAAGAAGA
1 GAAAAAAGAAAGAAGA
3252634 AGAGGGAAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 7 0.18
27 15 0.39
28 1 0.03
29 15 0.39
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (29 bp):
GAAAAAAGAAAGAAGAGGAAAGGAGAAGA
Found at i:3252605 original size:66 final size:65
Alignment explanation
Indices: 3252469--3252666 Score: 228
Period size: 66 Copynumber: 3.0 Consensus size: 65
3252459 GGTGGGGGGG
* *
3252469 AAGGAGAGG-GAA-AGAAAGAAAGAAAGGAAGGAAGGAAGGAGAGGAAA-GAAAGAAAAAGAAGG
1 AAGGAAAGGAGAAGAGAAA-AAA-AAAGGAAAGAA-GAAGGAGAGGAAAGGAAAG-AAAA-AA-G
3252531 AAAGAA
60 AAAGAA
* *
3252537 AAGGAAATGAGAAGAGAAAAAAAAAGGAAAGAAGAAGAAGAGGAAAGGAGAAGAAAAAAGAAAGA
1 AAGGAAAGGAGAAGAGAAAAAAAAAGGAAAGAAGAAGGAGAGGAAAGGA-AAGAAAAAAGAAAGA
3252602 A
65 A
* * *
3252603 AAGGAAAGGAGAAGAGAAAAAAAAAAG-AAGAAGAGGGA-AGG-AAGGAAAGAAAAAAAAAAGAA
1 AAGGAAAGGAGAAGAGAAAAAAAAAGGAAAGAAGAAGGAGAGGAAAGGAAAGAAAAAAGAAAGAA
3252665 AA
1 AA
3252667 AAAAAGGTAA
Statistics
Matches: 117, Mismatches: 9, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
62 17 0.15
63 5 0.04
64 3 0.03
65 9 0.08
66 32 0.27
67 14 0.12
68 23 0.20
69 9 0.08
70 5 0.04
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.01
Consensus pattern (65 bp):
AAGGAAAGGAGAAGAGAAAAAAAAAGGAAAGAAGAAGGAGAGGAAAGGAAAGAAAAAAGAAAGAA
Found at i:3252627 original size:33 final size:33
Alignment explanation
Indices: 3252515--3252670 Score: 151
Period size: 33 Copynumber: 4.6 Consensus size: 33
3252505 AGGAGAGGAA
*
3252515 AGAAAGAAAAAGAAGGAAAGAAAAGGAAATGAGAAG
1 AGAAA-AAAAA-AA-GAAAGAAAAGGAAAGGAGAAG
*
3252551 AGAAAAAAAAAGGAAAGAAGAA-GAAGAGGA-AAG
1 AGAAAAAAAAAAGAAAGAA-AAGGAA-AGGAGAAG
*
3252584 -GAGAAGAAAAAAGAAAGAAAAGGAAAGGAGAAG
1 AGA-AAAAAAAAAGAAAGAAAAGGAAAGGAGAAG
* *
3252617 AGAAAAAAAAAAG-AAGAAGAGGGAAGGAAGGAA-
1 AGAAAAAAAAAAGAAAGAAAAGGAAAGG-A-GAAG
*
3252650 AGAAAAAAAAAAGAAAAAAAA
1 AGAAAAAAAAAAGAAAGAAAA
3252671 AGGTAATTTT
Statistics
Matches: 102, Mismatches: 9, Indels: 20
0.78 0.07 0.15
Matches are distributed among these distances:
32 20 0.20
33 56 0.55
34 16 0.16
35 5 0.05
36 5 0.05
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.01
Consensus pattern (33 bp):
AGAAAAAAAAAAGAAAGAAAAGGAAAGGAGAAG
Found at i:3252631 original size:16 final size:15
Alignment explanation
Indices: 3252513--3252671 Score: 54
Period size: 16 Copynumber: 9.9 Consensus size: 15
3252503 GAAGGAGAGG
*
3252513 AAAGAAAG-AAAAAG
1 AAAGAAAGAAAAAAA
*
3252527 AAGGAAAGAAAAGGAAA
1 AAAGAAAGAAAA--AAA
**
3252544 TGAGAAGAGAAAAAAA
1 AAAGAA-AGAAAAAAA
* *
3252560 AAGGAAAGAAGAAGAA
1 AAAGAAAGAA-AAAAA
* * *
3252576 GAGGAAAGGAGAAGAAA
1 AAAGAAA-GA-AAAAAA
3252593 AAAGAAAGAAAAGGAAA
1 AAAGAAAGAAAA--AAA
**
3252610 GGAGAAGAGAAAAAAA
1 AAAGAA-AGAAAAAAA
**
3252626 AAAG-AAGAAGAGGGAAGG
1 AAAGAAAGAA-A---AAAA
*
3252644 AAGGAAAGAAAAAAA
1 AAAGAAAGAAAAAAA
3252659 AAAGAAA-AAAAAA
1 AAAGAAAGAAAAAA
3252672 GGTAATTTTT
Statistics
Matches: 105, Mismatches: 25, Indels: 30
0.66 0.16 0.19
Matches are distributed among these distances:
14 17 0.16
15 19 0.18
16 23 0.22
17 22 0.21
18 19 0.18
19 5 0.05
ACGTcount: A:0.71, C:0.00, G:0.28, T:0.01
Consensus pattern (15 bp):
AAAGAAAGAAAAAAA
Found at i:3253431 original size:27 final size:27
Alignment explanation
Indices: 3253401--3253456 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
3253391 AAAGAGAGTG
*
3253401 ATGGAGGGGAATAAAAAAGCGGCACCA
1 ATGGAGAGGAATAAAAAAGCGGCACCA
*
3253428 ATGGAGAGGAATAAAAAGGCGGCACCA
1 ATGGAGAGGAATAAAAAAGCGGCACCA
3253455 AT
1 AT
3253457 ATGTGGCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.45, C:0.14, G:0.32, T:0.09
Consensus pattern (27 bp):
ATGGAGAGGAATAAAAAAGCGGCACCA
Found at i:3258461 original size:18 final size:18
Alignment explanation
Indices: 3258438--3258482 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
3258428 ATCCCAATGA
3258438 TCGCCACCACCTTCTTCT
1 TCGCCACCACCTTCTTCT
*
3258456 TCGCCAGCACCTTCTTCT
1 TCGCCACCACCTTCTTCT
*
3258474 TCACCACCA
1 TCGCCACCA
3258483 ACCATATCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.16, C:0.49, G:0.07, T:0.29
Consensus pattern (18 bp):
TCGCCACCACCTTCTTCT
Found at i:3259209 original size:19 final size:18
Alignment explanation
Indices: 3259181--3259216 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3259171 TATATTGGTA
3259181 AATAAAAATAATAACTAAC
1 AATAAAAATAAT-ACTAAC
*
3259200 AATAATAATAATACTAA
1 AATAAAAATAATACTAA
3259217 AAAAATTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (18 bp):
AATAAAAATAATACTAAC
Found at i:3259593 original size:438 final size:437
Alignment explanation
Indices: 3258777--3259653 Score: 1718
Period size: 438 Copynumber: 2.0 Consensus size: 437
3258767 TGAAAACTTG
*
3258777 TAAAAAATTTTTGATATCCTTCTCTCACAACGTCTAAGTATTTTTGCATTAATCCTTGCCTTTAT
1 TAAAAAAATTTTGATATCCTTCTCTCACAACGTCTAAGTATTTTTGCATTAATCCTTGCCTTTAT
3258842 TTCATCGAACGATACATTTCTATTAAATCTCATTGCTATTTGTCGTCGACATTCAAATACACTTC
66 TTCATCGAACGATACATTTCTATTAAATCTCATTGCTATTTGTCGTCGACATTCAAATACACTTC
3258907 CAACACTTGTTGTCAAGATGACTCCATCGAAATAAACACATACAAGAAACTCAGCATCCATCTTC
131 CAACACTTGTTGTCAAGATGACTCCATCGAAATAAACACATACAAGAAACTCAGCATCCATCTTC
3258972 AATATTTAATCTGTAAAAAAACAAAATCTCATAAAAATTCTCGAACGGTAAATAAATTACTAATC
196 AATATTTAATCTGTAAAAAAACAAAATCTCATAAAAATTCTCGAACGGTAAATAAATTACTAATC
3259037 CTAATAACTAACACAATAATAATATTAATAATTTTATACTCAAAATAATACACACTAAAATTATT
261 CTAATAACTAACACAATAATAATATTAATAATTTTATACTCAAAATAATACACACTAAAATTATT
3259102 AATTAGGGTTTTACTAAAAATAATAACTAACTAACTATAATAATAATACTAGTTTTTTACTAACT
326 AATTAGGGTTTTACTAAAAATAATAACTAACTAACTATAATAATAATACTAGTTTTTTACTAACT
3259167 AGTTTATATTGGTAAATAAAAATAATAACTAACAATAATAATAATAC
391 AGTTTATATTGGTAAATAAAAATAATAACTAACAATAATAATAATAC
3259214 TAAAAAAATTTTGATATCCTTCTCTCACAACGTCTAAGTATTTTTGCATTAATCCTTGCCTTTAT
1 TAAAAAAATTTTGATATCCTTCTCTCACAACGTCTAAGTATTTTTGCATTAATCCTTGCCTTTAT
*
3259279 TTCATCGAACGATACATTTCTATTAAATCTCATTGCTATTTGTTGTCGACATTCAAATACACTTC
66 TTCATCGAACGATACATTTCTATTAAATCTCATTGCTATTTGTCGTCGACATTCAAATACACTTC
*
3259344 CAACACTTGTTGTCAAGATGACTCCATCGAAATAAACACATACAAGAAACTTAGCATCCATCTTC
131 CAACACTTGTTGTCAAGATGACTCCATCGAAATAAACACATACAAGAAACTCAGCATCCATCTTC
3259409 AATATTTAATCTGTAAAAAAAACAAAATCTCATAAAAATTCTCGAACGGTAAATAAATTACTAAT
196 AATATTTAATCTGT-AAAAAAACAAAATCTCATAAAAATTCTCGAACGGTAAATAAATTACTAAT
3259474 CCTAATAACTAACACAATAATAATATTAATAATTTTATACTCAAAATAATACACACTAAAATTAT
260 CCTAATAACTAACACAATAATAATATTAATAATTTTATACTCAAAATAATACACACTAAAATTAT
3259539 TAATTAGGGTTTTACTAAAAATAATAACTAACTAACTATAATAATAATACTAGTTTTTTACTAAC
325 TAATTAGGGTTTTACTAAAAATAATAACTAACTAACTATAATAATAATACTAGTTTTTTACTAAC
3259604 TAGTTTATATTGGTAAATAAAAATAATAACTAACAATAATAATAATAC
390 TAGTTTATATTGGTAAATAAAAATAATAACTAACAATAATAATAATAC
3259652 TA
1 TA
3259654 GTTTTTTACT
Statistics
Matches: 436, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
437 206 0.47
438 230 0.53
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.34
Consensus pattern (437 bp):
TAAAAAAATTTTGATATCCTTCTCTCACAACGTCTAAGTATTTTTGCATTAATCCTTGCCTTTAT
TTCATCGAACGATACATTTCTATTAAATCTCATTGCTATTTGTCGTCGACATTCAAATACACTTC
CAACACTTGTTGTCAAGATGACTCCATCGAAATAAACACATACAAGAAACTCAGCATCCATCTTC
AATATTTAATCTGTAAAAAAACAAAATCTCATAAAAATTCTCGAACGGTAAATAAATTACTAATC
CTAATAACTAACACAATAATAATATTAATAATTTTATACTCAAAATAATACACACTAAAATTATT
AATTAGGGTTTTACTAAAAATAATAACTAACTAACTATAATAATAATACTAGTTTTTTACTAACT
AGTTTATATTGGTAAATAAAAATAATAACTAACAATAATAATAATAC
Found at i:3259889 original size:11 final size:11
Alignment explanation
Indices: 3259869--3259910 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
3259859 TTAAAAATAC
3259869 CTTCTTTTTCT
1 CTTCTTTTTCT
*
3259880 CTTCTCTTTCT
1 CTTCTTTTTCT
3259891 C-TCTTTTTCT
1 CTTCTTTTTCT
3259901 CTTCTTTTTC
1 CTTCTTTTTC
3259911 GCAGCACCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (11 bp):
CTTCTTTTTCT
Found at i:3259896 original size:21 final size:21
Alignment explanation
Indices: 3259871--3259910 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3259861 AAAAATACCT
3259871 TCTTTTTCTCTTCTCTTTCTC
1 TCTTTTTCTCTTCTCTTTCTC
*
3259892 TCTTTTTCTCTTCTTTTTC
1 TCTTTTTCTCTTCTCTTTC
3259911 GCAGCACCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (21 bp):
TCTTTTTCTCTTCTCTTTCTC
Found at i:3260028 original size:27 final size:27
Alignment explanation
Indices: 3259990--3260062 Score: 110
Period size: 27 Copynumber: 2.7 Consensus size: 27
3259980 AACACGTGTA
3259990 GTGCCGCCAATGCCTTTGGCACCATTG
1 GTGCCGCCAATGCCTTTGGCACCATTG
** *
3260017 GTGCCGCCAATGGTTTTGGCACCTTTG
1 GTGCCGCCAATGCCTTTGGCACCATTG
*
3260044 GTGCCGCCAATGCCATTGG
1 GTGCCGCCAATGCCTTTGG
3260063 TCTGATCAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.14, C:0.30, G:0.29, T:0.27
Consensus pattern (27 bp):
GTGCCGCCAATGCCTTTGGCACCATTG
Found at i:3260167 original size:26 final size:28
Alignment explanation
Indices: 3260108--3260178 Score: 103
Period size: 26 Copynumber: 2.6 Consensus size: 28
3260098 TTTTTGTTTT
3260108 TTTAT-ATATTTTGGTAAATAATAAAAA
1 TTTATAATATTTTGGTAAATAATAAAAA
3260135 TAATTATAATATTTTGGTAAAT-A-AAAAA
1 T--TTATAATATTTTGGTAAATAATAAAAA
3260163 TTTATAATATTTTGGT
1 TTTATAATATTTTGGT
3260179 TATTTTTTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
26 15 0.37
27 1 0.02
28 6 0.15
29 5 0.12
30 14 0.34
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.46
Consensus pattern (28 bp):
TTTATAATATTTTGGTAAATAATAAAAA
Found at i:3267789 original size:20 final size:20
Alignment explanation
Indices: 3267752--3267790 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3267742 AAGTAGAAGT
* *
3267752 AATAAATAAATAATATAAAC
1 AATAAATAAACAACATAAAC
3267772 AATAAATAAACAACATAAA
1 AATAAATAAACAACATAAA
3267791 ATGATAAGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.21
Consensus pattern (20 bp):
AATAAATAAACAACATAAAC
Found at i:3269311 original size:19 final size:21
Alignment explanation
Indices: 3269273--3269312 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3269263 GTTTAATTTT
*
3269273 GATATTAATTTTAAATTTTGA
1 GATATTAATTTTAAAGTTTGA
3269294 GATATTAA-TTT-AAGTTTGA
1 GATATTAATTTTAAAGTTTGA
3269313 TGCTTCAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 3 0.17
21 8 0.44
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (21 bp):
GATATTAATTTTAAAGTTTGA
Found at i:3275596 original size:32 final size:31
Alignment explanation
Indices: 3275560--3275624 Score: 103
Period size: 32 Copynumber: 2.1 Consensus size: 31
3275550 TTCTCAAACC
3275560 TTGTTATATATATATACATACATACATACATT
1 TTGTTATATATATATACATACATACATA-ATT
* *
3275592 TTGTTATATATATATGCATACGTACATAATT
1 TTGTTATATATATATACATACATACATAATT
3275623 TT
1 TT
3275625 TTTAATTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 5 0.16
32 26 0.84
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (31 bp):
TTGTTATATATATATACATACATACATAATT
Found at i:3278372 original size:85 final size:85
Alignment explanation
Indices: 3278229--3278493 Score: 458
Period size: 85 Copynumber: 3.1 Consensus size: 85
3278219 GATGAGAAAA
*
3278229 TAGAAGAATGTTGCATTGAAATTACCTCAAAACATAGAGGGCAACCATGGTGGACTGCTCCTACC
1 TAGAAGAATGTTGCATTGAAATTACCTCAAAACATAGAGGACAACCATGGTGGACTGCTCCTACC
* * *
3278294 ACAAACGGATGGTACTTTTT
66 ACACATGGATGGTATTTTTT
*
3278314 TAGAAGAATGTTGCATTGAAATTACCTCAAAACATAGAGGACAACCATGGTGGACTGCTACTACC
1 TAGAAGAATGTTGCATTGAAATTACCTCAAAACATAGAGGACAACCATGGTGGACTGCTCCTACC
3278379 ACACATGGATGGTATTTTTT
66 ACACATGGATGGTATTTTTT
* *
3278399 TAGAAGAATGTTGCATTGAAATTACCTCAAAACATAGAGGACAACCATGGTGGATTACTCCTACC
1 TAGAAGAATGTTGCATTGAAATTACCTCAAAACATAGAGGACAACCATGGTGGACTGCTCCTACC
3278464 ACACATGGATGGTCATTTTTT
66 ACACATGGATGGT-ATTTTTT
3278485 TAGAAGAAT
1 TAGAAGAAT
3278494 TGAATGACTA
Statistics
Matches: 171, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
85 155 0.91
86 16 0.09
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (85 bp):
TAGAAGAATGTTGCATTGAAATTACCTCAAAACATAGAGGACAACCATGGTGGACTGCTCCTACC
ACACATGGATGGTATTTTTT
Found at i:3278538 original size:34 final size:35
Alignment explanation
Indices: 3278494--3278563 Score: 88
Period size: 37 Copynumber: 2.0 Consensus size: 35
3278484 TTAGAAGAAT
*
3278494 TGAATGACT-ACATTTTCGTACAATAAATGCGAAC
1 TGAATAACTAACATTTTCGTACAATAAATGCGAAC
* *
3278528 TGAATAACTACAACATTTTCTTACAATGAATGCGAA
1 TGAATAACT--AACATTTTCGTACAATAAATGCGAA
3278564 AGGAAATTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
34 8 0.27
37 22 0.73
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (35 bp):
TGAATAACTAACATTTTCGTACAATAAATGCGAAC
Found at i:3284295 original size:41 final size:41
Alignment explanation
Indices: 3284235--3284313 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 41
3284225 TTCATTTCAA
* * *
3284235 GTTTGGGGTTTGAAGTTTGA-GCTTGAAGTTTAGGGTTTAAG
1 GTTTGGGGTTTAAAATTTGATG-TTGAAGGTTAGGGTTTAAG
* *
3284276 GTTTGGTGTTTAAAATTTGATGTTTAAGGTTAGGGTTT
1 GTTTGGGGTTTAAAATTTGATGTTGAAGGTTAGGGTTT
3284314 TGGGATTTGA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
41 31 0.97
42 1 0.03
ACGTcount: A:0.20, C:0.01, G:0.33, T:0.46
Consensus pattern (41 bp):
GTTTGGGGTTTAAAATTTGATGTTGAAGGTTAGGGTTTAAG
Found at i:3284336 original size:14 final size:14
Alignment explanation
Indices: 3284319--3284366 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
3284309 GGTTTTGGGA
3284319 TTTGAGATTTGAGG
1 TTTGAGATTTGAGG
*
3284333 TTTGAGGTTTGAGG
1 TTTGAGATTTGAGG
*
3284347 TTTAAGATTTTG-GG
1 TTTGAGA-TTTGAGG
3284361 TTTGAG
1 TTTGAG
3284367 GGTTAGGGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 25 0.86
15 4 0.14
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.46
Consensus pattern (14 bp):
TTTGAGATTTGAGG
Found at i:3284362 original size:21 final size:21
Alignment explanation
Indices: 3284311--3284367 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
3284301 AAGGTTAGGG
* * *
3284311 TTTTGGGATTTGAGATTTGAGG
1 TTTTGGG-TTTGAGGTTTAAGA
**
3284333 TTTGAGGTTTGAGGTTTAAGA
1 TTTTGGGTTTGAGGTTTAAGA
3284354 TTTTGGGTTTGAGG
1 TTTTGGGTTTGAGG
3284368 GTTAGGGTTA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 23 0.82
22 5 0.18
ACGTcount: A:0.18, C:0.00, G:0.37, T:0.46
Consensus pattern (21 bp):
TTTTGGGTTTGAGGTTTAAGA
Found at i:3284867 original size:20 final size:20
Alignment explanation
Indices: 3284834--3284895 Score: 79
Period size: 20 Copynumber: 3.1 Consensus size: 20
3284824 AAAAATACTA
*
3284834 AATTTCTTATAGAATTATTG
1 AATTTCTTACAGAATTATTG
*
3284854 AATTTTTTACAGAATTATTG
1 AATTTCTTACAGAATTATTG
* * *
3284874 AATCTCTTACAAAATTCTTG
1 AATTTCTTACAGAATTATTG
3284894 AA
1 AA
3284896 CCTCTTATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (20 bp):
AATTTCTTACAGAATTATTG
Found at i:3284900 original size:20 final size:20
Alignment explanation
Indices: 3284846--3284902 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
3284836 TTTCTTATAG
** * *
3284846 AATTATTGAATTTTTTACAG
1 AATTATTGAACCTCTTACAA
*
3284866 AATTATTGAATCTCTTACAA
1 AATTATTGAACCTCTTACAA
*
3284886 AATTCTTGAACCTCTTA
1 AATTATTGAACCTCTTA
3284903 TAACATTGTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.35, C:0.14, G:0.07, T:0.44
Consensus pattern (20 bp):
AATTATTGAACCTCTTACAA
Found at i:3288246 original size:15 final size:14
Alignment explanation
Indices: 3288221--3288263 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
3288211 TGAAAATATA
*
3288221 TTTTTATATATCAT
1 TTTTTAAATATCAT
*
3288235 TATTTTAAATATAAAT
1 T-TTTTAAATAT-CAT
3288251 TTTTTAAATATCA
1 TTTTTAAATATCA
3288264 ACTATTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 2 0.08
15 19 0.79
16 3 0.12
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTTTAAATATCAT
Found at i:3288716 original size:13 final size:14
Alignment explanation
Indices: 3288689--3288717 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3288679 AAAATAACGA
3288689 TTTTTGAAATAATT
1 TTTTTGAAATAATT
3288703 TTTTTGAAAT-ATT
1 TTTTTGAAATAATT
3288716 TT
1 TT
3288718 AATATAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (14 bp):
TTTTTGAAATAATT
Done.