Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 59 of 240
Found at i:19531280 original size:39 final size:39
Alignment explanation
Indices: 19531237--19531315 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
19531227 TCGAGTTATT
*
19531237 TAAGTTAATCAATTTATTCAGATCAACTCGAATAAAAAA
1 TAAGTTAATCAAGTTATTCAGATCAACTCGAATAAAAAA
*
19531276 TAAGTTAATCAAGTTATTCGGATCAACTCGAATAAAAAA
1 TAAGTTAATCAAGTTATTCAGATCAACTCGAATAAAAAA
19531315 T
1 T
19531316 TAAATTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.30
Consensus pattern (39 bp):
TAAGTTAATCAAGTTATTCAGATCAACTCGAATAAAAAA
Found at i:19531770 original size:16 final size:16
Alignment explanation
Indices: 19531749--19531779 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19531739 AATTCCTTTA
19531749 AAATTAGAAATATTAT
1 AAATTAGAAATATTAT
*
19531765 AAATTAGTAATATTA
1 AAATTAGAAATATTA
19531780 AATTTAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (16 bp):
AAATTAGAAATATTAT
Found at i:19532579 original size:3 final size:3
Alignment explanation
Indices: 19532566--19532605 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
19532556 AAAATAATTC
19532566 AAG AA- AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
19532606 TATGGGGTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:19539303 original size:17 final size:17
Alignment explanation
Indices: 19539281--19539317 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
19539271 TTAGTAACTT
19539281 CGGCTGAGTTTGTATGG
1 CGGCTGAGTTTGTATGG
19539298 CGGCTGAGTTTGTATGG
1 CGGCTGAGTTTGTATGG
19539315 CGG
1 CGG
19539318 TGCGTTTGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.11, C:0.14, G:0.43, T:0.32
Consensus pattern (17 bp):
CGGCTGAGTTTGTATGG
Found at i:19543249 original size:21 final size:21
Alignment explanation
Indices: 19543225--19543269 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
19543215 AAAAATTGTC
* * * *
19543225 AATATTTAATTATTTAATTTT
1 AATATTCAAATATATAAATTT
19543246 AATATTCAAATATATAAATTT
1 AATATTCAAATATATAAATTT
19543267 AAT
1 AAT
19543270 TTAAATTTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
AATATTCAAATATATAAATTT
Found at i:19544904 original size:16 final size:17
Alignment explanation
Indices: 19544871--19544905 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
19544861 ATTTGAATCA
*
19544871 TTTTTAATTGCTATATT
1 TTTTTAATTGCTAAATT
19544888 TTTTTAATT-CTAAATT
1 TTTTTAATTGCTAAATT
19544904 TT
1 TT
19544906 CAGTCTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.66
Consensus pattern (17 bp):
TTTTTAATTGCTAAATT
Found at i:19549798 original size:48 final size:48
Alignment explanation
Indices: 19549732--19549865 Score: 187
Period size: 48 Copynumber: 2.8 Consensus size: 48
19549722 CGAGATAATG
* * * *
19549732 GGAATCCAAGTGGCGGCTGGAGTCGAGAACAAAGGGATAGAGATTACA
1 GGAATCCGAGCGGTGGCTGGAGTCGAGAACAAAGGGATAGAGAGTACA
**
19549780 GGAATCCGAGCGGTGGCTGGAGTCGAGAACAAAGGGATAGAGAGTATG
1 GGAATCCGAGCGGTGGCTGGAGTCGAGAACAAAGGGATAGAGAGTACA
* * *
19549828 GGAATCCGAGCGGTGGCTGGGGCCAAGAACAAAGGGAT
1 GGAATCCGAGCGGTGGCTGGAGTCGAGAACAAAGGGAT
19549866 CGGAACACCC
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 77 1.00
ACGTcount: A:0.32, C:0.15, G:0.40, T:0.13
Consensus pattern (48 bp):
GGAATCCGAGCGGTGGCTGGAGTCGAGAACAAAGGGATAGAGAGTACA
Found at i:19550322 original size:19 final size:20
Alignment explanation
Indices: 19550300--19550343 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
19550290 TTGGTACATA
* *
19550300 TTTTAC-TAAATTGTTTTTT
1 TTTTACATAAATTGTGTTTC
*
19550319 TTTTACATAATTTGTGTTTC
1 TTTTACATAAATTGTGTTTC
19550339 TTTTA
1 TTTTA
19550344 TTATTTTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.66
Consensus pattern (20 bp):
TTTTACATAAATTGTGTTTC
Found at i:19551567 original size:27 final size:26
Alignment explanation
Indices: 19551517--19551586 Score: 97
Period size: 27 Copynumber: 2.7 Consensus size: 26
19551507 CAAATTATAT
19551517 ATTAAATATATAT-TTTTTACTTTTA
1 ATTAAATATATATATTTTTACTTTTA
* *
19551542 ATTAAATATTAAATATTTTTATTTTTA
1 ATTAAATA-TATATATTTTTACTTTTA
*
19551569 ATCAAATATATATATTTT
1 ATTAAATATATATATTTT
19551587 ATATATATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
25 8 0.21
26 13 0.33
27 18 0.46
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (26 bp):
ATTAAATATATATATTTTTACTTTTA
Found at i:19554653 original size:21 final size:22
Alignment explanation
Indices: 19554613--19554659 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
19554603 CTCTGCTCAA
*
19554613 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
*
19554634 ACTCCACCTGCTGTGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
19554656 ACTC
1 ACTC
19554660 ACTCCTTCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.23
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:19563578 original size:20 final size:20
Alignment explanation
Indices: 19563555--19563595 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
19563545 TTAAATCCAT
* *
19563555 TTGATTTAAATCAAATCAAA
1 TTGATTGAAATCAAATAAAA
*
19563575 TTGATTGGAATCAAATAAAA
1 TTGATTGAAATCAAATAAAA
19563595 T
1 T
19563596 CATGATATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.34
Consensus pattern (20 bp):
TTGATTGAAATCAAATAAAA
Found at i:19565456 original size:33 final size:34
Alignment explanation
Indices: 19565411--19565519 Score: 100
Period size: 34 Copynumber: 3.3 Consensus size: 34
19565401 AATGCAACAT
* *
19565411 ACATGC-TATAACAGATCA-ATATGGTAGCAA-TA
1 ACATGCTTATAACAGAT-ATATATAGCAGCAATTA
*
19565443 ACATGCTTATAACAAATATATATAGCAGCAATTA
1 ACATGCTTATAACAGATATATATAGCAGCAATTA
* * * *
19565477 TCATGCTTATAACAGAT-TATGATAGTAGTAATAA
1 ACATGCTTATAACAGATATAT-ATAGCAGCAATTA
*
19565511 ACTTGCTTA
1 ACATGCTTA
19565520 ACATGTATTT
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
32 7 0.11
33 22 0.35
34 34 0.54
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.31
Consensus pattern (34 bp):
ACATGCTTATAACAGATATATATAGCAGCAATTA
Found at i:19565839 original size:27 final size:27
Alignment explanation
Indices: 19565807--19565957 Score: 119
Period size: 27 Copynumber: 5.4 Consensus size: 27
19565797 AACAGGGGAC
19565807 AAAATTGTAAAATCTAAAAAATAGGGG
1 AAAATTGTAAAATCTAAAAAATAGGGG
* * *
19565834 ATAATTGTAAAATATAAAAAA-ATGGGA
1 AAAATTGTAAAATCTAAAAAATA-GGGG
* * * *
19565861 AAAACTGTAAAATCTGAAGAATAGGTGC
1 AAAATTGTAAAATCTAAAAAATAGG-GG
* *
19565889 AAAACTATAAAA--TAAGAAAAGTAAGGGG
1 AAAATTGTAAAATCTAA-AAAA-T-AGGGG
*
19565917 AAAATTGTAAAATTTGAAAAAAATAGGGG
1 AAAATTGTAAAATCT--AAAAAATAGGGG
19565946 CAAAATTGTAAA
1 -AAAATTGTAAA
19565958 TTTGTAAAAT
Statistics
Matches: 98, Mismatches: 15, Indels: 19
0.74 0.11 0.14
Matches are distributed among these distances:
26 3 0.03
27 43 0.44
28 25 0.26
29 8 0.08
30 13 0.13
31 4 0.04
32 2 0.02
ACGTcount: A:0.56, C:0.04, G:0.19, T:0.22
Consensus pattern (27 bp):
AAAATTGTAAAATCTAAAAAATAGGGG
Found at i:19569566 original size:22 final size:22
Alignment explanation
Indices: 19569538--19569584 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
19569528 ATAAAATAAA
* *
19569538 TTTATTTTAATCAAATTAATAT
1 TTTATTTTAATCAAACTAAAAT
*
19569560 TTTATTTTGATCAAACTAAAAT
1 TTTATTTTAATCAAACTAAAAT
19569582 TTT
1 TTT
19569585 TCATTTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTATTTTAATCAAACTAAAAT
Found at i:19579905 original size:117 final size:117
Alignment explanation
Indices: 19579699--19579933 Score: 407
Period size: 117 Copynumber: 2.0 Consensus size: 117
19579689 ACTCGCCATC
* *
19579699 TGGCGAATTGTGTGATTGTGCTTGCAGTTATAAAAGGATCTGCTTGAAGTATCAGTAAATAGTTA
1 TGGCGAATTATGTGATTGTGCTTGCAGCTATAAAAGGATCTGCTTGAAGTATCAGTAAATAGTTA
*
19579764 AATGTTTTCATCTAGAACTCTCTAAGTTCTTTTGAACTTACTTAGTTACCTT
66 AATGTTTTCATCTAGAACTCTCTAAGTTCTTTTAAACTTACTTAGTTACCTT
* * *
19579816 TGGCGAGTTATGTGATTGTGGTTGCAGCTATAAAAGGATCTGCTTGAAGTATTAGTAAATAGTTA
1 TGGCGAATTATGTGATTGTGCTTGCAGCTATAAAAGGATCTGCTTGAAGTATCAGTAAATAGTTA
*
19579881 AATGTTTTCATCTGGAACTCTCTAAGTTCTTTTAAACTTACTTAGTTACCTT
66 AATGTTTTCATCTAGAACTCTCTAAGTTCTTTTAAACTTACTTAGTTACCTT
19579933 T
1 T
19579934 CCTTATCAGG
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
117 111 1.00
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.40
Consensus pattern (117 bp):
TGGCGAATTATGTGATTGTGCTTGCAGCTATAAAAGGATCTGCTTGAAGTATCAGTAAATAGTTA
AATGTTTTCATCTAGAACTCTCTAAGTTCTTTTAAACTTACTTAGTTACCTT
Found at i:19585411 original size:27 final size:27
Alignment explanation
Indices: 19585381--19585434 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
19585371 AAAAATTATT
19585381 TTAAAAAAAT-TAAAAATCATTAAAATA
1 TTAAAAAAATATAAAAAT-ATTAAAATA
* * *
19585408 TTAAAGAAGTATAAAAATTTTAAAATA
1 TTAAAAAAATATAAAAATATTAAAATA
19585435 CATATTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (27 bp):
TTAAAAAAATATAAAAATATTAAAATA
Found at i:19589521 original size:43 final size:43
Alignment explanation
Indices: 19589464--19589792 Score: 311
Period size: 43 Copynumber: 7.7 Consensus size: 43
19589454 TATTACATAT
* * * * *
19589464 CGATTCCACTGTCCCAGACAGGGTCTTATGCGAAATCAAATAA
1 CGATGCCAATGTCCCAGACATGGTCTTATACGTAATCAAATAA
* *
19589507 CGATGCCAATGTCCCAGACATGGTTTTATACGTAATCACAGT-A
1 CGATGCCAATGTCCCAGACATGGTCTTATACGTAATCA-AATAA
* * * * * * *
19589550 CAATGCTAATGTCCCAGACATGGTCTTACATGTTATCACATAT
1 CGATGCCAATGTCCCAGACATGGTCTTATACGTAATCAAATAA
* * *
19589593 CGATGCCACTGTCCCAGACAGGGTCTTATACGTAATCACAGT-A
1 CGATGCCAATGTCCCAGACATGGTCTTATACGTAATCA-AATAA
* * * * * * * * *
19589636 CAATGCTAATGTCCGAAACATGGTCTTACATGTTATCACATAT
1 CGATGCCAATGTCCCAGACATGGTCTTATACGTAATCAAATAA
* * * * *
19589679 TGATGCCACTGTCCCAGACAGGGTCTTATACGAAATCATATAA
1 CGATGCCAATGTCCCAGACATGGTCTTATACGTAATCAAATAA
* *
19589722 CGATGCCAATGTCCCAGACATGGTCTTATACGTAATCACATTA
1 CGATGCCAATGTCCCAGACATGGTCTTATACGTAATCAAATAA
* *
19589765 CAATGCCAATGTCCCAAACATGGTCTTA
1 CGATGCCAATGTCCCAGACATGGTCTTA
19589793 CATGTTATCA
Statistics
Matches: 223, Mismatches: 59, Indels: 8
0.77 0.20 0.03
Matches are distributed among these distances:
42 2 0.01
43 218 0.98
44 3 0.01
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (43 bp):
CGATGCCAATGTCCCAGACATGGTCTTATACGTAATCAAATAA
Found at i:19589622 original size:86 final size:86
Alignment explanation
Indices: 19589498--19589792 Score: 387
Period size: 86 Copynumber: 3.4 Consensus size: 86
19589488 CTTATGCGAA
* * * *
19589498 ATCAAATAACGATGCCAATGTCCCAGACATGGTTTTATACGTAATCACAGTACAATGCTAATGTC
1 ATCACATATCGATGCCAATGTCCCAGACAGGGTCTTATACGTAATCACAGTACAATGCTAATGTC
19589563 CCAGACATGGTCTTACATGTT
66 CCAGACATGGTCTTACATGTT
*
19589584 ATCACATATCGATGCCACTGTCCCAGACAGGGTCTTATACGTAATCACAGTACAATGCTAATGTC
1 ATCACATATCGATGCCAATGTCCCAGACAGGGTCTTATACGTAATCACAGTACAATGCTAATGTC
* *
19589649 CGAAACATGGTCTTACATGTT
66 CCAGACATGGTCTTACATGTT
* * * * * *
19589670 ATCACATATTGATGCCACTGTCCCAGACAGGGTCTTATACGAAATCATA-TAACGATGCCAATGT
1 ATCACATATCGATGCCAATGTCCCAGACAGGGTCTTATACGTAATCACAGT-ACAATGCTAATGT
* * *
19589734 CCCAGACATGGTCTTATACGTA
65 CCCAGACATGGTCTTACATGTT
* * *
19589756 ATCACAT-TACAATGCCAATGTCCCAAACATGGTCTTA
1 ATCACATAT-CGATGCCAATGTCCCAGACAGGGTCTTA
19589793 CATGTTATCA
Statistics
Matches: 185, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
85 2 0.01
86 183 0.99
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (86 bp):
ATCACATATCGATGCCAATGTCCCAGACAGGGTCTTATACGTAATCACAGTACAATGCTAATGTC
CCAGACATGGTCTTACATGTT
Found at i:19589674 original size:129 final size:129
Alignment explanation
Indices: 19589435--19589802 Score: 443
Period size: 129 Copynumber: 2.9 Consensus size: 129
19589425 TGTCATATCA
* * * * * *
19589435 CAGATATGTTCTTACATGTTATTACATATCGATTCCACTGTCCCAGACAGGGTCTTATGCGAAAT
1 CAGACATGGTCTTACATGTTATCACATATCGATGCCACTGTCCCAGACAGGGTCTTATACGTAAT
* * * * * * *
19589500 CA-AATAACGATGCCAATGTCCCAGACATGGTTTTATACGTAATCACAGTA-CAATGCTAATGTC
66 CACAAT-ACAATGCCAATGTCCCAAACATGGTCTTACATGTTATCACA-TATCAATGCCAATGTC
19589563 C
129 C
19589564 CAGACATGGTCTTACATGTTATCACATATCGATGCCACTGTCCCAGACAGGGTCTTATACGTAAT
1 CAGACATGGTCTTACATGTTATCACATATCGATGCCACTGTCCCAGACAGGGTCTTATACGTAAT
* * * ** *
19589629 CACAGTACAATGCTAATGTCCGAAACATGGTCTTACATGTTATCACATATTGATGCCACTGTCC
66 CACAATACAATGCCAATGTCCCAAACATGGTCTTACATGTTATCACATATCAATGCCAATGTCC
* * * ** * * * *
19589693 CAGACAGGGTCTTATACGAAATCATATAACGATGCCAATGTCCCAGACATGGTCTTATACGTAAT
1 CAGACATGGTCTTACATGTTATCACATATCGATGCCACTGTCCCAGACAGGGTCTTATACGTAAT
*
19589758 CACATTACAATGCCAATGTCCCAAACATGGTCTTACATGTTATCA
66 CACAATACAATGCCAATGTCCCAAACATGGTCTTACATGTTATCA
19589803 AATCTTGATA
Statistics
Matches: 206, Mismatches: 31, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
128 2 0.01
129 202 0.98
130 2 0.01
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (129 bp):
CAGACATGGTCTTACATGTTATCACATATCGATGCCACTGTCCCAGACAGGGTCTTATACGTAAT
CACAATACAATGCCAATGTCCCAAACATGGTCTTACATGTTATCACATATCAATGCCAATGTCC
Found at i:19592024 original size:18 final size:19
Alignment explanation
Indices: 19592001--19592037 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
19591991 GAATTTAAAC
*
19592001 TCTTTTATTTA-TTATTTA
1 TCTTTTATTAATTTATTTA
19592019 TCTTTTATTAATTTATTTA
1 TCTTTTATTAATTTATTTA
19592038 ATTAAAGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.70
Consensus pattern (19 bp):
TCTTTTATTAATTTATTTA
Found at i:19622283 original size:36 final size:36
Alignment explanation
Indices: 19622243--19622312 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
19622233 ATCATTTAAT
* *
19622243 CCAAACTTAATCTCCTAACTTCTAACAAGTAATCTG
1 CCAAACTCAATCTCCTAACTTCTAACAAGAAATCTG
* *
19622279 CCAAACTCAATCTCCTATCTTCTCACAAGAAATC
1 CCAAACTCAATCTCCTAACTTCTAACAAGAAATC
19622313 GACTAATCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.36, C:0.31, G:0.04, T:0.29
Consensus pattern (36 bp):
CCAAACTCAATCTCCTAACTTCTAACAAGAAATCTG
Found at i:19624776 original size:19 final size:20
Alignment explanation
Indices: 19624733--19624776 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
19624723 TTTACTTGGA
19624733 ATTTTTTTTATTTTAACATG
1 ATTTTTTTTATTTTAACATG
* * *
19624753 GTTTTTTTTCTTTTTA-ATG
1 ATTTTTTTTATTTTAACATG
19624772 ATTTT
1 ATTTT
19624777 GACTGGAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.18, C:0.05, G:0.07, T:0.70
Consensus pattern (20 bp):
ATTTTTTTTATTTTAACATG
Found at i:19626091 original size:27 final size:27
Alignment explanation
Indices: 19626061--19626127 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
19626051 AGGGAAGCAG
19626061 GTTGGCGGCACCAAACAAGGGAACCCT
1 GTTGGCGGCACCAAACAAGGGAACCCT
** *
19626088 GTTGGCGGCACCAAACAAGGGTTCCTT
1 GTTGGCGGCACCAAACAAGGGAACCCT
*
19626115 ATTGGCGGCACCA
1 GTTGGCGGCACCA
19626128 CCCTTGAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.25, C:0.28, G:0.30, T:0.16
Consensus pattern (27 bp):
GTTGGCGGCACCAAACAAGGGAACCCT
Found at i:19626197 original size:18 final size:18
Alignment explanation
Indices: 19626174--19626353 Score: 83
Period size: 19 Copynumber: 10.0 Consensus size: 18
19626164 GAAGGAGAGG
19626174 GGAAG-AAGAAGAAAGAAA
1 GGAAGAAAGAA-AAAGAAA
19626192 GGAAGAAAGAAAAAG-AA
1 GGAAGAAAGAAAAAGAAA
* * * *
19626209 TG-A-AAAGGAAAGGATA
1 GGAAGAAAGAAAAAGAAA
19626225 GGAAAGAAAGAAAAAG-AA
1 GG-AAGAAAGAAAAAGAAA
* * **
19626243 GGAAAGGAAAGGAAAGGGGA
1 GG-AA-GAAAGAAAAAGAAA
19626263 GGAAAGAAAGAAAAAG-AA
1 GG-AAGAAAGAAAAAGAAA
*
19626281 GGAAAGAAAAGGAAAAGAGAA
1 GG-AAG-AAAGAAAAAGA-AA
*
19626302 GAGAA-AAAAAAAAAGAAA
1 G-GAAGAAAGAAAAAGAAA
* * *
19626320 -GAAG-AAGAAGAGGGAA
1 GGAAGAAAGAAAAAGAAA
19626336 GGAAGGAAA-AAAAAGAAA
1 GGAA-GAAAGAAAAAGAAA
19626354 ATAAGCTAAT
Statistics
Matches: 123, Mismatches: 24, Indels: 30
0.69 0.14 0.17
Matches are distributed among these distances:
15 8 0.07
16 14 0.11
17 6 0.05
18 32 0.26
19 51 0.41
20 6 0.05
21 5 0.04
22 1 0.01
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (18 bp):
GGAAGAAAGAAAAAGAAA
Found at i:19626207 original size:10 final size:10
Alignment explanation
Indices: 19626176--19626328 Score: 73
Period size: 10 Copynumber: 15.1 Consensus size: 10
19626166 AGGAGAGGGG
*
19626176 AAGAAGAAGA
1 AAGAAAAAGA
19626186 AAGAAAGGAAGA
1 AAGAAA--AAGA
19626198 AAGAAAAAGA
1 AAGAAAAAGA
* *
19626208 ATGAAAAGGA
1 AAGAAAAAGA
19626218 AAGGATAGGAAAGA
1 AA-GA-A--AAAGA
19626232 AAGAAAAAG-
1 AAGAAAAAGA
* *
19626241 AAGGAAAGGA
1 AAGAAAAAGA
* * *
19626251 AAGGAAAGGG
1 AAGAAAAAGA
* *
19626261 GAG-GAAAGA
1 AAGAAAAAGA
19626270 AAGAAAAAGA
1 AAGAAAAAGA
* *
19626280 AGGAAAGA-A
1 AAGAAAAAGA
*
19626289 AAGGAAAAGA
1 AAGAAAAAGA
*
19626299 GAAGAGAAA-A
1 -AAGAAAAAGA
19626309 AA-AAAAAGA
1 AAGAAAAAGA
*
19626318 AAGAAGAAGA
1 AAGAAAAAGA
19626328 A
1 A
19626329 GAGGGAAGGA
Statistics
Matches: 108, Mismatches: 23, Indels: 24
0.70 0.15 0.15
Matches are distributed among these distances:
8 4 0.04
9 23 0.21
10 53 0.49
11 8 0.07
12 12 0.11
13 2 0.02
14 6 0.06
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (10 bp):
AAGAAAAAGA
Found at i:19626207 original size:22 final size:23
Alignment explanation
Indices: 19626176--19626354 Score: 77
Period size: 24 Copynumber: 7.7 Consensus size: 23
19626166 AGGAGAGGGG
*
19626176 AAGAAGAAGAAAG-AAAGGAAGA
1 AAGAAAAAGAAAGAAAAGGAAGA
*
19626198 AAGAAAAAGAATGAAAAGGAAAGGA
1 AAGAAAAAGAAAGAAAAGG-AA-GA
* * *
19626223 TAG-GAAAGAAAGAAAAAGAAGGA
1 AAGAAAAAGAAAGAAAAGGAA-GA
* * ***
19626246 AAGGAAAGGAAAGGGGAGGAAAGA
1 AAGAAAAAGAAAGAAAAGG-AAGA
*
19626270 AAGAAAAAG-AAGGAAA-GAA-A
1 AAGAAAAAGAAAGAAAAGGAAGA
* * *
19626290 AGGAAAAGAGAAGAGAAAA-AAAAA
1 AAGAAAA-AGAA-AGAAAAGGAAGA
*
19626314 AAGAAAGAAG-AAGAAGAGGGAAGGA
1 AAGAAA-AAGAAAGAA-AAGGAA-GA
*
19626339 AGGAAAAA-AAAGAAAA
1 AAGAAAAAGAAAGAAAA
19626355 TAAGCTAATT
Statistics
Matches: 117, Mismatches: 26, Indels: 27
0.69 0.15 0.16
Matches are distributed among these distances:
20 7 0.06
21 4 0.03
22 17 0.15
23 27 0.23
24 49 0.42
25 13 0.11
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (23 bp):
AAGAAAAAGAAAGAAAAGGAAGA
Found at i:19626230 original size:38 final size:35
Alignment explanation
Indices: 19626191--19626320 Score: 133
Period size: 34 Copynumber: 3.7 Consensus size: 35
19626181 GAAGAAAGAA
* *
19626191 AGGAAGAAAGAAAAAGAATGAAAAGGAAAGGATAGG
1 AGGAAGAAAGAAAAAGAA-GGAAAGGAAAGGAAAGG
19626227 A--AAGAAAGAAAAAGAAGGAAAGGAAAGGAAAGGGG
1 AGGAAGAAAGAAAAAGAAGGAAAGGAAAGGAAA--GG
* *
19626262 AGGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAAG
1 AGG-AAGAAAGAAAAAGAAGGAAAGGAAAGGAAAGG
* *
19626298 A-GAAGAGAA-AAAAAAAAAGAAAG
1 AGGAAGA-AAGAAAAAGAAGGAAAG
19626321 AAGAAGAAGA
Statistics
Matches: 82, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
33 13 0.16
34 31 0.38
35 6 0.07
36 3 0.04
38 29 0.35
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.02
Consensus pattern (35 bp):
AGGAAGAAAGAAAAAGAAGGAAAGGAAAGGAAAGG
Found at i:19626320 original size:34 final size:34
Alignment explanation
Indices: 19626176--19626353 Score: 107
Period size: 34 Copynumber: 5.1 Consensus size: 34
19626166 AGGAGAGGGG
*
19626176 AAGAAGAAG-AAAGA-AAGGAAGAAAGAAAAAGA
1 AAGAAGAAGAAAAGAGAAGGAAGAAAAAAAAAGA
* * *
19626208 ATGAA-AAGGAAAG-GATAGGAAAGAAAGAAAAAGA
1 AAGAAGAAGAAAAGAGA-AGG-AAGAAAAAAAAAGA
* * * *
19626242 AGGAAAGGAAAGGAAAGGGGAGGAAAGAAAGAAAAAGAAGGA
1 AAG-AA-G-AAGAAAAGAGAAGG-AAG-AA-AAAAA-AA-GA
19626284 AAGAA-AAGGAAAAGAGAAGAGAA-AAAAAAAAAGA
1 AAGAAGAA-GAAAAGAGAAG-GAAGAAAAAAAAAGA
* * *
19626318 AAGAAGAAGAAGAGGGAAGGAAGGAAAAAAAAGA
1 AAGAAGAAGAAAAGAGAAGGAAGAAAAAAAAAGA
19626352 AA
1 AA
19626354 ATAAGCTAAT
Statistics
Matches: 118, Mismatches: 11, Indels: 32
0.73 0.07 0.20
Matches are distributed among these distances:
31 3 0.03
32 9 0.08
33 6 0.05
34 44 0.37
35 6 0.05
36 5 0.04
37 2 0.02
38 17 0.14
39 13 0.11
40 5 0.04
41 4 0.03
42 4 0.03
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.01
Consensus pattern (34 bp):
AAGAAGAAGAAAAGAGAAGGAAGAAAAAAAAAGA
Found at i:19626347 original size:38 final size:39
Alignment explanation
Indices: 19626197--19626354 Score: 116
Period size: 38 Copynumber: 4.1 Consensus size: 39
19626187 AGAAAGGAAG
* *
19626197 AAAGAAA-AAGAATGAAAAGGAAAGGATAGGAAAGAAAGAA
1 AAAGAAAGAAGAA-GAAGAGGAAAGGA-AGGAAAGAAAAAA
* * * *
19626237 AAAGAAGGAA-AGGAA-AGGAAAGGGGAGGAAAGAAAGAA
1 AAAGAAAGAAGAAGAAGAGGAAA-GGAAGGAAAGAAAAAA
* *
19626275 AAAGAAGGAAAGAA-AAG-GAAAAGAGAA-GAGAA-AAAAAA
1 AAAGAAAG-AAGAAGAAGAGGAAAG-GAAGGA-AAGAAAAAA
*
19626313 AAAGAAAGAAGAAGAAGAGGGAAGGAAGGAAA-AAAAAGA
1 AAAGAAAGAAGAAGAAGAGGAAAGGAAGGAAAGAAAAA-A
19626352 AAA
1 AAA
19626355 TAAGCTAATT
Statistics
Matches: 97, Mismatches: 10, Indels: 23
0.75 0.08 0.18
Matches are distributed among these distances:
37 5 0.05
38 55 0.57
39 27 0.28
40 8 0.08
41 2 0.02
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (39 bp):
AAAGAAAGAAGAAGAAGAGGAAAGGAAGGAAAGAAAAAA
Found at i:19627058 original size:8 final size:8
Alignment explanation
Indices: 19627045--19627069 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
19627035 AATATTTTGG
19627045 TAATATTT
1 TAATATTT
19627053 TAATATTT
1 TAATATTT
19627061 TAATATTT
1 TAATATTT
19627069 T
1 T
19627070 TGTAATCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TAATATTT
Found at i:19627171 original size:27 final size:28
Alignment explanation
Indices: 19627121--19627189 Score: 115
Period size: 27 Copynumber: 2.5 Consensus size: 28
19627111 AATAAAAAAA
19627121 TTACCAAAATAT-TATAACTTTTTTTTAT
1 TTACCAAAATATATATAAC-TTTTTTTAT
19627149 TTACCAAAATATATATAA-TTTTTTTAT
1 TTACCAAAATATATATAACTTTTTTTAT
19627176 TTACCAAAATATAT
1 TTACCAAAATATAT
19627190 CAAAAAAAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
27 23 0.57
28 12 0.30
29 5 0.12
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (28 bp):
TTACCAAAATATATATAACTTTTTTTAT
Found at i:19629475 original size:15 final size:14
Alignment explanation
Indices: 19629435--19629463 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
19629425 TTTTTGTATC
19629435 AATTTAATTATTCT
1 AATTTAATTATTCT
19629449 AATTTAATTATTCT
1 AATTTAATTATTCT
19629463 A
1 A
19629464 GTTTTAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTTAATTATTCT
Found at i:19629723 original size:14 final size:14
Alignment explanation
Indices: 19629706--19629750 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
19629696 CTTTCCTCCC
19629706 CTTTCCTTTTCTTT
1 CTTTCCTTTTCTTT
*
19629720 CTTTCTTTTTCTTT
1 CTTTCCTTTTCTTT
* *
19629734 CTTTCCTCTCCTTT
1 CTTTCCTTTTCTTT
19629748 CTT
1 CTT
19629751 CTTCTTCCCC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (14 bp):
CTTTCCTTTTCTTT
Found at i:19629735 original size:38 final size:36
Alignment explanation
Indices: 19629674--19629756 Score: 103
Period size: 38 Copynumber: 2.2 Consensus size: 36
19629664 CATAAATTTT
19629674 TTTTCTCTTCTTCCTTTCTTTTCTTTCCTCCCCTTTCC
1 TTTTCT-TTCTTCCTTTCTTTTCTTTCCTCCCCTTT-C
* * *
19629712 TTTTCTTTCTTTCTTTTTCTTTCTTTCCTCTCCTTTC
1 TTTTCTTTCTTCCTTTCT-TTTCTTTCCTCCCCTTTC
19629749 TTCTTCTT
1 TT-TTCTT
19629757 CCCCTCTCCT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
37 13 0.32
38 27 0.68
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (36 bp):
TTTTCTTTCTTCCTTTCTTTTCTTTCCTCCCCTTTC
Found at i:19629746 original size:33 final size:33
Alignment explanation
Indices: 19629681--19629751 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
19629671 TTTTTTTCTC
*
19629681 TTCTTCCTTTCTTTTCTTTCCTCCCCTTTCCTT
1 TTCTTCCTTTCTTTTCTTTCCTCCCCTCTCCTT
* **
19629714 TTCTTTCTTTCTTTTTCTTT-CTTTCCTCTCC-T
1 TTCTTCCTTTC-TTTTCTTTCCTCCCCTCTCCTT
19629746 TTCTTC
1 TTCTTC
19629752 TTCTTCCCCT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
32 6 0.19
33 18 0.56
34 8 0.25
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (33 bp):
TTCTTCCTTTCTTTTCTTTCCTCCCCTCTCCTT
Found at i:19629770 original size:38 final size:38
Alignment explanation
Indices: 19629693--19629770 Score: 86
Period size: 38 Copynumber: 2.1 Consensus size: 38
19629683 CTTCCTTTCT
* ** **
19629693 TTTCTTTCCTCCCCTTTCCTTTTCTTTCTTTCTTTTTC
1 TTTCTTTCCTCCCCTTTCCTTTTCTTCCCCTCTCCTTC
*
19629731 TTTCTTTCCTCTCCTTT-CTTCTTCTTCCCCTCTCCTTC
1 TTTCTTTCCTCCCCTTTCCTT-TTCTTCCCCTCTCCTTC
19629769 TT
1 TT
19629771 CCCCCCACCA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
37 3 0.09
38 30 0.91
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (38 bp):
TTTCTTTCCTCCCCTTTCCTTTTCTTCCCCTCTCCTTC
Found at i:19629843 original size:27 final size:27
Alignment explanation
Indices: 19629805--19629871 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
19629795 AATTCAAGGG
19629805 TGGTGCCGCCAACAAGGAACCCTTGTT
1 TGGTGCCGCCAACAAGGAACCCTTGTT
* **
19629832 TGGTGCCGCCAACAGGGTTCCCTTGTT
1 TGGTGCCGCCAACAAGGAACCCTTGTT
19629859 TGGTGCCGCCAAC
1 TGGTGCCGCCAAC
19629872 TTGCTTCCCT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.16, C:0.31, G:0.28, T:0.24
Consensus pattern (27 bp):
TGGTGCCGCCAACAAGGAACCCTTGTT
Found at i:19629879 original size:27 final size:27
Alignment explanation
Indices: 19629805--19629881 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 27
19629795 AATTCAAGGG
**
19629805 TGGTGCCGCCAACAAGG-AACCCTTGTT
1 TGGTGCCGCCAAC-AGGCTTCCCTTGTT
*
19629832 TGGTGCCGCCAACAGGGTTCCCTTGTT
1 TGGTGCCGCCAACAGGCTTCCCTTGTT
**
19629859 TGGTGCCGCCAACTTGCTTCCCT
1 TGGTGCCGCCAACAGGCTTCCCT
19629882 CCACCCAGGG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
26 3 0.07
27 41 0.93
ACGTcount: A:0.14, C:0.32, G:0.26, T:0.27
Consensus pattern (27 bp):
TGGTGCCGCCAACAGGCTTCCCTTGTT
Found at i:19629953 original size:16 final size:17
Alignment explanation
Indices: 19629914--19629953 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
19629904 AGTCCAGGTT
19629914 TTTTTTTCTGTTTTTTA
1 TTTTTTTCTGTTTTTTA
*
19629931 TTTTTTT-TGTTTTTTG
1 TTTTTTTCTGTTTTTTA
19629947 TTTTTTT
1 TTTTTTT
19629954 ATATATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.03, C:0.03, G:0.07, T:0.88
Consensus pattern (17 bp):
TTTTTTTCTGTTTTTTA
Found at i:19629962 original size:24 final size:24
Alignment explanation
Indices: 19629912--19629963 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
19629902 TCAGTCCAGG
* *
19629912 TTTT-TTTTTCTGTTTTTTATTTT
1 TTTTGTTTTTCTGTTTTTTATATA
19629935 TTTTGTTTTT-TGTTTTTTTATATA
1 TTTTGTTTTTCTG-TTTTTTATATA
19629959 TTTTG
1 TTTTG
19629964 GTAAATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.08, C:0.02, G:0.08, T:0.83
Consensus pattern (24 bp):
TTTTGTTTTTCTGTTTTTTATATA
Found at i:19630012 original size:27 final size:27
Alignment explanation
Indices: 19629953--19630024 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
19629943 TTTGTTTTTT
* **
19629953 TATATATTTTGGTAAATAAAAAAATTA
1 TATATATTTTGGTAAACAAAAAAAAAA
*
19629980 TATATATTTTGTTAAACAAAAAAAAAA
1 TATATATTTTGGTAAACAAAAAAAAAA
19630007 GTTATAATATTTTGGTAA
1 --TAT-ATATTTTGGTAA
19630025 TTTTTTATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
27 23 0.62
29 3 0.08
30 11 0.30
ACGTcount: A:0.50, C:0.01, G:0.08, T:0.40
Consensus pattern (27 bp):
TATATATTTTGGTAAACAAAAAAAAAA
Found at i:19631950 original size:30 final size:31
Alignment explanation
Indices: 19631905--19631964 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
19631895 GGAGGTGGGA
*
19631905 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
19631936 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
19631965 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:19635358 original size:23 final size:23
Alignment explanation
Indices: 19635328--19635699 Score: 462
Period size: 23 Copynumber: 16.7 Consensus size: 23
19635318 TTAAGTTTAG
19635328 GGTTAGGGTTTTCAACTTAATTA
1 GGTTAGGGTTTTCAACTTAATTA
19635351 GGTTAGGGTTTTCAACTTAATTA
1 GGTTAGGGTTTTCAACTTAATTA
* *
19635374 -GTTAGTGTTTT-AATTTAATTA
1 GGTTAGGGTTTTCAACTTAATTA
19635395 GGTTAGGGTTTTCAACTTAATTA
1 GGTTAGGGTTTTCAACTTAATTA
*
19635418 GGTTAGGGTTTTCAACTTAAATA
1 GGTTAGGGTTTTCAACTTAATTA
* *
19635441 GGTTAGGGTTTTTAATTTAATTA
1 GGTTAGGGTTTTCAACTTAATTA
* *
19635464 GGTTAGGCTTTTCAACTT-A--G
1 GGTTAGGGTTTTCAACTTAATTA
***** *
19635484 GGTTTTTAATTT-AA-TTAGGTTA
1 GGTTAGGGTTTTCAACTTA-ATTA
*
19635506 GG-----CTTTTCAACTTAATTA
1 GGTTAGGGTTTTCAACTTAATTA
*
19635524 GGTTAGGGTTTTCAACCTAATTA
1 GGTTAGGGTTTTCAACTTAATTA
19635547 GGTTAGGGTTTTCAACTTAATTA
1 GGTTAGGGTTTTCAACTTAATTA
*
19635570 GGTTAGGGTTTTCAACTTAAATA
1 GGTTAGGGTTTTCAACTTAATTA
* *
19635593 GGTTAGGGTTTTTAATTTAATTA
1 GGTTAGGGTTTTCAACTTAATTA
* *
19635616 GGTTAGGGTTTTTAATTTAATTA
1 GGTTAGGGTTTTCAACTTAATTA
*
19635639 GGTTAGAGTTTTCAACTTAATTA
1 GGTTAGGGTTTTCAACTTAATTA
19635662 GGTTAGGGTTTTCAACTTAATTA
1 GGTTAGGGTTTTCAACTTAATTA
19635685 GGTTAGGGTTTTCAA
1 GGTTAGGGTTTTCAA
19635700 TTTTTATCAC
Statistics
Matches: 303, Mismatches: 33, Indels: 26
0.84 0.09 0.07
Matches are distributed among these distances:
17 3 0.01
18 9 0.03
19 5 0.02
20 7 0.02
21 9 0.03
22 23 0.08
23 247 0.82
ACGTcount: A:0.27, C:0.07, G:0.21, T:0.45
Consensus pattern (23 bp):
GGTTAGGGTTTTCAACTTAATTA
Found at i:19635461 original size:46 final size:46
Alignment explanation
Indices: 19635328--19635699 Score: 523
Period size: 46 Copynumber: 8.3 Consensus size: 46
19635318 TTAAGTTTAG
19635328 GGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAACTTAATTA
1 GGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAACTTAATTA
* *
19635374 -GTTAGTGTTTT-AATTTAATTAGGTTAGGGTTTTCAACTTAATTA
1 GGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAACTTAATTA
* * *
19635418 GGTTAGGGTTTTCAACTTAAATAGGTTAGGGTTTTTAATTTAATTA
1 GGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAACTTAATTA
* * *
19635464 GGTTAGGCTTTTCAAC---------TTAGGGTTTTTAATTTAATTA
1 GGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAACTTAATTA
* *
19635501 GGTTAGGCTTTTCAACTTAATTAGGTTAGGGTTTTCAACCTAATTA
1 GGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAACTTAATTA
*
19635547 GGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAACTTAAATA
1 GGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAACTTAATTA
* * * *
19635593 GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAATTA
1 GGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAACTTAATTA
*
19635639 GGTTAGAGTTTTCAACTTAATTAGGTTAGGGTTTTCAACTTAATTA
1 GGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAACTTAATTA
19635685 GGTTAGGGTTTTCAA
1 GGTTAGGGTTTTCAA
19635700 TTTTTATCAC
Statistics
Matches: 290, Mismatches: 25, Indels: 22
0.86 0.07 0.07
Matches are distributed among these distances:
37 37 0.13
44 32 0.11
45 20 0.07
46 201 0.69
ACGTcount: A:0.27, C:0.07, G:0.21, T:0.45
Consensus pattern (46 bp):
GGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAACTTAATTA
Found at i:19635490 original size:37 final size:37
Alignment explanation
Indices: 19635443--19635519 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
19635433 CTTAAATAGG
19635443 TTAGGGTTTTTAATTTAATTAGGTTAGGCTTTTCAAC
1 TTAGGGTTTTTAATTTAATTAGGTTAGGCTTTTCAAC
19635480 TTAGGGTTTTTAATTTAATTAGGTTAGGCTTTTCAAC
1 TTAGGGTTTTTAATTTAATTAGGTTAGGCTTTTCAAC
19635517 TTA
1 TTA
19635520 ATTAGGTTAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.25, C:0.08, G:0.18, T:0.49
Consensus pattern (37 bp):
TTAGGGTTTTTAATTTAATTAGGTTAGGCTTTTCAAC
Found at i:19635702 original size:69 final size:69
Alignment explanation
Indices: 19635328--19635699 Score: 523
Period size: 69 Copynumber: 5.6 Consensus size: 69
19635318 TTAAGTTTAG
* *
19635328 GGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAACTTAATTA-GTTAGTGTTTT-AATTTA
1 GGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAACTTA
19635391 ATTA
66 ATTA
* * *
19635395 GGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAACTTAAATAGGTTAGGGTTTTTAATTTA
1 GGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAACTTA
19635460 ATTA
66 ATTA
* * * *
19635464 GGTTAGGCTTTTCAAC---------TTAGGGTTTTTAATTTAATTAGGTTAGGCTTTTCAACTTA
1 GGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAACTTA
19635520 ATTA
66 ATTA
*
19635524 GGTTAGGGTTTTCAACCTAATTAGGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAACTTA
1 GGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAACTTA
*
19635589 AATA
66 ATTA
* * * * *
19635593 GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGAGTTTTCAACTTA
1 GGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAACTTA
19635658 ATTA
66 ATTA
19635662 GGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAA
1 GGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAA
19635700 TTTTTATCAC
Statistics
Matches: 270, Mismatches: 24, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
60 53 0.20
67 45 0.17
68 10 0.04
69 162 0.60
ACGTcount: A:0.27, C:0.07, G:0.21, T:0.45
Consensus pattern (69 bp):
GGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAACTTA
ATTA
Found at i:19635730 original size:25 final size:25
Alignment explanation
Indices: 19635701--19635793 Score: 150
Period size: 25 Copynumber: 3.7 Consensus size: 25
19635691 GGTTTTCAAT
*
19635701 TTTTATCACATCAAATAAACTTTTA
1 TTTTATTACATCAAATAAACTTTTA
* *
19635726 TTTTATTACATCATATAAACTTCTA
1 TTTTATTACATCAAATAAACTTTTA
19635751 TTTTATTACATCAAATAAACTTTTA
1 TTTTATTACATCAAATAAACTTTTA
*
19635776 TTTTATTATATCAAATAA
1 TTTTATTACATCAAATAA
19635794 TATCAAAATA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 62 1.00
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (25 bp):
TTTTATTACATCAAATAAACTTTTA
Found at i:19638222 original size:22 final size:23
Alignment explanation
Indices: 19638196--19638248 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
19638186 ATGAATTCAT
19638196 GAGAATTTTGAAAGGAAAT-TGA
1 GAGAATTTTGAAAGGAAATATGA
** *
19638218 GAGAAAATTGAGAGGAAATATGA
1 GAGAATTTTGAAAGGAAATATGA
*
19638241 GAGGATTT
1 GAGAATTT
19638249 GTAGTGAAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.45, C:0.00, G:0.30, T:0.25
Consensus pattern (23 bp):
GAGAATTTTGAAAGGAAATATGA
Found at i:19638240 original size:51 final size:51
Alignment explanation
Indices: 19638104--19638228 Score: 173
Period size: 51 Copynumber: 2.5 Consensus size: 51
19638094 CTATTTTAAA
* *
19638104 AAAGGAAATTGAGAGCAAATTGAAATTAAATATGACTTTGAGAGATTTTTG
1 AAAGGAAATTGAGAGAAAATTGAAATTAAATATGAATTTGAGAGATTTTTG
* * *
19638155 GAATGAAATTGAGAGGAAATTGAAATTAAATATGAATTCATGAGA-A-TTTTG
1 AAAGGAAATTGAGAGAAAATTGAAATTAAATATGAATT--TGAGAGATTTTTG
19638206 AAAGGAAATTGAGAGAAAATTGA
1 AAAGGAAATTGAGAGAAAATTGA
19638229 GAGGAAATAT
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
51 59 0.91
52 1 0.02
53 5 0.08
ACGTcount: A:0.46, C:0.02, G:0.22, T:0.29
Consensus pattern (51 bp):
AAAGGAAATTGAGAGAAAATTGAAATTAAATATGAATTTGAGAGATTTTTG
Found at i:19638241 original size:12 final size:11
Alignment explanation
Indices: 19638203--19638245 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
19638193 CATGAGAATT
*
19638203 TTGAAAGGAAA
1 TTGAGAGGAAA
*
19638214 TTGAGAGAAAA
1 TTGAGAGGAAA
19638225 TTGAGAGGAAA
1 TTGAGAGGAAA
19638236 TATGAGAGGA
1 T-TGAGAGGA
19638246 TTTGTAGTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
11 20 0.71
12 8 0.29
ACGTcount: A:0.49, C:0.00, G:0.33, T:0.19
Consensus pattern (11 bp):
TTGAGAGGAAA
Found at i:19651447 original size:24 final size:24
Alignment explanation
Indices: 19651415--19651467 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
19651405 TATTTATAGG
* **
19651415 TAAATATATTATGTTAATAAATAT
1 TAAATATATCATACTAATAAATAT
*
19651439 TAAATATATCATACTCATAAATAT
1 TAAATATATCATACTAATAAATAT
19651463 TAAAT
1 TAAAT
19651468 CTTTTAGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.42
Consensus pattern (24 bp):
TAAATATATCATACTAATAAATAT
Found at i:19655832 original size:24 final size:24
Alignment explanation
Indices: 19655800--19655852 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
19655790 TAATCAAAGT
* *
19655800 TAAATATATTATATTGATAAATAC
1 TAAATATATTATACTCATAAATAC
19655824 TAAATATATTATACTCATAAATAC
1 TAAATATATTATACTCATAAATAC
19655848 TAAAT
1 TAAAT
19655853 CTTCTAGAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.40
Consensus pattern (24 bp):
TAAATATATTATACTCATAAATAC
Found at i:19657287 original size:35 final size:35
Alignment explanation
Indices: 19657243--19657309 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
19657233 ATAAAAGTAC
19657243 ATAAATTATAATAAATTAAAAT-AATA-GAATGTCTA
1 ATAAATTATAA-AAA-TAAAATAAATACGAATGTCTA
* *
19657278 ATAATTTATAAACATAAAATAAATACGAATGT
1 ATAAATTATAAAAATAAAATAAATACGAATGT
19657310 TTGAAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 6 0.21
34 6 0.21
35 16 0.57
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (35 bp):
ATAAATTATAAAAATAAAATAAATACGAATGTCTA
Found at i:19662264 original size:18 final size:19
Alignment explanation
Indices: 19662223--19662274 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
19662213 TATCTAAAAC
19662223 AATTTAAATTTAAGTAATT
1 AATTTAAATTTAAGTAATT
*
19662242 AATTTATATTT-AGTTAA-T
1 AATTTAAATTTAAG-TAATT
19662260 AATTTTAATATTTAA
1 AA-TTTAA-ATTTAA
19662275 ATTTAAATCC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
18 5 0.19
19 17 0.63
20 4 0.15
21 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (19 bp):
AATTTAAATTTAAGTAATT
Found at i:19664298 original size:29 final size:29
Alignment explanation
Indices: 19664242--19664298 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
19664232 TGACATTTCA
*
19664242 ATAAATTATATTTTTACATAAATTTTTTT
1 ATAAATTATATTTTTACATAAATCTTTTT
* *
19664271 ATAAA-TATATTTTTTATATAACTCTTTT
1 ATAAATTATA-TTTTTACATAAATCTTTT
19664299 AACCTAATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (29 bp):
ATAAATTATATTTTTACATAAATCTTTTT
Found at i:19674696 original size:14 final size:14
Alignment explanation
Indices: 19674677--19674716 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
19674667 TTGATTGGCA
19674677 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
19674691 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
19674705 GGAAAATGTTTT
1 GTAAAATGTTTT
19674717 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:19674729 original size:34 final size:35
Alignment explanation
Indices: 19674685--19674751 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
19674675 CAGTAAAATG
* *
19674685 TTTTCCGTAAAATGA-TTTCTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
*
19674719 TTTTCTGTAAAATGACTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTT
19674752 TCTGGTGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 14 0.48
35 15 0.52
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
Found at i:19674738 original size:20 final size:20
Alignment explanation
Indices: 19674700--19674739 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
19674690 CGTAAAATGA
**
19674700 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGACTTACT
*
19674720 TTTCTGTAAAATGACTTACT
1 TTTCTGGAAAATGACTTACT
19674740 GGAAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTCTGGAAAATGACTTACT
Found at i:19679728 original size:13 final size:13
Alignment explanation
Indices: 19679710--19679735 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19679700 CCAGAAACTG
19679710 ATTTGCAGAAAAC
1 ATTTGCAGAAAAC
19679723 ATTTGCAGAAAAC
1 ATTTGCAGAAAAC
19679736 TACCCATTTG
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:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (13 bp):
ATTTGCAGAAAAC
Found at i:19679856 original size:16 final size:16
Alignment explanation
Indices: 19679835--19679866 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
19679825 ATCAAGAAAG
19679835 TAGAGGAGGAAAAACA
1 TAGAGGAGGAAAAACA
19679851 TAGAGGAGGAAAAACA
1 TAGAGGAGGAAAAACA
19679867 GCAGAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.06, G:0.31, T:0.06
Consensus pattern (16 bp):
TAGAGGAGGAAAAACA
Found at i:19682809 original size:30 final size:30
Alignment explanation
Indices: 19682766--19682841 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 30
19682756 CACCGGCAGA
* *
19682766 GACACA-GA-CATGTGTCTCAGCCATGTGT
1 GACACATGACCATGTGTCTCAACCATGTAT
*
19682794 GACACATGACCATGTGTCTCAACCGTGTAT
1 GACACATGACCATGTGTCTCAACCATGTAT
*
19682824 GACACATGGCCATGTGTC
1 GACACATGACCATGTGTC
19682842 CCTTATATCT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
28 6 0.14
29 2 0.05
30 34 0.81
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (30 bp):
GACACATGACCATGTGTCTCAACCATGTAT
Found at i:19684810 original size:14 final size:15
Alignment explanation
Indices: 19684791--19684819 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
19684781 TCATAGTAAC
19684791 ATTTTATA-AAAAAT
1 ATTTTATATAAAAAT
19684805 ATTTTATATAAAAAT
1 ATTTTATATAAAAAT
19684820 GCCCTCATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTTTATATAAAAAT
Found at i:19685420 original size:14 final size:14
Alignment explanation
Indices: 19685386--19685414 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19685376 TCTTGTAAGT
19685386 AAAC-AAGTTTTTC
1 AAACTAAGTTTTTC
19685399 AAACTAAGTTTTTC
1 AAACTAAGTTTTTC
19685413 AA
1 AA
19685415 GGTAAGGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (14 bp):
AAACTAAGTTTTTC
Found at i:19687695 original size:29 final size:29
Alignment explanation
Indices: 19687644--19687720 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
19687634 CTTTAATTTT
* *
19687644 TAATATAATTCAGTCTTTATATTTTTATAATG
1 TAAT-TAATT-AGT-TTAATATTTTTATAACG
*
19687676 CT-ATTAATTAGTTTAATATTTTTGTAACG
1 -TAATTAATTAGTTTAATATTTTTATAACG
19687705 TAATTAATTAGTTTAA
1 TAATTAATTAGTTTAA
19687721 ATAGTTAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 1 0.03
29 28 0.70
30 3 0.08
31 5 0.12
32 2 0.05
33 1 0.03
ACGTcount: A:0.35, C:0.05, G:0.08, T:0.52
Consensus pattern (29 bp):
TAATTAATTAGTTTAATATTTTTATAACG
Found at i:19691337 original size:2 final size:2
Alignment explanation
Indices: 19691330--19691377 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
19691320 TTTCAGTACG
19691330 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
19691372 TC TC TC
1 TC TC TC
19691378 ACGCGCACGC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:19696345 original size:63 final size:63
Alignment explanation
Indices: 19696211--19696363 Score: 175
Period size: 63 Copynumber: 2.4 Consensus size: 63
19696201 CCTGGAGAAT
* * * * * * *
19696211 GTGTTGATGCA-AAGAATGATTGTGCGTGTTGTAGAGCTTGTGTAAAATAAACTGGTGTTAAAT
1 GTGTTGATGCAGGA-AATGATTGTGTGTGTTGTAGAGCTTATGTAAAATAAACTAGAGCTAAAG
* *
19696274 GTGCTGATGCAGGAAATGATTGTGTGTGTTGT-GATGCTTATGTAAAATAAACTAGAGCTGAAG
1 GTGTTGATGCAGGAAATGATTGTGTGTGTTGTAGA-GCTTATGTAAAATAAACTAGAGCTAAAG
* *
19696337 GTGTTGATGCAGGGAATTATTGTGTGT
1 GTGTTGATGCAGGAAATGATTGTGTGT
19696364 CTTATTATGT
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
62 2 0.03
63 73 0.96
64 1 0.01
ACGTcount: A:0.28, C:0.07, G:0.31, T:0.35
Consensus pattern (63 bp):
GTGTTGATGCAGGAAATGATTGTGTGTGTTGTAGAGCTTATGTAAAATAAACTAGAGCTAAAG
Found at i:19697206 original size:22 final size:21
Alignment explanation
Indices: 19697176--19697216 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
19697166 ATAAAAATGA
*
19697176 TAATGATATTATCAAATGAATT
1 TAATCATATTA-CAAATGAATT
*
19697198 TAATCATATTACAAGTGAA
1 TAATCATATTACAAATGAA
19697217 AATTCGTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.37
Consensus pattern (21 bp):
TAATCATATTACAAATGAATT
Found at i:19699148 original size:45 final size:44
Alignment explanation
Indices: 19699084--19699190 Score: 119
Period size: 45 Copynumber: 2.4 Consensus size: 44
19699074 TTTAGGGCAC
* * * *
19699084 GTTTGGTTCACTGTAATGGAATAGAGGC-GTAATAGTAATTCAAT-T
1 GTTTGGTTGAATGGAATGGAATAGA-ACTGTAATAGT-ATTC-ATGT
*
19699129 GTTTGGTTGAATGGAATGGAATAGAACTGTAATAGTATTCTTGT
1 GTTTGGTTGAATGGAATGGAATAGAACTGTAATAGTATTCATGT
*
19699173 GTTTGGTTGAATAGAATG
1 GTTTGGTTGAATGGAATG
19699191 ATGTTGTAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
43 1 0.02
44 23 0.43
45 30 0.56
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.37
Consensus pattern (44 bp):
GTTTGGTTGAATGGAATGGAATAGAACTGTAATAGTATTCATGT
Found at i:19699414 original size:56 final size:54
Alignment explanation
Indices: 19699314--19699539 Score: 163
Period size: 61 Copynumber: 3.9 Consensus size: 54
19699304 TAAATAATGA
* * * *
19699314 ATAATTTAATCATATT-TTAACATAATTATTATTAAATATAATTTAATAAAAATAT
1 ATAATTTAATAAAATTCTTAATATAATTATTCTT--ATATAATTTAATAAAAATAT
* *
19699369 ATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATAT
1 ATAATTTAATAAAATTCTTAATA-TAATTATTCTTATAT-AATTTA--ATAA--A-AATAT
* * * *
19699430 ATAATATT-ATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAATTCAAT
1 ATAAT-TTAATAAAAT-T--CTTAATATAATTATTCTT--ATATAATTTAATAAAAAT--AT
*
19699491 ATAATTTAATAAAATTC--AATATAATTATTCTTATATGAATTTACTAAAA
1 ATAATTTAATAAAATTCTTAATATAATTATTCTTATAT-AATTTAATAAAA
19699540 TCATAATATA
Statistics
Matches: 137, Mismatches: 16, Indels: 36
0.72 0.08 0.19
Matches are distributed among these distances:
54 4 0.03
55 29 0.21
56 24 0.18
57 9 0.07
58 3 0.02
59 2 0.01
60 5 0.04
61 31 0.23
62 6 0.04
63 9 0.07
64 11 0.08
65 4 0.03
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (54 bp):
ATAATTTAATAAAATTCTTAATATAATTATTCTTATATAATTTAATAAAAATAT
Found at i:19699428 original size:37 final size:37
Alignment explanation
Indices: 19699366--19699437 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 37
19699356 TTAATAAAAA
*
19699366 TATATAATTTAATAAAATTCTTAATAT-TAAATATTCT
1 TATATAATTTAATAAAATTCATAATATAT-AATATTCT
*
19699403 TATATGAATTTACTAAAA-TCATAATATATAATATT
1 TATAT-AATTTAATAAAATTCATAATATATAATATT
19699438 ATAAAATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
37 19 0.61
38 12 0.39
ACGTcount: A:0.47, C:0.06, G:0.01, T:0.46
Consensus pattern (37 bp):
TATATAATTTAATAAAATTCATAATATATAATATTCT
Found at i:19699448 original size:22 final size:24
Alignment explanation
Indices: 19699403--19699449 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
19699393 TAAATATTCT
19699403 TATATGAATTTACTAAAATCATAA
1 TATATGAATTTACTAAAATCATAA
19699427 TATAT-AATATTA-TAAAAT-ATAA
1 TATATGAAT-TTACTAAAATCATAA
19699449 T
1 T
19699450 TTAAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 5 0.23
23 9 0.41
24 8 0.36
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (24 bp):
TATATGAATTTACTAAAATCATAA
Found at i:19699486 original size:10 final size:10
Alignment explanation
Indices: 19699468--19699516 Score: 62
Period size: 10 Copynumber: 4.9 Consensus size: 10
19699458 ATTATTATTA
*
19699468 AATATAATTT
1 AATATAATTC
*
19699478 AATAAAATTC
1 AATATAATTC
*
19699488 AATATAATTT
1 AATATAATTC
*
19699498 AATAAAATTC
1 AATATAATTC
19699508 AATATAATT
1 AATATAATT
19699517 ATTCTTATAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
10 32 1.00
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (10 bp):
AATATAATTC
Found at i:19699486 original size:26 final size:26
Alignment explanation
Indices: 19699430--19699479 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
19699420 ATCATAATAT
19699430 ATAA-TATTATAAAATATAATTTAAA
1 ATAATTATTATAAAATATAATTTAAA
*
19699455 ATAATTATTATTAAATATAATTTAA
1 ATAATTATTATAAAATATAATTTAA
19699480 TAAAATTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
ATAATTATTATAAAATATAATTTAAA
Found at i:19699493 original size:20 final size:20
Alignment explanation
Indices: 19699468--19699516 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
19699458 ATTATTATTA
19699468 AATATAATTTAATAAAATTC
1 AATATAATTTAATAAAATTC
19699488 AATATAATTTAATAAAATTC
1 AATATAATTTAATAAAATTC
19699508 AATATAATT
1 AATATAATT
19699517 ATTCTTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (20 bp):
AATATAATTTAATAAAATTC
Found at i:19699550 original size:119 final size:119
Alignment explanation
Indices: 19699329--19699564 Score: 395
Period size: 119 Copynumber: 2.0 Consensus size: 119
19699319 TTAATCATAT
*
19699329 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTC-TAATATT
*
19699394 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATATTATAAAATATAA
65 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
*
19699449 TTTAAAATAATTATTATTAAATATAATTTAATAAAATTCAATATAATTTAATAAAATTC-AATA-
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAAT--ATATAATTTAATAAAATTCTAATAT
*
19699512 TAATTATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATA
64 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATA
19699565 ATGTATAATC
Statistics
Matches: 110, Mismatches: 4, Indels: 5
0.92 0.03 0.04
Matches are distributed among these distances:
119 51 0.46
120 40 0.36
122 19 0.17
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.43
Consensus pattern (119 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTAATATTA
AATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
Found at i:19701024 original size:49 final size:49
Alignment explanation
Indices: 19700952--19701056 Score: 183
Period size: 49 Copynumber: 2.1 Consensus size: 49
19700942 CTTAAGAAAA
* * *
19700952 AAAATTAAAATTAAGTTTAATATCATGAATCAAAAGGTGAACACTTTAT
1 AAAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTAT
19701001 AAAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTAT
1 AAAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTAT
19701050 AAAATTA
1 AAAATTA
19701057 TAACACATGA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 53 1.00
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.31
Consensus pattern (49 bp):
AAAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTAT
Found at i:19703211 original size:27 final size:28
Alignment explanation
Indices: 19703172--19703242 Score: 69
Period size: 27 Copynumber: 2.5 Consensus size: 28
19703162 TCAATAATAA
*
19703172 ATGTAATTAAATTATAAGTATTT-TTAAAT
1 ATGTAA-T-AATTATAAATATTTGTTAAAT
19703201 ATGTAATAATTATCACAATATTTGTTAAAT
1 ATGTAATAATTAT-A-AATATTTGTTAAAT
19703231 -T-T-ATAATTATAA
1 ATGTAATAATTATAA
19703243 CAAATTTTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
25 1 0.03
26 1 0.03
27 14 0.37
28 3 0.08
29 13 0.34
30 6 0.16
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (28 bp):
ATGTAATAATTATAAATATTTGTTAAAT
Found at i:19704034 original size:25 final size:23
Alignment explanation
Indices: 19703995--19704047 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 23
19703985 TAAACTAAGG
*
19703995 TAAAATCGAAGAAATCAATTTAAA
1 TAAAATCAAAGAAAT-AATTTAAA
* *
19704019 TTAAAATCAAATAAATATTTTAAA
1 -TAAAATCAAAGAAATAATTTAAA
19704043 TAAAA
1 TAAAA
19704048 CCGAATTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 5 0.20
24 7 0.28
25 13 0.52
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.30
Consensus pattern (23 bp):
TAAAATCAAAGAAATAATTTAAA
Found at i:19704821 original size:24 final size:24
Alignment explanation
Indices: 19704794--19704845 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
19704784 TTAGTAAGTC
*
19704794 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
19704818 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
19704842 AAAT
1 AAAT
19704846 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:19706768 original size:24 final size:24
Alignment explanation
Indices: 19706741--19706792 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
19706731 TTAGTAAGTC
*
19706741 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
*
19706765 AAATATACTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
19706789 AAAT
1 AAAT
19706793 CTTCTAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.31
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:19712058 original size:17 final size:17
Alignment explanation
Indices: 19712038--19712083 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
19712028 AAAATAAAAT
*
19712038 AATTTTAAAAATTTTAA
1 AATTTAAAAAATTTTAA
*
19712055 AATTTAAAAAACTTTAA
1 AATTTAAAAAATTTTAA
* *
19712072 AACTTCAAAAAT
1 AATTTAAAAAAT
19712084 AACTTAATTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (17 bp):
AATTTAAAAAATTTTAA
Found at i:19713619 original size:17 final size:17
Alignment explanation
Indices: 19713592--19713629 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
19713582 TATACATTTC
19713592 TTTTGATTTTACTTTAAA
1 TTTTGATTTTA-TTTAAA
*
19713610 TTTT-ATTTTATTTCAA
1 TTTTGATTTTATTTAAA
19713626 TTTT
1 TTTT
19713630 TAATATTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
17 6 0.32
18 4 0.21
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (17 bp):
TTTTGATTTTATTTAAA
Found at i:19714244 original size:21 final size:20
Alignment explanation
Indices: 19714215--19714253 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
19714205 TCATGTTATA
19714215 TATTATAAAAATAATATACT
1 TATTATAAAAATAATATACT
*
19714235 TATTCATAAAAATATTATA
1 TATT-ATAAAAATAATATA
19714254 ATTTTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
TATTATAAAAATAATATACT
Found at i:19720533 original size:26 final size:25
Alignment explanation
Indices: 19720504--19720553 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
19720494 TAGTATTTTT
*
19720504 TTTAAATCTTATTAAACTCCTAAAAA
1 TTTAAATCTTA-TAAACCCCTAAAAA
* *
19720530 TTTACATTTTATAAACCCCTAAAA
1 TTTAAATCTTATAAACCCCTAAAA
19720554 GTACACCCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (25 bp):
TTTAAATCTTATAAACCCCTAAAAA
Found at i:19732427 original size:31 final size:31
Alignment explanation
Indices: 19732345--19732428 Score: 80
Period size: 31 Copynumber: 2.7 Consensus size: 31
19732335 ACATAATGGG
* * *
19732345 CTTAAATGATCTTTAATTA-TTTTACAAAGG
1 CTTAATTGATTTTTAATTATTTTTACAAAGA
* * * **
19732375 TTTAATTGCTTGTTTATTTATTTTTAGGAAGA
1 CTTAATTGATT-TTTAATTATTTTTACAAAGA
19732407 CTTAATTGATTTTTAATTATTT
1 CTTAATTGATTTTTAATTATTT
19732429 AAGTCTAAAA
Statistics
Matches: 41, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
30 7 0.17
31 17 0.41
32 17 0.41
ACGTcount: A:0.30, C:0.06, G:0.11, T:0.54
Consensus pattern (31 bp):
CTTAATTGATTTTTAATTATTTTTACAAAGA
Found at i:19732626 original size:11 final size:11
Alignment explanation
Indices: 19732610--19732634 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19732600 AAAGTTTTAA
19732610 ATATAAAAATT
1 ATATAAAAATT
19732621 ATATAAAAATT
1 ATATAAAAATT
19732632 ATA
1 ATA
19732635 GAAGTTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
ATATAAAAATT
Found at i:19732643 original size:55 final size:54
Alignment explanation
Indices: 19732560--19732665 Score: 119
Period size: 55 Copynumber: 1.9 Consensus size: 54
19732550 AAAAATATGC
*
19732560 AAAATATTACATAAATAATTAAAATTATAGAAA-TTATAGAAAAGTTTTAAATAT
1 AAAATATTACATAAATAATTAAAATTATAGAAACTTAT-GAAAAGTATTAAATAT
* * *
19732614 AAAA-ATTATATAAA-AATTATAGAAGTTATATAAACTTATTAAAAGTATTAAA
1 AAAATATTACATAAATAATTA-A-AA-TTATAGAAACTTATGAAAAGTATTAAA
19732666 AAGTTTTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
52 5 0.11
53 10 0.23
54 6 0.14
55 19 0.43
56 4 0.09
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.35
Consensus pattern (54 bp):
AAAATATTACATAAATAATTAAAATTATAGAAACTTATGAAAAGTATTAAATAT
Found at i:19732659 original size:20 final size:20
Alignment explanation
Indices: 19732611--19732693 Score: 70
Period size: 19 Copynumber: 4.3 Consensus size: 20
19732601 AAGTTTTAAA
*
19732611 TATAAAAATTATATAAAAAT
1 TATAAAAGTTATATAAAAAT
* *
19732631 TATAGAAGTTATAT-AAACT
1 TATAAAAGTTATATAAAAAT
19732650 TATTAAAAG-TAT-TAAAAAGT
1 TA-TAAAAGTTATATAAAAA-T
*
19732670 TTTAAAAGTT-T-TAAAAA-
1 TATAAAAGTTATATAAAAAT
19732687 TATAAAA
1 TATAAAA
19732694 AAAAATTTAT
Statistics
Matches: 52, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
17 6 0.12
18 1 0.02
19 25 0.48
20 20 0.38
ACGTcount: A:0.57, C:0.01, G:0.06, T:0.36
Consensus pattern (20 bp):
TATAAAAGTTATATAAAAAT
Found at i:19732982 original size:8 final size:8
Alignment explanation
Indices: 19732971--19733074 Score: 55
Period size: 8 Copynumber: 12.0 Consensus size: 8
19732961 ATTTTTTAAA
19732971 AAAATTAT
1 AAAATTAT
19732979 AAAATTAT
1 AAAATTAT
*
19732987 AAAATTTTAG
1 AAAA--TTAT
*
19732997 AAAATTGT
1 AAAATTAT
* *
19733005 AAAAATAG
1 AAAATTAT
*
19733013 AAAGTTAT
1 AAAATTAT
*
19733021 AAAAAATTAC
1 --AAAATTAT
*
19733031 ATAAGTTATT
1 A-AAATTA-T
*
19733041 AAAATTGTT
1 AAAATT-AT
19733050 AAATATTAT
1 AAA-ATTAT
*
19733059 AAAATTTT
1 AAAATTAT
19733067 AAAATTAT
1 AAAATTAT
19733075 TGGCCCTTTT
Statistics
Matches: 70, Mismatches: 18, Indels: 16
0.67 0.17 0.15
Matches are distributed among these distances:
8 36 0.51
9 17 0.24
10 17 0.24
ACGTcount: A:0.56, C:0.01, G:0.06, T:0.38
Consensus pattern (8 bp):
AAAATTAT
Found at i:19733000 original size:18 final size:18
Alignment explanation
Indices: 19732979--19733067 Score: 58
Period size: 18 Copynumber: 4.9 Consensus size: 18
19732969 AAAAAATTAT
19732979 AAAATTATAAAATTTTAG
1 AAAATTATAAAATTTTAG
* *
19732997 AAAATTGTAAAA--ATAG
1 AAAATTATAAAATTTTAG
* ** *
19733013 AAAGTTATAAAAAATTAC
1 AAAATTATAAAATTTTAG
*
19733031 ATAAGTTATTAAAATTGTTA-
1 A-AAATTA-TAAAATT-TTAG
*
19733051 AATATTATAAAATTTTA
1 AAAATTATAAAATTTTA
19733068 AAATTATTGG
Statistics
Matches: 56, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
16 13 0.23
17 3 0.05
18 21 0.38
19 10 0.18
20 6 0.11
21 3 0.05
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.37
Consensus pattern (18 bp):
AAAATTATAAAATTTTAG
Found at i:19733000 original size:26 final size:25
Alignment explanation
Indices: 19732970--19733072 Score: 80
Period size: 26 Copynumber: 3.9 Consensus size: 25
19732960 AATTTTTTAA
19732970 AAAAATTATAAAATTATAAAATTTT
1 AAAAATTATAAAATTATAAAATTTT
* * * * *
19732995 AGAAAATTGTAAAAATAGAAAGTTATA
1 A-AAAATTATAAAATTATAAAATT-TT
* *
19733022 AAAAATTACATAAGTTATTAAAATTGTT
1 AAAAATTATA-AAATTA-TAAAATT-TT
* *
19733050 AAATATTATAAAATTTTAAAATT
1 AAAAATTATAAAATTATAAAATT
19733073 ATTGGCCCTT
Statistics
Matches: 57, Mismatches: 17, Indels: 7
0.70 0.21 0.09
Matches are distributed among these distances:
25 1 0.02
26 32 0.56
27 10 0.18
28 14 0.25
ACGTcount: A:0.56, C:0.01, G:0.06, T:0.37
Consensus pattern (25 bp):
AAAAATTATAAAATTATAAAATTTT
Found at i:19736834 original size:14 final size:14
Alignment explanation
Indices: 19736815--19736841 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19736805 AATTGGTTTA
19736815 AAATCAAACTTAAT
1 AAATCAAACTTAAT
19736829 AAATCAAACTTAA
1 AAATCAAACTTAA
19736842 ATTTTTTTAA
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:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATCAAACTTAAT
Found at i:19737788 original size:14 final size:14
Alignment explanation
Indices: 19737771--19737808 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
19737761 GAGGACCGGA
19737771 GGTGGAGGTGGAT-T
1 GGTGGAGGTGG-TCT
*
19737785 GGTGGTGGTGGTCT
1 GGTGGAGGTGGTCT
19737799 GGTGGAGGTG
1 GGTGGAGGTG
19737809 AAGATTTTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 1 0.05
14 20 0.95
ACGTcount: A:0.08, C:0.03, G:0.61, T:0.29
Consensus pattern (14 bp):
GGTGGAGGTGGTCT
Found at i:19737969 original size:27 final size:29
Alignment explanation
Indices: 19737912--19737969 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
19737902 AACTTTTAAC
*
19737912 TTTTAAAAATAAAAAATATATGTATTGTA
1 TTTTAAAAATAAAAAATATATGTATTATA
*
19737941 TTTTAAAAATAAAGAATATA-GT-TTATA
1 TTTTAAAAATAAAAAATATATGTATTATA
19737968 TT
1 TT
19737970 CGGTTTATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 6 0.22
28 2 0.07
29 19 0.70
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (29 bp):
TTTTAAAAATAAAAAATATATGTATTATA
Found at i:19741842 original size:47 final size:47
Alignment explanation
Indices: 19741773--19741866 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
19741763 TAGACGAGGG
19741773 ACGTTCGATTTCACCGATCACCGTTGATCATTTTAGAACATAAATAC
1 ACGTTCGATTTCACCGATCACCGTTGATCATTTTAGAACATAAATAC
19741820 ACGTTCGATTTCACCGATCACCGTTGATCATTTTAGAACATAAATAC
1 ACGTTCGATTTCACCGATCACCGTTGATCATTTTAGAACATAAATAC
19741867 TATCAATCTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (47 bp):
ACGTTCGATTTCACCGATCACCGTTGATCATTTTAGAACATAAATAC
Found at i:19744578 original size:28 final size:28
Alignment explanation
Indices: 19744547--19744603 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
19744537 TAAAAAATTT
19744547 TAAAACAAATATTAAAACAAAAAACAAA
1 TAAAACAAATATTAAAACAAAAAACAAA
* * * *
19744575 TAAAACAATTCTTAAAACAATACACAAA
1 TAAAACAAATATTAAAACAAAAAACAAA
19744603 T
1 T
19744604 TGAAAATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.67, C:0.14, G:0.00, T:0.19
Consensus pattern (28 bp):
TAAAACAAATATTAAAACAAAAAACAAA
Found at i:19744720 original size:21 final size:21
Alignment explanation
Indices: 19744677--19744717 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
19744667 AATTAATAAT
*
19744677 AAAATAAAAATATATTTGATTA
1 AAAATAAAAATATATAT-ATTA
19744699 AAAAT-AAAATATATATATT
1 AAAATAAAAATATATATATT
19744718 TAATATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 10 0.56
22 5 0.28
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
AAAATAAAAATATATATATTA
Found at i:19750275 original size:37 final size:37
Alignment explanation
Indices: 19750225--19750298 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
19750215 TTGGAACATC
*
19750225 ACTGTAAGTTCCGTTTAACTATTGTTATTACTATCAT
1 ACTGTAAGTTCCGTTTAACTACTGTTATTACTATCAT
19750262 ACTGTAAGTTCCGTTTAACTACTGTTATTACTATCAT
1 ACTGTAAGTTCCGTTTAACTACTGTTATTACTATCAT
19750299 TATTAAAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.27, C:0.18, G:0.11, T:0.45
Consensus pattern (37 bp):
ACTGTAAGTTCCGTTTAACTACTGTTATTACTATCAT
Found at i:19750286 original size:20 final size:20
Alignment explanation
Indices: 19750225--19750286 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
19750215 TTGGAACATC
19750225 ACTGTAAGTTCCGTTTAACT
1 ACTGTAAGTTCCGTTTAACT
* * * * *
19750245 ATTGTTA-TTAC-TATCA-T
1 ACTGTAAGTTCCGTTTAACT
19750262 ACTGTAAGTTCCGTTTAACT
1 ACTGTAAGTTCCGTTTAACT
19750282 ACTGT
1 ACTGT
19750287 TATTACTATC
Statistics
Matches: 29, Mismatches: 10, Indels: 6
0.64 0.22 0.13
Matches are distributed among these distances:
17 6 0.21
18 6 0.21
19 6 0.21
20 11 0.38
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.44
Consensus pattern (20 bp):
ACTGTAAGTTCCGTTTAACT
Found at i:19754573 original size:18 final size:18
Alignment explanation
Indices: 19754550--19754594 Score: 74
Period size: 18 Copynumber: 2.5 Consensus size: 18
19754540 CGCAAAGAAG
19754550 GTAAGCAATC-CTTCTTAT
1 GTAAGCAA-CGCTTCTTAT
19754568 GTAAGCAACGCTTCTTAT
1 GTAAGCAACGCTTCTTAT
19754586 GTAAGCAAC
1 GTAAGCAAC
19754595 AAACCTGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 1 0.04
18 25 0.96
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (18 bp):
GTAAGCAACGCTTCTTAT
Found at i:19757670 original size:7 final size:7
Alignment explanation
Indices: 19757658--19757690 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
19757648 AAAGTATTTT
19757658 AAAATTA
1 AAAATTA
19757665 AAAATTA
1 AAAATTA
19757672 AAAATTA
1 AAAATTA
19757679 AAAATTA
1 AAAATTA
19757686 AAAAT
1 AAAAT
19757691 ATATATTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAAATTA
Found at i:19761775 original size:40 final size:38
Alignment explanation
Indices: 19761731--19761873 Score: 119
Period size: 40 Copynumber: 3.7 Consensus size: 38
19761721 CCAATACACC
* *
19761731 AATTTGGCACCCAGTGCCTTATCAGATATTTCGAAGTAA
1 AATTTGACACCCAGTGCCTCATC-GATATTTCGAAGTAA
* * * **
19761770 GAATTTGATACCTAGTGTCTCATCGACTAAATCGAAGT-A
1 -AATTTGACACCCAGTGCCTCATCGA-TATTTCGAAGTAA
* * *
19761809 AA-TTGGCACCCAATGCCTCATCGAATATATCCGAAGTAA
1 AATTTGACACCCAGTGCCTCATCG-ATAT-TTCGAAGTAA
*
19761848 TAATTTGACACCCAGTGTCTCATCGA
1 -AATTTGACACCCAGTGCCTCATCGA
19761874 CTCGAAGTCG
Statistics
Matches: 79, Mismatches: 18, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
37 18 0.23
38 9 0.11
39 4 0.05
40 30 0.38
41 18 0.23
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (38 bp):
AATTTGACACCCAGTGCCTCATCGATATTTCGAAGTAA
Found at i:19762745 original size:10 final size:10
Alignment explanation
Indices: 19762730--19762805 Score: 59
Period size: 10 Copynumber: 7.8 Consensus size: 10
19762720 AAACCCTAAC
19762730 CTTTCTTTCT
1 CTTTCTTTCT
19762740 CTTTCTTTC-
1 CTTTCTTTCT
19762749 CTTTCCTTTCT
1 CTTT-CTTTCT
*
19762760 GTTTCTTTCT
1 CTTTCTTTCT
* *
19762770 TTTTCGTT-T
1 CTTTCTTTCT
*
19762779 -GTTCTTTCT
1 CTTTCTTTCT
* *
19762788 ATTTCTTTTT
1 CTTTCTTTCT
*
19762798 ATTTCTTT
1 CTTTCTTT
19762806 ATTTGTTTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
8 5 0.09
9 6 0.11
10 41 0.75
11 3 0.05
ACGTcount: A:0.03, C:0.22, G:0.04, T:0.71
Consensus pattern (10 bp):
CTTTCTTTCT
Found at i:19762785 original size:18 final size:16
Alignment explanation
Indices: 19762731--19762805 Score: 64
Period size: 15 Copynumber: 4.7 Consensus size: 16
19762721 AACCCTAACC
*
19762731 TTTCTTTCTCTTTC-T
1 TTTCTTTCTTTTTCTT
* * *
19762746 TTCCTTTC-CTTTCTG
1 TTTCTTTCTTTTTCTT
19762761 TTTCTTTCTTTTTCGTT
1 TTTCTTTCTTTTTC-TT
*
19762778 TGTTCTTTCTATTTCTT
1 T-TTCTTTCTTTTTCTT
*
19762795 TTTATTTCTTT
1 TTTCTTTCTTT
19762806 ATTTGTTTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
14 5 0.10
15 14 0.29
16 12 0.25
17 5 0.10
18 12 0.25
ACGTcount: A:0.03, C:0.21, G:0.04, T:0.72
Consensus pattern (16 bp):
TTTCTTTCTTTTTCTT
Found at i:19762839 original size:9 final size:9
Alignment explanation
Indices: 19762820--19762888 Score: 53
Period size: 9 Copynumber: 8.3 Consensus size: 9
19762810 GTTTTTTATT
19762820 ATATAATATA
1 ATAT-ATATA
19762830 ATATATATA
1 ATATATATA
19762839 ATATATATA
1 ATATATATA
* *
19762848 CT-TA-ATC
1 ATATATATA
*
19762855 AT-TA-AGA
1 ATATATATA
19762862 ATATATAT-
1 ATATATATA
19762870 AT-TA-ATA
1 ATATATATA
19762877 ATATATATA
1 ATATATATA
19762886 ATA
1 ATA
19762889 AACTTATAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
6 2 0.04
7 12 0.25
8 8 0.17
9 22 0.46
10 4 0.08
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (9 bp):
ATATATATA
Found at i:19763723 original size:42 final size:43
Alignment explanation
Indices: 19763661--19763842 Score: 192
Period size: 42 Copynumber: 4.3 Consensus size: 43
19763651 AACTAGAAAA
* *
19763661 AAACGCCGCTAAAGATCAAGAACTTTAGCGGCGCTTTT-CAAC
1 AAACGCCGCTAAAGACCAAGAACTTTAGCGGCGCTTTTCCCAC
* *
19763703 AAACGCCGTTAAAGACCAAG-ACTTTAGTGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGAACTTTAGCGGCGCTTTTCCCAC
* * * * *
19763745 AAACGCCACAAAAGACCAAGACCTTTAGCTGTG-TTTTGCCCAC
1 AAACGCCGCTAAAGACCAAGAACTTTAGCGGCGCTTTT-CCCAC
* * * * * *
19763788 AAACGCCGCTAAAGAACAA-ACCTTTTGCGGCGCTTCTCGCAA
1 AAACGCCGCTAAAGACCAAGAACTTTAGCGGCGCTTTTCCCAC
19763830 AAACGCCGCTAAA
1 AAACGCCGCTAAA
19763843 AACATAATCT
Statistics
Matches: 116, Mismatches: 20, Indels: 8
0.81 0.14 0.06
Matches are distributed among these distances:
41 16 0.14
42 68 0.59
43 32 0.28
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.20
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCAAGAACTTTAGCGGCGCTTTTCCCAC
Found at i:19769505 original size:90 final size:88
Alignment explanation
Indices: 19769390--19769558 Score: 250
Period size: 88 Copynumber: 1.9 Consensus size: 88
19769380 AATCCCTAAC
* *
19769390 CCCTAACCCCTAACTATTAACCCCTAAACCTTATTTAATATATAAATTAAAAAATACTAATTAAT
1 CCCTAACCCCTAACTACTAACCCCTAAACCTTATTT-A-ATATAAATTAAAAAATACTAATTAAC
*
19769455 CTAAACCTTAAACCCTATCTCGAAT
64 CTAAACCCTAAACCCTATCTCGAAT
* *
19769480 CCCTAACCCCTAACCT-CTAACCCCTAAACCTTATTTAATATAGATTAAAACATACTAATTAACC
1 CCCTAACCCCTAA-CTACTAACCCCTAAACCTTATTTAATATAAATTAAAAAATACTAATTAACC
*
19769544 TAAACCCTAAGCCCT
65 TAAACCCTAAACCCT
19769559 GACTTGACAC
Statistics
Matches: 72, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
88 37 0.51
89 1 0.01
90 32 0.44
91 2 0.03
ACGTcount: A:0.40, C:0.29, G:0.02, T:0.29
Consensus pattern (88 bp):
CCCTAACCCCTAACTACTAACCCCTAAACCTTATTTAATATAAATTAAAAAATACTAATTAACCT
AAACCCTAAACCCTATCTCGAAT
Found at i:19769664 original size:14 final size:15
Alignment explanation
Indices: 19769645--19769677 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
19769635 TATAAACCAG
19769645 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
19769659 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
19769674 AATC
1 AATC
19769678 TATAAATCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:19769937 original size:30 final size:30
Alignment explanation
Indices: 19769902--19769992 Score: 100
Period size: 30 Copynumber: 3.1 Consensus size: 30
19769892 TTTAAAATTA
19769902 TTTTAAATAATAGTATTTTAATTTTTCTAT
1 TTTTAAATAATAGTATTTTAATTTTTCTAT
* *
19769932 TTTTAACA-AATA-T-TTTTCTATGTTTTTTA-
1 TTTTAA-ATAATAGTATTTT-AAT-TTTTCTAT
*
19769961 TTTTAGATAATAGTATTTTAATTTTTCTAT
1 TTTTAAATAATAGTATTTTAATTTTTCTAT
19769991 TT
1 TT
19769993 ATCCAATTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
28 5 0.10
29 18 0.37
30 21 0.43
31 5 0.10
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (30 bp):
TTTTAAATAATAGTATTTTAATTTTTCTAT
Found at i:19769986 original size:29 final size:28
Alignment explanation
Indices: 19769900--19769992 Score: 91
Period size: 29 Copynumber: 3.2 Consensus size: 28
19769890 ATTTTAAAAT
19769900 TATTTTAAATAATAGTATTTTAATTTTTC
1 TATTTT-AATAATAGTATTTTAATTTTTC
* * *
19769929 TATTTTTAACAA-A-TATTTTTCTATGTTTTT
1 TA-TTTTAATAATAGTA-TTTT-AAT-TTTTC
19769959 TATTTTAGATAATAGTATTTTAATTTTTC
1 TATTTTA-ATAATAGTATTTTAATTTTTC
19769988 TATTT
1 TATTT
19769993 ATCCAATTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
27 2 0.04
28 5 0.10
29 22 0.43
30 15 0.29
31 5 0.10
32 2 0.04
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.61
Consensus pattern (28 bp):
TATTTTAATAATAGTATTTTAATTTTTC
Found at i:19770155 original size:41 final size:40
Alignment explanation
Indices: 19770088--19770201 Score: 131
Period size: 41 Copynumber: 2.8 Consensus size: 40
19770078 AAATGTTTTT
* * *
19770088 GCGGCGCTTTTTC-AAAATGCCGCTAAAGCTCTGAGCATTA
1 GCGGCGC-TTTTCAAAAACGCCGCTAAAGCCCCGAGCATTA
**
19770128 GCGGCGCTTCTTGGAAAACGCCGCTAAAGCCCCGAGCATTA
1 GCGGCGCTT-TTCAAAAACGCCGCTAAAGCCCCGAGCATTA
* *
19770169 GCGGCGCTTTTTCAAAAACGCCACTAAATCCCC
1 GCGGCGC-TTTTCAAAAACGCCGCTAAAGCCCC
19770202 AAAAGGTTAA
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
39 2 0.03
40 9 0.14
41 50 0.79
42 2 0.03
ACGTcount: A:0.25, C:0.31, G:0.22, T:0.22
Consensus pattern (40 bp):
GCGGCGCTTTTCAAAAACGCCGCTAAAGCCCCGAGCATTA
Found at i:19770346 original size:40 final size:40
Alignment explanation
Indices: 19770292--19770368 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
19770282 GGCGCTTCCT
** * *
19770292 AAAAGCGCCGCTAATGCTCGATCTTTAGTGGCGTTTTATG
1 AAAAGCGCAACTAATGCTCGATCTTTAGCGACGTTTTATG
*
19770332 AAAAGCGCAACTAATGCTCGATTTTTAGCGACGTTTT
1 AAAAGCGCAACTAATGCTCGATCTTTAGCGACGTTTT
19770369 TTTGTCCAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.32
Consensus pattern (40 bp):
AAAAGCGCAACTAATGCTCGATCTTTAGCGACGTTTTATG
Found at i:19778629 original size:8 final size:8
Alignment explanation
Indices: 19778616--19778650 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
19778606 AATCATGAAC
19778616 AAAATTAT
1 AAAATTAT
19778624 AAAATTAT
1 AAAATTAT
*
19778632 AAAAATAT
1 AAAATTAT
*
19778640 AAAAGTAT
1 AAAATTAT
19778648 AAA
1 AAA
19778651 TATGTATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (8 bp):
AAAATTAT
Found at i:19778753 original size:4 final size:4
Alignment explanation
Indices: 19778744--19778774 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
19778734 AGTAAAATAA
19778744 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
19778775 ACTATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:19778800 original size:5 final size:6
Alignment explanation
Indices: 19778737--19778808 Score: 58
Period size: 6 Copynumber: 11.8 Consensus size: 6
19778727 AACATCAAGT
* * * * *
19778737 AAAATA AAAATA AATAA-A TAAATA AATAA-A TAAATA AAACTA TATATAA
1 AAAATA AAAATA AA-AATA AAAATA AA-AATA AAAATA AAAATA AAAAT-A
19778786 AAAATA AAAATA AAAATA AAAAT
1 AAAATA AAAATA AAAATA AAAAT
19778809 GTGTGTATAT
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
5 4 0.08
6 39 0.76
7 8 0.16
ACGTcount: A:0.76, C:0.01, G:0.00, T:0.22
Consensus pattern (6 bp):
AAAATA
Found at i:19778872 original size:24 final size:25
Alignment explanation
Indices: 19778845--19778898 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
19778835 AAATATAACA
19778845 AAAATATATGT-ATATATGA-ATTAT
1 AAAATATATGTAATATAT-ATATTAT
19778869 AAAATATATGTACATATATATATTAT
1 AAAATATATGTA-ATATATATATTAT
19778895 AAAA
1 AAAA
19778899 ATGTATAGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 11 0.41
25 1 0.04
26 15 0.56
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.39
Consensus pattern (25 bp):
AAAATATATGTAATATATATATTAT
Found at i:19779099 original size:23 final size:25
Alignment explanation
Indices: 19779072--19779119 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 25
19779062 TAAGATGATT
*
19779072 TATGAAGAAA-TTAA-ATATTAATA
1 TATGAAGAAACTTAATATAATAATA
19779095 TATGAAGAAACTTAATATAATAATA
1 TATGAAGAAACTTAATATAATAATA
19779120 CATAATGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.45
24 4 0.18
25 8 0.36
ACGTcount: A:0.56, C:0.02, G:0.08, T:0.33
Consensus pattern (25 bp):
TATGAAGAAACTTAATATAATAATA
Found at i:19795856 original size:21 final size:22
Alignment explanation
Indices: 19795832--19795874 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
19795822 ATCATCAATC
19795832 AAATAATACAAT-AT-AATTTAA
1 AAATAATA-AATAATAAATTTAA
*
19795853 AAATTATAAATAATAAATTTAA
1 AAATAATAAATAATAAATTTAA
19795875 TTCACTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 3 0.16
21 9 0.47
22 7 0.37
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
AAATAATAAATAATAAATTTAA
Found at i:19800507 original size:70 final size:69
Alignment explanation
Indices: 19800415--19801051 Score: 891
Period size: 70 Copynumber: 9.1 Consensus size: 69
19800405 TTTTCACACC
* * * *
19800415 AAAAATTGGACAACATATATACAACAATTTGGGCAGCATATATACATCAAATTGAGCAGCATTTT
1 AAAAATTGGACAGCATATATGCAACAATTTGGGCAGCATAAATACAACAAATTG-GCAGCATTTT
19800480 AGCAT
65 AGCAT
* * * * *
19800485 AAAAATTGGACAGCATATATACAACAATTTGGGCAGCCTATATATACCAAATTGAGCAGCATTTT
1 AAAAATTGGACAGCATATATGCAACAATTTGGGCAGCATAAATACAACAAATTG-GCAGCA-TTT
19800550 TA-CAT
64 TAGCAT
* ** * *
19800555 CAAAATTGGACAGCATATATAAAACAATTTGGGCAGCATAAATATAACAAATTGGGCAGCATTTA
1 AAAAATTGGACAGCATATATGCAACAATTTGGGCAGCATAAATACAACAAATT-GGCAGCATTTT
19800620 AGCAT
65 AGCAT
*
19800625 AAAAATTGGACAGCATATATGCAACAATTTGGGCAGCATAAATACAACAAATTGGGCAGCATTTA
1 AAAAATTGGACAGCATATATGCAACAATTTGGGCAGCATAAATACAACAAATT-GGCAGCATTTT
19800690 AGCAT
65 AGCAT
* *
19800695 AAAAATTGGACAGCATATATGCAACAATTTGGGCAGCATAAATACAACAAATTGGGCAACATTTA
1 AAAAATTGGACAGCATATATGCAACAATTTGGGCAGCATAAATACAACAAATT-GGCAGCATTTT
19800760 AGCAT
65 AGCAT
*
19800765 AAAAATTGGACAGCATATATGCAACAATTTGGGCAGCATAAATACAACGAATTGGACAGCATTTT
1 AAAAATTGGACAGCATATATGCAACAATTTGGGCAGCATAAATACAACAAATTGG-CAGCATTTT
19800830 AGCAT
65 AGCAT
* *
19800835 AAAAATTTGACAGCATATATGCACCAATTTGGGCAGCATAAATACAACAAATTGGACAGCATTTT
1 AAAAATTGGACAGCATATATGCAACAATTTGGGCAGCATAAATACAACAAATTGG-CAGCATTTT
19800900 AGCAT
65 AGCAT
* * * * *
19800905 AAAAATTTGACAGCATATGTGCAACAATTTGGGCAGCATATATATACCAAATTGAGCAGCATTTT
1 AAAAATTGGACAGCATATATGCAACAATTTGGGCAGCATAAATACAACAAATTG-GCAGCA-TTT
19800970 TA-CAT
64 TAGCAT
* * * * *
19800975 CAAAACTGGGCAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGGACAGCATTTA
1 AAAAATTGGACAGCATATATGCAACAATTTGGGCAGCATAAATACAACAAATTGG-CAGCATTTT
19801040 AGCAT
65 AGCAT
19801045 AAAAATT
1 AAAAATT
19801052 ACATGAACAT
Statistics
Matches: 521, Mismatches: 38, Indels: 16
0.91 0.07 0.03
Matches are distributed among these distances:
69 11 0.02
70 498 0.96
71 12 0.02
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.25
Consensus pattern (69 bp):
AAAAATTGGACAGCATATATGCAACAATTTGGGCAGCATAAATACAACAAATTGGCAGCATTTTA
GCAT
Found at i:19800712 original size:210 final size:210
Alignment explanation
Indices: 19800415--19801051 Score: 1006
Period size: 210 Copynumber: 3.0 Consensus size: 210
19800405 TTTTCACACC
* * * * *
19800415 AAAAATTGGACAACATATATACAACAATTTGGGCAGCATATATACATCAAATTGAGCAGCATTTT
1 AAAAATTGGACAGCATATATGCAACAATTTGGGCAGCATAAATACAACAAATTGGGCAGCATTTT
* *
19800480 AGCATAAAAATTGGACAGCATATATACAACAATTTGGGCAGCCTATATATACCAAATTGAGCAGC
66 AGCATAAAAATTGGACAGCATATATGCAACAATTTGGGCAGCATATATATACCAAATTGAGCAGC
* *
19800545 ATTTTTACATCAAAATTGGACAGCATATATAAAACAATTTGGGCAGCATAAATATAACAAATTGG
131 ATTTTTACATCAAAATTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGG
*
19800610 GCAGCATTTAAGCAT
196 ACAGCATTTAAGCAT
*
19800625 AAAAATTGGACAGCATATATGCAACAATTTGGGCAGCATAAATACAACAAATTGGGCAGCATTTA
1 AAAAATTGGACAGCATATATGCAACAATTTGGGCAGCATAAATACAACAAATTGGGCAGCATTTT
* * * * *
19800690 AGCATAAAAATTGGACAGCATATATGCAACAATTTGGGCAGCATAAATACAACAAATTGGGCAAC
66 AGCATAAAAATTGGACAGCATATATGCAACAATTTGGGCAGCATATATATACCAAATTGAGCAGC
* * * *
19800755 A-TTTAAGCATAAAAATTGGACAGCATATATGCAACAATTTGGGCAGCATAAATACAACGAATTG
131 ATTTTTA-CATCAAAATTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTG
*
19800819 GACAGCATTTTAGCAT
195 GACAGCATTTAAGCAT
* * *
19800835 AAAAATTTGACAGCATATATGCACCAATTTGGGCAGCATAAATACAACAAATTGGACAGCATTTT
1 AAAAATTGGACAGCATATATGCAACAATTTGGGCAGCATAAATACAACAAATTGGGCAGCATTTT
* *
19800900 AGCATAAAAATTTGACAGCATATGTGCAACAATTTGGGCAGCATATATATACCAAATTGAGCAGC
66 AGCATAAAAATTGGACAGCATATATGCAACAATTTGGGCAGCATATATATACCAAATTGAGCAGC
* *
19800965 ATTTTTACATCAAAACTGGGCAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGG
131 ATTTTTACATCAAAATTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGG
19801030 ACAGCATTTAAGCAT
196 ACAGCATTTAAGCAT
19801045 AAAAATT
1 AAAAATT
19801052 ACATGAACAT
Statistics
Matches: 386, Mismatches: 39, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
209 4 0.01
210 378 0.98
211 4 0.01
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.25
Consensus pattern (210 bp):
AAAAATTGGACAGCATATATGCAACAATTTGGGCAGCATAAATACAACAAATTGGGCAGCATTTT
AGCATAAAAATTGGACAGCATATATGCAACAATTTGGGCAGCATATATATACCAAATTGAGCAGC
ATTTTTACATCAAAATTGGACAGCATATATACAACAATTTGGGCAGCATAAATACAACAAATTGG
ACAGCATTTAAGCAT
Done.