Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 191 of 208
Found at i:58268283 original size:2 final size:2
Alignment explanation
Indices: 58268278--58268307 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
58268268 TTACTATTTC
58268278 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
58268308 AGAGGTTTCA
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:58268560 original size:62 final size:62
Alignment explanation
Indices: 58268491--58268616 Score: 252
Period size: 62 Copynumber: 2.0 Consensus size: 62
58268481 TTTAAAATGT
58268491 TTCTAAAATATAGATACATTAGTATCATTTTTTTTGTTATTGTTATTATTGTTATTGTTAGA
1 TTCTAAAATATAGATACATTAGTATCATTTTTTTTGTTATTGTTATTATTGTTATTGTTAGA
58268553 TTCTAAAATATAGATACATTAGTATCATTTTTTTTGTTATTGTTATTATTGTTATTGTTAGA
1 TTCTAAAATATAGATACATTAGTATCATTTTTTTTGTTATTGTTATTATTGTTATTGTTAGA
58268615 TT
1 TT
58268617 GTTATTTGCA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.29, C:0.05, G:0.11, T:0.56
Consensus pattern (62 bp):
TTCTAAAATATAGATACATTAGTATCATTTTTTTTGTTATTGTTATTATTGTTATTGTTAGA
Found at i:58268606 original size:15 final size:14
Alignment explanation
Indices: 58268586--58268622 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
58268576 ATCATTTTTT
*
58268586 TTGTTATTGTTATTA
1 TTGTTATTGTTA-GA
58268601 TTGTTATTGTTAGA
1 TTGTTATTGTTAGA
58268615 TTGTTATT
1 TTGTTATT
58268623 TGCATTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.19, C:0.00, G:0.16, T:0.65
Consensus pattern (14 bp):
TTGTTATTGTTAGA
Found at i:58271494 original size:20 final size:18
Alignment explanation
Indices: 58271469--58271507 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
58271459 TCCTTTAATT
*
58271469 TGTTTTTCATTGTTTTTTTA
1 TGTTTTT-ATT-TTGTTTTA
58271489 TGTTTTTATTTTGTTTTA
1 TGTTTTTATTTTGTTTTA
58271507 T
1 T
58271508 CTTATTATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 3 0.17
20 7 0.39
ACGTcount: A:0.10, C:0.03, G:0.10, T:0.77
Consensus pattern (18 bp):
TGTTTTTATTTTGTTTTA
Found at i:58272910 original size:16 final size:16
Alignment explanation
Indices: 58272885--58272918 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
58272875 TATGTTTTGC
* *
58272885 TTTGATTGCATGGCAT
1 TTTGACTGCATAGCAT
58272901 TTTGACTGCATAGCAT
1 TTTGACTGCATAGCAT
58272917 TT
1 TT
58272919 CATCCTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.44
Consensus pattern (16 bp):
TTTGACTGCATAGCAT
Found at i:58275080 original size:19 final size:19
Alignment explanation
Indices: 58275056--58275095 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
58275046 GTATATGTAA
58275056 TTTGTTTTAT-GTAAAGATT
1 TTTGTTTTATAGTAAAG-TT
*
58275075 TTTGTTTTCTAGTAAAGTT
1 TTTGTTTTATAGTAAAGTT
58275094 TT
1 TT
58275096 CTAAATGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.23, C:0.03, G:0.15, T:0.60
Consensus pattern (19 bp):
TTTGTTTTATAGTAAAGTT
Found at i:58281502 original size:13 final size:12
Alignment explanation
Indices: 58281484--58281519 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 12
58281474 CATGTTATGA
58281484 CTTCTCCATGGAG
1 CTTCTCCATGG-G
58281497 CTTCTCCATGGG
1 CTTCTCCATGGG
58281509 CTTTCTCCATG
1 C-TTCTCCATG
58281520 TGGTGTATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 2 0.09
13 20 0.91
ACGTcount: A:0.11, C:0.33, G:0.19, T:0.36
Consensus pattern (12 bp):
CTTCTCCATGGG
Found at i:58283445 original size:17 final size:17
Alignment explanation
Indices: 58283423--58283455 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
58283413 CATAAGAGAT
58283423 AAAAAAA-GATCATTCTA
1 AAAAAAATGA-CATTCTA
58283440 AAAAAAATGACATTCT
1 AAAAAAATGACATTCT
58283456 GCATTCATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.58, C:0.12, G:0.06, T:0.24
Consensus pattern (17 bp):
AAAAAAATGACATTCTA
Found at i:58283816 original size:132 final size:132
Alignment explanation
Indices: 58283578--58283840 Score: 382
Period size: 132 Copynumber: 2.0 Consensus size: 132
58283568 GAATAAACCA
* *
58283578 TTGAAAATAGCAGATCCTGTCTCCCCAAGCAGTGGCGGAGTAGATCAAAGACGGCAAATCTTATC
1 TTGAAAATAGCAGATCCTGTCTCCCCAAGCAGTAGCGGAGCAGATCAAAGACGGCAAATCTTATC
* **
58283643 TTCCTAAGATAGTGGAGAAGTAGATTTAAGCCATTAATCCTATCTCCCTGAGCAGCAATGGAGTA
66 TTCCCAAGATAGTGGAGAAACAGATTTAAGCCATTAATCCTATCTCCCTGAGCAGCAATGGAGTA
58283708 GG
131 GG
* * * * * * * *
58283710 TTGAAGATTGCAGATTCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGAATCTTATC
1 TTGAAAATAGCAGATCCTGTCTCCCCAAGCAGTAGCGGAGCAGATCAAAGACGGCAAATCTTATC
* * *
58283775 TTCCCAAGATAGTGGAGAAACAGATTTAGGCCATTAGTCCTATCTCCCTGAGCAGCAGTGGAGTA
66 TTCCCAAGATAGTGGAGAAACAGATTTAAGCCATTAATCCTATCTCCCTGAGCAGCAATGGAGTA
58283840 G
131 G
58283841 ATCGAAGACG
Statistics
Matches: 115, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
132 115 1.00
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (132 bp):
TTGAAAATAGCAGATCCTGTCTCCCCAAGCAGTAGCGGAGCAGATCAAAGACGGCAAATCTTATC
TTCCCAAGATAGTGGAGAAACAGATTTAAGCCATTAATCCTATCTCCCTGAGCAGCAATGGAGTA
GG
Found at i:58284622 original size:7 final size:8
Alignment explanation
Indices: 58284605--58284642 Score: 58
Period size: 8 Copynumber: 4.5 Consensus size: 8
58284595 TATTTACTTA
58284605 TTTTACTTT
1 TTTTA-TTT
58284614 TTTTATTT
1 TTTTATTT
58284622 TTTTATTTT
1 TTTTA-TTT
58284631 TTTTATTT
1 TTTTATTT
58284639 TTTT
1 TTTT
58284643 TAAAAACCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 15 0.54
9 13 0.46
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTATTT
Found at i:58284622 original size:8 final size:9
Alignment explanation
Indices: 58284597--58284644 Score: 62
Period size: 9 Copynumber: 5.4 Consensus size: 9
58284587 TTCCAGCTTA
*
58284597 TTTACTTAT
1 TTTACTTTT
58284606 TTTACTTTT
1 TTTACTTTT
58284615 TTTA-TTTT
1 TTTACTTTT
*
58284623 TTTATTTTT
1 TTTACTTTT
*
58284632 TTTATTTTT
1 TTTACTTTT
58284641 TTTA
1 TTTA
58284645 AAAACCAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
8 8 0.22
9 29 0.78
ACGTcount: A:0.15, C:0.04, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTACTTTT
Found at i:58284623 original size:9 final size:9
Alignment explanation
Indices: 58284605--58284644 Score: 64
Period size: 9 Copynumber: 4.6 Consensus size: 9
58284595 TATTTACTTA
*
58284605 TTTTACTTT
1 TTTTATTTT
58284614 TTTTA-TTT
1 TTTTATTTT
58284622 TTTTATTTT
1 TTTTATTTT
58284631 TTTTATTTT
1 TTTTATTTT
58284640 TTTTA
1 TTTTA
58284645 AAAACCAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 8 0.27
9 22 0.73
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTATTTT
Found at i:58284631 original size:17 final size:17
Alignment explanation
Indices: 58284605--58284642 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
58284595 TATTTACTTA
58284605 TTTTACTTTTTTTATTT
1 TTTTACTTTTTTTATTT
*
58284622 TTTTATTTTTTTTATTT
1 TTTTACTTTTTTTATTT
58284639 TTTT
1 TTTT
58284643 TAAAAACCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.11, C:0.03, G:0.00, T:0.87
Consensus pattern (17 bp):
TTTTACTTTTTTTATTT
Found at i:58285121 original size:3 final size:3
Alignment explanation
Indices: 58285107--58285154 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
58285097 TCATTACTGC
* * * *
58285107 TAT TAC TAT TAT TAT TAT TAA TAT TAT AAT AAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
58285155 ATTTTTATGA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:58295540 original size:40 final size:41
Alignment explanation
Indices: 58295444--58295541 Score: 137
Period size: 41 Copynumber: 2.4 Consensus size: 41
58295434 TGATCTCAGC
* * *
58295444 TTCGCACACTTAGTGCCCGTCATTTAACATCATTATTTAGT
1 TTCGCACACTTAGTGCTCGTCATTCAACATCATCATTTAGT
*
58295485 TTCGCACACTTAGTGCTCGAT-ATTCAACCTCATCATTTAG-
1 TTCGCACACTTAGTGCTCG-TCATTCAACATCATCATTTAGT
58295525 TTCGCACACTTAGTGCT
1 TTCGCACACTTAGTGCT
58295542 AATCAGATAG
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
40 17 0.33
41 34 0.65
42 1 0.02
ACGTcount: A:0.23, C:0.27, G:0.13, T:0.37
Consensus pattern (41 bp):
TTCGCACACTTAGTGCTCGTCATTCAACATCATCATTTAGT
Found at i:58296876 original size:51 final size:51
Alignment explanation
Indices: 58296816--58296947 Score: 167
Period size: 51 Copynumber: 2.6 Consensus size: 51
58296806 TGATAGGTCG
* *
58296816 CATGTGTAGTACTATGTGTAGGCTACTATGCGTACCGGATAGT-TTCAATCA
1 CATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTAAT-AATCA
* * * * * **
58296867 CGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGTAATGGTCA
1 CATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTAATAATCA
58296918 CATGTGTAGTACTATGTGCAGGCTACTATG
1 CATGTGTAGTACTATGTGCAGGCTACTATG
58296948 TGAACCGAAC
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
51 68 0.99
52 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (51 bp):
CATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTAATAATCA
Found at i:58296949 original size:26 final size:26
Alignment explanation
Indices: 58296869--58296949 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
58296859 TTCAATCACG
58296869 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* * *
58296895 CGTGTA-T-CGGATG-GTAATGG-TCAC-A
1 TGTGTAGTAC-TATGTG-CA-GGCT-ACTA
58296920 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
58296946 TGTG
1 TGTG
58296950 AACCGAACAT
Statistics
Matches: 40, Mismatches: 6, Indels: 18
0.62 0.09 0.28
Matches are distributed among these distances:
24 2 0.05
25 16 0.40
26 20 0.50
27 2 0.05
ACGTcount: A:0.22, C:0.15, G:0.30, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:58297043 original size:45 final size:45
Alignment explanation
Indices: 58296951--58297036 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
58296941 TACTATGTGA
* *
58296951 ACCGAACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATCCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTACGTGCTGATCCC
*
58296996 ACCGGACATCATTGATTAATAAGGTGGTTGCTACGTGCTGA
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTACGTGCTGA
58297037 ATCCACCTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.30
Consensus pattern (45 bp):
ACCGAACATCATTGATTAATAAGGTGGTTGCTACGTGCTGATCCC
Found at i:58297119 original size:30 final size:30
Alignment explanation
Indices: 58297083--58297142 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
58297073 TCGGGAAATT
58297083 GACTAAGTGTAATTGAATAATGAATATAGG
1 GACTAAGTGTAATTGAATAATGAATATAGG
58297113 GACTAAGTGTAATTGAATAATGAATATAGG
1 GACTAAGTGTAATTGAATAATGAATATAGG
58297143 TGTGGAATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.03, G:0.23, T:0.30
Consensus pattern (30 bp):
GACTAAGTGTAATTGAATAATGAATATAGG
Found at i:58297145 original size:23 final size:22
Alignment explanation
Indices: 58297119--58297162 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
58297109 TAGGGACTAA
58297119 GTGT-AATTGAATAATGAATATAG
1 GTGTGAATTGAAT--TGAATATAG
58297142 GTGTGGAATTGAATTGAATAT
1 GTGT-GAATTGAATTGAATAT
58297163 CGACTTAGAA
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:0.00, G:0.25, T:0.36
Consensus pattern (22 bp):
GTGTGAATTGAATTGAATATAG
Found at i:58297154 original size:25 final size:28
Alignment explanation
Indices: 58297088--58297162 Score: 79
Period size: 30 Copynumber: 2.8 Consensus size: 28
58297078 AAATTGACTA
*
58297088 AGTGTAATTGAATAATGAATATAGGGACT
1 AGTGGAATTGAATAATGAATATAGGGA-T
*
58297117 AAGTGTAATTGAATAATGAATATA-GG-T
1 -AGTGGAATTGAATAATGAATATAGGGAT
58297144 -GTGGAATTGAAT--TGAATAT
1 AGTGGAATTGAATAATGAATAT
58297163 CGACTTAGAA
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
23 7 0.16
25 11 0.25
27 1 0.02
29 2 0.05
30 23 0.52
ACGTcount: A:0.41, C:0.01, G:0.24, T:0.33
Consensus pattern (28 bp):
AGTGGAATTGAATAATGAATATAGGGAT
Found at i:58298612 original size:21 final size:20
Alignment explanation
Indices: 58298563--58298620 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
58298553 ATTAAATGGA
58298563 AATTGCAAATGATATTGTTTG
1 AATTG-AAATGATATTGTTTG
58298584 AATT-AAATGA-ATTGTTGTGG
1 AATTGAAATGATATTGTT-T-G
*
58298604 TATTGAAATGTATATTG
1 AATTGAAATG-ATATTG
58298621 GATTGAGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
18 6 0.19
19 7 0.23
20 4 0.13
21 9 0.29
22 1 0.03
23 4 0.13
ACGTcount: A:0.34, C:0.02, G:0.21, T:0.43
Consensus pattern (20 bp):
AATTGAAATGATATTGTTTG
Found at i:58301218 original size:31 final size:31
Alignment explanation
Indices: 58301143--58301220 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
58301133 CCACGTATGA
* * *
58301143 ATATG-AAATATATATTATATATTCCTAAAT
1 ATATGAAAATATATATAATATACTCCTAAAG
*
58301173 ATATGAAAAGATATATAATATACTCCTAAAAG
1 ATATGAAAATATATATAATATACTCCT-AAAG
*
58301205 ATAT-ACAATATATATA
1 ATATGAAAATATATATA
58301221 GTTAGGGTGG
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
30 5 0.12
31 28 0.70
32 7 0.17
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.36
Consensus pattern (31 bp):
ATATGAAAATATATATAATATACTCCTAAAG
Found at i:58301637 original size:59 final size:59
Alignment explanation
Indices: 58301562--58301686 Score: 169
Period size: 59 Copynumber: 2.1 Consensus size: 59
58301552 CCCATCCTGA
* * * * *
58301562 ATTGCATTCCTAACAAAGTGACAATCCACTTCAATTGCAATATGCAAGGCAAATTAACT
1 ATTGCATCCCAAACAAAGTGACAATACACTTCAATTGCAACATGCAACGCAAATTAACT
* * * *
58301621 ATTGCATCCCAAACAAAGTGACAATACACTTTACTTGCAACATGCAACGCAGATTGACT
1 ATTGCATCCCAAACAAAGTGACAATACACTTCAATTGCAACATGCAACGCAAATTAACT
58301680 ATTGCAT
1 ATTGCAT
58301687 ATTTAAATAT
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (59 bp):
ATTGCATCCCAAACAAAGTGACAATACACTTCAATTGCAACATGCAACGCAAATTAACT
Found at i:58308998 original size:106 final size:104
Alignment explanation
Indices: 58308597--58309045 Score: 533
Period size: 106 Copynumber: 4.3 Consensus size: 104
58308587 ATAAATTGTT
* *** * *
58308597 GTGTTTTGTGAGTTTTTAGTAATGTAAAAAATTTTTAAAAATAAT-TTTATAGTTATTTTGTTAA
1 GTGTTTTGTGATTTTTTAGTAATGT-AATTTTTTTTAAAAAAAATATTTATAGTTATTTTGTTAG
* *
58308661 TAGTTTATGATTATGTTATAAATTGTTAGTG--T--TTT-
65 TAATTTATGATTAGGTTATAAATTGTTAGTGTTTAGTTTA
* * * * *
58308696 GTGTTTTGTTATTTTTTAGTAATGTAATTTCTTTTAAAATAAATGTTATAGTTATTTATTTTGTT
1 GTGTTTTGTGATTTTTTAGTAATGTAATTTTTTTTAAAAAAAATATT-TA--TAGTTATTTTGTT
*
58308761 AGTAATTTATGGGATTAGGTTATAAATTGTTAGTATTTAGTTTA
63 AGTAATTTAT--GATTAGGTTATAAATTGTTAGTGTTTAGTTTA
* *
58308805 GGGTTTTGTGATTTTTTAGTAATGTAA---TTTTAAAAAAAAATAATTTTATAGTTATTTTGTTA
1 GTGTTTTGTGATTTTTTAGTAATGTAATTTTTTTTAAAAAAAAT-A-TTTATAGTTATTTTGTTA
*
58308867 GTAATTTATGATTAGGTTATATAAATTCTTAGTGTTTAGTTTA
64 GTAATTTATGATTAGG-T-TATAAATTGTTAGTGTTTAGTTTA
*
58308910 GTGTTTTGTGATTTTTTAGTAATGTAATTTTTTTTAAAAAAAATATTTATAGTTATTTGGTTAGT
1 GTGTTTTGTGATTTTTTAGTAATGTAATTTTTTTTAAAAAAAATATTTATAGTTATTTTGTTAGT
*
58308975 AATTTATGATTAGGTTATATAAATGGTTAGTGTTTAGTTTA
66 AATTTATGATTAGG-T-TATAAATTGTTAGTGTTTAGTTTA
*
58309016 GTGTTTTGTGATTTTTT--TAATTTAATTTTT
1 GTGTTTTGTGATTTTTTAGTAATGTAATTTTT
58309046 ATATAATGTA
Statistics
Matches: 304, Mismatches: 28, Indels: 31
0.84 0.08 0.09
Matches are distributed among these distances:
98 13 0.04
99 25 0.08
100 2 0.01
102 20 0.07
103 7 0.02
104 34 0.11
105 70 0.23
106 87 0.29
107 3 0.01
108 18 0.06
109 25 0.08
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.54
Consensus pattern (104 bp):
GTGTTTTGTGATTTTTTAGTAATGTAATTTTTTTTAAAAAAAATATTTATAGTTATTTTGTTAGT
AATTTATGATTAGGTTATAAATTGTTAGTGTTTAGTTTA
Found at i:58309030 original size:211 final size:203
Alignment explanation
Indices: 58308633--58309044 Score: 560
Period size: 211 Copynumber: 2.0 Consensus size: 203
58308623 AAAAATTTTT
* * *
58308633 AAAAATAATTTTATAGTTATTTTGTTAATAGTTTATGATTATGTTATAAATTGTTAGTGTTTTGT
1 AAAAATAATTTTATAGTTATTTTGTTAATAATTTATGATTAGGTTATAAATTCTTAGTGTTTTGT
* * * * *
58308698 GTTTTGTTATTTTTTAGTAATGTAATTTCTTTTAAAATAAATGTTATAGTTATTTATTTTGTTAG
66 GTTTTGTGATTTTTTAGTAATGTAATTTCTTTTAAAAAAAATATTATAG-TAGTTATTTGGTTAG
*
58308763 TAATTTATGGGATTAGGTTATAAATTGTTAGTATTTAGTTTAGGGTTTTGTGATTTTTTAGTAAT
130 TAATTTAT-GGATTAGGTTATAAATGGTTAGTATTTAGTTTAGGGTTTTGTGATTTTTT--TAAT
58308828 GTAATTTTAAAA
192 GTAATTTTAAAA
*
58308840 AAAAATAATTTTATAGTTATTTTGTTAGTAATTTATGATTAGGTTATATAAATTCTTAGTGTTTA
1 AAAAATAATTTTATAGTTATTTTGTTAATAATTTATGATTAGG-T-TATAAATTCTTAGTG--T-
*
58308905 GTTTAGTGTTTTGTGATTTTTTAGTAATGTAATTTTTTTTAAAAAAAATATT-TA-TAGTTATTT
61 -TTT-GTGTTTTGTGATTTTTTAGTAATGTAATTTCTTTTAAAAAAAATATTATAGTAGTTATTT
* *
58308968 GGTTAGTAATTTAT-GATTAGGTTATATAAATGGTTAGTGTTTAGTTTAGTGTTTTGTGATTTTT
124 GGTTAGTAATTTATGGATTAGG-T-TATAAATGGTTAGTATTTAGTTTAGGGTTTTGTGATTTTT
*
58309032 TTAATTTAATTTT
187 TTAATGTAATTTT
58309045 TATATAATGT
Statistics
Matches: 182, Mismatches: 14, Indels: 16
0.86 0.07 0.08
Matches are distributed among these distances:
207 40 0.22
208 1 0.01
209 32 0.18
210 1 0.01
211 60 0.33
213 5 0.03
214 43 0.24
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.54
Consensus pattern (203 bp):
AAAAATAATTTTATAGTTATTTTGTTAATAATTTATGATTAGGTTATAAATTCTTAGTGTTTTGT
GTTTTGTGATTTTTTAGTAATGTAATTTCTTTTAAAAAAAATATTATAGTAGTTATTTGGTTAGT
AATTTATGGATTAGGTTATAAATGGTTAGTATTTAGTTTAGGGTTTTGTGATTTTTTTAATGTAA
TTTTAAAA
Found at i:58310156 original size:50 final size:50
Alignment explanation
Indices: 58310098--58310199 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 50
58310088 TGTAGTAGAC
*
58310098 ATAGGCGAATGCCTCATATTGTTGCAGTCGTGGACACTTTACCGAATGCT
1 ATAGGCGAATGCCTCATATTGTTGCAGTCATGGACACTTTACCGAATGCT
58310148 ATAGGCGAATGCCTCATATTGTTGCAGTCATGGACACTTTACCGAATGCT
1 ATAGGCGAATGCCTCATATTGTTGCAGTCATGGACACTTTACCGAATGCT
58310198 AT
1 AT
58310200 TCTTGGCATC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (50 bp):
ATAGGCGAATGCCTCATATTGTTGCAGTCATGGACACTTTACCGAATGCT
Found at i:58311113 original size:33 final size:33
Alignment explanation
Indices: 58311076--58311151 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
58311066 TACCACTTCG
* *
58311076 GTACTACAGTCATCTCGGCTCATATCCACCACC
1 GTACTACACTCATCTCGGCCCATATCCACCACC
* * * *
58311109 GTACTCCACTCCTCTCGGCCCGTATCCACCGCC
1 GTACTACACTCATCTCGGCCCATATCCACCACC
*
58311142 GTACTCCACT
1 GTACTACACT
58311152 ACTTTCGGCT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.18, C:0.45, G:0.13, T:0.24
Consensus pattern (33 bp):
GTACTACACTCATCTCGGCCCATATCCACCACC
Found at i:58311160 original size:33 final size:33
Alignment explanation
Indices: 58311088--58311160 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
58311078 ACTACAGTCA
* * *
58311088 TCTCGGCTCATATCCACCACCGTACTCCACTCC
1 TCTCGGCCCGTATCCACCACCGTACTCCACTAC
*
58311121 TCTCGGCCCGTATCCACCGCCGTACTCCACTAC
1 TCTCGGCCCGTATCCACCACCGTACTCCACTAC
*
58311154 TTTCGGC
1 TCTCGGC
58311161 TAAAGTTCAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.15, C:0.47, G:0.14, T:0.25
Consensus pattern (33 bp):
TCTCGGCCCGTATCCACCACCGTACTCCACTAC
Found at i:58317885 original size:106 final size:106
Alignment explanation
Indices: 58317699--58317904 Score: 340
Period size: 106 Copynumber: 1.9 Consensus size: 106
58317689 TGAGCATTCC
* *
58317699 TATTTTTCGGGATTCGAGACATCGTGCCCTAACTTACGGGGCATAATTCTCTTCTCGATTAACTC
1 TATTTTTCGGGATTCGAGACATCGTGCCCTAACTTACGAGGCATAATTCTCTTCCCGATTAACTC
58317764 GAAATACGAAGACATTCTTCATAAAATTTGATTTAGTTTCT
66 GAAATACGAAGACATTCTTCATAAAATTTGATTTAGTTTCT
* * * *
58317805 TATTTTTGGGGATTCGAGACATCGTGTCCTAACTTATGAGGCATAATTTTCTTCCCGATTAACTC
1 TATTTTTCGGGATTCGAGACATCGTGCCCTAACTTACGAGGCATAATTCTCTTCCCGATTAACTC
* *
58317870 GAAATACGAATACATTTTTCATAAAATTTGATTTA
66 GAAATACGAAGACATTCTTCATAAAATTTGATTTA
58317905 ATTAACGATA
Statistics
Matches: 92, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
106 92 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (106 bp):
TATTTTTCGGGATTCGAGACATCGTGCCCTAACTTACGAGGCATAATTCTCTTCCCGATTAACTC
GAAATACGAAGACATTCTTCATAAAATTTGATTTAGTTTCT
Found at i:58321961 original size:26 final size:24
Alignment explanation
Indices: 58321923--58321974 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 24
58321913 TTTTTATATA
*
58321923 TATTTTGAATTTTGAATT-TTTAGT
1 TATTTTGAATTTTAAATTATTT-GT
58321947 TATTTTAGAATTTTTAAATTATTTGT
1 TATTTT-GAA-TTTTAAATTATTTGT
58321973 TA
1 TA
58321975 ATGTGGCATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 6 0.25
25 3 0.12
26 12 0.50
27 3 0.12
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.62
Consensus pattern (24 bp):
TATTTTGAATTTTAAATTATTTGT
Found at i:58324857 original size:31 final size:31
Alignment explanation
Indices: 58324819--58324921 Score: 111
Period size: 31 Copynumber: 3.4 Consensus size: 31
58324809 TAATCATATT
* *
58324819 AATATTAAATTAATAAAATATTATCTAGATA
1 AATATTAAATTAATAAAATAATATCTAAATA
** * *
58324850 AATATTAAATT-A-AATTTAATATCTCATATT
1 AATATTAAATTAATAAAATAATATCT-AAATA
* *
58324880 AATATTAAGTTAATAAAATACTATCTAAATA
1 AATATTAAATTAATAAAATAATATCTAAATA
58324911 AATATTAAATT
1 AATATTAAATT
58324922 TAATTTAATA
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
29 9 0.16
30 14 0.25
31 25 0.44
32 9 0.16
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (31 bp):
AATATTAAATTAATAAAATAATATCTAAATA
Found at i:58324912 original size:61 final size:61
Alignment explanation
Indices: 58324812--58324937 Score: 216
Period size: 61 Copynumber: 2.1 Consensus size: 61
58324802 TTAGAATTAA
* *
58324812 TCATATTAATATTAAATTAATAAAATATTATCTAGATAAATATTAAATTAAATTTAATATC
1 TCATATTAATATTAAATTAATAAAATACTATCTAAATAAATATTAAATTAAATTTAATATC
* *
58324873 TCATATTAATATTAAGTTAATAAAATACTATCTAAATAAATATTAAATTTAATTTAATATC
1 TCATATTAATATTAAATTAATAAAATACTATCTAAATAAATATTAAATTAAATTTAATATC
58324934 TCAT
1 TCAT
58324938 TTTATTATAT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (61 bp):
TCATATTAATATTAAATTAATAAAATACTATCTAAATAAATATTAAATTAAATTTAATATC
Found at i:58326370 original size:12 final size:12
Alignment explanation
Indices: 58326355--58326384 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
58326345 AATGATTAAA
58326355 TAAATTAAAAAT
1 TAAATTAAAAAT
*
58326367 TAAATTAGAAAT
1 TAAATTAAAAAT
58326379 TAAATT
1 TAAATT
58326385 CGGATTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (12 bp):
TAAATTAAAAAT
Found at i:58327516 original size:135 final size:135
Alignment explanation
Indices: 58327272--58327541 Score: 513
Period size: 136 Copynumber: 2.0 Consensus size: 135
58327262 TTCTATTTTT
58327272 GGCTTTTACAAAGTCAAAAGAATATGATAAGTCCTTAACTTTTTCCACATTTTTATTCGACCTCA
1 GGCTTTTACAAAGTCAAAAGAATATGATAAGTCCTTAACTTTTTCCACATTTTTATTCGACCTCA
*
58327337 TTTCATTGATTGTGTTTCAATTTGGTCATTTCTTGGTCGTTTTTTACTCTTAGCGTCCCAATTGC
66 TTTCATTGATTGTGTTTCAATTTGGTCATTTCCTGGTCGTTTTTTACTCTTAGCGTCCCAATTGC
58327402 ATCCA
131 ATCCA
58327407 GGCTTTTACAAAGTCAAAAGAATATGATAAGTCCTTAACTTTTTCCACATTTTTTATTCGACCTC
1 GGCTTTTACAAAGTCAAAAGAATATGATAAGTCCTTAACTTTTTCCACA-TTTTTATTCGACCTC
*
58327472 ATTTCATTGATTGTGTTTCAATTTGGTCATTTCCTGGTCGTTTTTTACTCTTAGTGTCCCAATTG
65 ATTTCATTGATTGTGTTTCAATTTGGTCATTTCCTGGTCGTTTTTTACTCTTAGCGTCCCAATTG
58327537 CATCC
130 CATCC
58327542 CTTATAAGAT
Statistics
Matches: 132, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
135 49 0.37
136 83 0.63
ACGTcount: A:0.23, C:0.20, G:0.13, T:0.43
Consensus pattern (135 bp):
GGCTTTTACAAAGTCAAAAGAATATGATAAGTCCTTAACTTTTTCCACATTTTTATTCGACCTCA
TTTCATTGATTGTGTTTCAATTTGGTCATTTCCTGGTCGTTTTTTACTCTTAGCGTCCCAATTGC
ATCCA
Found at i:58328711 original size:25 final size:25
Alignment explanation
Indices: 58328648--58328725 Score: 77
Period size: 25 Copynumber: 3.1 Consensus size: 25
58328638 CATTTGTGGT
* * *
58328648 GAATATTTTGTAAAGCTTTTGTGGT
1 GAATATTCTGTAAAGCTTTTATGGC
* * *
58328673 GAACT-CTCTATAAAGCCTTTATGGC
1 GAA-TATTCTGTAAAGCTTTTATGGC
*
58328698 GAATATTCTGTAAAGTTTTTATGGC
1 GAATATTCTGTAAAGCTTTTATGGC
58328723 GAA
1 GAA
58328726 CTCTCTGTAA
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
24 1 0.02
25 39 0.95
26 1 0.02
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.40
Consensus pattern (25 bp):
GAATATTCTGTAAAGCTTTTATGGC
Found at i:58328732 original size:25 final size:25
Alignment explanation
Indices: 58328656--58328736 Score: 92
Period size: 25 Copynumber: 3.2 Consensus size: 25
58328646 GTGAATATTT
* *
58328656 TGTAAAGCTTTTGTGGTGAACTCTC
1 TGTAAAGCTTTTATGGCGAACTCTC
* * *
58328681 TATAAAGCCTTTATGGCGAA-TATTC
1 TGTAAAGCTTTTATGGCGAACT-CTC
*
58328706 TGTAAAGTTTTTATGGCGAACTCTC
1 TGTAAAGCTTTTATGGCGAACTCTC
58328731 TGTAAA
1 TGTAAA
58328737 ACATTCTTGG
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
24 1 0.02
25 43 0.96
26 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (25 bp):
TGTAAAGCTTTTATGGCGAACTCTC
Found at i:58332920 original size:3 final size:3
Alignment explanation
Indices: 58332914--58332971 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
58332904 TTTCGTGTCT
58332914 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
58332962 TTA TTA TTA T
1 TTA TTA TTA T
58332972 GTCATTTTAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:58336627 original size:5 final size:5
Alignment explanation
Indices: 58336619--58336648 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
58336609 ATCACATTTC
58336619 CCCTG CCCTG CCCTG CCCTG CCCTG CCCTG
1 CCCTG CCCTG CCCTG CCCTG CCCTG CCCTG
58336649 GTTCTTAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.60, G:0.20, T:0.20
Consensus pattern (5 bp):
CCCTG
Found at i:58341677 original size:3 final size:3
Alignment explanation
Indices: 58341662--58341749 Score: 56
Period size: 3 Copynumber: 29.7 Consensus size: 3
58341652 TAGGTTTTTT
* * * *
58341662 TTA TT- TTA ATA TTA TTA ATA TTG TTA -TA TTGCA TCA TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT--A TTA TTA TTA TTA
* * * * *
58341706 TTA TTT TTA TTA TTA TTA CTA TTA TTA ATA TAA TAA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
58341750 GTCGAAACCG
Statistics
Matches: 64, Mismatches: 16, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
2 6 0.09
3 56 0.88
5 2 0.03
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:58342312 original size:98 final size:98
Alignment explanation
Indices: 58342143--58342439 Score: 465
Period size: 98 Copynumber: 3.0 Consensus size: 98
58342133 ATACAATAAA
* * *
58342143 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATC
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
58342208 CCTTTAGAATCCTAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCCTAAACTCGGAATATTTCCTTT
*
58342241 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGTACAATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
58342306 CCTTTAGAAT-CTCAAACTCGGAATATTTCCTTCAT
66 CCTTTAGAATCCT-AAACTCGGAATATTTCCTT--T
*
58342341 GA-TTTAAAAGAA-AGTCCGCTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAA
1 -ACTTTAAAAGAACA-TCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAA
* *
58342404 TTCCTTTAAAATCCCAAACTCGGAATATTTCCTTT
64 TTCCTTTAGAATCCTAAACTCGGAATATTTCCTTT
58342439 A
1 A
58342440 TGATTTTTAA
Statistics
Matches: 185, Mismatches: 8, Indels: 13
0.90 0.04 0.06
Matches are distributed among these distances:
97 3 0.02
98 91 0.49
99 1 0.01
100 88 0.48
101 2 0.01
ACGTcount: A:0.37, C:0.24, G:0.11, T:0.29
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTTTAGAATCCTAAACTCGGAATATTTCCTTT
Found at i:58342396 original size:100 final size:98
Alignment explanation
Indices: 58342145--58342445 Score: 464
Period size: 100 Copynumber: 3.0 Consensus size: 98
58342135 ACAATAAAAC
* * *
58342145 TTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATCCC
1 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
58342210 TTTAGAATCCTAAACTCGGAATATTTCCTT-T-A
66 TTTAGAATCC-AAACTCGGAATATTTCCTTATGA
*
58342242 CTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGTACAATTC
1 -TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTC
58342307 CTTTAGAATCTCAAACTCGGAATATTTCCTTCATGA
65 CTTTAGAATC-CAAACTCGGAATATTTCCTT-ATGA
*
58342343 TTTAAAAGAA-AGTCCGCTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTC
1 TTTAAAAGAACA-TCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTC
*
58342407 CTTTAAAATCCCAAACTCGGAATATTTCCTTTATGA
65 CTTTAGAAT-CCAAACTCGGAATATTTCC-TTATGA
58342443 TTT
1 TTT
58342446 TTAAAAAATC
Statistics
Matches: 189, Mismatches: 7, Indels: 12
0.91 0.03 0.06
Matches are distributed among these distances:
98 89 0.47
99 2 0.01
100 94 0.50
101 4 0.02
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (98 bp):
TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
TTTAGAATCCAAACTCGGAATATTTCCTTATGA
Found at i:58344640 original size:44 final size:44
Alignment explanation
Indices: 58344549--58344766 Score: 137
Period size: 44 Copynumber: 5.0 Consensus size: 44
58344539 CTGCAATTTC
* * **
58344549 AGGGAGATAAG-GCTTGCAATCTTCAATCTATTCCACTAATGCTT
1 AGGGAGATAAGATC-TGAAATCTTCAATCTATTCCACTGTTGCTT
58344593 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTG-TCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCT-T
* * * ** **
58344637 AGGG-GAGT-AGAATTACTG---GCTTCAATGTACTCCACTGTAACCAC
1 AGGGAGA-TAAG-A-T-CTGAAATCTTCAATCTATTCCACTGT-TGCTT
* * * * ** **
58344681 AGGGAGGTAAAATCT-ACCATCTTCGATCTGCTCCACTACTGCTT
1 AGGGAGATAAGATCTGA-AATCTTCAATCTATTCCACTGTTGCTT
58344725 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGC
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGC
58344767 CCAGGGAAGT
Statistics
Matches: 128, Mismatches: 31, Indels: 30
0.68 0.16 0.16
Matches are distributed among these distances:
42 2 0.02
43 23 0.18
44 81 0.63
45 19 0.15
46 3 0.02
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (44 bp):
AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCTT
Found at i:58344778 original size:132 final size:132
Alignment explanation
Indices: 58344580--58344844 Score: 458
Period size: 132 Copynumber: 2.0 Consensus size: 132
58344570 TTCAATCTAT
* * *
58344580 TCCACTAATGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCTAGGGGAGT
1 TCCACTAATGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGT
* * *
58344645 AGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTACCATCTTCGATCT
66 AGAATTACTAGCTTCAATGTACTCCACTGTAACCACAAGGAGGTAAAATCCACCATCTTCGATCT
58344710 GC
131 GC
*
58344712 TCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGT
1 TCCACTAATGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGT
*
58344777 AGAATTACTAGCTTCAATGTACTCCACTGTAACCACAAGGAGGTAAAATCCGCCATCTTCGATCT
66 AGAATTACTAGCTTCAATGTACTCCACTGTAACCACAAGGAGGTAAAATCCACCATCTTCGATCT
58344842 GC
131 GC
58344844 T
1 T
58344845 TCGCTGTCAA
Statistics
Matches: 125, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 125 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (132 bp):
TCCACTAATGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGT
AGAATTACTAGCTTCAATGTACTCCACTGTAACCACAAGGAGGTAAAATCCACCATCTTCGATCT
GC
Found at i:58344803 original size:43 final size:44
Alignment explanation
Indices: 58344613--58344806 Score: 119
Period size: 44 Copynumber: 4.4 Consensus size: 44
58344603 GATCTGAAAT
* * * * *
58344613 CTTCAATCTATTCCACTGTTGTCTAGGGGAGTAGAAT-TACTGG
1 CTTCAATCTACTCCACTGTTGCCCAGGGAAGTAGAATCTACTAG
* ** * * * *
58344656 CTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTACCAT
1 CTTCAATCTACTCCACTGTTGCC-CAGGGAAGTAGAATCTACTAG
* * ** ** * *
58344701 CTTCGATCTGCTCCACTACTGCTTAGGG-AGATA-AGATCTGA-AAT
1 CTTCAATCTACTCCACTGTTGCCCAGGGAAG-TAGA-ATCT-ACTAG
*
58344745 CTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAAT-TACTAG
1 CTTCAATCTACTCCACTGTTGCCCAGGGAAGTAGAATCTACTAG
*
58344788 CTTCAATGTACTCCACTGT
1 CTTCAATCTACTCCACTGT
58344807 AACCACAAGG
Statistics
Matches: 109, Mismatches: 34, Indels: 16
0.69 0.21 0.10
Matches are distributed among these distances:
42 1 0.01
43 39 0.36
44 47 0.43
45 22 0.20
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (44 bp):
CTTCAATCTACTCCACTGTTGCCCAGGGAAGTAGAATCTACTAG
Found at i:58348343 original size:21 final size:21
Alignment explanation
Indices: 58348317--58348356 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
58348307 GATTTAATCC
*
58348317 AAAAAAA-AAGAAAAAACAAG
1 AAAAAAATAAAAAAAAACAAG
*
58348337 AAAAAAATAAAAAGAAACAA
1 AAAAAAATAAAAAAAAACAA
58348357 AAACCTCTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.85, C:0.05, G:0.07, T:0.03
Consensus pattern (21 bp):
AAAAAAATAAAAAAAAACAAG
Found at i:58350693 original size:250 final size:254
Alignment explanation
Indices: 58350252--58350982 Score: 809
Period size: 250 Copynumber: 2.8 Consensus size: 254
58350242 CACAACGGTG
* * * * *
58350252 AATCTTACTTCCCTGGCGTTGCAGTGGAGCGGATTGAAGCCACAAT-GGCGAACCTTATCT-CCT
1 AATCTTACTTCCC-GGCGTTGCAGCGGAGCAGATTGAAGCCAC-GTCGGAGAATCTTATCTCCCT
* * * *
58350315 CGGTGTTAAGACTTGGATTAGCTGAAGTGGAGCGAATTAAAGCTGTGGGCAGCGAATCCTATCTC
64 -GGCGTTAAGACTTGAATTAGCTGAAGTGGAGCGGATTAAGGCTGTGGGCAGCGAATCCTATCTC
* * * *
58350380 TTTAGCATTACAGTGGAATGGGTTAAAGCCGCAGCGGCGAATCTTACTTCCCTAGCGGTGTAGGG
128 TTTGGCATTACAGTGGAATGGATTGAAGCCGCA-CGGCGAATCTTACTTCCCTGGCGGTGTAGGG
*
58350445 GACCAGATTGAAGCCACGAC-GACGAATCTCATTTCCCC-T-CA-TT-G-G-AGCCA-AACGAAA
192 GACCAGATTGAAGCCACGACAG-CGAATCTC-GTTCCCCATACAGTTAGAGAAGCCACAACGAAA
58350502 AATCTTACTTCTCCGGCGTTGCAGCGGAGCAGATTGAAGCCACGTCGGAGAATCTTATCTCCCTG
1 AATCTTACTTC-CCGGCGTTGCAGCGGAGCAGATTGAAGCCACGTCGGAGAATCTTATCTCCCTG
* *
58350567 GCGTTAAGACTTGAATTAGCTGAAGTGGAGTGGATTAAGGCTGTGGGCAGCAAATCCTATCTCTT
65 GCGTTAAGACTTGAATTAGCTGAAGTGGAGCGGATTAAGGCTGTGGGCAGCGAATCCTATCTCTT
* * **
58350632 TGGCATTACAGTGGAACGGATTGAAGCCGCGACGACGAATCTTACTTCAATGGCGGTGTAGGGGA
130 TGGCATTACAGTGGAATGGATTGAAGCCGC-ACGGCGAATCTTACTTCCCTGGCGGTGTAGGGGA
**
58350697 CCAGATTGAAGCCAAAACAGCGAATCTCGTTCCCCGATATAGCAGTTAAGTAGATTAAAGCCACA
194 CCAGATTGAAGCCACGACAGCGAATCTCGTTCCCC---ATA-CAGTT-AG-AG----AAGCCACA
* ***
58350762 ATGGCG
249 ACGAAA
* * * **
58350768 AATCTTACTTCCCCAGCGTTGCAGCGGAGTAGATTGAAGCCACGACGGTTAATCTTATCTCCCTG
1 AATCTTACTT-CCCGGCGTTGCAGCGGAGCAGATTGAAGCCACGTCGGAGAATCTTATCTCCCTG
* * *
58350833 GCATTAAGACTT-AGATTAGCTGAAGTGGAGCGGATTAAGGCCGTGGGTAGCGAATCCTATCTCT
65 GCGTTAAGACTTGA-ATTAGCTGAAGTGGAGCGGATTAAGGCTGTGGGCAGCGAATCCTATCTCT
* * ** * **
58350897 TTGGCATTACAGTGGAATAGATTGAAGCCACAACGGTAAATCTTACTTCCCTGGCAGTGTAGTAG
129 TTGGCATTACAGTGGAATGGATTGAAGCCGC-ACGGCGAATCTTACTTCCCTGGCGGTGTAGGGG
* *
58350962 AACAGATTGAAGCTACGACAG
193 ACCAGATTGAAGCCACGACAG
58350983 TAAATTGTAT
Statistics
Matches: 405, Mismatches: 52, Indels: 32
0.83 0.11 0.07
Matches are distributed among these distances:
249 7 0.02
250 189 0.47
251 7 0.02
253 1 0.00
255 2 0.00
256 2 0.00
258 1 0.00
260 1 0.00
265 6 0.01
266 188 0.46
267 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (254 bp):
AATCTTACTTCCCGGCGTTGCAGCGGAGCAGATTGAAGCCACGTCGGAGAATCTTATCTCCCTGG
CGTTAAGACTTGAATTAGCTGAAGTGGAGCGGATTAAGGCTGTGGGCAGCGAATCCTATCTCTTT
GGCATTACAGTGGAATGGATTGAAGCCGCACGGCGAATCTTACTTCCCTGGCGGTGTAGGGGACC
AGATTGAAGCCACGACAGCGAATCTCGTTCCCCATACAGTTAGAGAAGCCACAACGAAA
Found at i:58351096 original size:100 final size:100
Alignment explanation
Indices: 58350912--58351423 Score: 679
Period size: 100 Copynumber: 5.1 Consensus size: 100
58350902 ATTACAGTGG
* * * *
58350912 AATAGATTGAAGCCACAACGGTAAATCTTACTTCCCTGGCAGTGTAGTAGAACAGATTGAAGCTA
1 AATAGATTGAAGCCACAACAGTGAATCTTACTTCCCTGGCAGTGCAGTGGAACAGATTGAAGCTA
* * ** *
58350977 CGACAGTAAAT-TGTATTTCCCCGACATTGCAATTA
66 CAACGGCGAATCT-TGTTTCCCCGACATTGCAATTA
*
58351012 AATAGATTGAAGCCACAACAGTGAATCTTACTTCCCTGGCAGTGTAGTGGAACAGATTGAAGCTA
1 AATAGATTGAAGCCACAACAGTGAATCTTACTTCCCTGGCAGTGCAGTGGAACAGATTGAAGCTA
* * *
58351077 CGACGGCGAATATTGTTTCCCCGACATAGCAATTA
66 CAACGGCGAATCTTGTTTCCCCGACATTGCAATTA
* *
58351112 AATAGATCGAAGCCACAACAGCGAATCTTACTTCCCTGGC-GATGCAGTGGAACAGATTGAAGCT
1 AATAGATTGAAGCCACAACAGTGAATCTTACTTCCCTGGCAG-TGCAGTGGAACAGATTGAAGCT
* *
58351176 ACAACGGTGAATCTTATTTCCCCGACATTGCAATTA
65 ACAACGGCGAATCTTGTTTCCCCGACATTGCAATTA
* * * *
58351212 AAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGGTA
1 AATAGATTGAAGCCACAACAGTGAATCTTACTTCCCTGGCAGTGCAGTGGAACAGATTGAAGCTA
* *
58351277 CAACGGCGAATCTTGCTTCCCCGACATTACAATTA
66 CAACGGCGAATCTTGTTTCCCCGACATTGCAATTA
* * ** *
58351312 AAAAGACTGAAGCCACAAC-GACAAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCT
1 AATAGATTGAAGCCACAACAG-TGAATCTTACTTCCCTGGCAGTGCAGTGGAACAGATTGAAGCT
* * *
58351376 ACAACAGCGAATCTTGCTTCCCCGACATTGCAGTTA
65 ACAACGGCGAATCTTGTTTCCCCGACATTGCAATTA
* *
58351412 ATTAGACTGAAG
1 AATAGATTGAAG
58351424 ATAGCGAATC
Statistics
Matches: 374, Mismatches: 34, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
99 2 0.01
100 370 0.99
101 2 0.01
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.24
Consensus pattern (100 bp):
AATAGATTGAAGCCACAACAGTGAATCTTACTTCCCTGGCAGTGCAGTGGAACAGATTGAAGCTA
CAACGGCGAATCTTGTTTCCCCGACATTGCAATTA
Found at i:58351408 original size:50 final size:50
Alignment explanation
Indices: 58350901--58351409 Score: 365
Period size: 50 Copynumber: 10.2 Consensus size: 50
58350891 ATCTCTTTGG
* * ** * *
58350901 CATTACAGTGGAATAGATTGAAGCCACAACGGTAAATCTTACTTCCCTGG
1 CATTGCAGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTCCCCGA
* * * * * * ** *
58350951 CAGTGTAGTAGAACAGATTGAAGCTACGACAGTAAAT-TGTATTTCCCCGA
1 CATTGCAGTGGAACAGATTGAAGCCACAACGGCGAATCT-TACTTCCCCGA
* ** * * * * *
58351001 CATTGCAATTAAATAGATTGAAGCCACAACAGTGAATCTTACTTCCCTGG
1 CATTGCAGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTCCCCGA
* * * * * **
58351051 CAGTGTAGTGGAACAGATTGAAGCTACGACGGCGAATATTGTTTCCCCGA
1 CATTGCAGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTCCCCGA
* * ** * * * * *
58351101 CATAGCAATTAAATAGATCGAAGCCACAACAGCGAATCTTACTTCCCTGG
1 CATTGCAGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTCCCCGA
* * *
58351151 CGA-TGCAGTGGAACAGATTGAAGCTACAACGGTGAATCTTATTTCCCCGA
1 C-ATTGCAGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTCCCCGA
* ** * * * *
58351201 CATTGCAATTAAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCTGG
1 CATTGCAGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTCCCCGA
** ** *
58351251 CGGTGCAGTGGAACAGATTGAAGGTACAACGGCGAATCTTGCTTCCCCGA
1 CATTGCAGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTCCCCGA
* * ** * * * * * *
58351301 CATTACAATTAAAAAGACTGAAGCCACAACGACAAATCTTACTTCCCTGG
1 CATTGCAGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTCCCCGA
** * * *
58351351 CGGTGCAGTGGAACAGATTGAAGCTACAACAGCGAATCTTGCTTCCCCGA
1 CATTGCAGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTCCCCGA
58351401 CATTGCAGT
1 CATTGCAGT
58351410 TAATTAGACT
Statistics
Matches: 337, Mismatches: 118, Indels: 8
0.73 0.25 0.02
Matches are distributed among these distances:
49 2 0.01
50 333 0.99
51 2 0.01
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (50 bp):
CATTGCAGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTCCCCGA
Found at i:58352515 original size:16 final size:16
Alignment explanation
Indices: 58352491--58352521 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
58352481 GTGATTTTAT
*
58352491 TTTTGTTTTTTTCCTC
1 TTTTATTTTTTTCCTC
58352507 TTTTATTTTTTTCCT
1 TTTTATTTTTTTCCT
58352522 TCGATTTACT
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:0.03, C:0.16, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTTATTTTTTTCCTC
Found at i:58353139 original size:3 final size:3
Alignment explanation
Indices: 58353096--58353188 Score: 57
Period size: 3 Copynumber: 31.3 Consensus size: 3
58353086 TTTAGGTTTT
* * * *
58353096 TTA TT- TTA ATA TTA TTA ATA TTG TTA -TA TTGCA TCA TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT--A TTA TTA TTA TTA
* * * * * *
58353140 TTA TTT TTA TTT TTA TTA CTA TTA TTA ATA TAA TAA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
58353188 T
1 T
58353189 AACCATGTAT
Statistics
Matches: 67, Mismatches: 18, Indels: 10
0.71 0.19 0.11
Matches are distributed among these distances:
2 6 0.09
3 59 0.88
5 2 0.03
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:58353293 original size:22 final size:23
Alignment explanation
Indices: 58353240--58353293 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
58353230 TTATTTTTAT
58353240 AATTTATATATATACATACATAC
1 AATTTATATATATACATACATAC
* * * *
58353263 -TTTTTTATATATATATA-TTAC
1 AATTTATATATATACATACATAC
58353284 AATTTATATA
1 AATTTATATA
58353294 CGTATCTATA
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (23 bp):
AATTTATATATATACATACATAC
Found at i:58353421 original size:29 final size:27
Alignment explanation
Indices: 58353385--58353438 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
58353375 ATTTTCCATA
58353385 TTTTATAATCCATACATATATATATATAT
1 TTTTATAAT--ATACATATATATATATAT
* *
58353414 TTTTATAATATATATGTATATATAT
1 TTTTATAATATACATATATATATAT
58353439 TCATGCACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 14 0.61
29 9 0.39
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.52
Consensus pattern (27 bp):
TTTTATAATATACATATATATATATAT
Found at i:58354396 original size:12 final size:12
Alignment explanation
Indices: 58354379--58354417 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
58354369 AAATTAAAAA
58354379 AAATATAATAAT
1 AAATATAATAAT
**
58354391 AAATATTTTAA-
1 AAATATAATAAT
58354402 AAATATAATAAT
1 AAATATAATAAT
58354414 AAAT
1 AAAT
58354418 TTAAATTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
AAATATAATAAT
Found at i:58354407 original size:11 final size:11
Alignment explanation
Indices: 58354366--58354417 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
58354356 ATCCTAATTC
58354366 TAAAAAT-TAA
1 TAAAAATATAA
*
58354376 AAAAAATATAA
1 TAAAAATATAA
**
58354387 TAATAAATATTT
1 TAA-AAATATAA
58354399 TAAAAATATAA
1 TAAAAATATAA
58354410 TAATAAAT
1 TAA-AAAT
58354418 TTAAATTTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 6 0.18
11 14 0.42
12 13 0.39
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAAAATATAA
Found at i:58354433 original size:12 final size:13
Alignment explanation
Indices: 58354418--58354473 Score: 57
Period size: 12 Copynumber: 4.5 Consensus size: 13
58354408 AATAATAAAT
*
58354418 TTAAAT-TTTATA
1 TTAAATATTAATA
58354430 TT-AATATTAATA
1 TTAAATATTAATA
58354442 TTAAATA--AATA
1 TTAAATATTAATA
*
58354453 TAAATATATTAATA
1 TTAA-ATATTAATA
58354467 TTAAATA
1 TTAAATA
58354474 AAATAAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
11 10 0.28
12 12 0.33
13 7 0.19
14 7 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TTAAATATTAATA
Found at i:58354458 original size:17 final size:17
Alignment explanation
Indices: 58354411--58354459 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
58354401 AAAATATAAT
* *
58354411 AATAAATTTAAATTTTA
1 AATAAATATAAATATTA
* * *
58354428 TATTAATATTAATATTA
1 AATAAATATAAATATTA
58354445 AATAAATATAAATAT
1 AATAAATATAAATAT
58354460 ATTAATATTA
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATAAATATAAATATTA
Found at i:58354461 original size:25 final size:24
Alignment explanation
Indices: 58354433--58354480 Score: 87
Period size: 25 Copynumber: 2.0 Consensus size: 24
58354423 TTTTATATTA
58354433 ATATTAATATTAAATAAATATAAAT
1 ATATTAATATTAAATAAA-ATAAAT
58354458 ATATTAATATTAAATAAAATAAA
1 ATATTAATATTAAATAAAATAAA
58354481 AATCTCCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
ATATTAATATTAAATAAAATAAAT
Found at i:58354463 original size:19 final size:20
Alignment explanation
Indices: 58354439--58354478 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
58354429 ATTAATATTA
58354439 ATATTAA-A-TAAATATAAAT
1 ATATTAATATTAAATA-AAAT
58354458 ATATTAATATTAAATAAAAT
1 ATATTAATATTAAATAAAAT
58354478 A
1 A
58354479 AAAATCTCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 6 0.32
21 6 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATATTAATATTAAATAAAAT
Found at i:58376404 original size:22 final size:21
Alignment explanation
Indices: 58376379--58376423 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
58376369 AGTTCATCGT
* *
58376379 TTTAGGAATCTTATTTTTTTTA
1 TTTA-GAACCTTATCTTTTTTA
*
58376401 TTTAGCACCTTATCTTTTTTA
1 TTTAGAACCTTATCTTTTTTA
58376422 TT
1 TT
58376424 AATTGAGGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.20, C:0.11, G:0.07, T:0.62
Consensus pattern (21 bp):
TTTAGAACCTTATCTTTTTTA
Found at i:58378990 original size:60 final size:60
Alignment explanation
Indices: 58378892--58379010 Score: 220
Period size: 60 Copynumber: 2.0 Consensus size: 60
58378882 TTTATTTTTA
*
58378892 TAATTATTTTAAAATTAATTTGTTAGTAATTTAAGATTATGTTATAAATTGTTGTGTTTG
1 TAATTATTTTAAAATTAATTTATTAGTAATTTAAGATTATGTTATAAATTGTTGTGTTTG
*
58378952 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAATTGTTGTGTTT
1 TAATTATTTTAAAATTAATTTATTAGTAATTTAAGATTATGTTATAAATTGTTGTGTTT
58379011 AGTTTAGTAT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.54
Consensus pattern (60 bp):
TAATTATTTTAAAATTAATTTATTAGTAATTTAAGATTATGTTATAAATTGTTGTGTTTG
Found at i:58386163 original size:15 final size:15
Alignment explanation
Indices: 58386145--58386188 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
58386135 TCGTCCACCT
*
58386145 CCTCCTCCGCCTCCG
1 CCTCCTCCACCTCCG
*
58386160 CCTCCCCCACCTCCG
1 CCTCCTCCACCTCCG
*
58386175 CCCCCTCCACCTCC
1 CCTCCTCCACCTCC
58386189 TCCGGCACTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.05, C:0.73, G:0.07, T:0.16
Consensus pattern (15 bp):
CCTCCTCCACCTCCG
Found at i:58397289 original size:49 final size:50
Alignment explanation
Indices: 58397197--58397298 Score: 188
Period size: 49 Copynumber: 2.1 Consensus size: 50
58397187 TAAAACAACC
58397197 ATAGTTATGGTAGTTGTGCTTCCCTCCCCTTCAATGTAATAATATATATA
1 ATAGTTATGGTAGTTGTGCTTCCCTCCCCTTCAATGTAATAATATATATA
*
58397247 ATAGTTATGGTAGTTTTGCTT-CCTCCCCTTCAATGTAATAATATATATA
1 ATAGTTATGGTAGTTGTGCTTCCCTCCCCTTCAATGTAATAATATATATA
58397296 ATA
1 ATA
58397299 AAACCTAAAG
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
49 31 0.61
50 20 0.39
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (50 bp):
ATAGTTATGGTAGTTGTGCTTCCCTCCCCTTCAATGTAATAATATATATA
Found at i:58402912 original size:23 final size:23
Alignment explanation
Indices: 58402868--58402912 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
58402858 CTTCGTCTCC
*
58402868 TTCTTTCTCCCTTTTTTCTTTCT
1 TTCTTTCTCCCTTTTCTCTTTCT
** *
58402891 TTCTTTCTTTCTTTTCTGTTTC
1 TTCTTTCTCCCTTTTCTCTTTC
58402913 GTTTTTGCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.00, C:0.27, G:0.02, T:0.71
Consensus pattern (23 bp):
TTCTTTCTCCCTTTTCTCTTTCT
Found at i:58424013 original size:2 final size:2
Alignment explanation
Indices: 58424008--58424042 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
58423998 GAGTGTGTGT
58424008 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
58424043 CGCTGAGAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:58428349 original size:23 final size:22
Alignment explanation
Indices: 58428316--58428388 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 22
58428306 AGTTATAGTA
*
58428316 TTGCATTGAAGTGTCACTTTCAT
1 TTGCATCGAAGTG-CACTTTCAT
*
58428339 TTGCA-CAGAAGTGCCACATTTCAA
1 TTGCATC-GAAGTG-CAC-TTTCAT
*
58428363 TTGTATCGAAGTGCTACTTTCAT
1 TTGCATCGAAGTGC-ACTTTCAT
58428386 TTG
1 TTG
58428389 TGCACATAGG
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
23 23 0.56
24 17 0.41
25 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (22 bp):
TTGCATCGAAGTGCACTTTCAT
Found at i:58428389 original size:23 final size:23
Alignment explanation
Indices: 58428323--58428389 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 23
58428313 GTATTGCATT
*
58428323 GAAGTG-TCACTTTCATTTGCACA
1 GAAGTGCT-ACTTTCATTTGTACA
* *
58428346 GAAGTGCCACATTTCAATTGTATC-
1 GAAGTGCTAC-TTTCATTTGTA-CA
58428370 GAAGTGCTACTTTCATTTGT
1 GAAGTGCTACTTTCATTTGT
58428390 GCACATAGGA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
23 17 0.47
24 18 0.50
25 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.37
Consensus pattern (23 bp):
GAAGTGCTACTTTCATTTGTACA
Found at i:58433765 original size:26 final size:26
Alignment explanation
Indices: 58433727--58433776 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
58433717 CCTAATTCCT
*
58433727 AAAAAACCTTAACCCTAACAAAATAA
1 AAAAAACCCTAACCCTAACAAAATAA
*
58433753 AAAAAACCCTAACCCTATCAAAAT
1 AAAAAACCCTAACCCTAACAAAAT
58433777 TTTTCTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.58, C:0.26, G:0.00, T:0.16
Consensus pattern (26 bp):
AAAAAACCCTAACCCTAACAAAATAA
Found at i:58434429 original size:15 final size:16
Alignment explanation
Indices: 58434403--58434433 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
58434393 AAAAATCATA
58434403 AGCCCAGGCCCGGCCC
1 AGCCCAGGCCCGGCCC
58434419 AGCCC-GGCCCGGCCC
1 AGCCCAGGCCCGGCCC
58434434 TTTTTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.10, C:0.58, G:0.32, T:0.00
Consensus pattern (16 bp):
AGCCCAGGCCCGGCCC
Found at i:58434493 original size:11 final size:11
Alignment explanation
Indices: 58434473--58434541 Score: 72
Period size: 11 Copynumber: 6.4 Consensus size: 11
58434463 TAAAAATTAA
58434473 AAAAAGTATTTT
1 AAAAA-TATTTT
58434485 AAAAATATTTT
1 AAAAATATTTT
**
58434496 --AAA-ATTAA
1 AAAAATATTTT
58434504 AAAAAGTATTTT
1 AAAAA-TATTTT
*
58434516 AAAAGTATTTT
1 AAAAATATTTT
58434527 AAAAATATTTT
1 AAAAATATTTT
58434538 AAAA
1 AAAA
58434542 TTAAAAAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
8 3 0.06
9 3 0.06
10 3 0.06
11 26 0.55
12 12 0.26
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:58434503 original size:31 final size:31
Alignment explanation
Indices: 58434458--58434530 Score: 128
Period size: 31 Copynumber: 2.3 Consensus size: 31
58434448 CCCAAAAATT
58434458 TATTTTAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATTAAAAAAAGTATTTTAAAAA
*
58434490 TATTTTAAAATTAAAAAAAGTATTTTAAAAG
1 TATTTTAAAATTAAAAAAAGTATTTTAAAAA
58434521 TATTTTAAAA
1 TATTTTAAAA
58434531 ATATTTTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
31 34 0.85
32 6 0.15
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (31 bp):
TATTTTAAAATTAAAAAAAGTATTTTAAAAA
Found at i:58446786 original size:57 final size:57
Alignment explanation
Indices: 58446698--58446808 Score: 206
Period size: 57 Copynumber: 1.9 Consensus size: 57
58446688 ATATTAGAAA
58446698 ATACACCCATTAGAGATTAGAACTCATAACACATTTAGAGAATATTT-TGTTTACGTT
1 ATACACCCATTAGAGATTAGAACTCATAACACATTTAGAGAAT-TTTGTGTTTACGTT
58446755 ATACACCCATTAGAGATTAGAACTCATAACACATTTAGAGAATTTTGTGTTTAC
1 ATACACCCATTAGAGATTAGAACTCATAACACATTTAGAGAATTTTGTGTTTAC
58446809 ATTTTGAGAG
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
56 3 0.06
57 50 0.94
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (57 bp):
ATACACCCATTAGAGATTAGAACTCATAACACATTTAGAGAATTTTGTGTTTACGTT
Found at i:58457299 original size:22 final size:22
Alignment explanation
Indices: 58457271--58457344 Score: 112
Period size: 22 Copynumber: 3.4 Consensus size: 22
58457261 TATTTTCCTC
*
58457271 CTCTCATGTTTCACGTACTAAG
1 CTCTCATGTTTAACGTACTAAG
58457293 CTCTCATGTTTAACGTACTAAG
1 CTCTCATGTTTAACGTACTAAG
* *
58457315 CTCTCATGTTTAACGAACTAAA
1 CTCTCATGTTTAACGTACTAAG
*
58457337 CCCTCATG
1 CTCTCATG
58457345 GCTAAGATAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.34
Consensus pattern (22 bp):
CTCTCATGTTTAACGTACTAAG
Found at i:58463611 original size:24 final size:24
Alignment explanation
Indices: 58463549--58463624 Score: 73
Period size: 24 Copynumber: 3.1 Consensus size: 24
58463539 AGCTTCTTGA
**
58463549 TTAATGGCTCTCCAGAA-CTTCCCG
1 TTAATGGCTCT-TTGAAGCTTCCCG
* *
58463573 ATATATGGCTATTTGAAGCTTCCCG
1 TTA-ATGGCTCTTTGAAGCTTCCCG
* *
58463598 TTAATGGCTCTTTGGAGCTACCCG
1 TTAATGGCTCTTTGAAGCTTCCCG
58463622 TTA
1 TTA
58463625 TTACCTCGTA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
24 26 0.62
25 16 0.38
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.34
Consensus pattern (24 bp):
TTAATGGCTCTTTGAAGCTTCCCG
Found at i:58463722 original size:25 final size:25
Alignment explanation
Indices: 58463661--58463716 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
58463651 GGCTCTTATG
*
58463661 AGCTTCCCGTTATACAGCCCGGATA
1 AGCTTCCCGTTATACAGCCCGAATA
58463686 AGCTTCCCGTTATACAGCCCGAATA
1 AGCTTCCCGTTATACAGCCCGAATA
58463711 AGCTTC
1 AGCTTC
58463717 TTGTTACATG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (25 bp):
AGCTTCCCGTTATACAGCCCGAATA
Found at i:58463736 original size:25 final size:25
Alignment explanation
Indices: 58463708--58463755 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
58463698 TACAGCCCGA
* *
58463708 ATAAGCTTCTTGTTACATGGCTCAC
1 ATAAGCTTCCTATTACATGGCTCAC
*
58463733 ATAAGCTTCCTATTATATGGCTC
1 ATAAGCTTCCTATTACATGGCTC
58463756 GAGAGATGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.38
Consensus pattern (25 bp):
ATAAGCTTCCTATTACATGGCTCAC
Found at i:58463766 original size:12 final size:12
Alignment explanation
Indices: 58463749--58463773 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
58463739 TTCCTATTAT
58463749 ATGGCTCGAGAG
1 ATGGCTCGAGAG
58463761 ATGGCTCGAGAG
1 ATGGCTCGAGAG
58463773 A
1 A
58463774 GGGCATCCCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.16, G:0.40, T:0.16
Consensus pattern (12 bp):
ATGGCTCGAGAG
Found at i:58466001 original size:33 final size:35
Alignment explanation
Indices: 58465947--58466025 Score: 83
Period size: 33 Copynumber: 2.3 Consensus size: 35
58465937 GCCGTGTCGC
*
58465947 CAAGCCATGTGAACCCAAATTT-TACCTAAA-AAT
1 CAAGCCATTTGAACCCAAATTTATACCTAAACAAT
* * *
58465980 CAAGCCATTTGAAGTCC-AATTTATATCTAAACATT
1 CAAGCCATTTGAA-CCCAAATTTATACCTAAACAAT
*
58466015 CAAACCATTTG
1 CAAGCCATTTG
58466026 GGAACACATT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
33 17 0.45
34 9 0.24
35 12 0.32
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.29
Consensus pattern (35 bp):
CAAGCCATTTGAACCCAAATTTATACCTAAACAAT
Found at i:58469425 original size:28 final size:29
Alignment explanation
Indices: 58469377--58469446 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 29
58469367 AGGGGTCCGA
*
58469377 TGCCGCCTGACAACATTCCTCCAAAT-GG
1 TGCCGCCTGACAACATCCCTCCAAATGGG
* ** **
58469405 TGTCGCCTGACAATGTCCCTCCACTTGGG
1 TGCCGCCTGACAACATCCCTCCAAATGGG
58469434 TGCCGCCTGACAA
1 TGCCGCCTGACAA
58469447 ATCTCTTCCA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
28 20 0.59
29 14 0.41
ACGTcount: A:0.20, C:0.36, G:0.21, T:0.23
Consensus pattern (29 bp):
TGCCGCCTGACAACATCCCTCCAAATGGG
Found at i:58487472 original size:21 final size:20
Alignment explanation
Indices: 58487444--58487533 Score: 103
Period size: 21 Copynumber: 4.4 Consensus size: 20
58487434 GGGCCAATGG
*
58487444 GTAA-TTTTGTATGTATATT
1 GTAATTTTTGTATGAATATT
58487463 GTAACTTTTTGTATGAATATT
1 GTAA-TTTTTGTATGAATATT
* *
58487484 GTAATTATTTTATAATTAATATT
1 GTAA-T-TTTTGT-ATGAATATT
58487507 GTAA-TTTTGTATGAATATT
1 GTAATTTTTGTATGAATATT
58487526 GTAATTTT
1 GTAATTTT
58487534 GTAATTTTAT
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
19 16 0.27
20 8 0.13
21 19 0.32
22 5 0.08
23 12 0.20
ACGTcount: A:0.31, C:0.01, G:0.12, T:0.56
Consensus pattern (20 bp):
GTAATTTTTGTATGAATATT
Found at i:58487525 original size:19 final size:19
Alignment explanation
Indices: 58487444--58487577 Score: 106
Period size: 19 Copynumber: 6.3 Consensus size: 19
58487434 GGGCCAATGG
*
58487444 GTAATTTTGTATGTATATT
1 GTAATTTTGTATGAATATT
58487463 GTAACTTTTTGTATGAATATT
1 GTAA--TTTTGTATGAATATT
* *
58487484 GTAATTATTTTATAATTAATATT
1 GT-A--ATTTTGT-ATGAATATT
58487507 GTAATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
58487526 GTAATTTTGTAATTTTATATGAATATT
1 GTAATTTTG--------TATGAATATT
*
58487553 ATAATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
58487572 GTAATT
1 GTAATT
58487578 ATTTTATAAT
Statistics
Matches: 94, Mismatches: 7, Indels: 28
0.73 0.05 0.22
Matches are distributed among these distances:
19 36 0.38
20 6 0.06
21 16 0.17
22 7 0.07
23 10 0.11
24 1 0.01
27 18 0.19
ACGTcount: A:0.33, C:0.01, G:0.12, T:0.54
Consensus pattern (19 bp):
GTAATTTTGTATGAATATT
Found at i:58487538 original size:27 final size:27
Alignment explanation
Indices: 58487500--58487663 Score: 101
Period size: 27 Copynumber: 6.2 Consensus size: 27
58487490 ATTTTATAAT
*
58487500 TAATATTGTAATTTTGTATGAATATTG
1 TAATTTTGTAATTTTGTATGAATATTG
* *
58487527 TAATTTTGTAATTTTATATGAATATTA
1 TAATTTTGTAATTTTGTATGAATATTG
* *
58487554 TAATTTTGTATGAATATTGTA--ATTATT-
1 TAATTTTG--T-AATTTTGTATGAATATTG
* ** * ** *
58487581 TTATAAT-TAATTTTATATTTATAGTTTT
1 TAATTTTGTAATTTTGTATGAATA--TTG
* *
58487609 TGA-TTAGT-ATTTTGTATGAATATTG
1 TAATTTTGTAATTTTGTATGAATATTG
58487634 TAA--TTGTAATTTTGTATGAATATTG
1 TAATTTTGTAATTTTGTATGAATATTG
58487659 TAATT
1 TAATT
58487664 ATTTTATAAT
Statistics
Matches: 102, Mismatches: 23, Indels: 24
0.68 0.15 0.16
Matches are distributed among these distances:
23 7 0.07
24 4 0.04
25 26 0.25
27 49 0.48
28 8 0.08
29 1 0.01
30 7 0.07
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (27 bp):
TAATTTTGTAATTTTGTATGAATATTG
Found at i:58487587 original size:88 final size:87
Alignment explanation
Indices: 58487444--58488215 Score: 305
Period size: 88 Copynumber: 8.5 Consensus size: 87
58487434 GGGCCAATGG
* * *
58487444 GTAATTTTGTATGTATATTGTAACTTTTTGTATGAATATTGTAATTATTTTATAATTAATATTGT
1 GTAATTTTATATGAATATTATAA--TTTTGTATGAATATTGTAATTATTTTATAATTAAT-TTGT
58487509 AATTTTGTATGAATATTGTAATTTT
63 AATTTTGTATGAATATTGTAATTTT
58487534 GTAATTTTATATGAATATTATAATTTTGTATGAATATTGTAATTATTTTATAATTAATTT-TATA
1 GTAATTTTATATGAATATTATAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTGTA-A
* *
58487598 TTTATAGTTTTTG-AT-TAGT-ATTTT
65 TTT-T-G--TATGAATATTGTAATTTT
** * *
58487622 GT-A-TGAATATTGTA-ATTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGT-
1 GTAATTTTATA-TGAATATTATAATTTTGTATGAATATTGTAATTATTTTATAATTAA-TTTGTA
* * * *
58487683 A--TT-TAT-AGT-TTTTGA-TTA
64 ATTTTGTATGAATATTGTAATTTT
* * * * *
58487701 GT-ATTTTGTATGAATATTTTAATTATTTTAT-AATTAATTTTGTATTTATATTT-T--TTGATT
1 GTAATTTTATATGAATATTATAATT-TTGTATGAA-T-A--TTGTAATTAT-TTTATAATTAATT
*
58487761 AGT-ATTTTGTATGAATATTGTAATTTT
60 TGTAATTTTGTATGAATATTGTAATTTT
* * * * * *
58487788 GTAATTTTGTATGAATAGTGTAATTATTTTATAATTAATTTTGTACTTATAGTTT-T--TT-ATT
1 GTAATTTTATATGAATA-T-T-ATAATTTTGT-ATGAATATTGTAATTAT--TTTATAATTAATT
*
58487849 AGT-ATTTTGTATGAATATTGTAATTTT
60 TGTAATTTTGTATGAATATTGTAATTTT
** * * * * * *
58487876 GT-ATGAATATTAT-AATTTTGTAATTTTATATGAATTTTGTAATTTTGTAATTTTGT-ATGAAT
1 GTAAT-TTTA-TATGAATATTATAATTTTGTATGAATATTGTAA---T-T-ATTTTATAATTAAT
58487938 ATTGTAATATTGTTTGTATGAATATTGTAATTTT
59 -TTGT-A-A-T-TTTGTATGAATATTGTAATTTT
*
58487972 GTAATTTTATATGAATATTGTAATTTTGTAATTTTGTATGAATATTGTAATTATTGTATAATTAA
1 GTAATTTTATATGAATA-T-T-A-----TAATTTTGTATGAATATTGTAATTATTTTATAATTAA
* * **
58488037 TTTTGT-ATTTATAGTTTTGGAT-TAAT-ATTTT
58 -TTTGTAATTT-T-G-TATGAATATTGTAATTTT
** * *
58488068 GT-A-TGAATATTGTAATTTTGTAATTTTGTATGAATATTGTAATTTTATAATTTTGTATGAATA
1 GTAATTTTATA-TG-AATATTATAATTTTGTATGAATATTGTAA---T-T-A-TTT-TAT--A-A
* *
58488131 TTATAATTTTGTAATTTTATATGAATTTTGTAATTTT
54 -T-TAATTT-GTAATTTTGTATGAATATTGTAATTTT
* *
58488168 GTAATTTTGTATGAATATTGTAATATTGTTTGTATGAATATTGTAATT
1 GTAATTTTATATGAATA-T-T-ATAAT-TTTGTATGAATATTGTAATT
58488216 TTGTAATTTT
Statistics
Matches: 524, Mismatches: 72, Indels: 162
0.69 0.09 0.21
Matches are distributed among these distances:
79 13 0.02
80 14 0.03
81 11 0.02
82 4 0.01
83 3 0.01
84 25 0.05
85 13 0.02
86 52 0.10
87 24 0.05
88 127 0.24
89 17 0.03
90 28 0.05
91 14 0.03
92 3 0.01
93 1 0.00
94 8 0.02
95 13 0.02
96 41 0.08
97 8 0.02
98 12 0.02
99 11 0.02
100 26 0.05
101 11 0.02
102 4 0.01
103 3 0.01
104 38 0.07
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (87 bp):
GTAATTTTATATGAATATTATAATTTTGTATGAATATTGTAATTATTTTATAATTAATTTGTAAT
TTTGTATGAATATTGTAATTTT
Found at i:58487706 original size:27 final size:27
Alignment explanation
Indices: 58487676--58487772 Score: 77
Period size: 27 Copynumber: 3.3 Consensus size: 27
58487666 TTTATAATTA
*
58487676 ATTTTGTATTTATAGTTTTTGATTAGT
1 ATTTTGTATTTATAATTTTTGATTAGT
* * * *
58487703 ATTTTGTATGAATATTTTAATTATTTTATAATT
1 ATTTTG--T--AT-TTATAATT-TTTGATTAGT
*
58487736 AATTTTGTATTTATATTTTTTGATTAGT
1 -ATTTTGTATTTATAATTTTTGATTAGT
58487764 ATTTTGTAT
1 ATTTTGTAT
58487773 GAATATTGTA
Statistics
Matches: 53, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
27 15 0.28
28 7 0.13
29 7 0.13
30 2 0.04
31 2 0.04
32 7 0.13
33 7 0.13
34 6 0.11
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (27 bp):
ATTTTGTATTTATAATTTTTGATTAGT
Found at i:58487711 original size:61 final size:61
Alignment explanation
Indices: 58487642--58487785 Score: 270
Period size: 61 Copynumber: 2.4 Consensus size: 61
58487632 TGTAATTGTA
58487642 ATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTTGATTAGT
1 ATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTTGATTAGT
* *
58487703 ATTTTGTATGAATATTTTAATTATTTTATAATTAATTTTGTATTTATATTTTTTGATTAGT
1 ATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTTGATTAGT
58487764 ATTTTGTATGAATATTGTAATT
1 ATTTTGTATGAATATTGTAATT
58487786 TTGTAATTTT
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 80 1.00
ACGTcount: A:0.30, C:0.00, G:0.10, T:0.60
Consensus pattern (61 bp):
ATTTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTTGATTAGT
Found at i:58487794 original size:27 final size:27
Alignment explanation
Indices: 58487764--58488324 Score: 583
Period size: 27 Copynumber: 21.0 Consensus size: 27
58487754 TTTGATTAGT
58487764 ATTTTGTATGAATATTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
*
58487791 ATTTTGTATGAATAGTGTAA---T-T-
1 ATTTTGTATGAATATTGTAATTTTGTA
* * * * *
58487813 ATTTTATAATTAATTTTGTACTTATAGT-
1 ATTTTGT-ATGAATATTGTAATT-TTGTA
* * *
58487841 -TTTT-TATTAGTATTTTGTATGAATATTGTA
1 ATTTTGTA-T-GAATATTG--T-AATTTTGTA
*
58487871 ATTTTGTATGAATATTATAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
* *
58487898 ATTTTATATGAATTTTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
*
58487925 ATTTTGTATGAATATTGTAATATTG--
1 ATTTTGTATGAATATTGTAATTTTGTA
58487950 --TTTGTATGAATATTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
*
58487975 ATTTTATATGAATATTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
58488002 ATTTTGTATGAATATTGTAATTATTGTATA
1 ATTTTGTATGAATATTGTAATT-TTG--TA
* * *
58488032 ATTAATT-T-TGTAT-TTATAGTTTTGGATTAA
1 ATT--TTGTATGAATATTGTAATTTT-G--T-A
58488062 TATTTTGTATGAATATTGTAATTTTGTA
1 -ATTTTGTATGAATATTGTAATTTTGTA
*
58488090 ATTTTGTATGAATATTGTAATTTTATA
1 ATTTTGTATGAATATTGTAATTTTGTA
*
58488117 ATTTTGTATGAATATTATAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
* *
58488144 ATTTTATATGAATTTTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
*
58488171 ATTTTGTATGAATATTGTAATATTG--
1 ATTTTGTATGAATATTGTAATTTTGTA
58488196 --TTTGTATGAATATTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
*
58488221 ATTTTATATGAATATTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
*
58488248 ATTTTGTATGAATATTGTAATATTG--
1 ATTTTGTATGAATATTGTAATTTTGTA
58488273 --TTTGTATGAATATTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
*
58488298 ATTTTATATGAATATTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
58488325 TGAATATTGT
Statistics
Matches: 449, Mismatches: 48, Indels: 74
0.79 0.08 0.13
Matches are distributed among these distances:
22 6 0.01
23 76 0.17
24 1 0.00
25 1 0.00
26 2 0.00
27 296 0.66
28 8 0.02
29 15 0.03
30 18 0.04
31 14 0.03
32 12 0.03
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (27 bp):
ATTTTGTATGAATATTGTAATTTTGTA
Found at i:58487874 original size:19 final size:19
Alignment explanation
Indices: 58487852--58488380 Score: 261
Period size: 19 Copynumber: 28.2 Consensus size: 19
58487842 TTTTATTAGT
58487852 ATTTTGTATGAATATTGTA
1 ATTTTGTATGAATATTGTA
*
58487871 ATTTTGTATGAATATTATA
1 ATTTTGTATGAATATTGTA
**
58487890 ATTTTGTAAT-TTTATATG-A
1 ATTTTGT-ATGAATAT-TGTA
*
58487909 ATTTTG--T-AATTTTGTA
1 ATTTTGTATGAATATTGTA
58487925 ATTTTGTATGAATATTGTAA
1 ATTTTGTATGAATATTGT-A
58487945 TATTGTTTGTATGAATATTGTA
1 -A-T-TTTGTATGAATATTGTA
**
58487967 ATTTTGTAAT-TTTATATG-A
1 ATTTTGT-ATGAATAT-TGTA
* *
58487986 ATATTG--T-AATTTTGTA
1 ATTTTGTATGAATATTGTA
58488002 ATTTTGTATGAATATTGTA
1 ATTTTGTATGAATATTGTA
58488021 ATTATTGTAT--A-A-T-TA
1 ATT-TTGTATGAATATTGTA
* *
58488036 ATTTTGTATTTATAGTTTTGGATTAA
1 ATTTTGTA-TGA-A-TATT-G--T-A
58488062 TATTTTGTATGAATATTGTA
1 -ATTTTGTATGAATATTGTA
*
58488082 ATTTTG--T-AATTTTGTATGA
1 ATTTTGTATGAATATTG--T-A
* * *
58488101 ATATTG--T-AATTTTATA
1 ATTTTGTATGAATATTGTA
*
58488117 ATTTTGTATGAATATTATA
1 ATTTTGTATGAATATTGTA
**
58488136 ATTTTGTAAT-TTTATATG-A
1 ATTTTGT-ATGAATAT-TGTA
*
58488155 ATTTTG--T-AATTTTGTA
1 ATTTTGTATGAATATTGTA
58488171 ATTTTGTATGAATATTGTAA
1 ATTTTGTATGAATATTGT-A
58488191 TATTGTTTGTATGAATATTGTA
1 -A-T-TTTGTATGAATATTGTA
**
58488213 ATTTTGTAAT-TTTATATG-A
1 ATTTTGT-ATGAATAT-TGTA
* *
58488232 ATATTG--T-AATTTTGTA
1 ATTTTGTATGAATATTGTA
58488248 ATTTTGTATGAATATTGTA
1 ATTTTGTATGAATATTGTA
* *
58488267 ATATTGTTTG--TA-TG-A
1 ATTTTGTATGAATATTGTA
* *
58488282 ATATTG--T-AATTTTGTA
1 ATTTTGTATGAATATTGTA
*
58488298 ATTTTATATGAATATTGTA
1 ATTTTGTATGAATATTGTA
58488317 ATTTTGTATGAATATTGTAA
1 ATTTTGTATGAATATTGT-A
58488337 TATTGTTTGTATGAATATTGTA
1 -A-T-TTTGTATGAATATTGTA
58488359 ATTTTGTATGAATATTGTA
1 ATTTTGTATGAATATTGTA
58488378 ATT
1 ATT
58488381 ATTCTATAAT
Statistics
Matches: 401, Mismatches: 46, Indels: 126
0.70 0.08 0.22
Matches are distributed among these distances:
13 1 0.00
14 6 0.01
15 23 0.06
16 58 0.14
17 5 0.01
18 9 0.02
19 193 0.48
20 27 0.07
21 8 0.02
22 6 0.01
23 49 0.12
24 3 0.01
25 2 0.00
26 3 0.01
27 8 0.02
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (19 bp):
ATTTTGTATGAATATTGTA
Found at i:58487969 original size:77 final size:77
Alignment explanation
Indices: 58487852--58488366 Score: 628
Period size: 77 Copynumber: 6.6 Consensus size: 77
58487842 TTTTATTAGT
* *
58487852 ATTTTGTATGAATATTGT-A-A-T-TTTGTATGAATATTATAATTTTGTAATTTTATATGAATTT
1 ATTTTGTATGAATATTGTAATATTGTTTGTATGAATATTGTAATTTTGTAATTTTATATGAATAT
58487913 TGTAATTTTGTA
66 TGTAATTTTGTA
58487925 ATTTTGTATGAATATTGTAATATTGTTTGTATGAATATTGTAATTTTGTAATTTTATATGAATAT
1 ATTTTGTATGAATATTGTAATATTGTTTGTATGAATATTGTAATTTTGTAATTTTATATGAATAT
58487990 TGTAATTTTGTA
66 TGTAATTTTGTA
* * * * * * ** *
58488002 ATTTTGTATGAATATTGTAATTATTGTAT-AATTAATTTTGT-A-TTTATAGTTTTGGATTAATA
1 ATTTTGTATGAATATTGTAA-TATTGTTTGTATGAATATTGTAATTTTGTAATTTTATATGAATA
58488064 TTTTGTATGAATATTGTAATTTTGTA
65 --TTG--T--A-A---T---TTTGTA
** *
58488090 ATTTTGTATGAATATTGTAATTTTATAATTTTGTATGAATATTATAATTTTGTAATTTTATATGA
1 ATTTTGTATGAATATTGTAA---TAT-TGTTTGTATGAATATTGTAATTTTGTAATTTTATATGA
*
58488155 ATTTTGTAATTTTGTA
62 ATATTGTAATTTTGTA
58488171 ATTTTGTATGAATATTGTAATATTGTTTGTATGAATATTGTAATTTTGTAATTTTATATGAATAT
1 ATTTTGTATGAATATTGTAATATTGTTTGTATGAATATTGTAATTTTGTAATTTTATATGAATAT
58488236 TGTAATTTTGTA
66 TGTAATTTTGTA
58488248 ATTTTGTATGAATATTGTAATATTGTTTGTATGAATATTGTAATTTTGTAATTTTATATG-A-A-
1 ATTTTGTATGAATATTGTAATATTGTTTGTATGAATATTGTAATTTTGTAATTTTATATGAATAT
58488310 --T-A--TTGTA
66 TGTAATTTTGTA
58488317 ATTTTGTATGAATATTGTAATATTGTTTGTATGAATATTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAATATTGTTTGTATGAATATTGTAATTTTGTA
58488367 TGAATATTGT
Statistics
Matches: 390, Mismatches: 28, Indels: 52
0.83 0.06 0.11
Matches are distributed among these distances:
69 55 0.14
71 1 0.00
72 1 0.00
73 18 0.05
74 1 0.00
75 17 0.04
76 3 0.01
77 192 0.49
78 10 0.03
79 1 0.00
81 27 0.07
82 1 0.00
84 1 0.00
85 1 0.00
87 1 0.00
88 27 0.07
90 5 0.01
91 2 0.01
92 11 0.03
93 1 0.00
94 14 0.04
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (77 bp):
ATTTTGTATGAATATTGTAATATTGTTTGTATGAATATTGTAATTTTGTAATTTTATATGAATAT
TGTAATTTTGTA
Found at i:58487995 original size:211 final size:215
Alignment explanation
Indices: 58487764--58488247 Score: 680
Period size: 219 Copynumber: 2.3 Consensus size: 215
58487754 TTTGATTAGT
* *
58487764 ATTTTGTATGAATATTGTAATTTTGTAATTTTGTATGAATAGTGTAATTATTTTATAATTAATTT
1 ATTTTGTATGAATATTGTAATTTTGTAATTTTGTATGAATATTGTAATTATTGTATAATTAATTT
** *
58487829 TGTACTTATAGTTTTTTATTAGTATTTTGTATG-A-A-T-A-TTGTAATTTTGTATGAATATTAT
66 TGTACTTATAGTTTTGGATTAATATTTTGTATGAATATTAATTTGTAATTTTGTATGAATATTAT
* * * *
58487889 AATTTTGTAATTTTATATGAATTTTGTAATTTTGTAATTTTGTATGAATATTGTAATATTG-TTT
131 AATTTTATAATTTTATATGAATATTATAATTTTGTAATTTTATATGAATATTGTAATATTGATTT
*
58487953 GTATGAATATTGTAATTTTG
196 GTATGAATATTGTAATATTG
*
58487973 TAATTTTATATGAATATTGTAATTTTGTAATTTTGTATGAATATTGTAATTATTGTATAATTAAT
1 --ATTTTGTATGAATATTGTAATTTTGTAATTTTGTATGAATATTGTAATTATTGTATAATTAAT
*
58488038 TTTGTATTTATAGTTTTGGATTAATATTTTGTATGAATATTGTAATTTTGTAATTTTGTATGAAT
64 TTTGTACTTATAGTTTTGGATTAATATTTTGTATGAATA-T-TAA-TTTGTAATTTTGTATGAAT
* * * *
58488103 ATTGTAATTTTATAATTTTGTATGAATATTATAATTTTGTAATTTTATATGAATTTTGTAATTTT
126 ATTATAATTTTATAATTTTATATGAATATTATAATTTTGTAATTTTATATGAATATTGTAATATT
58488168 GTAATTTTGTATGAATATTGTAATATTG
191 G--A-TTTGTATGAATATTGTAATATTG
*
58488196 --TTTGTATGAATATTGTAATTTTGTAATTTTATATGAATATTGTAATT-TTGTA
1 ATTTTGTATGAATATTGTAATTTTGTAATTTTGTATGAATATTGTAATTATTGTA
58488248 ATTTTGTATG
Statistics
Matches: 243, Mismatches: 18, Indels: 17
0.87 0.06 0.06
Matches are distributed among these distances:
211 91 0.37
212 1 0.00
213 1 0.00
216 1 0.00
217 1 0.00
218 5 0.02
219 121 0.50
223 22 0.09
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (215 bp):
ATTTTGTATGAATATTGTAATTTTGTAATTTTGTATGAATATTGTAATTATTGTATAATTAATTT
TGTACTTATAGTTTTGGATTAATATTTTGTATGAATATTAATTTGTAATTTTGTATGAATATTAT
AATTTTATAATTTTATATGAATATTATAATTTTGTAATTTTATATGAATATTGTAATATTGATTT
GTATGAATATTGTAATATTG
Found at i:58488076 original size:13 final size:13
Alignment explanation
Indices: 58488036--58488078 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
58488026 TGTATAATTA
*
58488036 ATTTTGTATTTAT
1 ATTTTGTATTAAT
*
58488049 AGTTTTGGATTAAT
1 A-TTTTGTATTAAT
*
58488063 ATTTTGTATGAAT
1 ATTTTGTATTAAT
58488076 ATT
1 ATT
58488079 GTAATTTTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.58
Consensus pattern (13 bp):
ATTTTGTATTAAT
Found at i:58488337 original size:246 final size:249
Alignment explanation
Indices: 58487869--58488363 Score: 765
Period size: 246 Copynumber: 2.0 Consensus size: 249
58487859 ATGAATATTG
58487869 TAATTTTGTATGAATATTATAATTTTGTAATTTTATATGAATTTTGTAATTTTGTAATTTTGTAT
1 TAATTTTGTATGAATATTATAATTTTGTAATTTTATATGAATTTTGTAATTTTGTAATTTTGTAT
58487934 GAATATTGTAATATTGTTTGTATGAATATTGTAATTTTGTAATTTTATATGAATATTGTAATTTT
66 GAATATTGTAATATTGTTTGTATGAATATTGTAATTTTGTAATTTTATATGAATATTGTAATTTT
* * * * *
58487999 GTAATTTTGTATGAATATTGTAATTATTGTATAATTAATTTTGTATTTATAGTTTTGGATTAATA
131 GTAATTTTGTATGAATATTGTAATTATTGTATAATGAATATTGTATTTATAATTTTAGATGAATA
*
58488064 TTTTGTATGAATATTGTAATTTTGT-A-A-T-TTTGTATGAATATTGTAATTTTA
196 TTTTGTATG-ATATTGTAATATTGTAATATTGTTTGTATGAATATTGTAATTTTA
58488115 TAATTTTGTATGAATATTATAATTTTGTAATTTTATATGAATTTTGTAATTTTGTAATTTTGTAT
1 TAATTTTGTATGAATATTATAATTTTGTAATTTTATATGAATTTTGTAATTTTGTAATTTTGTAT
58488180 GAATATTGTAATATTGTTTGTATGAATATTGTAATTTTGTAATTTTATATGAATATTGTAATTTT
66 GAATATTGTAATATTGTTTGTATGAATATTGTAATTTTGTAATTTTATATGAATATTGTAATTTT
* * * *
58488245 GTAATTTTGTATGAATATTGTAA-TATTGTTTGTATGAATATTGTAATTTTGTAATTTTATATGA
131 GTAATTTTGTATGAATATTGTAATTATTGTAT-AATGAATATTGT-A-TTTATAATTTTAGATGA
*
58488309 ATA--TTGTA--ATTTTGTATGAATATTGTAATATTGTTTGTATGAATATTGTAATTTT
193 ATATTTTGTATGATATTG--T-AATATTGTAATATTGTTTGTATGAATATTGTAATTTT
58488364 GTATGAATAT
Statistics
Matches: 228, Mismatches: 11, Indels: 16
0.89 0.04 0.06
Matches are distributed among these distances:
243 5 0.02
245 8 0.04
246 174 0.76
247 2 0.01
248 16 0.07
249 1 0.00
250 22 0.10
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.55
Consensus pattern (249 bp):
TAATTTTGTATGAATATTATAATTTTGTAATTTTATATGAATTTTGTAATTTTGTAATTTTGTAT
GAATATTGTAATATTGTTTGTATGAATATTGTAATTTTGTAATTTTATATGAATATTGTAATTTT
GTAATTTTGTATGAATATTGTAATTATTGTATAATGAATATTGTATTTATAATTTTAGATGAATA
TTTTGTATGATATTGTAATATTGTAATATTGTTTGTATGAATATTGTAATTTTA
Found at i:58488338 original size:27 final size:26
Alignment explanation
Indices: 58488308--58488366 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 26
58488298 ATTTTATATG
58488308 AATATTGTAATTTTGTATGAATATTGT
1 AATATTGTAA-TTTGTATGAATATTGT
58488335 AATATTG---TTTGTATGAATATTGT
1 AATATTGTAATTTGTATGAATATTGT
*
58488358 AATTTTGTA
1 AATATTGTA
58488367 TGAATATTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
23 22 0.76
27 7 0.24
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (26 bp):
AATATTGTAATTTGTATGAATATTGT
Found at i:58488642 original size:15 final size:16
Alignment explanation
Indices: 58488606--58488642 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
58488596 TCATTTAATT
58488606 TTTTATATAATGTAAC
1 TTTTATATAATGTAAC
*
58488622 TTTTATATTATGTAA-
1 TTTTATATAATGTAAC
58488637 TTTTAT
1 TTTTAT
58488643 TTGATTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (16 bp):
TTTTATATAATGTAAC
Found at i:58488742 original size:27 final size:27
Alignment explanation
Indices: 58488707--58488788 Score: 85
Period size: 27 Copynumber: 3.0 Consensus size: 27
58488697 ATAAAATAAT
*
58488707 ACCATTGGCGCCTCTCAACAT-GGCACC
1 ACCAATGGCGCCTCTC-ACATAGGCACC
* * *
58488734 ACTAATGGCACCTCTCAGATAGGCACC
1 ACCAATGGCGCCTCTCACATAGGCACC
* * *
58488761 ACCATTGGCGCCTCTGAGATAGGCACC
1 ACCAATGGCGCCTCTCACATAGGCACC
58488788 A
1 A
58488789 ATACTATGTA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
26 3 0.07
27 43 0.93
ACGTcount: A:0.26, C:0.35, G:0.21, T:0.18
Consensus pattern (27 bp):
ACCAATGGCGCCTCTCACATAGGCACC
Found at i:58488902 original size:52 final size:52
Alignment explanation
Indices: 58488845--58488943 Score: 137
Period size: 52 Copynumber: 1.9 Consensus size: 52
58488835 TTATATTTTA
*
58488845 TAAAAAAAATTTAATA-TAAAATATTCATTGGCGCCTATCTAATAGGCGCCAT
1 TAAAAAAAA-TTAATATTAAAATATTCATTGGCACCTATCTAATAGGCGCCAT
****
58488897 TAAAAAAAATTAATATTTTTTTATTCATTGGCACCTATCTAATAGGC
1 TAAAAAAAATTAATATTAAAATATTCATTGGCACCTATCTAATAGGC
58488944 TCTAATAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
51 6 0.15
52 35 0.85
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.35
Consensus pattern (52 bp):
TAAAAAAAATTAATATTAAAATATTCATTGGCACCTATCTAATAGGCGCCAT
Found at i:58493092 original size:68 final size:67
Alignment explanation
Indices: 58492978--58493109 Score: 196
Period size: 68 Copynumber: 2.0 Consensus size: 67
58492968 TTTATATTTT
* *
58492978 AATTTTGTAATTTATTTTTTTCAAATTTCTTTTAGAAATTAAAATATTTAAATTTTAAGATTTTG
1 AATTTTGTAATTTATTTTTTTCAAATCTCTTTTAGAAATTAAAATATTTAAAATTTAAGATTTTG
58493043 AA
66 AA
*
58493045 AATTTTGGATAATTTATTATTTTT-AAATCT-TTTTGGAAATTAAAATATTTAAAATTTAAGATT
1 AATTTT-G-TAATTTATT-TTTTTCAAATCTCTTTTAGAAATTAAAATATTTAAAATTTAAGATT
58493108 TT
63 TT
58493110 TGAATTAATC
Statistics
Matches: 59, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
67 6 0.10
68 34 0.58
69 14 0.24
70 5 0.08
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (67 bp):
AATTTTGTAATTTATTTTTTTCAAATCTCTTTTAGAAATTAAAATATTTAAAATTTAAGATTTTG
AA
Found at i:58493557 original size:3 final size:3
Alignment explanation
Indices: 58493551--58493575 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
58493541 AATAAATATA
58493551 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
58493576 TTAATTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:58498590 original size:22 final size:21
Alignment explanation
Indices: 58498564--58498634 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 21
58498554 AGTTGAATTT
58498564 ATCTATATAATTTTAATATCA
1 ATCTATATAATTTTAATATCA
*
58498585 AGTCTATA-CATTTTCAA-ATCA
1 A-TCTATATAATTTT-AATATCA
*
58498606 ATCTA-ATATATTTATTATATCA
1 ATCTATATA-ATTT-TAATATCA
58498628 ATCTATA
1 ATCTATA
58498635 ATAAATAGAC
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
19 1 0.03
20 4 0.10
21 16 0.40
22 18 0.45
23 1 0.03
ACGTcount: A:0.41, C:0.13, G:0.01, T:0.45
Consensus pattern (21 bp):
ATCTATATAATTTTAATATCA
Found at i:58498605 original size:21 final size:19
Alignment explanation
Indices: 58498569--58498636 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 19
58498559 AATTTATCTA
58498569 TATAATTTTAATATCAAGTC
1 TATAATTTTAATATCAA-TC
58498589 TATACATTTTCAA-ATCAATC
1 TATA-ATTTT-AATATCAATC
*
58498609 TAATATATTTATTATATCAATC
1 T-ATA-ATTT-TAATATCAATC
58498631 TATAAT
1 TATAAT
58498637 AAATAGACAA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
20 9 0.22
21 21 0.51
22 11 0.27
ACGTcount: A:0.41, C:0.12, G:0.01, T:0.46
Consensus pattern (19 bp):
TATAATTTTAATATCAATC
Found at i:58499606 original size:30 final size:29
Alignment explanation
Indices: 58499545--58499623 Score: 76
Period size: 30 Copynumber: 2.8 Consensus size: 29
58499535 TATAAAAAAT
*
58499545 TTAATAAAT-AAAAAAT-ATATAAAATTA
1 TTAAAAAATAAAAAAATAATATAAAATTA
* *
58499572 TTAAATATTAAATTAAAATAATAT-AAA-TA
1 TTAAAAAATAAA--AAAATAATATAAAATTA
58499601 TTTAAAAAATAAAAAAATAATAT
1 -TTAAAAAATAAAAAAATAATAT
58499624 GAGCAGACTT
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
27 6 0.14
28 12 0.29
29 2 0.05
30 18 0.43
31 4 0.10
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (29 bp):
TTAAAAAATAAAAAAATAATATAAAATTA
Found at i:58506251 original size:6 final size:6
Alignment explanation
Indices: 58506242--58506269 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
58506232 TATATTTATA
58506242 GGATAG GGATAG GGATAG GGATAG GGAT
1 GGATAG GGATAG GGATAG GGATAG GGAT
58506270 CAAAAAGCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.50, T:0.18
Consensus pattern (6 bp):
GGATAG
Found at i:58509154 original size:16 final size:16
Alignment explanation
Indices: 58509133--58509164 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
58509123 GATTTGGGAG
58509133 ATTTTCTTTTTATTTT
1 ATTTTCTTTTTATTTT
58509149 ATTTTCTTTTTATTTT
1 ATTTTCTTTTTATTTT
58509165 TTTCTGTAAT
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:0.12, C:0.06, G:0.00, T:0.81
Consensus pattern (16 bp):
ATTTTCTTTTTATTTT
Found at i:58515047 original size:23 final size:24
Alignment explanation
Indices: 58514999--58515062 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
58514989 TAAGGCTATA
*
58514999 AAAATATTAAAAAACTTAGAAATT
1 AAAATATTAAAAAATTTAGAAATT
*
58515023 AAAATA-TAGAAAAATTTA-AATTT
1 AAAATATTA-AAAAATTTAGAAATT
58515046 AAACATATTAAAAAATT
1 AAA-ATATTAAAAAATT
58515063 AAAGAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
23 9 0.26
24 24 0.69
25 2 0.06
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (24 bp):
AAAATATTAAAAAATTTAGAAATT
Found at i:58520222 original size:20 final size:20
Alignment explanation
Indices: 58520163--58520249 Score: 59
Period size: 21 Copynumber: 4.2 Consensus size: 20
58520153 TTCTGTTTTA
* *
58520163 TTTTATTTTTACTCTT-TTAT
1 TTTTATGTTTAATCTTGTT-T
* * *
58520183 TTTTATTATTTCATCGTGTTT
1 TTTTA-TGTTTAATCTTGTTT
58520204 TTTTATGTTTAATCTTGTTT
1 TTTTATGTTTAATCTTGTTT
* * * *
58520224 TTATTTTGTTTGATTTTATTT
1 TT-TTATGTTTAATCTTGTTT
58520245 TTTTA
1 TTTTA
58520250 ACTTTATTAT
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
20 21 0.40
21 29 0.56
22 2 0.04
ACGTcount: A:0.15, C:0.06, G:0.07, T:0.72
Consensus pattern (20 bp):
TTTTATGTTTAATCTTGTTT
Found at i:58531548 original size:24 final size:24
Alignment explanation
Indices: 58531521--58531567 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 24
58531511 ACTTCGCAAA
58531521 TTTTTTTACAATTATGGT-TTAAATT
1 TTTTTTTA-AATTA-GGTCTTAAATT
58531546 TTTTTTTAAATTAGGTCTTAAA
1 TTTTTTTAAATTAGGTCTTAAA
58531568 CTTGATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 3 0.14
24 10 0.48
25 8 0.38
ACGTcount: A:0.30, C:0.04, G:0.09, T:0.57
Consensus pattern (24 bp):
TTTTTTTAAATTAGGTCTTAAATT
Found at i:58532234 original size:14 final size:14
Alignment explanation
Indices: 58532189--58532234 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
58532179 TTGACCTAAA
58532189 AAAAATATTTA-T-
1 AAAAATATTTATTC
58532201 AAAAATAATTCTAGTTC
1 AAAAAT-ATT-TA-TTC
58532218 AAAAATATTTATTC
1 AAAAATATTTATTC
58532232 AAA
1 AAA
58532235 TGATCTGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
12 6 0.21
13 3 0.10
14 8 0.28
15 2 0.07
16 4 0.14
17 6 0.21
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (14 bp):
AAAAATATTTATTC
Found at i:58534321 original size:24 final size:24
Alignment explanation
Indices: 58534281--58534349 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
58534271 TTATTTTCTT
58534281 AATAATTAT-TT-A-ATTAAATAA
1 AATAATTATATTAATATTAAATAA
*
58534302 AA-ACTGTATATTAATATTAAATAA
1 AATAAT-TATATTAATATTAAATAA
*
58534326 AATAATTATATTAATATAAAATAA
1 AATAATTATATTAATATTAAATAA
58534350 CCCCCCCCCT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
20 2 0.05
21 5 0.12
22 2 0.05
23 1 0.03
24 28 0.70
25 2 0.05
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (24 bp):
AATAATTATATTAATATTAAATAA
Found at i:58534879 original size:23 final size:23
Alignment explanation
Indices: 58534852--58534903 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
58534842 GAGGGTTTTA
58534852 TTTTATTTAATATTAAT-ATAATT
1 TTTTATTTAAT-TTAATAATAATT
* * *
58534875 TTTTACTTAATTTTATAATTATT
1 TTTTATTTAATTTAATAATAATT
58534898 TTTTAT
1 TTTTAT
58534904 AATTTATTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTTATTTAATTTAATAATAATT
Found at i:58537827 original size:37 final size:37
Alignment explanation
Indices: 58537786--58537860 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
58537776 TCTCAGCAAA
*
58537786 TGGATTTTATTAATTATAGAAAGGTACAACTAAGAGG
1 TGGATTTTATTAATTATAAAAAGGTACAACTAAGAGG
58537823 TGGATTTTATTAATTATAAAAAGGTACAACTAAGAGG
1 TGGATTTTATTAATTATAAAAAGGTACAACTAAGAGG
58537860 T
1 T
58537861 ATGTTATGGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.33
Consensus pattern (37 bp):
TGGATTTTATTAATTATAAAAAGGTACAACTAAGAGG
Found at i:58546045 original size:3 final size:3
Alignment explanation
Indices: 58546037--58546079 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
58546027 TTACAATCAT
58546037 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
58546080 TAAATTTTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:58546735 original size:22 final size:22
Alignment explanation
Indices: 58546697--58546740 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
58546687 TCTCTTTCTC
*
58546697 TGTTTCTATTCTGTTCTTCTTT
1 TGTTTCTATTCTGTTCTACTTT
*
58546719 TGTTTCTTTGTCT-TTCTACTTT
1 TGTTTCTAT-TCTGTTCTACTTT
58546741 ACTTACTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.05, C:0.18, G:0.09, T:0.68
Consensus pattern (22 bp):
TGTTTCTATTCTGTTCTACTTT
Found at i:58546916 original size:5 final size:5
Alignment explanation
Indices: 58546908--58546972 Score: 82
Period size: 5 Copynumber: 13.2 Consensus size: 5
58546898 TATTTAATTT
*
58546908 ATATA ATATA ATATA ATACA ATATA ATATA ATATA ATATA TTATATA ATA-A
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA --ATATA ATATA
58546959 A-ATA ATAT- ATATA A
1 ATATA ATATA ATATA A
58546973 AACATAAAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
3 1 0.02
4 8 0.15
5 39 0.74
7 5 0.09
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:58552055 original size:18 final size:18
Alignment explanation
Indices: 58552032--58552075 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
58552022 AATTTTTATG
*
58552032 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGGATA
58552050 ATTGGGTTGGGTTGGATA
1 ATTGGGTTGGGTTGGATA
*
58552068 CTTGGGTT
1 ATTGGGTT
58552076 TGGATTGAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.11, C:0.02, G:0.45, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGGATA
Found at i:58555367 original size:26 final size:26
Alignment explanation
Indices: 58555334--58555396 Score: 92
Period size: 26 Copynumber: 2.4 Consensus size: 26
58555324 TTTACTTGAG
58555334 TAAAATTTTGACAATTTTACCCTCT-A
1 TAAAATTTTGACAATTTTACCC-CTAA
**
58555360 TAAAATTTTGATGATTTTACCCCTAA
1 TAAAATTTTGACAATTTTACCCCTAA
58555386 TAAAATTTTGA
1 TAAAATTTTGA
58555397 GAAATTCGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
25 2 0.06
26 32 0.94
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (26 bp):
TAAAATTTTGACAATTTTACCCCTAA
Found at i:58562780 original size:2 final size:2
Alignment explanation
Indices: 58562775--58562802 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
58562765 ATATAAGTTC
58562775 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58562803 TTAAGTATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58563037 original size:18 final size:18
Alignment explanation
Indices: 58563009--58563043 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
58562999 AATCGTTTCG
58563009 TACCATATTTGTATACATA
1 TACCATATTTGTA-ACATA
58563028 TACC-TATTTGTAACAT
1 TACCATATTTGTAACAT
58563044 GTATTTAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 8 0.50
19 4 0.25
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (18 bp):
TACCATATTTGTAACATA
Found at i:58575250 original size:26 final size:25
Alignment explanation
Indices: 58575207--58575291 Score: 161
Period size: 25 Copynumber: 3.4 Consensus size: 25
58575197 GAGTACAATC
58575207 TTTAAAAGGTTGGCAGATTCTCATA
1 TTTAAAAGGTTGGCAGATTCTCATA
58575232 TTTAAAAGGATTGGCAGATTCTCATA
1 TTTAAAAGG-TTGGCAGATTCTCATA
58575258 TTTAAAAGGTTGGCAGATTCTCATA
1 TTTAAAAGGTTGGCAGATTCTCATA
58575283 TTTAAAAGG
1 TTTAAAAGG
58575292 AACCCATATT
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
25 34 0.58
26 25 0.42
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.35
Consensus pattern (25 bp):
TTTAAAAGGTTGGCAGATTCTCATA
Found at i:58576414 original size:31 final size:31
Alignment explanation
Indices: 58576355--58576414 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
58576345 GGAGGTGGGA
*
58576355 TGGGAAGGGAATAAAAGTTTTAGGGAAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGAAAAAG
*
58576386 TGGG-AGGGAGTAAAAATTTT-GGGAGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGA-AAAA
58576415 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 4 0.15
30 18 0.69
31 4 0.15
ACGTcount: A:0.43, C:0.00, G:0.37, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGAAAAAG
Found at i:58576825 original size:10 final size:10
Alignment explanation
Indices: 58576810--58576835 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
58576800 CCCCTACTAA
58576810 AGAGAGGGAG
1 AGAGAGGGAG
58576820 AGAGAGGGAG
1 AGAGAGGGAG
58576830 AGAGAG
1 AGAGAG
58576836 AGGAAGGGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (10 bp):
AGAGAGGGAG
Found at i:58579754 original size:18 final size:17
Alignment explanation
Indices: 58579731--58579764 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
58579721 TAATTAAATG
58579731 ATGTAATTATTATTTTTT
1 ATGTAATTATT-TTTTTT
58579749 ATGTAATTATTTTTTT
1 ATGTAATTATTTTTTT
58579765 AAATTTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (17 bp):
ATGTAATTATTTTTTTT
Done.