Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004507.1 Hibiscus syriacus cultivar Beakdansim tig00009942_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1776135
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 8
Found at i:624144 original size:17 final size:16
Alignment explanation
Indices: 624117--624151 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
624107 ATATTTTTAA
624117 TATTTTGTATTTAATT
1 TATTTTGTATTTAATT
*
624133 TATTTATGTATTTTATT
1 TATTT-TGTATTTAATT
624150 TA
1 TA
624152 ATTAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.69
Consensus pattern (16 bp):
TATTTTGTATTTAATT
Found at i:626214 original size:127 final size:119
Alignment explanation
Indices: 625952--626215 Score: 255
Period size: 127 Copynumber: 2.1 Consensus size: 119
625942 CCGCCACCTT
*
625952 CATAGAGTTTTATGACCCTCCTGGAGGCTATTATGGGTCTATGTTTGCAGATCCGACTTGGGTTC
1 CATACAGTTTTATGACCCTCCTGGAGGCTATTATGGGTCTATGTTTGCAGATCCGACTTGGGTTC
* * * * * *
626017 ATACGATATTTGGCGGGTTCATCGCCTTCACCTGGTTTTATGATCCCGCCGCCGCCACCTT
66 ATACGATATTTGGCGGGTTCA-CGCCTTCACC-----TCATGAT-CCGCAGCAGACACATC
*
626078 CATAGAGTTTTATGACCCCTCCTGGAGGCTATTATGGGTCTATGTTTGCAGATCCGACTTGGGAT
1 CATACAGTTTTATGA-CCCTCCTGGAGGCTATTATGGGTCTATGTTTGCAGATCCGACTTGGG-T
*
626143 TCATATACTAGATATTTGGCGGGTTCA-GCCTCATCACC-CATGGT-CGCAGCATAGACACATC
64 TC--ATAC--GATATTTGGCGGGTTCACGCCT--TCACCTCATGATCCGCAGC--AGACACATC
*
626204 CTGTACAGTTTT
1 C-ATACAGTTTT
626216 CACACTCAGC
Statistics
Matches: 118, Mismatches: 9, Indels: 21
0.80 0.06 0.14
Matches are distributed among these distances:
124 5 0.04
126 25 0.21
127 55 0.47
128 3 0.03
130 8 0.07
132 22 0.19
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.33
Consensus pattern (119 bp):
CATACAGTTTTATGACCCTCCTGGAGGCTATTATGGGTCTATGTTTGCAGATCCGACTTGGGTTC
ATACGATATTTGGCGGGTTCACGCCTTCACCTCATGATCCGCAGCAGACACATC
Found at i:626541 original size:13 final size:12
Alignment explanation
Indices: 626518--626567 Score: 55
Period size: 13 Copynumber: 3.9 Consensus size: 12
626508 TTGTATTTAT
626518 TACTTTTTATTG
1 TACTTTTTATTG
*
626530 TAGTTGTTTATTG
1 TACTT-TTTATTG
*
626543 GACTTTTTATTG
1 TACTTTTTATTG
626555 TAACTTTATTATT
1 T-ACTTT-TTATT
626568 ATTTATCATT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
12 11 0.35
13 15 0.48
14 5 0.16
ACGTcount: A:0.20, C:0.06, G:0.12, T:0.62
Consensus pattern (12 bp):
TACTTTTTATTG
Found at i:630611 original size:21 final size:21
Alignment explanation
Indices: 630581--630620 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
630571 TATCAAGTTT
*
630581 ATTCCGTCATCCATAACAATC
1 ATTCCATCATCCATAACAATC
*
630602 ATTCCATCATTCATAACAA
1 ATTCCATCATCCATAACAA
630621 ATGTATTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.30, G:0.03, T:0.30
Consensus pattern (21 bp):
ATTCCATCATCCATAACAATC
Found at i:631668 original size:29 final size:31
Alignment explanation
Indices: 631621--631684 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 31
631611 TTATATCATC
*
631621 ATCACTAAACTTTCAAAATTTTCA-A-TTTA
1 ATCACTAAACTTTCAAAATTCTCATATTTTA
* **
631650 ATCACTTAACTTTTGAAATTCTCATATTTTA
1 ATCACTAAACTTTCAAAATTCTCATATTTTA
631681 ATCA
1 ATCA
631685 TCATGACTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 20 0.69
30 1 0.03
31 8 0.28
ACGTcount: A:0.38, C:0.17, G:0.02, T:0.44
Consensus pattern (31 bp):
ATCACTAAACTTTCAAAATTCTCATATTTTA
Found at i:631772 original size:14 final size:14
Alignment explanation
Indices: 631753--631808 Score: 60
Period size: 15 Copynumber: 3.9 Consensus size: 14
631743 TTTTATTAAT
631753 ATATTAATAAAATA
1 ATATTAATAAAATA
*
631767 ATATTAATTAAATTA
1 ATATTAA-TAAAATA
* *
631782 AAATT-TTAAAATTA
1 ATATTAATAAAA-TA
631796 ATATTAATAAAAT
1 ATATTAATAAAAT
631809 TTAGTACAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
13 4 0.12
14 14 0.42
15 15 0.45
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATTAATAAAATA
Found at i:631842 original size:23 final size:23
Alignment explanation
Indices: 631746--631844 Score: 86
Period size: 23 Copynumber: 4.4 Consensus size: 23
631736 ATTATTATTT
631746 TATTAATATATTAATAAAA--TAA
1 TATTAATATA-TAATAAAATTTAA
631768 TATTAAT-TA-AATTAAAATTTTAA
1 TATTAATATATAA-TAAAA-TTTAA
* *
631791 AATTAATAT-TAATAAAATTTAG
1 TATTAATATATAATAAAATTTAA
*
631813 TA-CAATATCATAATAAAA-TTAA
1 TATTAATAT-ATAATAAAATTTAA
631835 TATTAATATA
1 TATTAATATA
631845 ATGCATATCA
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
19 2 0.03
20 5 0.08
21 7 0.11
22 18 0.29
23 27 0.44
24 3 0.05
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (23 bp):
TATTAATATATAATAAAATTTAA
Found at i:634071 original size:15 final size:14
Alignment explanation
Indices: 634038--634071 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
634028 CCTTATCTCA
634038 TTATTTTTTAAAAT
1 TTATTTTTTAAAAT
634052 TTATTTTTTAAAAT
1 TTATTTTTTAAAAT
634066 TGTATT
1 T-TATT
634072 AAAAATCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (14 bp):
TTATTTTTTAAAAT
Found at i:634743 original size:195 final size:190
Alignment explanation
Indices: 634416--634804 Score: 699
Period size: 195 Copynumber: 2.0 Consensus size: 190
634406 AAAGTTTTTA
*
634416 TTTTTAGTTTGAAACTTTGGAAAATTTTATATTTTTCTCTATATATATATATAAGAAATTTTCTA
1 TTTTTAGTTTGAAACTTTGGAAAATTTTATATTTTTCTATATATATATATATAAGAAATTTTCTA
634481 ATTTTATATTAATTTGTATTTTCATGATTTGTTTAATTTTTTTTATAATTATATAATTATAAGTT
66 ATTTTATATTAATTTGTATTTTCATGATTTGTTTAATTTTTTTTATAATTATATAATTATAAGTT
634546 AACGCGGTCTCATGTA-TGTAGTTTGCTTGTTTTAAAGCAGTAAATAAATTAAATTGCTCC
131 AACGCGGTCTCATGTAGTGTA-TTTGCTTGTTTTAAAGCAGTAAATAAATTAAATTGCTCC
634606 TTTTTAGTTTGAAACTTTGGAAAATTTTATTATTTTTCTATATATATATATATAAGAAATTTTCT
1 TTTTTAGTTTGAAACTTTGGAAAATTTTA-TATTTTTCTATATATATATATATAAGAAATTTTCT
634671 AATTTTTATGATTAATTTTTGTATTTTCATGATTTGTTTAATTTTTTTTATAATTATATAATTAT
65 AA-TTTTAT-ATTAA--TTTGTATTTTCATGATTTGTTTAATTTTTTTTATAATTATATAATTAT
634736 AAGTTAACGCGGTCTCATGTAGTTGTATTTGCTTGTTTTAAAGCAGTAAATAAATTAAATTGCTC
126 AAGTTAACGCGGTCTCATGTAG-TGTATTTGCTTGTTTTAAAGCAGTAAATAAATTAAATTGCTC
634801 C
190 C
634802 TTT
1 TTT
634805 CTTACAGGTA
Statistics
Matches: 191, Mismatches: 1, Indels: 8
0.95 0.00 0.04
Matches are distributed among these distances:
190 29 0.15
191 36 0.19
192 6 0.03
193 5 0.03
195 69 0.36
196 42 0.22
197 4 0.02
ACGTcount: A:0.31, C:0.07, G:0.11, T:0.51
Consensus pattern (190 bp):
TTTTTAGTTTGAAACTTTGGAAAATTTTATATTTTTCTATATATATATATATAAGAAATTTTCTA
ATTTTATATTAATTTGTATTTTCATGATTTGTTTAATTTTTTTTATAATTATATAATTATAAGTT
AACGCGGTCTCATGTAGTGTATTTGCTTGTTTTAAAGCAGTAAATAAATTAAATTGCTCC
Found at i:634906 original size:2 final size:2
Alignment explanation
Indices: 634899--634948 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
634889 AATGATTTTG
634899 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
634941 TA TA TA TA
1 TA TA TA TA
634949 GAGAGAGAGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:635850 original size:18 final size:18
Alignment explanation
Indices: 635816--635853 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
635806 ATATATTTTT
*
635816 TAATATTTTTTGGTAAAA
1 TAATATTTTTTGCTAAAA
635834 TAATATTTTTAT-CTAAAA
1 TAATATTTTT-TGCTAAAA
635852 TA
1 TA
635854 TTAATTTCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (18 bp):
TAATATTTTTTGCTAAAA
Found at i:636469 original size:11 final size:12
Alignment explanation
Indices: 636427--636480 Score: 83
Period size: 12 Copynumber: 4.6 Consensus size: 12
636417 GTTATTTAAA
*
636427 CGGGTATTGGGC
1 CGGGTATTGGGT
636439 CGGGTATTGGGT
1 CGGGTATTGGGT
636451 CGGGTATTGGGT
1 CGGGTATTGGGT
*
636463 C-GGTATTGGGC
1 CGGGTATTGGGT
636474 CGGGTAT
1 CGGGTAT
636481 ATATATATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
11 10 0.26
12 29 0.74
ACGTcount: A:0.09, C:0.13, G:0.48, T:0.30
Consensus pattern (12 bp):
CGGGTATTGGGT
Found at i:636471 original size:23 final size:24
Alignment explanation
Indices: 636427--636480 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 24
636417 GTTATTTAAA
*
636427 CGGGTATTGGGCCGGGTATTGGGT
1 CGGGTATTGGGCCGGGTATTGGGC
*
636451 CGGGTATTGGGTC-GGTATTGGGC
1 CGGGTATTGGGCCGGGTATTGGGC
636474 CGGGTAT
1 CGGGTAT
636481 ATATATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
23 16 0.57
24 12 0.43
ACGTcount: A:0.09, C:0.13, G:0.48, T:0.30
Consensus pattern (24 bp):
CGGGTATTGGGCCGGGTATTGGGC
Found at i:636542 original size:24 final size:24
Alignment explanation
Indices: 636479--636542 Score: 85
Period size: 24 Copynumber: 2.6 Consensus size: 24
636469 TGGGCCGGGT
636479 ATATATATATATATATTTAAATTAA
1 ATATATATATAT-TATTTAAATTAA
*
636504 ATATATATATTTTATTTAAATTAA
1 ATATATATATATTATTTAAATTAA
*
636528 ATTTAT-TAATATTAT
1 ATATATAT-ATATTAT
636543 ATATATATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
23 1 0.03
24 23 0.66
25 11 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
ATATATATATATTATTTAAATTAA
Found at i:638569 original size:30 final size:31
Alignment explanation
Indices: 638526--638583 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
638516 AATAAAAAAA
* * *
638526 TTAATTTATTTAT-AAAAAAGCTCTAAACTT
1 TTAATTAAATTATAAAAAAAACTCTAAACTT
638556 TTAATTAAATTATAAAAAAAACTCTAAA
1 TTAATTAAATTATAAAAAAAACTCTAAA
638584 AAACTAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 11 0.46
31 13 0.54
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.38
Consensus pattern (31 bp):
TTAATTAAATTATAAAAAAAACTCTAAACTT
Found at i:639396 original size:22 final size:22
Alignment explanation
Indices: 639341--639398 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
639331 GACAAAATCT
639341 TTATTGACAACAAT-AACAGCA
1 TTATTGACAACAATAAACAGCA
* *
639362 TCT-TT-ATAACAATAAACTGCA
1 T-TATTGACAACAATAAACAGCA
639383 TTATTGACAACAATAA
1 TTATTGACAACAATAA
639399 CAACATCTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
20 8 0.27
21 12 0.40
22 10 0.33
ACGTcount: A:0.47, C:0.17, G:0.07, T:0.29
Consensus pattern (22 bp):
TTATTGACAACAATAAACAGCA
Found at i:640210 original size:17 final size:16
Alignment explanation
Indices: 640187--640225 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
640177 AAACAATATC
* *
640187 TAATTTTGATATAATA
1 TAATTTTCAAATAATA
640203 TGAATTTTCAAATAATA
1 T-AATTTTCAAATAATA
640220 TAATTT
1 TAATTT
640226 GTTAAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (16 bp):
TAATTTTCAAATAATA
Found at i:642854 original size:2 final size:2
Alignment explanation
Indices: 642847--642876 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
642837 TTATAATCCG
642847 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
642877 TTAAATTTTA
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):
AT
Found at i:642999 original size:17 final size:17
Alignment explanation
Indices: 642977--643011 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
642967 AATTATCGAG
642977 TTGAATTTTTTGAATAA
1 TTGAATTTTTTGAATAA
642994 TTGAATTTTTTGAATAA
1 TTGAATTTTTTGAATAA
643011 T
1 T
643012 GCAGTTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.54
Consensus pattern (17 bp):
TTGAATTTTTTGAATAA
Found at i:643194 original size:41 final size:41
Alignment explanation
Indices: 643126--643203 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
643116 CTTACCCGAA
* * *
643126 CCCCTCGAAGATGCATTGGAGTTCATGCGTCTTCCCCTGCT
1 CCCCTCGAAGACGCATTGGAATCCATGCGTCTTCCCCTGCT
*
643167 CCCCTCGAAGACGCA-TGGTAATCCATGCTTCTTCCCC
1 CCCCTCGAAGACGCATTGG-AATCCATGCGTCTTCCCC
643204 CTGCATGCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 3 0.09
41 29 0.91
ACGTcount: A:0.17, C:0.37, G:0.19, T:0.27
Consensus pattern (41 bp):
CCCCTCGAAGACGCATTGGAATCCATGCGTCTTCCCCTGCT
Found at i:643425 original size:25 final size:24
Alignment explanation
Indices: 643391--643582 Score: 192
Period size: 25 Copynumber: 7.7 Consensus size: 24
643381 CTTCCCCCCT
* *
643391 CATGCTACACTCGTAGTCCCCCTTG
1 CATGCAACACTCGT-GGCCCCCTTG
* * *
643416 CACGCAACACCCGT-GACCCCTACTG
1 CATGCAACACTCGTGGCCCCCT--TG
*
643441 CATGCAACACCCGTGG-CCCCTACTG
1 CATGCAACACTCGTGGCCCCCT--TG
*
643466 CATGCAACACTCGTGGCCCCCACTG
1 CATGCAACACTCGTGGCCCCC-TTG
*
643491 CATGCAACACTCGTGGCCCCCACTG
1 CATGCAACACTCGTGGCCCCC-TTG
*
643516 CATGCAACACTCGTGGCCCCCACTG
1 CATGCAACACTCGTGGCCCCC-TTG
643541 CATGCAACACTCGTGGCCCCTACTT-
1 CATGCAACACTCGTGGCCCC--CTTG
643566 CATGCAACACTCGTGGC
1 CATGCAACACTCGTGGC
643583 GTGGCCACCG
Statistics
Matches: 151, Mismatches: 9, Indels: 14
0.87 0.05 0.08
Matches are distributed among these distances:
23 5 0.03
25 139 0.92
26 6 0.04
27 1 0.01
ACGTcount: A:0.20, C:0.43, G:0.19, T:0.18
Consensus pattern (24 bp):
CATGCAACACTCGTGGCCCCCTTG
Found at i:643445 original size:50 final size:48
Alignment explanation
Indices: 643384--643582 Score: 224
Period size: 50 Copynumber: 4.0 Consensus size: 48
643374 TTGGCAACTT
* * * *
643384 CCCCC-CT-CATGCTACACTCGTAGTCCCCCTTGCACGCAACACCCGTGA
1 CCCCCACTGCATGCAACACTCGT-G-CCCCCTTGCATGCAACACTCGTGG
* * *
643432 CCCCTACTGCATGCAACACCCGTGGCCCCTACTGCATGCAACACTCGTGG
1 CCCCCACTGCATGCAACACTCGTGCCCCCT--TGCATGCAACACTCGTGG
*
643482 CCCCCACTGCATGCAACACTCGTGGCCCCCACTGCATGCAACACTCGTGG
1 CCCCCACTGCATGCAACACTCGT-GCCCCC-TTGCATGCAACACTCGTGG
643532 CCCCCACTGCATGCAACACTCGTGGCCCCTACTT-CATGCAACACTCGTGG
1 CCCCCACTGCATGCAACACTCGT-GCCCC--CTTGCATGCAACACTCGTGG
643582 C
1 C
643583 GTGGCCACCG
Statistics
Matches: 131, Mismatches: 12, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
48 9 0.07
49 3 0.02
50 112 0.85
51 6 0.05
52 1 0.01
ACGTcount: A:0.20, C:0.44, G:0.18, T:0.18
Consensus pattern (48 bp):
CCCCCACTGCATGCAACACTCGTGCCCCCTTGCATGCAACACTCGTGG
Found at i:643581 original size:75 final size:75
Alignment explanation
Indices: 643384--643582 Score: 269
Period size: 75 Copynumber: 2.7 Consensus size: 75
643374 TTGGCAACTT
* * * * * * *
643384 CCCCC-CT-CATGCTACACTCGTAGTCCCCC-TTGCACGCAACACCCGTGACCCCTACTGCATGC
1 CCCCCACTGCATGCAACACTCGT-GGCCCCCACTGCATGCAACACTCGTGGCCCCCACTGCATGC
643446 AACACCCGTGG
65 AACACCCGTGG
*
643457 CCCCTACTGCATGCAACACTCGTGGCCCCCACTGCATGCAACACTCGTGGCCCCCACTGCATGCA
1 CCCCCACTGCATGCAACACTCGTGGCCCCCACTGCATGCAACACTCGTGGCCCCCACTGCATGCA
*
643522 ACACTCGTGG
66 ACACCCGTGG
* *
643532 CCCCCACTGCATGCAACACTCGTGGCCCCTACTTCATGCAACACTCGTGGC
1 CCCCCACTGCATGCAACACTCGTGGCCCCCACTGCATGCAACACTCGTGGC
643583 GTGGCCACCG
Statistics
Matches: 111, Mismatches: 12, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
73 4 0.04
74 8 0.07
75 99 0.89
ACGTcount: A:0.20, C:0.44, G:0.18, T:0.18
Consensus pattern (75 bp):
CCCCCACTGCATGCAACACTCGTGGCCCCCACTGCATGCAACACTCGTGGCCCCCACTGCATGCA
ACACCCGTGG
Found at i:648375 original size:22 final size:22
Alignment explanation
Indices: 648347--648395 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
648337 ATATCCGAAC
648347 ATAAAAT-TAAAAAGTTCAAAAT
1 ATAAAATATAAAAA-TTCAAAAT
* *
648369 ATAAAATATAATAATTCATAAT
1 ATAAAATATAAAAATTCAAAAT
648391 ATAAA
1 ATAAA
648396 TAATTCATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (22 bp):
ATAAAATATAAAAATTCAAAAT
Found at i:648399 original size:16 final size:15
Alignment explanation
Indices: 648373--648408 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
648363 CAAAATATAA
648373 AATATAATAATTCAT
1 AATATAATAATTCAT
648388 AATATAAATAATTCAT
1 AATAT-AATAATTCAT
*
648404 TATAT
1 AATAT
648409 TTTATATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (15 bp):
AATATAATAATTCAT
Found at i:648831 original size:13 final size:13
Alignment explanation
Indices: 648797--648837 Score: 64
Period size: 13 Copynumber: 3.0 Consensus size: 13
648787 AAAATATTAA
648797 ATTTAATAAATTTT
1 ATTTAATAAA-TTT
648811 ATTTTAATAAATTT
1 A-TTTAATAAATTT
648825 ATTTAATAAATTT
1 ATTTAATAAATTT
648838 TATTAAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 12 0.46
14 5 0.19
15 9 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTTAATAAATTT
Found at i:648843 original size:13 final size:14
Alignment explanation
Indices: 648797--648846 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
648787 AAAATATTAA
648797 ATTTAATAAATTTT
1 ATTTAATAAATTTT
648811 ATTTTAATAAA-TTT
1 A-TTTAATAAATTTT
648825 ATTTAATAAATTTT
1 ATTTAATAAATTTT
*
648839 ATTAAATA
1 ATTTAATA
648847 TAAAAGTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
13 9 0.27
14 15 0.45
15 9 0.27
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
ATTTAATAAATTTT
Found at i:648943 original size:23 final size:22
Alignment explanation
Indices: 648917--648960 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
648907 AATTTATATC
648917 ATTTAAAAATAAATAAAATAATG
1 ATTTAAAAAT-AATAAAATAATG
** *
648940 ATTTTTAAATATTAAAATAAT
1 ATTTAAAAATAATAAAATAAT
648961 TGTTATTGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
ATTTAAAAATAATAAAATAATG
Found at i:653112 original size:18 final size:18
Alignment explanation
Indices: 653089--653176 Score: 113
Period size: 18 Copynumber: 4.9 Consensus size: 18
653079 GAGGGTCTAC
653089 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
*
653107 GTGGTCATTCGGGACATA
1 GTGGTCCTTCGGGACATA
* * *
653125 ATGGTCATTCGGGACACA
1 GTGGTCCTTCGGGACATA
* *
653143 GTGGTCCTTCGGGATATG
1 GTGGTCCTTCGGGACATA
*
653161 GTGGTCCTACGGGACA
1 GTGGTCCTTCGGGACA
653177 AATTCTACGC
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 60 1.00
ACGTcount: A:0.19, C:0.20, G:0.34, T:0.26
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:662278 original size:31 final size:31
Alignment explanation
Indices: 662235--662303 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 31
662225 TTCTAAAACC
*
662235 CTAATTTCTTAAATT-TTGACACCA-TAACGTT
1 CTAAATTCTTAAATTATT-ACA-CATTAACGTT
*
662266 CTAAATTCTTAAATTATTTCACATTAACGTT
1 CTAAATTCTTAAATTATTACACATTAACGTT
662297 CTAAATT
1 CTAAATT
662304 ATTTTTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 2 0.06
31 30 0.88
32 2 0.06
ACGTcount: A:0.35, C:0.17, G:0.04, T:0.43
Consensus pattern (31 bp):
CTAAATTCTTAAATTATTACACATTAACGTT
Found at i:662613 original size:27 final size:25
Alignment explanation
Indices: 662562--662625 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 25
662552 ATATAACTTA
662562 AAATAT-TTTTA-TATCAACTTATT
1 AAATATATTTTATTATCAACTTATT
*
662585 AAATATATTTTATTATTAACTTAATTT
1 AAATATATTTTATTATCAACTT-A-TT
*
662612 AAAAATATTTTATT
1 AAATATATTTTATT
662626 TTTATTTTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 6 0.17
24 5 0.14
25 8 0.23
26 1 0.03
27 15 0.43
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (25 bp):
AAATATATTTTATTATCAACTTATT
Found at i:662646 original size:27 final size:27
Alignment explanation
Indices: 662561--662625 Score: 82
Period size: 25 Copynumber: 2.5 Consensus size: 27
662551 TATATAACTT
*
662561 AAAATATTTT-TATATCAACTT-A-TTA
1 AAAATATTTTAT-TATTAACTTAATTTA
*
662586 AATATATTTTATTATTAACTTAATTTA
1 AAAATATTTTATTATTAACTTAATTTA
662613 AAAATATTTTATT
1 AAAATATTTTATT
662626 TTTATTTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 17 0.50
26 2 0.06
27 15 0.44
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (27 bp):
AAAATATTTTATTATTAACTTAATTTA
Found at i:664731 original size:19 final size:19
Alignment explanation
Indices: 664703--664743 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
664693 CAAAAAGAAA
*
664703 AAAATGAAT-AATAAATAAT
1 AAAATAAATAAAT-AATAAT
664722 AAAATAAATAAATAATAAT
1 AAAATAAATAAATAATAAT
664741 AAA
1 AAA
664744 TAATGTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (19 bp):
AAAATAAATAAATAATAAT
Found at i:664745 original size:26 final size:27
Alignment explanation
Indices: 664695--664747 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
664685 ATGCTAAACA
664695 AAAAGAAAAAAATGAATAATAAATAAT
1 AAAAGAAAAAAATGAATAATAAATAAT
* *
664722 AAAATAAATAAAT-AATAATAAATAAT
1 AAAAGAAAAAAATGAATAATAAATAAT
664748 GTATTATCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.23
Consensus pattern (27 bp):
AAAAGAAAAAAATGAATAATAAATAAT
Found at i:665256 original size:33 final size:33
Alignment explanation
Indices: 665218--665299 Score: 103
Period size: 33 Copynumber: 2.5 Consensus size: 33
665208 AGTCCTACTT
* * *
665218 AGACTCAAATGC-TTCGGTTTTAGTGTTTCAATA
1 AGACTCAAATACGTT-GGTTTTAATATTTCAATA
*
665251 GGACTCAAATACGTTGGTTTTAATATTTCAATA
1 AGACTCAAATACGTTGGTTTTAATATTTCAATA
*
665284 AGATTCAAATACGTTG
1 AGACTCAAATACGTTG
665300 ATTTATTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
33 40 0.95
34 2 0.05
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (33 bp):
AGACTCAAATACGTTGGTTTTAATATTTCAATA
Found at i:666564 original size:110 final size:110
Alignment explanation
Indices: 666422--666622 Score: 357
Period size: 110 Copynumber: 1.8 Consensus size: 110
666412 GAAATTGTTT
666422 GTTGACAATCAGCCGCCCCTTCATCGTGAAGTTGAGCTTATGTTGTCTTGAGTCCAATATCCTTC
1 GTTGACAATCAGCCGCCCCTTCATCGTGAAGTTGAGCTTATGTTGTCTTGAGTCCAATATCCTTC
666487 GTTGTGAAGTTGAAATTGACTCTGAATGAAATTGAAAAGTTATTC
66 GTTGTGAAGTTGAAATTGACTCTGAATGAAATTGAAAAGTTATTC
* * * *
666532 GTTGACAATCAGTCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAATATCCTTC
1 GTTGACAATCAGCCGCCCCTTCATCGTGAAGTTGAGCTTATGTTGTCTTGAGTCCAATATCCTTC
*
666597 GTTGTGAAGTTGAAATTGGCTCTGAA
66 GTTGTGAAGTTGAAATTGACTCTGAA
666623 ATTGGGAAGC
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
110 86 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (110 bp):
GTTGACAATCAGCCGCCCCTTCATCGTGAAGTTGAGCTTATGTTGTCTTGAGTCCAATATCCTTC
GTTGTGAAGTTGAAATTGACTCTGAATGAAATTGAAAAGTTATTC
Found at i:670624 original size:19 final size:19
Alignment explanation
Indices: 670596--670636 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
670586 CAAAAAGGGA
*
670596 AAAATGAAT-AATAAATAAT
1 AAAATAAATAAAT-AATAAT
670615 AAAATAAATAAATAATAAT
1 AAAATAAATAAATAATAAT
670634 AAA
1 AAA
670637 TAATGTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (19 bp):
AAAATAAATAAATAATAAT
Found at i:671145 original size:33 final size:33
Alignment explanation
Indices: 671108--671189 Score: 121
Period size: 33 Copynumber: 2.5 Consensus size: 33
671098 AGTCCTACTT
* *
671108 GGACTCAAATGC-TTCGGTTTTAGTGTTTCAATA
1 GGACTCAAATACGTT-GGTTTTAGTATTTCAATA
671141 GGACTCAAATACGTTGGTTTTAGTATTTCAATA
1 GGACTCAAATACGTTGGTTTTAGTATTTCAATA
*
671174 AGACTCAAATACGTTG
1 GGACTCAAATACGTTG
671190 ATTTATTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
33 43 0.96
34 2 0.04
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.37
Consensus pattern (33 bp):
GGACTCAAATACGTTGGTTTTAGTATTTCAATA
Found at i:671257 original size:3 final size:3
Alignment explanation
Indices: 671243--671273 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
671233 GGCCTGCAAA
671243 AAT AAT AA- AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
671274 ATAAATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:671288 original size:15 final size:16
Alignment explanation
Indices: 671242--671296 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 16
671232 GGGCCTGCAA
*
671242 AAAT-AATAAAATAAT
1 AAATAAATATAATAAT
671257 -AAT-AATAATAATAAT
1 AAATAAAT-ATAATAAT
671272 AAATAAATATAAT-AT
1 AAATAAATATAATAAT
*
671287 AATTAAATAT
1 AAATAAATAT
671297 TTTTGTAGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
14 6 0.17
15 18 0.51
16 8 0.23
17 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATAAATATAATAAT
Found at i:672443 original size:19 final size:19
Alignment explanation
Indices: 672419--672460 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
672409 AGCCTAAAAA
672419 AATTAAATACCATTGATAT
1 AATTAAATACCATTGATAT
* *
672438 AATTAAATTCTATTGATAT
1 AATTAAATACCATTGATAT
672457 AATT
1 AATT
672461 TTGATATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (19 bp):
AATTAAATACCATTGATAT
Found at i:674005 original size:20 final size:20
Alignment explanation
Indices: 673980--674026 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
673970 TTTTGCAGTA
673980 CCGAATTGTTAGAGTTTGAC
1 CCGAATTGTTAGAGTTTGAC
674000 CCGAATTGTTAGAGTTTGAC
1 CCGAATTGTTAGAGTTTGAC
*
674020 TCGAATT
1 CCGAATT
674027 CAAAGATACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (20 bp):
CCGAATTGTTAGAGTTTGAC
Found at i:679706 original size:14 final size:15
Alignment explanation
Indices: 679666--679708 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
679656 TTGGTTTTCC
679666 GGAAAATGAATTACT
1 GGAAAATGAATTACT
*
679681 -GAAATTTGAATT-CT
1 GGAAA-ATGAATTACT
679695 GGAAAATGAATTAC
1 GGAAAATGAATTAC
679709 ATTTCTGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (15 bp):
GGAAAATGAATTACT
Found at i:679740 original size:14 final size:14
Alignment explanation
Indices: 679718--679751 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
679708 CATTTCTGGA
*
679718 AAAACGTTTTCCGG
1 AAAATGTTTTCCGG
*
679732 AAAATGTTTTCCGT
1 AAAATGTTTTCCGG
679746 AAAATG
1 AAAATG
679752 AATTATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (14 bp):
AAAATGTTTTCCGG
Found at i:680044 original size:23 final size:23
Alignment explanation
Indices: 679995--680057 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
679985 GTGTTATATT
* * **
679995 ATATTTAAAAAATATTAATTAGT
1 ATATTTTAAATATATTAATTAAA
*
680018 ATATTTTAAATATATTTATTAAA
1 ATATTTTAAATATATTAATTAAA
680041 ATATTATTTAAATATAT
1 ATA-T-TTTAAATATAT
680058 AAATAATATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
23 21 0.64
24 1 0.03
25 11 0.33
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
ATATTTTAAATATATTAATTAAA
Found at i:680051 original size:12 final size:12
Alignment explanation
Indices: 680017--680057 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
680007 TATTAATTAG
680017 TATA-TTTTAAA
1 TATATTTTTAAA
680028 TATATTTATTAAA
1 TATATTT-TTAAA
680041 -ATATTATTTAAA
1 TATATT-TTTAAA
680053 TATAT
1 TATAT
680058 AAATAATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 4 0.15
12 12 0.46
13 10 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TATATTTTTAAA
Found at i:680085 original size:19 final size:20
Alignment explanation
Indices: 680033--680085 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
680023 TTAAATATAT
680033 TTATTAAA-ATATTATTTAA
1 TTATTAAATATATTATTTAA
* *
680052 ATATATAAATAATATTA-TTCA
1 TTAT-TAAAT-ATATTATTTAA
680073 TTATTAAATATAT
1 TTATTAAATATAT
680086 ACATTTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 7 0.25
20 9 0.32
21 6 0.21
22 6 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATTAAATATATTATTTAA
Found at i:680183 original size:22 final size:23
Alignment explanation
Indices: 680158--680201 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
680148 GATTATTTTA
680158 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
680180 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
680202 AATAAATACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:680444 original size:42 final size:42
Alignment explanation
Indices: 680386--680503 Score: 164
Period size: 42 Copynumber: 2.8 Consensus size: 42
680376 ATGAATTACA
* * *
680386 TTCCGGAAAACCAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGAAAAACGAATTACGTGAAACAAACACGGCAAAACATT
* *
680428 TTCCGAAAAACGAATTACGTGAAACAAACACGACAAAATATT
1 TTCCGAAAAACGAATTACGTGAAACAAACACGGCAAAACATT
* *
680470 TTCCGAAAAATGAATTACGGGAAACAAAACACGG
1 TTCCGAAAAACGAATTACGTGAAAC-AAACACGG
680504 TAATTCAAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
42 60 0.90
43 7 0.10
ACGTcount: A:0.47, C:0.19, G:0.16, T:0.17
Consensus pattern (42 bp):
TTCCGAAAAACGAATTACGTGAAACAAACACGGCAAAACATT
Found at i:680823 original size:3 final size:3
Alignment explanation
Indices: 680809--680843 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
680799 CCTACCCCTC
* *
680809 CTT CTC CTT CTT CTT CTC CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
680844 ACCTCTACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (3 bp):
CTT
Found at i:680826 original size:12 final size:12
Alignment explanation
Indices: 680809--680843 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
680799 CCTACCCCTC
680809 CTTCTCCTTCTT
1 CTTCTCCTTCTT
680821 CTTCTCCTTCTT
1 CTTCTCCTTCTT
*
680833 CTTCTTCTTCT
1 CTTCTCCTTCT
680844 ACCTCTACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (12 bp):
CTTCTCCTTCTT
Found at i:683560 original size:14 final size:14
Alignment explanation
Indices: 683541--683588 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
683531 GTCGCGTCAG
683541 ATATTTTTTAAAAT
1 ATATTTTTTAAAAT
*
683555 ATATTTTTAAAAAT
1 ATATTTTTTAAAAT
*
683569 ATTTATTTTTTAAAAA
1 A--TATTTTTTAAAAT
683585 ATAT
1 ATAT
683589 AGACGTGATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 17 0.59
16 12 0.41
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
ATATTTTTTAAAAT
Found at i:684271 original size:15 final size:14
Alignment explanation
Indices: 684251--684284 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
684241 CTGATTGGAG
*
684251 AATTTAATTTATTTT
1 AATTTAATATA-TTT
684266 AATTTAATATATTT
1 AATTTAATATATTT
684280 AATTT
1 AATTT
684285 TTACCAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
AATTTAATATATTT
Found at i:688588 original size:21 final size:21
Alignment explanation
Indices: 688562--688658 Score: 133
Period size: 21 Copynumber: 4.6 Consensus size: 21
688552 TATATATAGT
*
688562 CATTCATAAGGACGAGAAGAC
1 CATTCATAAAGACGAGAAGAC
*
688583 CATTCATAAAGATGAGAAGAC
1 CATTCATAAAGACGAGAAGAC
* *
688604 CATTCATAAAGATGATAAGAC
1 CATTCATAAAGACGAGAAGAC
688625 CATTCATAAAGAC-ATGAAGAC
1 CATTCATAAAGACGA-GAAGAC
*
688646 CCTTCATAAAGAC
1 CATTCATAAAGAC
688659 ATGAAGATCA
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
20 1 0.01
21 68 0.99
ACGTcount: A:0.45, C:0.19, G:0.16, T:0.20
Consensus pattern (21 bp):
CATTCATAAAGACGAGAAGAC
Found at i:688659 original size:21 final size:21
Alignment explanation
Indices: 688562--688670 Score: 125
Period size: 21 Copynumber: 5.2 Consensus size: 21
688552 TATATATAGT
*
688562 CATTCATAAGGACGA-GAAGAC
1 CATTCATAAAGAC-ATGAAGAC
*
688583 CATTCATAAAGATGA-GAAGAC
1 CATTCATAAAGA-CATGAAGAC
*
688604 CATTCATAAAGATGAT-AAGAC
1 CATTCATAAAGA-CATGAAGAC
688625 CATTCATAAAGACATGAAGAC
1 CATTCATAAAGACATGAAGAC
* *
688646 CCTTCATAAAGACATGAAGAT
1 CATTCATAAAGACATGAAGAC
688667 CATT
1 CATT
688671 TCACATTGGA
Statistics
Matches: 79, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
20 2 0.03
21 77 0.97
ACGTcount: A:0.45, C:0.17, G:0.17, T:0.21
Consensus pattern (21 bp):
CATTCATAAAGACATGAAGAC
Found at i:688940 original size:7 final size:7
Alignment explanation
Indices: 688917--688956 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
688907 TAACACCTCG
688917 TGCA-TT
1 TGCATTT
* *
688923 TGCACTC
1 TGCATTT
688930 TGCATTT
1 TGCATTT
688937 TGCATTT
1 TGCATTT
688944 TGCATTT
1 TGCATTT
688951 TGCATT
1 TGCATT
688957 GCATGTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
6 4 0.13
7 26 0.87
ACGTcount: A:0.15, C:0.20, G:0.15, T:0.50
Consensus pattern (7 bp):
TGCATTT
Found at i:692488 original size:125 final size:125
Alignment explanation
Indices: 692264--692512 Score: 360
Period size: 125 Copynumber: 2.0 Consensus size: 125
692254 AAGTTAGGAT
* * *
692264 ATATTGGGGCACGACTGAACCCACATCATGTTGAGATGATAAGATTCAGACCAAGAAGATATGAA
1 ATATTGGGGCACGACTGAACCCACATCATATTGAGATGACAAGATACAGACCAAGAAGATATGAA
* *
692329 GAATGAGCCTTACAATTTGAAGTGATGGGACATTTTGAAGGCCTGTACCGGTATAAGTTA
66 GAATGAGCCTTACAATTTGAAGTGATGGGACATTTTGAAGGCCCGTACCAGTATAAGTTA
* *
692389 ATATTGGGGCACGACTGAACCCATATCATATTGAGATGACAAGATACAGACCAAGAAGGCCT-TG
1 ATATTGGGGCACGACTGAACCCACATCATATTGAGATGACAAGATACAGACCAAGAA-G-ATATG
* * *
692453 -AGAATGGGCCTTACAATTTGAGGTGTTGTGG-CATTTTGAAGGCCCGTACCAGTATAAGTT
64 AAGAATGAGCCTTACAATTTGAAGTGATG-GGACATTTTGAAGGCCCGTACCAGTATAAGTT
692513 GACGTTGCGG
Statistics
Matches: 111, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
125 105 0.95
126 5 0.05
127 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (125 bp):
ATATTGGGGCACGACTGAACCCACATCATATTGAGATGACAAGATACAGACCAAGAAGATATGAA
GAATGAGCCTTACAATTTGAAGTGATGGGACATTTTGAAGGCCCGTACCAGTATAAGTTA
Found at i:693880 original size:36 final size:37
Alignment explanation
Indices: 693784--693916 Score: 196
Period size: 37 Copynumber: 3.6 Consensus size: 37
693774 ATGAGATTGG
* *
693784 AGCAAAGTCAATCTTAAGCCTTCACTGAAGAGTAGTGA
1 AGCAAA-TCCATCTTAAGCCTTCACCGAAGAGTAGTGA
* *
693822 AGCAAATCCATCTTAATCCTTCACCAAAGAGTAGTGA
1 AGCAAATCCATCTTAAGCCTTCACCGAAGAGTAGTGA
*
693859 AGCAAA-CCATCTTAAGTCTTCACCGAAGAGTAGTGA
1 AGCAAATCCATCTTAAGCCTTCACCGAAGAGTAGTGA
*
693895 AGCAAATCCATTTTAAGCCTTC
1 AGCAAATCCATCTTAAGCCTTC
693917 TAAGAAGAAT
Statistics
Matches: 85, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
36 33 0.39
37 46 0.54
38 6 0.07
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.25
Consensus pattern (37 bp):
AGCAAATCCATCTTAAGCCTTCACCGAAGAGTAGTGA
Found at i:693936 original size:73 final size:73
Alignment explanation
Indices: 693780--693942 Score: 197
Period size: 73 Copynumber: 2.2 Consensus size: 73
693770 ACATATGAGA
* * *
693780 TTGGAGCAAAGTCAATCTTAAGCCTTCACTGAAGAGTAGTGAAGCAAATCCATCTTAATCCTTCA
1 TTGGAGCAAA--CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCTTAAGCCTTCA
*
693845 CCAAAGAGTAG
64 -CAAAGAATAG
* * *
693856 -TGAAGCAAACCATCTTAAGTCTTCACCGAAGAGTAGTGAAGCAAATCCATTTTAAGCCTTCTA-
1 TTGGAGCAAACCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCTTAAGCCTTC-AC
693919 AGAAGAAT-G
65 A-AAGAATAG
693928 TTGGAGCAAACCATC
1 TTGGAGCAAACCATC
693943 AGATTATCAG
Statistics
Matches: 76, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
72 2 0.03
73 65 0.86
74 1 0.01
75 8 0.11
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (73 bp):
TTGGAGCAAACCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCTTAAGCCTTCACA
AAGAATAG
Found at i:694390 original size:54 final size:54
Alignment explanation
Indices: 694323--694585 Score: 377
Period size: 54 Copynumber: 4.9 Consensus size: 54
694313 GTGAAGCAAG
*
694323 AGAAGATGTTCGAGTTCCATACTTCCTAGAGAAAGAGGGAGTGAACCCGTAAGA
1 AGAAGATGTTCGAGTTCCATACTTCCTAGAGAAAGAGGGAGCGAACCCGTAAGA
* **
694377 AGAAGATGTTCGAGTTTCATACTTCCTAGAGAAAGAGGGAGCGAACCCGTTTGA
1 AGAAGATGTTCGAGTTCCATACTTCCTAGAGAAAGAGGGAGCGAACCCGTAAGA
* * * * **
694431 AGAATATGTTCGAGTTCTATACTCCCTAGAGAAAGAGAGAGCGAACCCGTTTGA
1 AGAAGATGTTCGAGTTCCATACTTCCTAGAGAAAGAGGGAGCGAACCCGTAAGA
* *
694485 AGAAGATG-TCTGAGTTCTATACTCCCT-GAAGAAAGAGGGAGCGAACCCGTAAGA
1 AGAAGATGTTC-GAGTTCCATACTTCCTAG-AGAAAGAGGGAGCGAACCCGTAAGA
*
694539 AGAAGATGTTCGAGTTCCATACTTTCTAGAGAAAGAGGGAGCGAACC
1 AGAAGATGTTCGAGTTCCATACTTCCTAGAGAAAGAGGGAGCGAACC
694586 TGTTTGTTCA
Statistics
Matches: 189, Mismatches: 16, Indels: 8
0.89 0.08 0.04
Matches are distributed among these distances:
53 3 0.02
54 183 0.97
55 3 0.02
ACGTcount: A:0.34, C:0.17, G:0.27, T:0.22
Consensus pattern (54 bp):
AGAAGATGTTCGAGTTCCATACTTCCTAGAGAAAGAGGGAGCGAACCCGTAAGA
Found at i:694627 original size:55 final size:54
Alignment explanation
Indices: 694378--695493 Score: 896
Period size: 55 Copynumber: 20.9 Consensus size: 54
694368 CCCGTAAGAA
*
694378 GAAGA-TGTTCGAGT-TTCATACT-TCCT-AGAGAAAGAGGGAGCGAACCCG--T-TT
1 GAAGATTGTTCGAGTCTT-ATACTCT-CTGA-AGAAATAGGGAGCGAA-CCGATTGTT
* * * * **
694429 GAAGAATATGTTCGAGT-TCTATACTCCCT-AGAGAAAGAGAGAGCGAACCCGTTTGAA
1 GAAG-AT-TGTTCGAGTCT-TATACTCTCTGA-AGAAATAGGGAGCGAA-CCGATTGTT
* * * **
694486 GAAGA-TG-TCTGAGT-TCTATACTCCCTGAAGAAAGAGGGAGCGAACCCG-TAAGAA
1 GAAGATTGTTC-GAGTCT-TATACTCTCTGAAGAAATAGGGAGCGAA-CCGAT-TGTT
* * * *
694540 GAAGA-TGTTCGAGT-TCCATACTTTCT-AGAGAAAGAGGGAGCGAACCTGTTTGTT
1 GAAGATTGTTCGAGTCT-TATACTCTCTGA-AGAAATAGGGAGCGAACC-GATTGTT
* * *
694594 CAAAATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGC-AGACACGATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCGA-AC-CGATTGTT
* *
694649 GAAGATTGCTCGAGTCTTATACTCTCTGAAGGAATAGGGAGC-AGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCGA-AC-CGATTGTT
* * *
694704 GAATATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAAACATGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCGAAC-CGATTGTT
*
694759 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGAGAGC-ATACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCGA-AC-CGATTGTT
* * *
694814 GAAAATTGTTCGAGTCTTATACTCTCTGAAGAAATAGAGAGCAAACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCGAAC-CGATTGTT
* *
694869 GAAGATTGTTCTAGTCTTATACTCTCTGAAGAAATAGGAAGC-AGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCGA-AC-CGATTGTT
* *
694924 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAAACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGC-GAACCGATTGTT
*
694979 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAAACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGC-GAACCGATTGTT
695034 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGATA-CGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGC-GA-ACCGATTGTT
*
695089 GAAAATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGC-ATA-C-------
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCGA-ACCGATTGTT
* * **
695135 -ACGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGATAA-C-------
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCGAACCGATTGTT
* *
695180 -ACGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGC-AGACACGTTTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCGA-AC-CGATTGTT
** * * * * *
695234 GAAGGCTGTTCAAGTCCTATACTCTCTGAAGGAATAGGGAGCAAACACGTTTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCGAAC-CGATTGTT
* * * * **
695289 GAAGA----TCGAGTCCTATACTCTCTGAAGGAATAAGGAGCGGACACTTTTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCGAAC-CGATTGTT
* * * *
695340 GAAGATTTGTTCAAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAC-ATTTGTT
1 GAAGA-TTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCGAAC-CGA-TTGTT
* * * *
695396 GAAGA----TCGAGTCCTATACTCTCTGAA-AGAATAGGGAACAAACCCG-TTTTAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGA-AATAGGGAGCGAA-CCGATTGT-T
* * * * * *
695447 GAAGATTGTTTGAGTTTTACACTCCCTGAAGCAAGAGGGAGCGAACC
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCGAACC
695494 CGCTGGTCGA
Statistics
Matches: 932, Mismatches: 78, Indels: 107
0.83 0.07 0.10
Matches are distributed among these distances:
44 1 0.00
45 79 0.08
46 1 0.00
47 1 0.00
50 3 0.00
51 87 0.09
52 2 0.00
53 10 0.01
54 124 0.13
55 562 0.60
56 57 0.06
57 5 0.01
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (54 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCGAACCGATTGTT
Found at i:694713 original size:110 final size:110
Alignment explanation
Indices: 694589--695488 Score: 1065
Period size: 110 Copynumber: 8.4 Consensus size: 110
694579 GCGAACCTGT
* * * *
694589 TTGTTCAAAATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATTGAAGA
1 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAAACACGATTGTTGAAGA
* *
694654 TTGCTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGA
66 TTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA
* *
694699 TTGTTGAATATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAAACATGATTGTTGAAGA
1 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAAACACGATTGTTGAAGA
* *
694764 TTGTTCGAGTCTTATACTCTCTGAAGAAATAGAGAGCATACACGA
66 TTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA
* *
694809 TTGTTGAAAATTGTTCGAGTCTTATACTCTCTGAAGAAATAGAGAGCAAACACGATTGTTGAAGA
1 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAAACACGATTGTTGAAGA
* *
694874 TTGTTCTAGTCTTATACTCTCTGAAGAAATAGGAAGCAGACACGA
66 TTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA
*
694919 TTGTTGAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAA-ACGATTGTTGAAG
1 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCA-AACACGATTGTTGAAG
*
694983 ATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAAACGA
65 ATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA
* * *
695029 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGATACGATTGTTGAAAA
1 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAAACACGATTGTTGAAGA
*
695094 TTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCATACAC--
66 TTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA
*
695137 --------GATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAG-ATAACAC----------G
1 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCA-AACACGATTGTTGAAG
*
695183 ATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGT
65 ATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA
** * * * *
695229 TTGTTGAAGGCTGTTCAAGTCCTATACTCTCTGAAGGAATAGGGAGCAAACACGTTTGTTGAAGA
1 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAAACACGATTGTTGAAGA
* * * * **
695294 ----TCGAGTCCTATACTCTCTGAAGGAATAAGGAGCGGACACTT
66 TTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA
* * * **
695335 TTGTTGAAGATTTGTTCAAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAC-ATTTGTTGAA
1 TTGTTGAAGA-TTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAAACACGA-TTGTTGAA
* * * *
695399 GA----TCGAGTCCTATACTCTCTGAA-AGAATAGGGAACAAACCCG-
64 GATTGTTCGAGTCTTATACTCTCTGAAGA-AATAGGGAGCAGACACGA
* * * * * * *
695441 TTTTATGAAGATTGTTTGAGTTTTACACTCCCTGAAGCAAGAGGGAGC
1 TTGT-TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGC
695489 GAACCCGCTG
Statistics
Matches: 698, Mismatches: 64, Indels: 60
0.85 0.08 0.07
Matches are distributed among these distances:
90 43 0.06
99 1 0.00
100 77 0.11
101 1 0.00
106 77 0.11
107 88 0.13
109 1 0.00
110 408 0.58
111 2 0.00
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.29
Consensus pattern (110 bp):
TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAAACACGATTGTTGAAGA
TTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA
Found at i:694769 original size:165 final size:164
Alignment explanation
Indices: 694589--695431 Score: 1058
Period size: 165 Copynumber: 5.3 Consensus size: 164
694579 GCGAACCTGT
* * *
694589 TTGTTCAAAATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATTGAAGA
1 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGA
* *
694654 TTGCTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAATATTGTTCGAGT
66 TTG-TCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGT
* *
694719 CTTATACTCTCTGAAGAAATAGGGAGCAAACATGA
130 CTTATACTCTCTGAAGAAATAGGGAGCAGACACGA
* * *
694754 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGAGAGCATACACGATTGTTGAAAA
1 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGA
* * *
694819 TTGTTCGAGTCTTATACTCTCTGAAGAAATAGAGAGCAAACACGATTGTTGAAGATTGTTCTAGT
66 TTG-TCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGT
*
694884 CTTATACTCTCTGAAGAAATAGGAAGCAGACACGA
130 CTTATACTCTCTGAAGAAATAGGGAGCAGACACGA
* *
694919 TTGTTGAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAAACGATTGTTGAAGA
1 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGA
*
694984 TTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAAACGATTGTTGAAGATTGTTCGAGT
66 TTG-TCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGT
*
695049 CTTATACTCTCTGAAGAAATAGGGAGCAGATACGA
130 CTTATACTCTCTGAAGAAATAGGGAGCAGACACGA
* *
695084 TTGTTGAAAATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCATACACGA---TT---G-
1 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGA
* * *
695142 -T-TCGAGTCTCATACTCTCTGAAGAAATAGGGAG-ATA-AC--------ACGATTGTTCGAGTC
66 TTGTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTC
*
695195 TTATACTCTCTGAAGAAATAGGGAGCAGACACGT
131 TTATACTCTCTGAAGAAATAGGGAGCAGACACGA
** * * * * *
695229 TTGTTGAAGGCTGTTCAAGTCCTATACTCTCTGAAGGAATAGGGAGCAAACACGTTTGTTGAAGA
1 TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGA
* * * * ** *
695294 ---TCGAGTCCTATACTCTCTGAAGGAATAAGGAGCGGACACTTTTGTTGAAGATTTGTTCAAGT
66 TTGTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGA-TTGTTCGAGT
* * *
695356 CCTATACTCTCTGAAGGAATAGGGAGCGGACAC-A
130 CTTATACTCTCTGAAGAAATAGGGAGCAGACACGA
*
695390 TTTGTTGAAGA----TCGAGTCCTATACTCTCTGAA-AGAATAGGGA
1 -TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGA-AATAGGGA
695432 ACAAACCCGT
Statistics
Matches: 600, Mismatches: 58, Indels: 47
0.85 0.08 0.07
Matches are distributed among these distances:
145 93 0.16
148 2 0.00
151 29 0.05
152 1 0.00
153 4 0.01
154 2 0.00
155 31 0.05
157 1 0.00
158 28 0.05
159 1 0.00
161 3 0.00
162 50 0.08
165 355 0.59
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.29
Consensus pattern (164 bp):
TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGA
TTGTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTC
TTATACTCTCTGAAGAAATAGGGAGCAGACACGA
Found at i:695033 original size:45 final size:45
Alignment explanation
Indices: 694982--695233 Score: 245
Period size: 45 Copynumber: 5.2 Consensus size: 45
694972 GATTGTTGAA
694982 GATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAAAC
1 GATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAAAC
*
695027 GATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGATACGATTGTT
1 ----------GATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGA-A--A----C
* *
695089 GAAAATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCATACAC
1 G---ATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAAAC
* *
695137 GATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAG-ATAACAC
1 GATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAA-AC
*
695182 GATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACAC
1 GATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAAAC
*
695227 GTTTGTT
1 GATTGTT
695234 GAAGGCTGTT
Statistics
Matches: 175, Mismatches: 10, Indels: 34
0.80 0.05 0.16
Matches are distributed among these distances:
44 3 0.02
45 83 0.47
46 2 0.01
48 1 0.01
52 2 0.01
55 82 0.47
56 1 0.01
58 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (45 bp):
GATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAAAC
Found at i:695371 original size:56 final size:56
Alignment explanation
Indices: 695184--695453 Score: 294
Period size: 51 Copynumber: 5.0 Consensus size: 56
695174 GATAACACGA
* * * *
695184 TTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGTTTGTTGAAG-G
1 TTGTTCAAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTGAAGAT
* *
695239 CTGTTCAAGTCCTATACTCTCTGAAGGAATAGGGAGCAAACACGTTTGTTGAAGA-
1 TTGTTCAAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTGAAGAT
* * * *
695294 ----TCGAGTCCTATACTCTCTGAAGGAATAAGGAGCGGACACTTTTGTTGAAGAT
1 TTGTTCAAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTGAAGAT
* *
695346 TTGTTCAAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACATTTGTTGAAGA-
1 TTGTTCAAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTGAAGAT
* * * * *
695401 ----TCGAGTCCTATACTCTCTGAAAGAATAGGGAACAAACCCGTTT-TATGAAGAT
1 TTGTTCAAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGT-TGAAGAT
695453 T
1 T
695454 GTTTGAGTTT
Statistics
Matches: 186, Mismatches: 20, Indels: 20
0.82 0.09 0.09
Matches are distributed among these distances:
50 1 0.01
51 88 0.47
55 49 0.26
56 48 0.26
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (56 bp):
TTGTTCAAGTCCTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTGAAGAT
Found at i:698613 original size:37 final size:39
Alignment explanation
Indices: 698553--698642 Score: 96
Period size: 37 Copynumber: 2.4 Consensus size: 39
698543 TCTTAACTAA
* * * *
698553 AAATATATTTTAATATTATCTTAATTTA-TAAAT-TTAT
1 AAATATATTATATTATTACCTTAAATTATTAAATATTAT
*
698590 AAATATATTATATTTTTACCTTAAATTATTAAATATTAT
1 AAATATATTATATTATTACCTTAAATTATTAAATATTAT
**
698629 TTAT-TATTATATTA
1 AAATATATTATATTA
698643 ACTTAAAAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
37 23 0.53
38 14 0.33
39 6 0.14
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.54
Consensus pattern (39 bp):
AAATATATTATATTATTACCTTAAATTATTAAATATTAT
Found at i:698663 original size:25 final size:24
Alignment explanation
Indices: 698630--698720 Score: 83
Period size: 27 Copynumber: 3.5 Consensus size: 24
698620 AAATATTATT
*
698630 TATTATTATATTAACTTAAAAATATA
1 TATT-TTATTTTAA-TTAAAAATATA
698656 TATTTTATTTTAATTTTAAAAAATATA
1 TATTTTATTTTAA--TT-AAAAATATA
**
698683 TATTATTCTATTTTAATTTTAAATATA
1 TA-T-TT-TATTTTAATTAAAAATATA
698710 TATTTTATTTT
1 TATTTTATTTT
698721 TATCTTAACT
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
24 6 0.11
25 10 0.18
26 7 0.12
27 20 0.36
28 3 0.05
29 2 0.04
30 8 0.14
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
TATTTTATTTTAATTAAAAATATA
Found at i:698710 original size:29 final size:30
Alignment explanation
Indices: 698647--698718 Score: 98
Period size: 29 Copynumber: 2.5 Consensus size: 30
698637 ATATTAACTT
698647 AAAAATATATA-T-TT-TATTTTAATTTTA
1 AAAAATATATATTATTCTATTTTAATTTTA
698674 AAAAATATATATTATTCTATTTTAATTTT-
1 AAAAATATATATTATTCTATTTTAATTTTA
* *
698703 AAATATATATTTTATT
1 AAAAATATATATTATT
698719 TTTATCTTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
27 11 0.28
28 1 0.03
29 16 0.40
30 12 0.30
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (30 bp):
AAAAATATATATTATTCTATTTTAATTTTA
Found at i:698721 original size:25 final size:25
Alignment explanation
Indices: 698649--698744 Score: 88
Period size: 27 Copynumber: 3.7 Consensus size: 25
698639 ATTAACTTAA
698649 AAATATATATTTTA-TTTTAATTTT
1 AAATATATATTTTATTTTTAATTTT
*
698673 AAAAAATATATATTATTCTATTTTAATTTT
1 ---AAATATATATT-TTAT-TTTTAATTTT
*
698703 AAATATATATTTTATTTTT-ATCTT
1 AAATATATATTTTATTTTTAATTTT
* * *
698727 AACTATAAAATTTATTTT
1 AAATATATATTTTATTTT
698745 ATCTTAATTG
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
24 19 0.32
25 4 0.07
26 3 0.05
27 22 0.37
28 2 0.03
30 10 0.17
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (25 bp):
AAATATATATTTTATTTTTAATTTT
Found at i:698728 original size:24 final size:24
Alignment explanation
Indices: 698680--698751 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 24
698670 TTTAAAAAAT
* * *
698680 ATATATTATTCTATTTTAATTTTAA
1 ATATA-TATTTTATTTTTATCTTAA
698705 ATATATATTTTATTTTTATCTTAA
1 ATATATATTTTATTTTTATCTTAA
* * *
698729 CTATAAAATTTA-TTTTATCTTAA
1 ATATATATTTTATTTTTATCTTAA
698752 TTGTAAAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
23 11 0.27
24 25 0.61
25 5 0.12
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (24 bp):
ATATATATTTTATTTTTATCTTAA
Found at i:698761 original size:54 final size:54
Alignment explanation
Indices: 698648--698762 Score: 128
Period size: 54 Copynumber: 2.1 Consensus size: 54
698638 TATTAACTTA
* *
698648 AAAATATATATTTTATTTTAATTTTAAAAAATATATATTATTCTATTTTAATTT
1 AAAATATATATTTTATTTTAATCTTAAAAAATATATATTATTCTATCTTAATTT
* * * *
698702 TAAATATATATTTTATTTTTATCTTAACTATAA-A-AT-TTATTTTATCTTAATTGT
1 AAAATATATATTTTATTTTAATCTTAA--AAAATATATATTATTCTATCTTAATT-T
698756 AAAATAT
1 AAAATAT
698763 TATAAGAATA
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
53 14 0.27
54 33 0.65
55 1 0.02
56 3 0.06
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (54 bp):
AAAATATATATTTTATTTTAATCTTAAAAAATATATATTATTCTATCTTAATTT
Found at i:698765 original size:24 final size:23
Alignment explanation
Indices: 698713--698765 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 23
698703 AAATATATAT
698713 TTTATTTTTATCTTAACTATAAAA
1 TTTA-TTTTATCTTAACTATAAAA
* *
698737 TTTATTTTATCTTAATTGTAAAA
1 TTTATTTTATCTTAACTATAAAA
698760 TATTAT
1 T-TTAT
698766 AAGAATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 18 0.69
24 8 0.31
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.57
Consensus pattern (23 bp):
TTTATTTTATCTTAACTATAAAA
Found at i:698862 original size:27 final size:26
Alignment explanation
Indices: 698796--698863 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 26
698786 AAGTTAAGGT
*
698796 AAAAAACATATATTTTTTAAGTTTAA
1 AAAAAATATATATTTTTTAAGTTTAA
* * *
698822 AAAAGATTAAATATTTTTT-ATTTTAA
1 AAAA-AATATATATTTTTTAAGTTTAA
698848 GAATAAAATATATATT
1 -AA-AAAATATATATT
698864 CAATTTTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
26 10 0.30
27 21 0.64
28 2 0.06
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.44
Consensus pattern (26 bp):
AAAAAATATATATTTTTTAAGTTTAA
Found at i:700198 original size:17 final size:19
Alignment explanation
Indices: 700176--700210 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
700166 GATTCAAAGA
700176 ATTAATT-C-AAAATAAAT
1 ATTAATTCCAAAAATAAAT
700193 ATTAATTCCAAAAATAAA
1 ATTAATTCCAAAAATAAA
700211 AAAGATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 1 0.06
19 8 0.50
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.31
Consensus pattern (19 bp):
ATTAATTCCAAAAATAAAT
Found at i:701072 original size:24 final size:24
Alignment explanation
Indices: 701040--701085 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
701030 CAATGACTTG
701040 AACTCGAGACATTACTTAAACGTC
1 AACTCGAGACATTACTTAAACGTC
701064 AACTCGAGACATTACTTAAACG
1 AACTCGAGACATTACTTAAACG
701086 ATATCAATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.39, C:0.24, G:0.13, T:0.24
Consensus pattern (24 bp):
AACTCGAGACATTACTTAAACGTC
Found at i:709786 original size:2 final size:2
Alignment explanation
Indices: 709779--709886 Score: 72
Period size: 2 Copynumber: 57.5 Consensus size: 2
709769 TAAAATGATA
* * *
709779 AT AT AT AT A- AT AT A- AT AT AT AT ACT AT AT AT AT -T TT AA AA
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
* * * *
709819 AT -T GT AT AT AT -T TT TT A- AT AT AT AT AT AT TT CAT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
709858 AT AT AT AT AT AT AT AT AT AT -T A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
709887 CATTTTTAAA
Statistics
Matches: 88, Mismatches: 7, Indels: 22
0.75 0.06 0.19
Matches are distributed among these distances:
1 9 0.10
2 76 0.86
3 3 0.03
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:709885 original size:16 final size:15
Alignment explanation
Indices: 709776--709886 Score: 81
Period size: 14 Copynumber: 7.7 Consensus size: 15
709766 TTTTAAAATG
709776 ATAATATATATA-AT
1 ATAATATATATATAT
709790 ATAATATATATACTAT
1 ATAATATATATA-TAT
* * *
709806 AT-ATAT-TTTAAAA
1 ATAATATATATATAT
** *
709819 ATTGTATATAT-TTT
1 ATAATATATATATAT
*
709833 TTAATATATATATAT
1 ATAATATATATATAT
* *
709848 TTCATA-ATATATAT
1 ATAATATATATATAT
709862 AT-ATATATATATAT
1 ATAATATATATATAT
709876 ATTAATATATA
1 A-TAATATATA
709887 CATTTTTAAA
Statistics
Matches: 75, Mismatches: 14, Indels: 14
0.73 0.14 0.14
Matches are distributed among these distances:
13 6 0.08
14 44 0.59
15 14 0.19
16 11 0.15
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.50
Consensus pattern (15 bp):
ATAATATATATATAT
Found at i:712625 original size:19 final size:19
Alignment explanation
Indices: 712597--712648 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
712587 AATGCATTTA
* *
712597 ATGCACCGATGCACAAGCT
1 ATGCATCGATGCACAAGAT
* *
712616 ATGCATCGATGTACGAGAT
1 ATGCATCGATGCACAAGAT
712635 ATGCATCGATGCAC
1 ATGCATCGATGCAC
712649 CCTCAATGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.21
Consensus pattern (19 bp):
ATGCATCGATGCACAAGAT
Found at i:718506 original size:44 final size:45
Alignment explanation
Indices: 718444--718566 Score: 128
Period size: 44 Copynumber: 2.8 Consensus size: 45
718434 TTGTGCATAA
* * *
718444 TGCATCGATACACTATGAAATGCATAGATGCATCCCT-TTTAATG
1 TGCATCGATACACAATGAAATGCATCGATGCATCCCTCTTGAATG
* *
718488 TGCATCGATCCATC-ATGAAGATGCACCGATGCA--CCTCTTGAATG
1 TGCATCGATACA-CAATGAA-ATGCATCGATGCATCCCTCTTGAATG
* * *
718532 GGCATCGATGCACAATGACATGCATCGATGCATCC
1 TGCATCGATACACAATGAAATGCATCGATGCATCC
718567 GTCGGGTTTT
Statistics
Matches: 65, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
43 16 0.25
44 36 0.55
45 13 0.20
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (45 bp):
TGCATCGATACACAATGAAATGCATCGATGCATCCCTCTTGAATG
Found at i:720132 original size:27 final size:27
Alignment explanation
Indices: 720102--720154 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
720092 TCCCGGAGCC
* * *
720102 AGTTCTTCACGTGCTCCTCCTGCTCCT
1 AGTTATTCACGTGCTCCACCTCCTCCT
*
720129 AGTTATTCTCGTGCTCCACCTCCTCC
1 AGTTATTCACGTGCTCCACCTCCTCC
720155 GACACCGGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.09, C:0.42, G:0.13, T:0.36
Consensus pattern (27 bp):
AGTTATTCACGTGCTCCACCTCCTCCT
Found at i:720824 original size:16 final size:16
Alignment explanation
Indices: 720803--720836 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
720793 ATTTAACACA
720803 AAGGGGGAGAAGTGTT
1 AAGGGGGAGAAGTGTT
720819 AAGGGGGAGAAGTGTT
1 AAGGGGGAGAAGTGTT
720835 AA
1 AA
720837 AATAAGGGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.47, T:0.18
Consensus pattern (16 bp):
AAGGGGGAGAAGTGTT
Found at i:726955 original size:22 final size:22
Alignment explanation
Indices: 726930--726974 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
726920 GCTAAACAAT
726930 GTTAAACAAAACTCTTTAATGG
1 GTTAAACAAAACTCTTTAATGG
*
726952 GTTAAACAAAGCTCTTTAATGG
1 GTTAAACAAAACTCTTTAATGG
726974 G
1 G
726975 AGGCAACCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (22 bp):
GTTAAACAAAACTCTTTAATGG
Found at i:731084 original size:21 final size:21
Alignment explanation
Indices: 731060--731124 Score: 68
Period size: 20 Copynumber: 3.3 Consensus size: 21
731050 ATCATTGTAA
731060 TTATTTCTTTTTATATTTATT
1 TTATTTCTTTTTATATTTATT
*
731081 TTATTCCCTTTTT-TA-TTATT
1 TTATT-TCTTTTTATATTTATT
*
731101 TTA--T-TTTTCATATTTATT
1 TTATTTCTTTTTATATTTATT
731119 TTATTT
1 TTATTT
731125 TAATATTGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 11
0.72 0.06 0.22
Matches are distributed among these distances:
16 4 0.11
17 2 0.06
18 8 0.22
20 9 0.25
21 7 0.19
22 6 0.17
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (21 bp):
TTATTTCTTTTTATATTTATT
Found at i:731130 original size:17 final size:18
Alignment explanation
Indices: 731096--731136 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
731086 CCCTTTTTTA
*
731096 TTATTTTATTTTTCATAT
1 TTATTTTATTTTTAATAT
731114 TTATTTTA-TTTTAATAT
1 TTATTTTATTTTTAATAT
*
731131 TGATTT
1 TTATTT
731137 CATCTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (18 bp):
TTATTTTATTTTTAATAT
Found at i:732059 original size:41 final size:41
Alignment explanation
Indices: 731998--732077 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 41
731988 CGTTATGATT
*
731998 TTTTTCTTTTGCTAAAATTATTAATTCATCACACTAACTCC
1 TTTTTCTTTTACTAAAATTATTAATTCATCACACTAACTCC
* * * *
732039 TTTTTCTTTTACTGAGATTATTAATTCATTATACTAACT
1 TTTTTCTTTTACTAAAATTATTAATTCATCACACTAACT
732078 TATTTTCTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.29, C:0.17, G:0.04, T:0.50
Consensus pattern (41 bp):
TTTTTCTTTTACTAAAATTATTAATTCATCACACTAACTCC
Found at i:732107 original size:19 final size:21
Alignment explanation
Indices: 732079--732122 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
732069 ATACTAACTT
*
732079 ATTTTC-TTTTGTTTTTT-TC
1 ATTTTCTTTTTATTTTTTATC
*
732098 ATTTTGTTTTTATTTTTTATC
1 ATTTTCTTTTTATTTTTTATC
732119 ATTT
1 ATTT
732123 GCATTATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.24
20 10 0.48
21 6 0.29
ACGTcount: A:0.11, C:0.07, G:0.05, T:0.77
Consensus pattern (21 bp):
ATTTTCTTTTTATTTTTTATC
Found at i:733767 original size:11 final size:10
Alignment explanation
Indices: 733747--733771 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
733737 ATTGACCCCT
733747 AAAAATAAAA
1 AAAAATAAAA
733757 AAAAATAAAA
1 AAAAATAAAA
733767 AAAAA
1 AAAAA
733772 CATTTCCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:737153 original size:199 final size:202
Alignment explanation
Indices: 736773--737210 Score: 519
Period size: 200 Copynumber: 2.2 Consensus size: 202
736763 GTTAAATTTT
* * * ** * *
736773 AAACCGATGTCTTTAA-CCTAAGAAGAAGATCAAGGTTGGTTGTGATTTGGCAACAATGAACCAC
1 AAACCGAGGTCTTTAAGCC-AAGAAGAAGACCTAGGTTGACTATGATTTAGCAACAATGAACCAC
* * * * * **
736837 TTCTCAGTCAAAATTCGACATAGTTTAAGATGAGAAGAGATATTTATCGACCAAAAACTTTTGAG
65 TTCTCAGTCAAAATTCAACATAGCTTAAGATGAGAAAAGATATATATCAACCAAAAACTTCCGAG
* * *
736902 TTCGATTTCACTCAACTCGAGAGTGCATCAAATGCATGGTAGCATCGAGGAACTACCTTCTGATC
130 TTCGATTTCACTCAACTCGAAAGTGCATCAAACGCATGGTAGCATCGAGGAACTACCTTCCGATC
*
736967 AAAAT-TC
195 AAAATATA
* *
736974 TAATCGAGGTCTTTAAGCCAAGAAGAA-ACCTAGGTTGACTATGATTTAGCAACAA-GAAACCAC
1 AAACCGAGGTCTTTAAGCCAAGAAGAAGACCTAGGTTGACTATGATTTAGCAACAATG-AACCAC
* * * * * * *
737037 TTTTCAGTCATATTTCAACATAGCTTAAGTTGAGAAAAGCTATATGTCAACC-AAAGCTTCCGAG
65 TTCTCAGTCAAAATTCAACATAGCTTAAGATGAGAAAAGATATATATCAACCAAAAACTTCCGAG
* * * *
737101 TTTGATTTCACTCAGCTCGAAAGTGCATCGACCGCATGGTAGCAGT-GAGGAACTACCTTCCGAT
130 TTCGATTTCACTCAACTCGAAAGTGCATCAAACGCATGGTAGCA-TCGAGGAACTACCTTCCGAT
737165 CAAAATATA
194 CAAAATATA
*
737174 AAACCGAGGTCTTTAAGCCAGGAAGAAGACCTAGGTT
1 AAACCGAGGTCTTTAAGCCAAGAAGAAGACCTAGGTT
737211 ACCTAATTTA
Statistics
Matches: 198, Mismatches: 34, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
199 71 0.36
200 95 0.48
201 30 0.15
202 2 0.01
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (202 bp):
AAACCGAGGTCTTTAAGCCAAGAAGAAGACCTAGGTTGACTATGATTTAGCAACAATGAACCACT
TCTCAGTCAAAATTCAACATAGCTTAAGATGAGAAAAGATATATATCAACCAAAAACTTCCGAGT
TCGATTTCACTCAACTCGAAAGTGCATCAAACGCATGGTAGCATCGAGGAACTACCTTCCGATCA
AAATATA
Found at i:737336 original size:169 final size:168
Alignment explanation
Indices: 737048--737714 Score: 721
Period size: 169 Copynumber: 4.0 Consensus size: 168
737038 TTTCAGTCAT
* * * * *
737048 ATTT-CAACATAGCTTAAGTTGAGAA-AAGCTATATGTCAACCAAAGCTTCCGAGTTTGATTTCA
1 ATTTACAACATAACTTAAGTCGAGAAGAA-CTATATGTAAACCAAAGCTTTCGAGTTTGATTCCA
* * * *
737111 CTCAGCTCGAAAGTGCATCGACCGCATGGTAGCAGTGAGGAACTACCTTCCGATCAAAATATAAA
65 TTCAGCACGAGAGTGCATCGACCGCATGGTAGCAGTGAGGAACTACCTTTCGATCAAAAT-TAAA
*
737176 ACCGAGGTCTTTAAGCCAGGAAGAAGACCTAGGTTACCTA
129 ACCGAGGTCTTTAAGCCAAGAAGAAGACCTAGGTTACCTA
* ** * *
737216 ATTTACAACATAGCTTAAGTCGAGAAGAACTACCTATAAACCAAAGCTTTCGAGTTTAATTCCAT
1 ATTTACAACATAACTTAAGTCGAGAAGAACTATATGTAAACCAAAGCTTTCGAGTTTGATTCCAT
* * * **
737281 TCAGCACGAGAGTGCATCGACTGCATGATAGTAGTGAGGAACTATTTTTCGATCAAAATTCAAAA
66 TCAGCACGAGAGTGCATCGACCGCATGGTAGCAGTGAGGAACTACCTTTCGATCAAAATT-AAAA
* ** *
737346 CTGAGGTCTTTAAGCCAAGAAGAAGACAAAGGTTACCAA
130 CCGAGGTCTTTAAGCCAAGAAGAAGACCTAGGTTACCTA
* * * *
737385 ATTTACAACTTAACTAAAGTCGAGAAGAGCTATCTGTAAACCAAAGCTTTCGAGTTTGATTCCAT
1 ATTTACAACATAACTTAAGTCGAGAAGAACTATATGTAAACCAAAGCTTTCGAGTTTGATTCCAT
* * * * * * *
737450 TCAGTACGAGAGTGCATTGACCGTATGGTAGCAGCGAGTAACTACCTTTC-AGTAAAAATTCAAA
66 TCAGCACGAGAGTGCATCGACCGCATGGTAGCAGTGAGGAACTACCTTTCGA-TCAAAATTAAAA
** * *
737514 CCGATATCTTTAAGCCAAGAAGAATACCTAGGTTGCCTA
130 CCGAGGTCTTTAAGCCAAGAAGAAGACCTAGGTTACCTA
* * *
737553 ATTTACAGCATAACTTAAGTCGAGAAGAGCTATATGTAAA-CAAAGCTTTCAAGTTTGATTCCAT
1 ATTTACAACATAACTTAAGTCGAGAAGAACTATATGTAAACCAAAGCTTTCGAGTTTGATTCCAT
* * ** ** * ** * * * ** * **
737617 TCAACATGAGAGCACATTAACCGTATGGTAGCAACGATGAACTACCTTCCGGTTGAATTTTTAAC
66 TCAGCACGAGAGTGCATCGACCGCATGGTAGCAGTGAGGAACTACCTTTCGATCAAAATTAAAAC
* *
737682 CGAGGTTTTTAAGCCAAGAAGAAGACCAAGGTT
131 CGAGGTCTTTAAGCCAAGAAGAAGACCTAGGTT
737715 GACTGCGATT
Statistics
Matches: 419, Mismatches: 75, Indels: 11
0.83 0.15 0.02
Matches are distributed among these distances:
167 99 0.24
168 76 0.18
169 242 0.58
170 2 0.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (168 bp):
ATTTACAACATAACTTAAGTCGAGAAGAACTATATGTAAACCAAAGCTTTCGAGTTTGATTCCAT
TCAGCACGAGAGTGCATCGACCGCATGGTAGCAGTGAGGAACTACCTTTCGATCAAAATTAAAAC
CGAGGTCTTTAAGCCAAGAAGAAGACCTAGGTTACCTA
Found at i:738503 original size:22 final size:21
Alignment explanation
Indices: 738475--738547 Score: 85
Period size: 22 Copynumber: 3.3 Consensus size: 21
738465 ATTGCTATTG
*
738475 TATATATATGGCTTTGAAAATA
1 TATATATAT-GTTTTGAAAATA
738497 TATATATATAGTTTTGAAAAATA
1 TATATATAT-GTTTTG-AAAATA
738520 TATAATATAAT-TTTTGAAAATA
1 TAT-ATAT-ATGTTTTGAAAATA
738542 TATATA
1 TATATA
738548 ATATATATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
21 3 0.07
22 23 0.50
23 14 0.30
24 4 0.09
25 2 0.04
ACGTcount: A:0.47, C:0.01, G:0.08, T:0.44
Consensus pattern (21 bp):
TATATATATGTTTTGAAAATA
Found at i:738527 original size:24 final size:24
Alignment explanation
Indices: 738478--738554 Score: 97
Period size: 23 Copynumber: 3.3 Consensus size: 24
738468 GCTATTGTAT
* *
738478 ATATATGGCTTTG-AAAATATAT-
1 ATATATAGTTTTGAAAAATATATA
738500 ATATATAGTTTTGAAAAATATATA
1 ATATATAGTTTTGAAAAATATATA
*
738524 ATATA-ATTTTTGAAAATATATATA
1 ATATATAGTTTTGAAAA-ATATATA
738548 ATATATA
1 ATATATA
738555 TAATTTTTGA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.23
23 19 0.40
24 17 0.35
25 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.08, T:0.43
Consensus pattern (24 bp):
ATATATAGTTTTGAAAAATATATA
Found at i:738528 original size:28 final size:27
Alignment explanation
Indices: 738494--738567 Score: 86
Period size: 24 Copynumber: 2.8 Consensus size: 27
738484 GGCTTTGAAA
738494 ATATATATATATAGTTTTGAAAA-ATAT
1 ATATATATATATA-TTTTGAAAATATAT
738521 ATA-ATATA-AT-TTTTGAAAATATAT
1 ATATATATATATATTTTGAAAATATAT
738545 ATA-ATATATATAATTTTTGAAAA
1 ATATATATATAT-A-TTTTGAAAA
738568 CTTTAGTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
23 9 0.21
24 12 0.29
25 4 0.10
26 5 0.12
27 3 0.07
28 9 0.21
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (27 bp):
ATATATATATATATTTTGAAAATATAT
Found at i:738600 original size:12 final size:12
Alignment explanation
Indices: 738583--738608 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
738573 GTTTTTGAAA
738583 ATATAATATATT
1 ATATAATATATT
738595 ATATAATATATT
1 ATATAATATATT
738607 AT
1 AT
738609 GTAGTTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATATAATATATT
Found at i:738662 original size:56 final size:55
Alignment explanation
Indices: 738558--738664 Score: 135
Period size: 56 Copynumber: 1.9 Consensus size: 55
738548 ATATATATAA
* * * * *
738558 TTTTTGAAAACTTTAGTTTTTGAAAATATAATATATTATATAATATATTATGTAG
1 TTTTTGAAAACTATAATTTTTGAAAATATAATATAGTATAAAACATATTATGTAG
*
738613 TTTTTGAAAATCTATAATTTTT-AATATATATATATAGTATAAAACATATTAT
1 TTTTTGAAAA-CTATAATTTTTGAAAATATA-ATATAGTATAAAACATATTAT
738665 TATTACTACT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
55 17 0.39
56 27 0.61
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.49
Consensus pattern (55 bp):
TTTTTGAAAACTATAATTTTTGAAAATATAATATAGTATAAAACATATTATGTAG
Found at i:738705 original size:10 final size:9
Alignment explanation
Indices: 738676--738738 Score: 71
Period size: 10 Copynumber: 7.1 Consensus size: 9
738666 ATTACTACTA
738676 ATTTATTTT
1 ATTTATTTT
738685 -TTTA-TTT
1 ATTTATTTT
738692 -TTTATTTT
1 ATTTATTTT
738700 CATTTATTTT
1 -ATTTATTTT
738710 CATTTACTTTT
1 -ATTTA-TTTT
738721 ATTTATTTT
1 ATTTATTTT
738730 -TTTATTTT
1 ATTTATTTT
738738 A
1 A
738739 ATTTTTAGGA
Statistics
Matches: 49, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
7 7 0.14
8 15 0.31
9 4 0.08
10 19 0.39
11 4 0.08
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (9 bp):
ATTTATTTT
Found at i:739660 original size:2 final size:2
Alignment explanation
Indices: 739653--739680 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
739643 GATTGGGGTT
739653 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
739681 AGGGACTGGT
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):
TA
Found at i:740118 original size:21 final size:20
Alignment explanation
Indices: 740084--740122 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
740074 AAAAATTAAA
740084 ATATTATTTTTAATATTTAT
1 ATATTATTTTTAATATTTAT
*
740104 ATATTTTTATTTAATATTT
1 ATATTATT-TTTAATATTT
740123 TTTGTCCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
ATATTATTTTTAATATTTAT
Found at i:741836 original size:21 final size:20
Alignment explanation
Indices: 741810--741848 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
741800 ATTGGACAAA
741810 AAATATTAAATAAAAATATAT
1 AAATATTAAA-AAAAATATAT
*
741831 AAATATTAAAAATAATAT
1 AAATATTAAAAAAAATAT
741849 TTTAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATATTAAAAAAAATATAT
Found at i:747253 original size:21 final size:22
Alignment explanation
Indices: 747214--747256 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
747204 GAGGGGTCAT
747214 AAAACCCTACGGTGATGGCATC
1 AAAACCCTACGGTGATGGCATC
* *
747236 AAAA-CCTACTGTGGTGGCATC
1 AAAACCCTACGGTGATGGCATC
747257 TGAAATAGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (22 bp):
AAAACCCTACGGTGATGGCATC
Found at i:748904 original size:22 final size:23
Alignment explanation
Indices: 748870--748914 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
748860 AATATAAACT
748870 AATATTATAAATAAATAA-ATAA
1 AATATTATAAATAAATAACATAA
*
748892 AATATTCAT-AATAATTAACATAA
1 AATATT-ATAAATAAATAACATAA
748915 CACAATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (23 bp):
AATATTATAAATAAATAACATAA
Found at i:760535 original size:15 final size:15
Alignment explanation
Indices: 760497--760537 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
760487 AGAGACTAAT
*
760497 TTATTTTTATATAAA
1 TTATTTTTTTATAAA
*
760512 TTATTTTTTTATGAA
1 TTATTTTTTTATAAA
760527 TTATTTTTTTA
1 TTATTTTTTTA
760538 AATGTGGCGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (15 bp):
TTATTTTTTTATAAA
Found at i:765365 original size:11 final size:12
Alignment explanation
Indices: 765341--765378 Score: 76
Period size: 12 Copynumber: 3.2 Consensus size: 12
765331 TAACTTTTCA
765341 TTTTATTCCTTT
1 TTTTATTCCTTT
765353 TTTTATTCCTTT
1 TTTTATTCCTTT
765365 TTTTATTCCTTT
1 TTTTATTCCTTT
765377 TT
1 TT
765379 CGGTAGACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTATTCCTTT
Found at i:767406 original size:18 final size:18
Alignment explanation
Indices: 767383--767420 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
767373 ATGGCAATAA
*
767383 GACCAGCACTGTTGTATG
1 GACCAGCACTGCTGTATG
*
767401 GACCAGTACTGCTGTATG
1 GACCAGCACTGCTGTATG
767419 GA
1 GA
767421 TCAAAATGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (18 bp):
GACCAGCACTGCTGTATG
Found at i:778525 original size:21 final size:21
Alignment explanation
Indices: 778501--778541 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
778491 AGTTTATTTT
778501 TAAACTTTGTTTCAATTATCG
1 TAAACTTTGTTTCAATTATCG
778522 TAAACTTTGTTTCAATTATC
1 TAAACTTTGTTTCAATTATC
778542 AAACTTGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.15, G:0.07, T:0.49
Consensus pattern (21 bp):
TAAACTTTGTTTCAATTATCG
Found at i:778580 original size:33 final size:32
Alignment explanation
Indices: 778531--778607 Score: 109
Period size: 33 Copynumber: 2.4 Consensus size: 32
778521 GTAAACTTTG
* *
778531 TTTCAATTATCAAACTTGAAAGTTTTTAAGTA
1 TTTCAATTATCGAACTTGAAAGTATTTAAGTA
* *
778563 TTTGAATTTATCGAACTTGGAAGTATTTAAGTA
1 TTTCAA-TTATCGAACTTGAAAGTATTTAAGTA
778596 TTTCAATTATCG
1 TTTCAATTATCG
778608 TAAACTTTGT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
32 11 0.28
33 28 0.72
ACGTcount: A:0.34, C:0.09, G:0.13, T:0.44
Consensus pattern (32 bp):
TTTCAATTATCGAACTTGAAAGTATTTAAGTA
Found at i:779859 original size:42 final size:41
Alignment explanation
Indices: 779774--779874 Score: 123
Period size: 42 Copynumber: 2.5 Consensus size: 41
779764 TCCGGTTCGC
* *
779774 AAATGATCGATCCCTTCAC-AAAAGGTCGATCCCTCAATAA
1 AAATGATCGATCCCTTCTCTAGAAGGTCGATCCCTCAATAA
* * * *
779814 AAATGATTGATTCCTTCTCTAGAAGGATCGATCCCTCGATGA
1 AAATGATCGATCCCTTCTCTAGAAGG-TCGATCCCTCAATAA
*
779856 AAATTATCGATCCCTTCTC
1 AAATGATCGATCCCTTCTC
779875 CTAATAGATT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
40 16 0.32
41 5 0.10
42 29 0.58
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.29
Consensus pattern (41 bp):
AAATGATCGATCCCTTCTCTAGAAGGTCGATCCCTCAATAA
Found at i:781569 original size:21 final size:22
Alignment explanation
Indices: 781521--781571 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
781511 GTCATAAGGA
*
781521 GAGGAATTAGGGAATTCAAGTT
1 GAGGAATTGGGGAATTCAAGTT
* *
781543 TA-GAATTGGGGAATTCGA-TT
1 GAGGAATTGGGGAATTCAAGTT
781563 GAGGAATTG
1 GAGGAATTG
781572 AGAATTGAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 3 0.12
21 20 0.83
22 1 0.04
ACGTcount: A:0.33, C:0.04, G:0.33, T:0.29
Consensus pattern (22 bp):
GAGGAATTGGGGAATTCAAGTT
Found at i:785883 original size:57 final size:58
Alignment explanation
Indices: 785814--785924 Score: 181
Period size: 59 Copynumber: 1.9 Consensus size: 58
785804 GATATTTACC
*
785814 TTACTTATAAGTTACAA-TTGATGAAGTTGTGAGATTTTG-AATTTATAATAAATTATA
1 TTACTTATAAGTTACAATTTGATGAAGTTGTAAGA-TTTGAAATTTATAATAAATTATA
785871 TTACTTATAAGTTACAATTTTGATGAAGTTGTAAGATTTGAAATTTATAATAAA
1 TTACTTATAAGTTACAA-TTTGATGAAGTTGTAAGATTTGAAATTTATAATAAA
785925 CTACGATAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
57 17 0.34
58 4 0.08
59 29 0.58
ACGTcount: A:0.40, C:0.04, G:0.14, T:0.43
Consensus pattern (58 bp):
TTACTTATAAGTTACAATTTGATGAAGTTGTAAGATTTGAAATTTATAATAAATTATA
Found at i:786178 original size:23 final size:24
Alignment explanation
Indices: 786148--786197 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
786138 TTTTTATGTA
786148 ATAATTAA-TTAATAA-TTT-AAAT
1 ATAATTAACTTAA-AATTTTAAAAT
786170 ATAATTTAACTTAAAATTTTAAAAT
1 ATAA-TTAACTTAAAATTTTAAAAT
786195 ATA
1 ATA
786198 TAAAAGATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.17
23 6 0.25
24 7 0.29
25 7 0.29
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
ATAATTAACTTAAAATTTTAAAAT
Found at i:786628 original size:2 final size:2
Alignment explanation
Indices: 786621--786774 Score: 101
Period size: 2 Copynumber: 78.5 Consensus size: 2
786611 ATGTTTAATG
* *
786621 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA ACT -T AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * * *
786663 AT AT ACT -T AT AT AT AT AT AT GT GT GT AC AT AT AT -T AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
786704 AT TT AGT -T AT GT AT AT ACT -T AT AT AT AT AC AT AT ACT -T AT
1 AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT
*
786744 AT AT -T AT AT ACT TT AT A- AT -T AT AT AT AT AT A
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT A
786775 GCCATATGAT
Statistics
Matches: 121, Mismatches: 16, Indels: 30
0.72 0.10 0.18
Matches are distributed among these distances:
1 9 0.07
2 107 0.88
3 5 0.04
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:788597 original size:2 final size:2
Alignment explanation
Indices: 788590--788620 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
788580 CTGAAAATGT
788590 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
788621 GATAATGTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:788682 original size:28 final size:28
Alignment explanation
Indices: 788624--788682 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
788614 TATATATGAT
* **
788624 AATGTGCTAAGTGAAAAGGTTCTACGTG
1 AATGTGCTAAGTGAAAAAGTTCTACACG
788652 AATGTGCTAAGTGAAAAAGTTCTACACG
1 AATGTGCTAAGTGAAAAAGTTCTACACG
788680 AAT
1 AAT
788683 ATATCCTATG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (28 bp):
AATGTGCTAAGTGAAAAAGTTCTACACG
Found at i:788938 original size:23 final size:23
Alignment explanation
Indices: 788903--788959 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
788893 TCCTTTGGGA
*
788903 CAAAACTATGTGGCACTTCGGTG
1 CAAATCTATGTGGCACTTCGGTG
* *
788926 CAATTCTATGTGGCACTTTGGTG
1 CAAATCTATGTGGCACTTCGGTG
788949 CAAAT-TATGTG
1 CAAATCTATGTG
788960 AATTGTGGTG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 6 0.20
23 24 0.80
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.33
Consensus pattern (23 bp):
CAAATCTATGTGGCACTTCGGTG
Found at i:792399 original size:21 final size:20
Alignment explanation
Indices: 792255--792507 Score: 127
Period size: 20 Copynumber: 12.7 Consensus size: 20
792245 AAATAACCAA
* *
792255 CAAATTCGCAACGCG-ATCT
1 CAAATTCGCAACACGAATTT
** * *
792274 CAAATTCGCAATGCGAACTC
1 CAAATTCGCAACACGAATTT
* ** * *
792294 CAATTTCGCAATGCGAACTC
1 CAAATTCGCAACACGAATTT
* *
792314 CAATTTCGCAACAC-AGTTT
1 CAAATTCGCAACACGAATTT
*
792333 CCAAATTCGCAACACGAATTA
1 -CAAATTCGCAACACGAATTT
*** * *
792354 CTTTTTCACAACGCG-ATTT
1 CAAATTCGCAACACGAATTT
792373 CCAAATTCGCAACACGGAATTT
1 -CAAATTCGCAACAC-GAATTT
*
792395 CAAATTCGCAACTC-AATTT
1 CAAATTCGCAACACGAATTT
* * *
792414 CTGAATTCGCAACAAGATTTT
1 C-AAATTCGCAACACGAATTT
*
792435 CTAATTCGCAACACGAATTT
1 CAAATTCGCAACACGAATTT
**** * * *
792455 TGTTTTTGCAACTCGATTTT
1 CAAATTCGCAACACGAATTT
**
792475 TGAATTCGCAACACGAATTT
1 CAAATTCGCAACACGAATTT
* *
792495 TAATTTCGCAACA
1 CAAATTCGCAACA
792508 TCTTTTATTT
Statistics
Matches: 180, Mismatches: 46, Indels: 15
0.75 0.19 0.06
Matches are distributed among these distances:
19 25 0.14
20 129 0.72
21 22 0.12
22 4 0.02
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.30
Consensus pattern (20 bp):
CAAATTCGCAACACGAATTT
Found at i:792441 original size:101 final size:100
Alignment explanation
Indices: 792318--792506 Score: 238
Period size: 101 Copynumber: 1.9 Consensus size: 100
792308 GAACTCCAAT
792318 TTCGCAACACAGTTTCCAAATTCGCAACACGAATTACT-TTTTCACAACGCGATTTCCAAATTCG
1 TTCGCAACACAGTTTCCAAATTCGCAACACGAATT-CTGTTTTCACAACGCGATTTCCAAATTCG
792382 CAACACGGAATTTCAAATTCGCAACTCAATTTCTGAA
65 CAACAC-GAATTTCAAATTCGCAACTCAATTTCTGAA
* * * ** * ***
792419 TTCGCAACA-AGATTTTCTAATTCGCAACACGAATTTTGTTTTTGCAACTCGATTTTTGAATTCG
1 TTCGCAACACAG-TTTCCAAATTCGCAACACGAATTCTGTTTTCACAACGCGATTTCCAAATTCG
* *
792483 CAACACGAATTTTAATTTCGCAAC
65 CAACACGAATTTCAAATTCGCAAC
792507 ATCTTTTATT
Statistics
Matches: 75, Mismatches: 11, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
100 19 0.25
101 56 0.75
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.33
Consensus pattern (100 bp):
TTCGCAACACAGTTTCCAAATTCGCAACACGAATTCTGTTTTCACAACGCGATTTCCAAATTCGC
AACACGAATTTCAAATTCGCAACTCAATTTCTGAA
Found at i:794364 original size:21 final size:21
Alignment explanation
Indices: 794334--794385 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
794324 CCTGCTACAA
* *
794334 TGCTATAGTGCATCGATGCAT
1 TGCTACAGTGCATCGATGCAC
*
794355 TGCTACAGTGTATCGATGCAC
1 TGCTACAGTGCATCGATGCAC
794376 TGCTACAGTG
1 TGCTACAGTG
794386 ATTTTCGTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31
Consensus pattern (21 bp):
TGCTACAGTGCATCGATGCAC
Found at i:795065 original size:31 final size:31
Alignment explanation
Indices: 795027--795151 Score: 189
Period size: 31 Copynumber: 4.0 Consensus size: 31
795017 CCCGAAGGAC
* * *
795027 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
795058 CAGTCCATATATCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
795089 CAGTTCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
795120 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
795151 C
1 C
795152 CCTCGACCCT
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 86 1.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:795878 original size:11 final size:11
Alignment explanation
Indices: 795862--795890 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
795852 CATCAGTACA
795862 CAAAATAGCTT
1 CAAAATAGCTT
795873 CAAAATAGCTT
1 CAAAATAGCTT
795884 CAAAATA
1 CAAAATA
795891 TCCATGCATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.52, C:0.17, G:0.07, T:0.24
Consensus pattern (11 bp):
CAAAATAGCTT
Found at i:798151 original size:12 final size:12
Alignment explanation
Indices: 798134--798174 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
798124 AGCAAAAAGA
*
798134 AATCAAAATCGC
1 AATCAAAATCAC
*
798146 AATCAAAATCAA
1 AATCAAAATCAC
*
798158 AATCAAAATCCC
1 AATCAAAATCAC
798170 AATCA
1 AATCA
798175 CAACCGGCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.56, C:0.24, G:0.02, T:0.17
Consensus pattern (12 bp):
AATCAAAATCAC
Found at i:798155 original size:6 final size:6
Alignment explanation
Indices: 798133--798167 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
798123 AAGCAAAAAG
* *
798133 AAATCA AAATCG CAATCA AAATCA AAATCA AAATC
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATC
798168 CCAATCACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.60, C:0.20, G:0.03, T:0.17
Consensus pattern (6 bp):
AAATCA
Done.