Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015557.1 Corchorus olitorius cultivar O-4 contig15590, 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: 111076
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:5471 original size:30 final size:31
Alignment explanation
Indices: 5428--5529 Score: 79
Period size: 31 Copynumber: 3.3 Consensus size: 31
5418 TGCAATATTT
*
5428 TATACT-TCTAAAGATGCTGT-TTTTAT-TTA
1 TATACTGTCCAAAGATGCT-TATTTTATGTTA
*
5457 TGTACTGTCCAAAGAT-CTTACTTTTATGTTA
1 TATACTGTCCAAAGATGCTTA-TTTTATGTTA
* * *
5488 TATAGTTTCCAAAGATGC-TATCTTTTTGTTGA
1 TATACTGTCCAAAGATGCTTAT-TTTATGTT-A
*
5520 TATAATGTCC
1 TATACTGTCC
5530 CAAGGTTTCA
Statistics
Matches: 58, Mismatches: 8, Indels: 11
0.75 0.10 0.14
Matches are distributed among these distances:
28 1 0.02
29 7 0.12
30 15 0.26
31 25 0.43
32 10 0.17
ACGTcount: A:0.26, C:0.14, G:0.13, T:0.47
Consensus pattern (31 bp):
TATACTGTCCAAAGATGCTTATTTTATGTTA
Found at i:9962 original size:8 final size:8
Alignment explanation
Indices: 9949--9988 Score: 71
Period size: 8 Copynumber: 4.9 Consensus size: 8
9939 AATTGGGGTT
9949 TTTTTTTA
1 TTTTTTTA
9957 TTTTTTTA
1 TTTTTTTA
9965 TTTTTTTA
1 TTTTTTTA
9973 TTTTTTTA
1 TTTTTTTA
9981 TTTCTTTT
1 TTT-TTTT
9989 CCTAAGAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 27 0.87
9 4 0.13
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTTTA
Found at i:10097 original size:21 final size:21
Alignment explanation
Indices: 10072--10117 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
10062 TTGAGCAGTC
10072 GGATTTGAATTGATTTTGAGA
1 GGATTTGAATTGATTTTGAGA
10093 GGATTTGAATTGATTTTGAGA
1 GGATTTGAATTGATTTTGAGA
10114 GGAT
1 GGAT
10118 AACAAGAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.41
Consensus pattern (21 bp):
GGATTTGAATTGATTTTGAGA
Found at i:13127 original size:97 final size:97
Alignment explanation
Indices: 12970--13157 Score: 308
Period size: 97 Copynumber: 1.9 Consensus size: 97
12960 TATCCTATTC
*
12970 CTTTTGTATTCTCAGGCAAAAAAGGCAAAGAAAAATATGTAGGTACTTCATGTCAATGTGTCATC
1 CTTTAGTATTCTCAGGCAAAAAAGGCAAAG-AAAATATGTAGGTACTTCATGTCAATGTGTCATC
13035 GAATATAGGTTCAT-CCCATAAGACCAGCAGAGTA
65 GAATATAGGTTC-TCCCCAT-AGACCAGCAGAGTA
*
13069 CTTTAGTATTCTCAGGCAAAAAAGGCAAAG-AAATATGTAGGTTCTTCATGTCAATGTGTCATCG
1 CTTTAGTATTCTCAGGCAAAAAAGGCAAAGAAAATATGTAGGTACTTCATGTCAATGTGTCATCG
*
13133 AATGTAGGTTCTCCCCATAGACCAG
66 AATATAGGTTCTCCCCATAGACCAG
13158 AGTCCTGTAT
Statistics
Matches: 85, Mismatches: 3, Indels: 5
0.91 0.03 0.05
Matches are distributed among these distances:
96 8 0.09
97 48 0.56
99 29 0.34
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (97 bp):
CTTTAGTATTCTCAGGCAAAAAAGGCAAAGAAAATATGTAGGTACTTCATGTCAATGTGTCATCG
AATATAGGTTCTCCCCATAGACCAGCAGAGTA
Found at i:23347 original size:61 final size:62
Alignment explanation
Indices: 23249--23368 Score: 208
Period size: 61 Copynumber: 2.0 Consensus size: 62
23239 TTTAAGTTTA
*
23249 TAAGTTTATACGGACTGTCATTTTGCATCCAA-TTTTTTATTTTGATCAAAACGCATCCCTT
1 TAAGTTTATACGGACTGACATTTTGCATCCAACTTTTTTATTTTGATCAAAACGCATCCCTT
23310 TAAGTTTATACGGACT-ACAATTTTGCATCCAACTTTTTTATTTTGATCAAAACGCATCC
1 TAAGTTTATACGGACTGAC-ATTTTGCATCCAACTTTTTTATTTTGATCAAAACGCATCC
23369 TAAAGTTTTA
Statistics
Matches: 56, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
60 1 0.02
61 29 0.52
62 26 0.46
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.41
Consensus pattern (62 bp):
TAAGTTTATACGGACTGACATTTTGCATCCAACTTTTTTATTTTGATCAAAACGCATCCCTT
Found at i:24346 original size:35 final size:35
Alignment explanation
Indices: 24300--24368 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
24290 ATAATAATAT
24300 CTCCTATTGCCATCATACATTTGGTCTGTTGATAC
1 CTCCTATTGCCATCATACATTTGGTCTGTTGATAC
24335 CTCCTATTGCCATCATACATTTGGTCTGTTGATA
1 CTCCTATTGCCATCATACATTTGGTCTGTTGATA
24369 GAGTGGATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.20, C:0.25, G:0.14, T:0.41
Consensus pattern (35 bp):
CTCCTATTGCCATCATACATTTGGTCTGTTGATAC
Found at i:29522 original size:22 final size:22
Alignment explanation
Indices: 29490--29682 Score: 148
Period size: 22 Copynumber: 8.9 Consensus size: 22
29480 AATTACAGGG
* *
29490 AGATTAACAAAATCTCATAAGGA
1 AGATTATCAAAATTTCAT-AGGA
*
29513 AG-TTATCAAAA-ATCATAGGA
1 AGATTATCAAAATTTCATAGGA
*
29533 AGATTA-CAAAAATTCATAGGA
1 AGATTATCAAAATTTCATAGGA
* * **
29554 AGGTTTATTAAAATTTCATAGTT
1 A-GATTATCAAAATTTCATAGGA
*
29577 AGGTTATCAAAATTTCATATGG-
1 AGATTATCAAAATTTCATA-GGA
* * *
29599 AGTTTATCACAATTTCATAGGT
1 AGATTATCAAAATTTCATAGGA
*
29621 A-ATTATCAGAATTTCATAGCG-
1 AGATTATCAAAATTTCATAG-GA
* * *
29642 TGATTATCAAAATTTAATAGGGT
1 AGATTATCAAAATTTCATA-GGA
29665 AG-TTATCAAAATTTCATA
1 AGATTATCAAAATTTCATA
29683 AAAATATTTA
Statistics
Matches: 140, Mismatches: 20, Indels: 21
0.77 0.11 0.12
Matches are distributed among these distances:
20 11 0.08
21 34 0.24
22 78 0.56
23 17 0.12
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (22 bp):
AGATTATCAAAATTTCATAGGA
Found at i:29534 original size:20 final size:21
Alignment explanation
Indices: 29477--29555 Score: 76
Period size: 21 Copynumber: 3.8 Consensus size: 21
29467 TATAGCATCA
* *
29477 AAAAATT-ACAGGGAGATTA-
1 AAAAATTCATAGGAAGATTAC
29496 ACAAAATCTCATAAGGAAG-TTATC
1 A-AAAAT-TCAT-AGGAAGATTA-C
29520 AAAAA-TCATAGGAAGATTAC
1 AAAAATTCATAGGAAGATTAC
29540 AAAAATTCATAGGAAG
1 AAAAATTCATAGGAAG
29556 GTTTATTAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
19 1 0.02
20 17 0.34
21 18 0.36
22 4 0.08
23 9 0.18
24 1 0.02
ACGTcount: A:0.52, C:0.10, G:0.16, T:0.22
Consensus pattern (21 bp):
AAAAATTCATAGGAAGATTAC
Found at i:31064 original size:361 final size:364
Alignment explanation
Indices: 30393--31123 Score: 1308
Period size: 361 Copynumber: 2.0 Consensus size: 364
30383 GATAAACAAT
* *
30393 AGGTTAATCATTTAGATATTGTATGTTTTTAAACAGAAGACATTATATAAGCGAACTTTACAATT
1 AGGTTAATCATTTAGATATTGTATGTTTTTAAACAGAAAACATTATATAAGCAAACTTTACAATT
30458 TAGATGAAAAATATGTTTCAAGCAAATCCAGTTTTTCCATTTATAGATTAATAGTTGCTATTTAG
66 TAGATGAAAAATATGTTTCAAGCAAATCCAGTTTTTCCATTTATAGATTAATAGTTGCTATTTAG
30523 AAAAATAACAAATTTTAGATCATGTAACTTTGAAATATTTTTTTCAACATCAAATCATTGCATTC
131 AAAAATAACAAATTTTAGATCATGTAACTTTGAAATATTTTTTTCAACATCAAATCATTGCATTC
* * *
30588 AAGATAAGTAATTTTTAAACAATTCAAATTTTTTAACGTTCGGCGCGCCAGCACGAGCCGAACCA
196 AAGATAAGTAATTCTTAAACAATTCAAATTTTTTAACGCTCGACGCGCCAGCACGAGCCGAACCA
*
30653 CTTGAATATATGATAATTAATCAAATTGAATTCTGACTAAATTTAAAGTCCAGACTAGTCAAACC
261 CTTGAATATATGATAATTAATCAAATTGAATTCTGACTAAATTCAAAGTCCAGACTAGTCAAACC
30718 TGG-AAAAA-AAAAG-AAAAGGTCCCATAATATTATTGA
326 TGGAAAAAAGAAAAGAAAAAGGTCCCATAATATTATTGA
*
30754 AGGTTAATCATTTAGATATTGTATGTTTTTTAACAGAAAACATTATATAAGCAAACTTTACAATT
1 AGGTTAATCATTTAGATATTGTATGTTTTTAAACAGAAAACATTATATAAGCAAACTTTACAATT
30819 TAGATGAAAAATATGTTTCAAGCAAATCCA-TTTGTTCCATTTATAGATTAATAGTTGCTATTTA
66 TAGATGAAAAATATGTTTCAAGCAAATCCAGTTT-TTCCATTTATAGATTAATAGTTGCTATTTA
30883 GAAAAATAACAAATTTTAGATCATGTAACTTTGAAATATTTTTTTCAACATCAAATCATTGCATT
130 GAAAAATAACAAATTTTAGATCATGTAACTTTGAAATATTTTTTTCAACATCAAATCATTGCATT
*
30948 CAAGATAAGTAATTCTTAAACAATTCAAATTTTTTAACGCTCGACGCGCCAGCGCGAGCCGAACC
195 CAAGATAAGTAATTCTTAAACAATTCAAATTTTTTAACGCTCGACGCGCCAGCACGAGCCGAACC
* *
31013 ACTTGTATATATGATAATTAATCACATTGAATTCTGACTAAATTCAAAGTCCAGACTAGTCAAAC
260 ACTTGAATATATGATAATTAATCAAATTGAATTCTGACTAAATTCAAAGTCCAGACTAGTCAAAC
31078 CTGGAAAAAAAAAGAAAAGAAAAAGGTCCCATAATATTATTGA
325 CTGG---AAAAAAGAAAAGAAAAAGGTCCCATAATATTATTGA
31121 AGG
1 AGG
31124 GACTCCAAGA
Statistics
Matches: 353, Mismatches: 10, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
360 3 0.01
361 314 0.89
365 5 0.01
366 5 0.01
367 26 0.07
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (364 bp):
AGGTTAATCATTTAGATATTGTATGTTTTTAAACAGAAAACATTATATAAGCAAACTTTACAATT
TAGATGAAAAATATGTTTCAAGCAAATCCAGTTTTTCCATTTATAGATTAATAGTTGCTATTTAG
AAAAATAACAAATTTTAGATCATGTAACTTTGAAATATTTTTTTCAACATCAAATCATTGCATTC
AAGATAAGTAATTCTTAAACAATTCAAATTTTTTAACGCTCGACGCGCCAGCACGAGCCGAACCA
CTTGAATATATGATAATTAATCAAATTGAATTCTGACTAAATTCAAAGTCCAGACTAGTCAAACC
TGGAAAAAAGAAAAGAAAAAGGTCCCATAATATTATTGA
Found at i:36679 original size:3 final size:3
Alignment explanation
Indices: 36671--36726 Score: 57
Period size: 3 Copynumber: 20.0 Consensus size: 3
36661 TTTTGCATGG
* *
36671 GAT GAT GAT GAT GAT GAT G-T GAT GAG GAT -AT G-T GAT GAT GAA GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
36716 -CT GAT GAT GAT
1 GAT GAT GAT GAT
36727 ATATATAAAC
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
2 7 0.16
3 36 0.84
ACGTcount: A:0.32, C:0.02, G:0.34, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:36705 original size:13 final size:14
Alignment explanation
Indices: 36671--36722 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
36661 TTTTGCATGG
*
36671 GATGATGATGATGAT
1 GATG-TGATGAGGAT
36686 GATGTGATGAGGAT
1 GATGTGATGAGGAT
* *
36700 -ATGTGATGATGAA
1 GATGTGATGAGGAT
*
36713 GATCTGATGA
1 GATGTGATGA
36723 TGATATATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
13 11 0.34
14 17 0.53
15 4 0.12
ACGTcount: A:0.33, C:0.02, G:0.35, T:0.31
Consensus pattern (14 bp):
GATGTGATGAGGAT
Found at i:36707 original size:27 final size:27
Alignment explanation
Indices: 36676--36728 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
36666 CATGGGATGA
* *
36676 TGATGATGATGATGTGATGAGGATATG
1 TGATGATGAAGATCTGATGAGGATATG
*
36703 TGATGATGAAGATCTGATGATGATAT
1 TGATGATGAAGATCTGATGAGGATAT
36729 ATATAAACCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.32, C:0.02, G:0.32, T:0.34
Consensus pattern (27 bp):
TGATGATGAAGATCTGATGAGGATATG
Found at i:37915 original size:13 final size:13
Alignment explanation
Indices: 37897--37921 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
37887 GATAAGGGCC
37897 CTTTTTCTATTTT
1 CTTTTTCTATTTT
37910 CTTTTTCTATTT
1 CTTTTTCTATTT
37922 CCCTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (13 bp):
CTTTTTCTATTTT
Found at i:47290 original size:8 final size:8
Alignment explanation
Indices: 47279--47309 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
47269 CTTTCTTTTT
*
47279 GTTTTTTG
1 GTTTTTGG
47287 GTTTTTGG
1 GTTTTTGG
47295 GTTTTTGG
1 GTTTTTGG
47303 GTTTTTG
1 GTTTTTG
47310 ACTTTCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (8 bp):
GTTTTTGG
Found at i:47797 original size:8 final size:7
Alignment explanation
Indices: 47775--47812 Score: 51
Period size: 8 Copynumber: 5.3 Consensus size: 7
47765 AAACAAAACG
47775 AAAC-AA
1 AAACAAA
47781 AAACAAA
1 AAACAAA
47788 AAACAGAA
1 AAACA-AA
47796 AAACAGAA
1 AAACA-AA
47804 AAACAAA
1 AAACAAA
47811 AA
1 AA
47813 CGATACCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 4 0.13
7 11 0.37
8 15 0.50
ACGTcount: A:0.82, C:0.13, G:0.05, T:0.00
Consensus pattern (7 bp):
AAACAAA
Found at i:51525 original size:14 final size:13
Alignment explanation
Indices: 51495--51531 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
51485 ATTCTTGAAG
51495 AAAACAGAGC-AA
1 AAAACAGAGCAAA
51507 AAAACAGAGCAAGA
1 AAAACAGAGCAA-A
51521 AAAACAGAGCA
1 AAAACAGAGCA
51532 CTCTTTTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 10 0.43
13 1 0.04
14 12 0.52
ACGTcount: A:0.65, C:0.16, G:0.19, T:0.00
Consensus pattern (13 bp):
AAAACAGAGCAAA
Found at i:54072 original size:22 final size:23
Alignment explanation
Indices: 54045--54087 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
54035 CTTGCACTTT
*
54045 TTTTTTCTTTTCA-ATTTTCTCC
1 TTTTTTCTTTCCACATTTTCTCC
*
54067 TTTTTTGTTTCCACATTTTCT
1 TTTTTTCTTTCCACATTTTCT
54088 TCATGGCATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.09, C:0.21, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTTTTCTTTCCACATTTTCTCC
Found at i:70762 original size:108 final size:107
Alignment explanation
Indices: 70606--70881 Score: 403
Period size: 107 Copynumber: 2.6 Consensus size: 107
70596 ATAAAATTTT
*
70606 AATTTTAATTTGGA-CTAAACTTAGTG-AATTAGTTATATATTTTATTTCTAAAAACCCTATAAC
1 AATTTTAATTTGGAGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCT-AAAACCCTATAAC
* * * * * *
70669 AATAAGTTGTTAATTATGGAATTTACCCTTACAATACAAATAA
65 AATAAATTATTAATTATGAAATTTACCCTTAAAACAAAAATAA
*
70712 AATTTTAATTTGGAGCTAAACTTAGTGAAATTAGTTTTGTATTTTATTTCTAAAACCCTATAACA
1 AATTTTAATTTGGAGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAACA
* *
70777 ATAAATTATTAATTTTGAAATTTACTCTTAAAACAAAAATAA
66 ATAAATTATTAATTATGAAATTTACCCTTAAAACAAAAATAA
* * * *
70819 AATTTTAATTTGGGGCTACACTTAATGAAATTAGTTTTATATTTTATTTCTAAAACTCTATAA
1 AATTTTAATTTGGAGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAA
70882 AGAAAACCTT
Statistics
Matches: 153, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
106 14 0.09
107 118 0.77
108 21 0.14
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (107 bp):
AATTTTAATTTGGAGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAACA
ATAAATTATTAATTATGAAATTTACCCTTAAAACAAAAATAA
Found at i:85396 original size:15 final size:14
Alignment explanation
Indices: 85372--85401 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
85362 TCGATTTCTG
85372 AAAAAAAAAAAGAA
1 AAAAAAAAAAAGAA
85386 AAAAGAAAAAAAGAA
1 AAAA-AAAAAAAGAA
85401 A
1 A
85402 GGGAATATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGAA
Found at i:86730 original size:137 final size:137
Alignment explanation
Indices: 86484--86759 Score: 525
Period size: 137 Copynumber: 2.0 Consensus size: 137
86474 AATTCTCACG
*
86484 GAATGTGAGTTTAATTTGTAATTTGTTTGTTTGTTTATTTGGTTTGTAGGTAGGCATAGTTTCTA
1 GAATGTGAGTTTAATTTGTAATTTGATTGTTTGTTTATTTGGTTTGTAGGTAGGCATAGTTTCTA
*
86549 GTTTCTAGGTTCAATAGCAGGTATTATGAAATTTCAATTGTATTTGTTGGGGAAGGGGTTTGTTG
66 GTTTCTAGGTTCAAGAGCAGGTATTATGAAATTTCAATTGTATTTGTTGGGGAAGGGGTTTGTTG
86614 GCTCATA
131 GCTCATA
*
86621 GAATGTGAGTTTAATTTGTAATTTGATTGTTTGTTTATTTGGTTTGTAGGTAGGTATAGTTTCTA
1 GAATGTGAGTTTAATTTGTAATTTGATTGTTTGTTTATTTGGTTTGTAGGTAGGCATAGTTTCTA
86686 GTTTCTAGGTTCAAGAGCAGGTATTATGAAATTTCAATTGTATTTGTTGGGGAAGGGGTTTGTTG
66 GTTTCTAGGTTCAAGAGCAGGTATTATGAAATTTCAATTGTATTTGTTGGGGAAGGGGTTTGTTG
86751 GCTCATA
131 GCTCATA
86758 GA
1 GA
86760 TTAGCGTTTG
Statistics
Matches: 136, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
137 136 1.00
ACGTcount: A:0.22, C:0.05, G:0.27, T:0.45
Consensus pattern (137 bp):
GAATGTGAGTTTAATTTGTAATTTGATTGTTTGTTTATTTGGTTTGTAGGTAGGCATAGTTTCTA
GTTTCTAGGTTCAAGAGCAGGTATTATGAAATTTCAATTGTATTTGTTGGGGAAGGGGTTTGTTG
GCTCATA
Found at i:86784 original size:38 final size:38
Alignment explanation
Indices: 86728--86802 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
86718 TTCAATTGTA
*
86728 TTTGTTGGGGAAGGGGTTTGTTGGCTCATAGATTAGCG
1 TTTGTTGGGGAAGAGGTTTGTTGGCTCATAGATTAGCG
86766 TTTGTTGGGGAAGAGGTTTGTTGGCTCATAGATTAGC
1 TTTGTTGGGGAAGAGGTTTGTTGGCTCATAGATTAGC
86803 ATTTCGATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.17, C:0.08, G:0.37, T:0.37
Consensus pattern (38 bp):
TTTGTTGGGGAAGAGGTTTGTTGGCTCATAGATTAGCG
Found at i:89939 original size:19 final size:20
Alignment explanation
Indices: 89909--89972 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
89899 TTGACACTGT
89909 TTAGCAACTGTACAGATGAGA
1 TTAGC-ACTGTACAGATGAGA
* *
89930 TTA-CACTGTACATATTAGA
1 TTAGCACTGTACAGATGAGA
* *
89949 TTAGGTACTATACAGATGAGA
1 TTA-GCACTGTACAGATGAGA
89970 TTA
1 TTA
89973 TTAGAGCAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 16 0.46
20 1 0.03
21 18 0.51
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (20 bp):
TTAGCACTGTACAGATGAGA
Found at i:93663 original size:14 final size:14
Alignment explanation
Indices: 93641--93670 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
93631 TGTATCTTGC
93641 AATAATTACATTGT
1 AATAATTACATTGT
*
93655 AATATTTACATTGT
1 AATAATTACATTGT
93669 AA
1 AA
93671 CATGAGGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (14 bp):
AATAATTACATTGT
Found at i:95245 original size:23 final size:23
Alignment explanation
Indices: 95219--95262 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
95209 TTAAATCTAA
*
95219 TATCCTTATACCT-ATTTTATTTT
1 TATCATTATA-CTAATTTTATTTT
*
95242 TATCATTCTACTAATTTTATT
1 TATCATTATACTAATTTTATT
95263 AAAAAACTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 16 0.89
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (23 bp):
TATCATTATACTAATTTTATTTT
Found at i:95801 original size:16 final size:16
Alignment explanation
Indices: 95761--95794 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
95751 TTGGCCCAAA
*
95761 GTCACTCGGATTTTGG
1 GTCATTCGGATTTTGG
*
95777 GTCATTCGGCTTTTGG
1 GTCATTCGGATTTTGG
95793 GT
1 GT
95795 TTTTCGGGTC
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:0.09, C:0.18, G:0.32, T:0.41
Consensus pattern (16 bp):
GTCATTCGGATTTTGG
Found at i:100319 original size:322 final size:319
Alignment explanation
Indices: 99075--100939 Score: 1644
Period size: 322 Copynumber: 5.7 Consensus size: 319
99065 AAAATTTTGC
* * *
99075 AAAAATTGACCCGAAAATTTTTTTCCTTAATTTTTTTTGCCATAATA-TTCAGAAAAAAAGTATA
1 AAAAACTGACCCG-AAA-TTTTTTCCTGAA--TTTTTTGCCACAATACTT-AG-AAAAAA-TATA
* * *
99139 TAATTCAACGCAAAAAAGATTGAAGGGTATTTCACGATTCTGATATCATTTTTCCATTTTTTT-T
59 TAATTCAACGCAAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCATTTTTCCATTTTTTTCT
* *
99203 GAATTTATTTCTAATTAAATCGAAACAAGATTTAGATGTTCGTAAAAACAAATCCTTAAATCCAA
124 GAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAA
* * * * * **
99268 TGTGACTG-GAATTTGATTCGATGAATATAAATATTTCAAGGAGTCTTTACGCCAAAAATCATGC
189 TGTGGCTGAG-ATTTGGTTAGATGAATATAGATATTTCAAGGAATCTTTACTTCAAAAATCATGC
* * *
99332 AAAATTGA-TCTGA-GACCTTGGAACGCGTTTTTAG-AAAAACACCGTGATGGTACATGATTTCA
253 AAAATTGAGTC-GAGGTCC--CGAACGCGTTTTTAGCAAAAA-ACCGTGATGTTA-AT-A---CA
* *
99394 GCTAAAATTT-TGC-
309 -C---GATTTCGGCT
* * * *
99407 AAAAACTGACCCGAAAATTTTTTTCTTAATTTTTTG-CAGAATACTCAGAAAAAATATATAATTC
1 AAAAACTGACCCG-AAATTTTTTCCTGAATTTTTTGCCACAATACTTAGAAAAAATATATAATTC
* * * * * *
99471 AACACCAGAAAA-ATTGAAGGGTTTTTTACACTTCTAATATCGTTTTTCCATTTTTTTTTCTAAA
65 AAC-GCAAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCATTTTTCCA--TTTTTTTCTGAA
* * *
99535 TTTATTTCTAATTAAATCGAAACAAGATTCAGATGATTGTAAAAACAAATTCTTAAATCCAAATG
127 TTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCC-AATG
* * *
99600 TGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGTAGTCTTT-CTCTCTAAAATCATGCAA
191 TGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAATCTTTACT-TCAAAAATCATGCAA
* * * * * * *
99664 AATTGAGCCGAGGCCCCGAAAAGCGTTTTTA-CTAAAAAAAACCTTGATGGTTAGTGCAGGATTT
255 AATTGAGTCGAGGTCCCG-AACGCGTTTTTAGC---AAAAAACCGTGAT-GTTAATACACGATTT
99728 CGGCTAAAATTTT
315 CGGC--------T
* ** * * * *
99741 GCAAAAACTTATTCGAAATTTTTTTCCCTTAATTCTTTGCCACAATTCTTAGAAAAATTATATAA
1 --AAAAACTGACCCGAAA-TTTTTT-CCTGAATTTTTTGCCACAATACTTAGAAAAAATATATAA
* * *
99806 TTCAACGCCAAAATA-ATTGAAGGGTTTTTCACGCTTCTAATAT--TGTTTTCTGATCTTTTT-T
62 TTCAACG-CAAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCAT-TTTTC-CATTTTTTTCT
* * * * *
99867 GAATTTATTTTTATTTAAATCGAAACAAGATTCAAATGCTCAT-AAAACAAAT-CTGTAATTCCA
124 GAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCT-TAAATCCA
** * * * *
99930 ATGTGGCTGAGATTTGGTTAGATGAATATAGATGCTTCAAGGATTGTTTAAGTT-AAAAATTATG
188 ATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAATCTTT-ACTTCAAAAATCATG
* *
99994 CAAAACTGAGTCG-GGTCCCGAATCGCGTTTTTAGCTAAAAAACCGTGATGTTTAATACATGATT
252 CAAAATTGAGTCGAGGTCCCGAA-CGCGTTTTTAGC-AAAAAACCGTGATG-TTAATACACGATT
100058 TCGGCT
314 TCGGCT
* * * * * *
100064 AAAAACTGACCCGTAATTTTTTCCTGAATTATTTCCCAAAATAATTAGAAAAAAAAATATAATTC
1 AAAAACTGACCCGAAATTTTTTCCTGAATTTTTTGCCACAATACTTAG-AAAAAATATATAATTC
* * * ** * *
100129 AACGTAAAAAAGATTGACGGGCTTTTCACGCTTCTAATATTGTTTTTCCATTTTTTTCCGAATTA
65 AACGCAAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCATTTTTCCATTTTTTTCTGAATTT
* * * *
100194 AATTCTAATTAAATCGAAACAAGATTCAGAAGCTCGTAAAAGCAAATGCTTAAATCCAATGTGGC
130 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC
* *
100259 TAAGATTTGGTTTGATGAATATAGATATTTCAAGGAATCTTTACTTCAAAAATCATGC-AAATTG
195 TGAGATTTGGTTAGATGAATATAGATATTTCAAGGAATCTTTACTTCAAAAATCATGCAAAATTG
* * * * *
100323 AGCCGAGGTTCCAGAACGCGGTTTTAGGCAAAAACCCGTGATGGTTAGTACACGATTTCAGTTAA
260 AGTCGAGG-TCCCGAACGCGTTTTTA-GCAAAAAACCGTGAT-GTTAATACACGATTTC-G----
**
100388 AATTTT
317 ---GCT
* * * *
100394 ACAAAAACTGAACCGAAACGTTTTTCC-GCAATTTTTTGCCACAATACTCAGAAAAATTATATAA
1 --AAAAACTGACCCGAAA-TTTTTTCCTG-AATTTTTTGCCACAATACTTAGAAAAAATATATAA
* * * * *
100458 TTCAATGCAAAAAAAATTTGAATGG-TTTTCACGCTTTTAATATCATTTTTCCATTTTTTTTTCC
62 TTCAACGCAAAAAAGA-TTGAAGGGTTTTTCACGCTTCTAATATCATTTTTCCA--TTTTTTTCT
* * * *
100522 GAATTTATTTCTAATTAAATCGAAATAAGATTCATATCCTCGTAAAAACAAATCCTTAAATCCTA
124 GAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAA
** * * * * * *
100587 TGTTACTGAGATTTGGTTAGATGAACATAGATATTTTAAGGAATC-TAAATGCAAAAAACCATGC
189 TGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAATCTTTACTTC-AAAAATCATGC
* * * * * * * **
100651 AAAACTGAGTCGAGG-CCCG-ACACGTTTTCAGCCAAAGATCGTGATGGTAACGTAGGCGATTTC
253 AAAATTGAGTCGAGGTCCCGAACGCGTTTTTAGCAAAAAACCGTGATGTTAA--TACACGATTTC
100714 GGCT
316 GGCT
* * * ** *
100718 AAAATCTGACCTGAAAATTTTATT-CTCAATTTTTTTACACAATACTTTGAAAAAATATATAATT
1 AAAAACTGACCCG-AAATTTT-TTCCTGAATTTTTTGCCACAATACTTAGAAAAAATATATAATT
* *
100782 CAACGCCAAAAAGATTAAAGGGTTTTTCACGCTTCTAATATCATTTTTCCATTTTTTTCTGAATT
64 CAACGCAAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCATTTTTCCATTTTTTTCTGAATT
* *
100847 AATCTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
129 TATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
*
100912 CTGAAATTTGGTTCA-ATGAATATAGATA
194 CTGAGATTTGGTT-AGATGAATATAGATA
100940 GCTCAACTTG
Statistics
Matches: 1255, Mismatches: 202, Indels: 164
0.77 0.12 0.10
Matches are distributed among these distances:
319 25 0.02
320 151 0.12
321 72 0.06
322 189 0.15
323 18 0.01
324 5 0.00
325 2 0.00
326 45 0.04
327 12 0.01
328 17 0.01
329 69 0.05
330 80 0.06
331 57 0.05
332 120 0.10
333 112 0.09
334 130 0.10
335 53 0.04
336 23 0.02
337 16 0.01
338 59 0.05
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (319 bp):
AAAAACTGACCCGAAATTTTTTCCTGAATTTTTTGCCACAATACTTAGAAAAAATATATAATTCA
ACGCAAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCATTTTTCCATTTTTTTCTGAATTTA
TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCT
GAGATTTGGTTAGATGAATATAGATATTTCAAGGAATCTTTACTTCAAAAATCATGCAAAATTGA
GTCGAGGTCCCGAACGCGTTTTTAGCAAAAAACCGTGATGTTAATACACGATTTCGGCT
Found at i:100848 original size:654 final size:648
Alignment explanation
Indices: 99026--100939 Score: 2003
Period size: 654 Copynumber: 2.9 Consensus size: 648
99016 CGTGATTCCA
* * ** * * *
99026 GTTTTA-GCAAAAAAACCGTGATGG-TA-TATA--ATTTTGGCTAAAATTTTGCAAAAATTGACC
1 GTTTTACGAAAAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTACAAAAACTGAAC
** * * * *
99086 CGAAAATTTTTTTCCTTAATTTTTTTTGCCATAATATTCAGAAAAAAAGTATATAATTCAACGCA
66 CG-AAACGTTTTTCCCTAA--TTTTTTGCCACAATACTCAG--AAAAATTATATAATTCAACGCA
* * *
99151 AAAAAGATTGAAGGGTATTTCACGATTCTGATATCATTTTTCCATTTTTTTTGAATTTATTTCTA
126 AAAAAAATTGAAGGGT-TTTCACGCTTCTAATATCATTTTTCCATTTTTTTTGAATTTATTTCTA
* * *
99216 ATTAAATCGAAACAAGATTTAGATGTTCGTAAAAACAAATCCTTAAATCCAATGTGACTG-GAAT
190 ATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTGACTGAG-AT
* * * * * * *
99280 TTGATTCGATGAATATAAATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAATTGA-TCTG
254 TTGGTTAGATGAATATAGATATTTCAAGGAATC-TTAAGCAAAAAATCATGCAAAACTGAGTC-G
* * * *
99344 AGACCTTGGAACGCGTTTTTAG-AAAAACACCGTGATGGTACATGATTTCAGCTAAAATTT-TGC
317 AGGCC--CGAACGCGTTTTTAGCAAAAA-ACCGTGATGGTA-A-G---T-AGC---GATTTCGGC
* * * *
99407 -AAAAACTGACCCGAAAATTTTTTTCTTAA-TTTTTTGCAGAATACTCAGAAAAAATATATAATT
370 TAAAAACTGACCCGAAAA-TTTTTTCTCAATTTTTTTACAAAATACTTAGAAAAAATATATAATT
* * * *
99470 CAACACCAGAAAA-ATTGAAGGGTTTTTTACACTTCTAATATCGTTTTTCCATTTTTTTTTCTAA
434 CAACGCCA-AAAAGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCA--TTTTTTTCTGA
* * * *
99534 ATTTATTTCTAATTAAATCGAAACAAGATTCAGATGATTGTAAAAACAAATTCTTAAATCCAAAT
496 A-TTAATTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCC-AAT
* * * *
99599 GTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGTAGTCTTTCTCTCTAAAATCATGCAA
559 GTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAATCTTTCTCTCAAAAATCATGCAA
*
99664 AATTGAGCCGAGGCCCCGAAAAGCG
624 AATTGAGCCGAGGCCCAGAAAAGCG
* * * * * * * * **
99689 TTTTTACTAAAAAAAACCTTGATGGTTAGTGCAGGATTTCGGCTAAAATTTTGCAAAAACTTATT
1 GTTTTACGAAAAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTACAAAAACTGAAC
** * * * *
99754 CGAAATTTTTTTCCCTTAATTCTTTGCCACAATTCTTAGAAAAATTATATAATTCAACGCCAAAA
66 CGAAACGTTTTTCCC-TAATTTTTTGCCACAATACTCAGAAAAATTATATAATTCAACGCAAAAA
* * * * *
99819 TAATTGAAGGGTTTTTCACGCTTCTAATAT--TGTTTTCTGATCTTTTTTGAATTTATTTTTATT
130 AAATTGAAGGG-TTTTCACGCTTCTAATATCAT-TTTTC-CATTTTTTTTGAATTTATTTCTAAT
* * *
99882 TAAATCGAAACAAGATTCAAATGCTCAT-AAAACAAAT-CTGTAATTCCAATGTGGCTGAGATTT
192 TAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCT-TAAATCCAATGTGACTGAGATTT
** * * ** *
99945 GGTTAGATGAATATAGATGCTTCAAGGATTGTTTAAGTTAAAAATTATGCAAAACTGAGTCG-GG
256 GGTTAGATGAATATAGATATTTCAAGGAAT-CTTAAGCAAAAAATCATGCAAAACTGAGTCGAGG
*
100009 TCCCGAATCGCGTTTTTAGCTAAAAAACCGTGATGTTTAA-TA-CATGATTTCGGCTAAAAACTG
320 -CCCGAA-CGCGTTTTTAGC-AAAAAACCGTGATG-GTAAGTAGC--GATTTCGGCTAAAAACTG
* * * ** * * **
100072 ACCCG-TAATTTTTTCCTGAATTATTTCCCAAAATAATTAGAAAAAAAAATATAATTCAACGTAA
379 ACCCGAAAATTTTTT-CTCAATTTTTTTACAAAATACTTAG-AAAAAATATATAATTCAACGCCA
* * * *
100136 AAAAGATTGACGGGCTTTTCACGCTTCTAATATTGTTTTTCCATTTTTTTCCGAATTAAATTCTA
442 AAAAGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCTGAATT-AATTCTA
* * *
100201 ATTAAATCGAAACAAGATTCAGAAGCTCGTAAAAGCAAATGCTTAAATCCAATGTGGCTAAGATT
506 ATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATT
*
100266 TGGTTTGATGAATATAGATATTTCAAGGAATCTTTACT-TCAAAAATCATGC-AAATTGAGCCGA
571 TGGTTAGATGAATATAGATATTTCAAGGAATCTTT-CTCTCAAAAATCATGCAAAATTGAGCCGA
* *
100329 GGTTCCAG-AACGCG
635 GG-CCCAGAAAAGCG
** * *
100343 GTTTTA-GGCAAAAACCCGTGATGGTTAGTACACGATTTCAGTTAAAATTTTACAAAAACTGAAC
1 GTTTTACGAAAAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTACAAAAACTGAAC
*
100407 CGAAACGTTTTTCCGC-AATTTTTTGCCACAATACTCAGAAAAATTATATAATTCAATGCAAAAA
66 CGAAACGTTTTTCC-CTAATTTTTTGCCACAATACTCAGAAAAATTATATAATTCAACGCAAAAA
* *
100471 AAATTTGAATGGTTTTCACGCTTTTAATATCATTTTTCCATTTTTTTTTCCGAATTTATTTCTAA
130 AAA-TTGAAGGGTTTTCACGCTTCTAATATCATTTTTCCA-TTTTTTTT--GAATTTATTTCTAA
* * * * *
100536 TTAAATCGAAATAAGATTCATATCCTCGTAAAAACAAATCCTTAAATCCTATGTTACTGAGATTT
191 TTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTGACTGAGATTT
* * * *
100601 GGTTAGATGAACATAGATATTTTAAGGAATCTAAATGCAAAAAACCATGCAAAACTGAGTCGAGG
256 GGTTAGATGAATATAGATATTTCAAGGAATCTTAA-GCAAAAAATCATGCAAAACTGAGTCGAGG
* * * * * * *
100666 CCCG-ACACGTTTTCAGCCAAAGATCGTGATGGTAACGTAGGCGATTTCGGCTAAAATCTGACCT
320 CCCGAACGCGTTTTTAGCAAAAAACCGTGATGGTAA-GTA-GCGATTTCGGCTAAAAACTGACCC
* *
100730 GAAAATTTTATTCTCAATTTTTTTACACAATACTTTGAAAAAATATATAATTCAACGCCAAAAAG
383 GAAAATTTT-TTCTCAATTTTTTTACAAAATACTTAGAAAAAATATATAATTCAACGCCAAAAAG
* *
100795 ATTAAAGGGTTTTTCACGCTTCTAATATCATTTTTCCATTTTTTTCTGAATTAATCTCTAATTAA
447 ATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCTGAATTAAT-TCTAATTAA
100860 ATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAA-ATTTGGT
511 ATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCT-AAGATTTGGT
100924 TCA-ATGAATATAGATA
575 T-AGATGAATATAGATA
100940 GCTCAACTTG
Statistics
Matches: 1044, Mismatches: 160, Indels: 103
0.80 0.12 0.08
Matches are distributed among these distances:
652 66 0.06
653 90 0.09
654 211 0.20
655 141 0.14
656 154 0.15
657 35 0.03
658 53 0.05
661 3 0.00
662 15 0.01
663 96 0.09
664 118 0.11
665 3 0.00
666 17 0.02
667 12 0.01
668 30 0.03
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (648 bp):
GTTTTACGAAAAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTACAAAAACTGAAC
CGAAACGTTTTTCCCTAATTTTTTGCCACAATACTCAGAAAAATTATATAATTCAACGCAAAAAA
AATTGAAGGGTTTTCACGCTTCTAATATCATTTTTCCATTTTTTTTGAATTTATTTCTAATTAAA
TCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTGACTGAGATTTGGTTA
GATGAATATAGATATTTCAAGGAATCTTAAGCAAAAAATCATGCAAAACTGAGTCGAGGCCCGAA
CGCGTTTTTAGCAAAAAACCGTGATGGTAAGTAGCGATTTCGGCTAAAAACTGACCCGAAAATTT
TTTCTCAATTTTTTTACAAAATACTTAGAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGG
TTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCTGAATTAATTCTAATTAAATCGAAACAA
GATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGGTTAGATGAATAT
AGATATTTCAAGGAATCTTTCTCTCAAAAATCATGCAAAATTGAGCCGAGGCCCAGAAAAGCG
Found at i:101065 original size:21 final size:21
Alignment explanation
Indices: 101039--101085 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
101029 TCTCACAGAG
101039 AGGTTATCAAAA-ATCATAAGA
1 AGGTTA-CAAAATATCATAAGA
* *
101060 AGGTTACAAAATTTCATAGGA
1 AGGTTACAAAATATCATAAGA
101081 AGGTT
1 AGGTT
101086 TATTAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.28
Consensus pattern (21 bp):
AGGTTACAAAATATCATAAGA
Found at i:101119 original size:22 final size:22
Alignment explanation
Indices: 100999--101122 Score: 94
Period size: 22 Copynumber: 5.7 Consensus size: 22
100989 CATACTATAG
* *
100999 TATCAAAATATT-ATAGGGAGAT
1 TATCAAAAT-TTCATAGGAAGGT
* * *
101021 TAACAAAATCTCACA-GAGAGGT
1 TATCAAAATTTCATAGGA-AGGT
* *
101043 TATCAAAA-ATCATAAGAAGGT
1 TATCAAAATTTCATAGGAAGGT
101064 TA-CAAAATTTCATAGGAAGGTT
1 TATCAAAATTTCATAGGAAGG-T
* **
101086 TATTAAAATTTCATAGTTAGGT
1 TATCAAAATTTCATAGGAAGGT
*
101108 TATCAAAGTTTCATA
1 TATCAAAATTTCATA
101123 TTTCGTAGGT
Statistics
Matches: 81, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
20 5 0.06
21 22 0.27
22 39 0.48
23 15 0.19
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (22 bp):
TATCAAAATTTCATAGGAAGGT
Found at i:101168 original size:22 final size:22
Alignment explanation
Indices: 101140--101196 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
101130 GGTAAATTAT
* *
101140 CAAAATTCCATAACGTGGTTAC
1 CAAAATTTCATAACGTAGTTAC
* * *
101162 CAAAATTTAATAAGGTAGTTAT
1 CAAAATTTCATAACGTAGTTAC
101184 CAAAATTTCATAA
1 CAAAATTTCATAA
101197 AAATATTCAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.32
Consensus pattern (22 bp):
CAAAATTTCATAACGTAGTTAC
Found at i:101301 original size:2 final size:2
Alignment explanation
Indices: 101294--101322 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
101284 GGATATGTAT
101294 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 T
101323 TATCATGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.