Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2322
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: 72253
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Found at i:2900 original size:20 final size:21
Alignment explanation
Indices: 2860--2911 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
2850 CAATAGGGTG
*
2860 ATGTATCGATACATAAGTG-A
1 ATGTATCGATACATAACTGAA
**
2880 ATGTATCGATACATGTCTGAA
1 ATGTATCGATACATAACTGAA
2901 ATGTATCGATA
1 ATGTATCGATA
2912 TAAGACTATG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATAACTGAA
Found at i:3814 original size:479 final size:479
Alignment explanation
Indices: 2917--3878 Score: 1924
Period size: 479 Copynumber: 2.0 Consensus size: 479
2907 CGATATAAGA
2917 CTATGTCGAAGCAAATTTGCATTCTAGAATGAAAATGTATTGATACATTTTTCATTGTATCAATA
1 CTATGTCGAAGCAAATTTGCATTCTAGAATGAAAATGTATTGATACATTTTTCATTGTATCAATA
2982 CATTTTAGGTTTTTTACTCAAATGTATTAATACATTTTTCAATGTATCGATACATGCAGGTAATT
66 CATTTTAGGTTTTTTACTCAAATGTATTAATACATTTTTCAATGTATCGATACATGCAGGTAATT
3047 TTGCACATTCCGTGACATTTTCAGCTTTTTCCAAACACCTCCAATGCTCGATTCAAATGAGTTTT
131 TTGCACATTCCGTGACATTTTCAGCTTTTTCCAAACACCTCCAATGCTCGATTCAAATGAGTTTT
3112 TGCATCATAAATGATAAGAATTCATGTTAATATCAAATGTCAAACTTCAAATTCAAGCTCTGATC
196 TGCATCATAAATGATAAGAATTCATGTTAATATCAAATGTCAAACTTCAAATTCAAGCTCTGATC
3177 ATTTTTGGAGCACAAAGCCTCGCATTAATAAGAGATGGCATGATGAAGCACATTGTCATCATAAG
261 ATTTTTGGAGCACAAAGCCTCGCATTAATAAGAGATGGCATGATGAAGCACATTGTCATCATAAG
3242 GTTGCTAAGCATTCACTCCAACTACCCTATCTTCCTCTTAAGCTCTGACTAGCCACCATAACCTT
326 GTTGCTAAGCATTCACTCCAACTACCCTATCTTCCTCTTAAGCTCTGACTAGCCACCATAACCTT
3307 TAATCTCAGCCACCCTACTTAGCCACCACTGCAAGCAAACTCATCATTAATGTTAGAAAATGGAA
391 TAATCTCAGCCACCCTACTTAGCCACCACTGCAAGCAAACTCATCATTAATGTTAGAAAATGGAA
3372 AAGTCTCAAATACCCTCATTTTGG
456 AAGTCTCAAATACCCTCATTTTGG
3396 CTATGTCGAAGCAAATTTGCATTCTAGAATGAAAATGTATTGATACATTTTTCATTGTATCAATA
1 CTATGTCGAAGCAAATTTGCATTCTAGAATGAAAATGTATTGATACATTTTTCATTGTATCAATA
3461 CATTTTAGGTTTTTTACTCAAATGTATTAATACATTTTTCAATGTATCGATACATGCAGGTAATT
66 CATTTTAGGTTTTTTACTCAAATGTATTAATACATTTTTCAATGTATCGATACATGCAGGTAATT
3526 TTGCACATTCCGTGACATTTTCAGCTTTTTCCAAACACCTCCAATGCTCGATTCAAATGAGTTTT
131 TTGCACATTCCGTGACATTTTCAGCTTTTTCCAAACACCTCCAATGCTCGATTCAAATGAGTTTT
3591 TGCATCATAAATGATAAGAATTCATGTTAATATCAAATGTCAAACTTCAAATTCAAGCTCTGATC
196 TGCATCATAAATGATAAGAATTCATGTTAATATCAAATGTCAAACTTCAAATTCAAGCTCTGATC
3656 ATTTTTGGAGCACAAAGCCTCGCATTAATAAGAGATGGCATGATGAAGCACATTGTCATCATAAG
261 ATTTTTGGAGCACAAAGCCTCGCATTAATAAGAGATGGCATGATGAAGCACATTGTCATCATAAG
3721 GTTGCTAAGCATTCACTCCAACTACCCTATCTTCCTCTTAAGCTCTGACTAGCCACCATAACCTT
326 GTTGCTAAGCATTCACTCCAACTACCCTATCTTCCTCTTAAGCTCTGACTAGCCACCATAACCTT
3786 TAATCTCAGCCACCCTACTTAGCCACCACTGCAAGCAAACTCATCATTAATGTTAGAAAATGGAA
391 TAATCTCAGCCACCCTACTTAGCCACCACTGCAAGCAAACTCATCATTAATGTTAGAAAATGGAA
3851 AAGTCTCAAATACCCTCATTTTGG
456 AAGTCTCAAATACCCTCATTTTGG
3875 CTAT
1 CTAT
3879 AAAATTTTAC
Statistics
Matches: 483, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
479 483 1.00
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.33
Consensus pattern (479 bp):
CTATGTCGAAGCAAATTTGCATTCTAGAATGAAAATGTATTGATACATTTTTCATTGTATCAATA
CATTTTAGGTTTTTTACTCAAATGTATTAATACATTTTTCAATGTATCGATACATGCAGGTAATT
TTGCACATTCCGTGACATTTTCAGCTTTTTCCAAACACCTCCAATGCTCGATTCAAATGAGTTTT
TGCATCATAAATGATAAGAATTCATGTTAATATCAAATGTCAAACTTCAAATTCAAGCTCTGATC
ATTTTTGGAGCACAAAGCCTCGCATTAATAAGAGATGGCATGATGAAGCACATTGTCATCATAAG
GTTGCTAAGCATTCACTCCAACTACCCTATCTTCCTCTTAAGCTCTGACTAGCCACCATAACCTT
TAATCTCAGCCACCCTACTTAGCCACCACTGCAAGCAAACTCATCATTAATGTTAGAAAATGGAA
AAGTCTCAAATACCCTCATTTTGG
Found at i:4652 original size:20 final size:20
Alignment explanation
Indices: 4627--4701 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
4617 TTTTACCCAG
*
4627 ATGTATCGATACATTTTTCA
1 ATGTATCAATACATTTTTCA
* * * *
4647 ATGTATCGATACATGTATAA
1 ATGTATCAATACATTTTTCA
*
4667 ATGTATCAATACATTCTTCA
1 ATGTATCAATACATTTTTCA
*
4687 ATATATCAATACATT
1 ATGTATCAATACATT
4702 CTATCTTTTT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40
Consensus pattern (20 bp):
ATGTATCAATACATTTTTCA
Found at i:5649 original size:20 final size:22
Alignment explanation
Indices: 5609--5649 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
5599 TAGCCTTTGA
*
5609 CCATGCATTTTTTTACTATGTT
1 CCATGCATTTTTTAACTATGTT
5631 CCATGCA-TTTTTAAC-ATGT
1 CCATGCATTTTTTAACTATGT
5650 CTAGCATCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 7 0.39
22 7 0.39
ACGTcount: A:0.22, C:0.20, G:0.10, T:0.49
Consensus pattern (22 bp):
CCATGCATTTTTTAACTATGTT
Found at i:12956 original size:40 final size:42
Alignment explanation
Indices: 12912--13018 Score: 139
Period size: 40 Copynumber: 2.6 Consensus size: 42
12902 AAATTTAAAT
* *
12912 TAGAAACTCTTGTTTGATAAGGCATGGGCATGTTAA-AAAA-
1 TAGAAACTCTTGTTTGATAAGGCATGGGCACGTGAAGAAAAC
* * *
12952 TAGAAACTCTTGTTTAATAAGACGTGGGCACGTGAAGAAAAC
1 TAGAAACTCTTGTTTGATAAGGCATGGGCACGTGAAGAAAAC
*
12994 T-GAAACTCTTATTTGATAAGGCATG
1 TAGAAACTCTTGTTTGATAAGGCATG
13019 TGCGCGCTCT
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
40 31 0.55
41 24 0.43
42 1 0.02
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.29
Consensus pattern (42 bp):
TAGAAACTCTTGTTTGATAAGGCATGGGCACGTGAAGAAAAC
Found at i:19741 original size:21 final size:23
Alignment explanation
Indices: 19716--19768 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 23
19706 CACCCCACTT
19716 AAAATATTATTA-TATTAA-TAA
1 AAAATATTATTATTATTAATTAA
* * *
19737 AAAATATTTTTATTTTTAATTTA
1 AAAATATTATTATTATTAATTAA
19760 AAAATATTA
1 AAAATATTA
19769 AAATATTACC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 11 0.42
22 5 0.19
23 10 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AAAATATTATTATTATTAATTAA
Found at i:20365 original size:21 final size:21
Alignment explanation
Indices: 20341--20395 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
20331 AGTTGTATTT
* *
20341 TTTCATCTAAAAAATGCATTC
1 TTTCATCCAAAAAATGCATTA
**
20362 TTTCATCCAACCAATGCATTA
1 TTTCATCCAAAAAATGCATTA
20383 TTTCATCCAAAAA
1 TTTCATCCAAAAA
20396 TACCTTTTTC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.38, C:0.24, G:0.04, T:0.35
Consensus pattern (21 bp):
TTTCATCCAAAAAATGCATTA
Found at i:23444 original size:21 final size:20
Alignment explanation
Indices: 23420--23475 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 20
23410 AGTTATATTT
*
23420 TTTCATCTAAAAAATGCATTC
1 TTTCATC-AAAAAATGCATTA
*
23441 TTTCATCAAACCAATGCATTA
1 TTTCATCAAA-AAATGCATTA
23462 TTTCATCAAAAAAT
1 TTTCATCAAAAAAT
23476 ACCTTTTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.19
21 25 0.81
ACGTcount: A:0.41, C:0.20, G:0.04, T:0.36
Consensus pattern (20 bp):
TTTCATCAAAAAATGCATTA
Found at i:23990 original size:22 final size:20
Alignment explanation
Indices: 23965--24012 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 20
23955 TTTCTTAATG
23965 TTTTTAAAT-TTATTATATAAAA
1 TTTTTAAATATT-TTA-AT-AAA
*
23987 TTTTTTAATATTTTAATAAA
1 TTTTTAAATATTTTAATAAA
24007 TTTTTA
1 TTTTTA
24013 TATTAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 8 0.35
21 2 0.09
22 11 0.48
23 2 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTTAAATATTTTAATAAA
Found at i:24020 original size:34 final size:33
Alignment explanation
Indices: 23948--24024 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 33
23938 GTGAAATTTT
* *
23948 TTAATAATTTCTTAATGTTTTTAAATTTATTATA
1 TTAA-AATTTTTTAATATTTTTAAATTTATTATA
23982 -TAAAATTTTTTAATATTTTAATAAATTT-TTATA
1 TTAAAATTTTTTAATATTTT--TAAATTTATTATA
24015 TTAAAATTTT
1 TTAAAATTTT
24025 AATAATAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
32 14 0.37
33 8 0.21
34 16 0.42
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (33 bp):
TTAAAATTTTTTAATATTTTTAAATTTATTATA
Found at i:24217 original size:26 final size:26
Alignment explanation
Indices: 24160--24218 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
24150 TAGTAGAAAA
* * *
24160 TAATAATAA-ATAATATTTTTATTTT
1 TAATATTAATATAATATTTTTAATAT
24185 TAATATTAATATAATA-TTTTAATAT
1 TAATATTAATATAATATTTTTAATAT
24210 TAATTATTA
1 TAA-TATTA
24219 TTATTATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 18 0.62
26 11 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TAATATTAATATAATATTTTTAATAT
Found at i:24298 original size:21 final size:21
Alignment explanation
Indices: 24265--24306 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
24255 TTTGAACATT
24265 TTAATAATGAATACTT-TAATA
1 TTAATAATGAATA-TTATAATA
24286 TTAATAA-GTAATATTATAATA
1 TTAATAATG-AATATTATAATA
24307 ATGATGTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (21 bp):
TTAATAATGAATATTATAATA
Found at i:24777 original size:30 final size:30
Alignment explanation
Indices: 24741--24811 Score: 124
Period size: 30 Copynumber: 2.4 Consensus size: 30
24731 TTTTTCCATT
24741 TGTAAACTCCTTTTCTTGATAAGCCCTATC
1 TGTAAACTCCTTTTCTTGATAAGCCCTATC
* *
24771 TGTAAACTCCTTTTTTTTATAAGCCCTATC
1 TGTAAACTCCTTTTCTTGATAAGCCCTATC
24801 TGTAAACTCCT
1 TGTAAACTCCT
24812 ATTTGCAGCT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.24, C:0.25, G:0.08, T:0.42
Consensus pattern (30 bp):
TGTAAACTCCTTTTCTTGATAAGCCCTATC
Found at i:26924 original size:13 final size:13
Alignment explanation
Indices: 26908--26937 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
26898 ATACATTGTT
26908 CATTGTATCGATA
1 CATTGTATCGATA
26921 CATTGTATCGATA
1 CATTGTATCGATA
26934 CATT
1 CATT
26938 CAAGTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:29331 original size:50 final size:51
Alignment explanation
Indices: 29227--29349 Score: 133
Period size: 50 Copynumber: 2.4 Consensus size: 51
29217 AAATTTTTAG
* * * * **
29227 ATTTTTCATCTCGGGGATACT-TCAACCCTGGCTTTATTTCTACAATATTG
1 ATTTTTCATCTCGGGGATACTCTCAACCCCGGCTTTATTTCCAAAACATCA
* *
29277 ATTTTTCATCTCGGGGATACTCT-ATCCCCGGTTTTATTTCCAAAACATCA
1 ATTTTTCATCTCGGGGATACTCTCAACCCCGGCTTTATTTCCAAAACATCA
* *
29327 ATTTTTCATAATCGAGGATACTC
1 ATTTTTCAT-CTCGGGGATACTC
29350 CAATGTTGTT
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
50 49 0.80
51 12 0.20
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.40
Consensus pattern (51 bp):
ATTTTTCATCTCGGGGATACTCTCAACCCCGGCTTTATTTCCAAAACATCA
Found at i:29423 original size:79 final size:79
Alignment explanation
Indices: 29289--29632 Score: 284
Period size: 79 Copynumber: 4.4 Consensus size: 79
29279 TTTTCATCTC
* * * * * * *
29289 GGGGATACTCTATCCCCGGTTTTATTTCCAAAACATCAATTTTTCATAATCGAGGATACTCCAAT
1 GGGGATACTCCAACCCCGGCTTTATTTCTAAAACATCAATTTCTCACAATCGAGGATACTCCAAC
***
29354 GTTGTTATTTCAGA
66 CCCGTTATTTCAGA
* ** *
29368 GGGGATACTCCAACCCCGGCTTTATTTCTAAAATATTGATTTCTCACAATTGAGGATACTCCAAC
1 GGGGATACTCCAACCCCGGCTTTATTTCTAAAACATCAATTTCTCACAATCGAGGATACTCCAAC
** *
29433 CCCGTTATTTTGGC
66 CCCGTTATTTCAGA
* * * * *
29447 GGAGATACTCCAACCTCGGCCTTATTTCTAAAACTTCAATTT-TCCACAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCGGCTTTATTTCTAAAACATCAATTTCT-CACAATCGAGGATACTCCAA
29511 CCCCGTTATTTTCA-A
65 CCCCGTTA-TTTCAGA
* ** * * * *
29526 GGGGATACTCTAACCCCGATTTTATTT-TCAAAACGTCGATTT-TCTATAATC-AGGGATGCTCC
1 GGGGATACTCCAACCCCGGCTTTATTTCT-AAAACATCAATTTCTC-ACAATCGA-GGATACTCC
** * *
29588 AACCCTATTATTTCCGT
63 AACCCCGTTATTTCAGA
* **
29605 GGAGATACTCCAACCCCGATTTTATTTC
1 GGGGATACTCCAACCCCGGCTTTATTTC
29633 CAGAATACAG
Statistics
Matches: 212, Mismatches: 46, Indels: 13
0.78 0.17 0.05
Matches are distributed among these distances:
78 7 0.03
79 202 0.95
80 3 0.01
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGGCTTTATTTCTAAAACATCAATTTCTCACAATCGAGGATACTCCAAC
CCCGTTATTTCAGA
Found at i:29588 original size:158 final size:158
Alignment explanation
Indices: 29310--29668 Score: 368
Period size: 158 Copynumber: 2.3 Consensus size: 158
29300 ATCCCCGGTT
* * * ****
29310 TTATTTCCAAAACATCAATTTTTCATAATCGAGGATACTCCAATGTTGTTATTTCAGAGGGGATA
1 TTATTTCCAAAACTTCAATTTTCCATAATCGGGGATACTCCAACCCCGTTATTTCAGAGGGGATA
* * * * *
29375 CTCCAACCCCGGCTTTATTTCTAAAATATTGATTTCTCACAATTGAGGATACTCCAACCCCGTTA
66 CTCCAACCCCGACTTTATTTCTAAAACATCGATTTCTCACAATAGAGGATACTCCAACCCCATTA
** * *
29440 TTTTGGCGGAGATACTCCAACCTCGGCC
131 TTTCCGCGGAGATACTCCAACCCCGACC
* *
29468 TTATTTCTAAAACTTCAATTTTCCACAATCGGGGATACTCCAACCCCGTTATTTTCA-AGGGGAT
1 TTATTTCCAAAACTTCAATTTTCCATAATCGGGGATACTCCAACCCCGTTA-TTTCAGAGGGGAT
* * * * * *
29532 ACTCTAACCCCGATTTTATTT-TCAAAACGTCGATTT-TCTATAATCAG-GGATGCTCCAACCCT
65 ACTCCAACCCCGACTTTATTTCT-AAAACATCGATTTCTC-ACAAT-AGAGGATACTCCAACCCC
* **
29594 ATTATTTCCGTGGAGATACTCCAACCCCGATT
127 ATTATTTCCGCGGAGATACTCCAACCCCGACC
* *
29626 TTATTTCCAGAA-TACAGATTTTCCATAATCAGGGGATACTCCA
1 TTATTTCCAAAACTTCA-ATTTTCCATAATC-GGGGATACTCCA
29669 GCCCTGTTGT
Statistics
Matches: 164, Mismatches: 31, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
157 6 0.04
158 140 0.85
159 18 0.11
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (158 bp):
TTATTTCCAAAACTTCAATTTTCCATAATCGGGGATACTCCAACCCCGTTATTTCAGAGGGGATA
CTCCAACCCCGACTTTATTTCTAAAACATCGATTTCTCACAATAGAGGATACTCCAACCCCATTA
TTTCCGCGGAGATACTCCAACCCCGACC
Found at i:42083 original size:9 final size:8
Alignment explanation
Indices: 42068--42124 Score: 53
Period size: 9 Copynumber: 6.8 Consensus size: 8
42058 CTTCTTTTTT
42068 AAAAAAAC
1 AAAAAAAC
42076 AGAAAAAAC
1 A-AAAAAAC
42085 -AAAAAAC
1 AAAAAAAC
42092 AAAAAAAAC
1 -AAAAAAAC
*
42101 AATAACAAAA
1 AA-AA-AAAC
*
42111 AAAAAAAG
1 AAAAAAAC
42119 AAAAAA
1 AAAAAA
42125 TGAAAGAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
7 7 0.17
8 12 0.29
9 18 0.43
10 5 0.12
ACGTcount: A:0.86, C:0.09, G:0.04, T:0.02
Consensus pattern (8 bp):
AAAAAAAC
Found at i:42096 original size:15 final size:14
Alignment explanation
Indices: 42068--42117 Score: 64
Period size: 15 Copynumber: 3.4 Consensus size: 14
42058 CTTCTTTTTT
42068 AAAAAAACAGAAAAA
1 AAAAAAACA-AAAAA
42083 ACAAAAAACAAAAAA
1 A-AAAAAACAAAAAA
*
42098 AACAATAACAAAAAA
1 AA-AAAAACAAAAAA
42113 AAAAA
1 AAAAA
42118 GAAAAAATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 3 0.10
15 20 0.65
16 8 0.26
ACGTcount: A:0.86, C:0.10, G:0.02, T:0.02
Consensus pattern (14 bp):
AAAAAAACAAAAAA
Found at i:42115 original size:16 final size:16
Alignment explanation
Indices: 42069--42114 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
42059 TTCTTTTTTA
*
42069 AAAAAACAGAAAAAAC
1 AAAAAACAAAAAAAAC
42085 AAAAAACAAAAAAAAC
1 AAAAAACAAAAAAAAC
*
42101 -AATAACAAAAAAAA
1 AAAAAACAAAAAAAA
42115 AAAGAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
15 13 0.46
16 15 0.54
ACGTcount: A:0.85, C:0.11, G:0.02, T:0.02
Consensus pattern (16 bp):
AAAAAACAAAAAAAAC
Found at i:42134 original size:22 final size:20
Alignment explanation
Indices: 42068--42142 Score: 62
Period size: 22 Copynumber: 3.6 Consensus size: 20
42058 CTTCTTTTTT
* *
42068 AAAAAAACAGAAAAAACAAA
1 AAAAAAAAAGAAAAAATAAA
* *
42088 AAACAAAAA-AAACAATAACAA
1 AAAAAAAAAGAAAAAAT-A-AA
42109 AAAAAAAAAGAAAAAATGAAA
1 AAAAAAAAAGAAAAAAT-AAA
*
42130 GAAAAGAAAAGAA
1 -AAAAAAAAAGAA
42143 CTTGTTTAAG
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 5 0.12
20 8 0.19
21 12 0.28
22 18 0.42
ACGTcount: A:0.83, C:0.07, G:0.08, T:0.03
Consensus pattern (20 bp):
AAAAAAAAAGAAAAAATAAA
Found at i:43268 original size:94 final size:97
Alignment explanation
Indices: 43095--43286 Score: 248
Period size: 94 Copynumber: 2.0 Consensus size: 97
43085 ATCTAAACTT
* * * *
43095 TCTCCTTTCACTTTTTAGTCCTCAAAGAGCAGGATTCCTTCTCCTTTTGAAGCCCACACAAGTTG
1 TCTCCTTTCACTCTTCAGTCCTCAAAGAGCAGGATGCCTTCTCC---TAAAGCCCACACAAGTTG
* *
43160 GTGGCATTTCCCAGT-CCTCAAAGAGCATGACGCTC
63 ATGGCATTTCCCAGTCCCT-AAAGAGCAGGACGCTC
*
43195 TCTCCTTTCACTCTTCAGTCCTCAAAGAGCAGGATGCCTT-T-C-AAAGCCCACACCAGTTGATG
1 TCTCCTTTCACTCTTCAGTCCTCAAAGAGCAGGATGCCTTCTCCTAAAGCCCACACAAGTTGATG
*
43257 GCATTTTCCAGTCCCTAAAGAGCAGGACGC
66 GCATTTCCCAGTCCCTAAAGAGCAGGACGC
43287 CTTTTAAAGC
Statistics
Matches: 83, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
94 41 0.49
95 3 0.04
98 1 0.01
99 1 0.01
100 37 0.45
ACGTcount: A:0.23, C:0.31, G:0.18, T:0.28
Consensus pattern (97 bp):
TCTCCTTTCACTCTTCAGTCCTCAAAGAGCAGGATGCCTTCTCCTAAAGCCCACACAAGTTGATG
GCATTTCCCAGTCCCTAAAGAGCAGGACGCTC
Found at i:43404 original size:61 final size:61
Alignment explanation
Indices: 43231--43836 Score: 727
Period size: 61 Copynumber: 10.0 Consensus size: 61
43221 GAGCAGGATG
* * * *
43231 CCTTTCAAAGCCCACACCAGTTGATGGCATTTTCCAGTCC-CTAAAGAGCAGGACG------
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTC-AAAGAGCAGGACGCCTTTT
* * * *
43286 CCTTTTAAAGCCTACACAAGCTGGTGGCACCTT-CAGTCCTCAAAGAGCAGGATGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGACGCCTTTT
* * * * * *
43346 CCTTTTAAAGCCCATACGAGTTTGTGGCACTTTCCAATCCTCAATGAGCAGGGCGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGACGCCTTTT
* * * *
43407 TCTTTTAAAAGCCCACACAAGTTGGTGGCAC-CTCCAGTCTTCAAAGAGCATGACGCCTTTT
1 CCTTTT-AAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGACGCCTTTT
* *
43468 CCTTTTAAAGCCCACACAAGTTGGTTGCACTTTCCAGTCCTCAAAGAGCAGGACACCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGACGCCTTTT
* * *
43529 CCTTTTAAAAGCCCACACAAGTTGGTGGCAC-CTCCAGTCCTCAAAGAGCAAGACGCATTTT
1 CCTTTT-AAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGACGCCTTTT
*
43590 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCAC-TTTCCAGTCCTCAAAGAGCAGGACGCCTTTT
* * *
43652 TCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGATG-C-TTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGACGCCTTTT
* * * *
43711 CTCTTTGCAAAGCCCACACAA-TTGGTGGCACCTTCTAGTCCTCAAAAAGCAGGACGCCTTTT
1 C-CTTT-TAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGACGCCTTTT
* * * **
43773 -CTTTTCAAAGCCTACACGAGTTGTTGGCACTTTTTAGTCCTCAAAGAGCAGGACGCCTTTT
1 CCTTTT-AAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGACGCCTTTT
43834 CCT
1 CCT
43837 CCTCTCCCTT
Statistics
Matches: 472, Mismatches: 59, Indels: 33
0.84 0.10 0.06
Matches are distributed among these distances:
54 18 0.04
55 27 0.06
59 3 0.01
60 126 0.27
61 194 0.41
62 104 0.22
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (61 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGACGCCTTTT
Found at i:43946 original size:86 final size:85
Alignment explanation
Indices: 43845--44136 Score: 290
Period size: 86 Copynumber: 3.4 Consensus size: 85
43835 CTCCTCTCCC
* **
43845 TTGTCCTCAAAGAGCATGACACATTTCATTTCCTTCTTTTCCCTTTTGTTCTCAAATTGCAAGAT
1 TTGTCCTCAAAGAGCAGGACACATTTCATTTCCTTCTTTT-CCTTTTGTTCTCAAAAAGCAAGAT
*
43910 GCTTTTTTTTTCTTTTTTCCT
65 GCATTTTTTTTCTTTTTTCCT
* * * * *
43931 TTGTCCTCAAAGAGCAGGACACACTTCA-TTCTTTCTTTTTCCTTCTAGTTCTCAAAGAGCAGGA
1 TTGTCCTCAAAGAGCAGGACACATTTCATTTCCTTC-TTTTCCTT-TTGTTCTCAAAAAGCAAGA
* * *
43995 CGCACTTTATTCTCTTTTTTCCT
64 TGCA-TTTTTTTTCTTTTTTCCT
* * * *
44018 TTGTCCTCAAAAAGCAGGACACATTTAATTTCC-T-TTTTCC-TTTG-TCTTTAAAAGGCAAGAT
1 TTGTCCTCAAAGAGCAGGACACATTTCATTTCCTTCTTTTCCTTTTGTTC-TCAAAAAGCAAGAT
*
44079 GCATTTTATTTCATTTTTTCCT
65 GCATTTTTTTTC-TTTTTTCCT
* * *
44101 TAGTCCCCAAGGAGCAGGAC-CTATTTCATTCTCCTT
1 TTGTCCTCAAAGAGCAGGACAC-ATTTCATT-TCCTT
44137 TTCCTTAATC
Statistics
Matches: 168, Mismatches: 29, Indels: 19
0.78 0.13 0.09
Matches are distributed among these distances:
82 9 0.05
83 46 0.27
84 4 0.02
85 17 0.10
86 47 0.28
87 42 0.25
88 3 0.02
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.43
Consensus pattern (85 bp):
TTGTCCTCAAAGAGCAGGACACATTTCATTTCCTTCTTTTCCTTTTGTTCTCAAAAAGCAAGATG
CATTTTTTTTCTTTTTTCCT
Found at i:44034 original size:42 final size:41
Alignment explanation
Indices: 43809--44163 Score: 215
Period size: 41 Copynumber: 8.5 Consensus size: 41
43799 GCACTTTTTA
* ** * *
43809 GTCCTCAAAGAGCAGGACGC-CTT-TTC-CTCCTCTCCCTT
1 GTCCTCAAAGAGCAGGACGCATTTATTCTCTTTTTTCCTTT
* *
43847 GTCCTCAAAGAGCATGACACATTTCATT-TCCTTCTTTTCCCTTTT
1 GTCCTCAAAGAGCAGGACGCATTT-ATTCT-CTT-TTTT-CC-TTT
* ** * * * * *
43892 GTTCTCAAATTGCAAGATGCTTTTTTTTTCTTTTTTCCTTT
1 GTCCTCAAAGAGCAGGACGCATTTATTCTCTTTTTTCCTTT
* * *
43933 GTCCTCAAAGAGCAGGACACACTTCATTCTTTCTTTTTCCTTCT
1 GTCCTCAAAGAGCAGGACGCA-TTTATTCTCT-TTTTTCCTT-T
*
43977 AGTTCTCAAAGAGCAGGACGCACTTTATTCTCTTTTTTCCTTT
1 -GTCCTCAAAGAGCAGGACGCA-TTTATTCTCTTTTTTCCTTT
* * *
44020 GTCCTCAAAAAGCAGGACACATTTAATT-TCCTTTTTCCTTT
1 GTCCTCAAAGAGCAGGACGCATTT-ATTCTCTTTTTTCCTTT
* * * * *
44061 GTCTTTAAA-AGGCAAGATGCATTTTATT-TCATTTTTTCCTTA
1 GTCCTCAAAGA-GCAGGACGCA-TTTATTCTC-TTTTTTCCTTT
* * * *
44103 GTCCCCAAGGAGCAGGAC-CTATTTCATTCTC-CTTTTCCTTA
1 GTCCTCAAAGAGCAGGACGC-ATTT-ATTCTCTTTTTTCCTTT
*
44144 ATCCTCAAAGAGCAGGACGC
1 GTCCTCAAAGAGCAGGACGC
44164 CGCCTTCCTT
Statistics
Matches: 244, Mismatches: 51, Indels: 40
0.73 0.15 0.12
Matches are distributed among these distances:
38 18 0.07
39 2 0.01
40 1 0.00
41 81 0.33
42 58 0.24
43 19 0.08
44 17 0.07
45 48 0.20
ACGTcount: A:0.21, C:0.26, G:0.13, T:0.40
Consensus pattern (41 bp):
GTCCTCAAAGAGCAGGACGCATTTATTCTCTTTTTTCCTTT
Found at i:44039 original size:87 final size:85
Alignment explanation
Indices: 43805--44164 Score: 269
Period size: 83 Copynumber: 4.3 Consensus size: 85
43795 GTTGGCACTT
* ** * * *
43805 TTTAGTCCTCAAAGAGCAGGACGCC-TTTTC-CTCCTCTCCCTTGTCCTCAAAGAGCATGACACA
1 TTTAGTTCTCAAAGAGCAGGACGCCTTTTTCTCTTTTTTCCTTTGTCCTCAAAGAGCAGGACACA
*
43868 TTTCATTTCCTTCTTTTCCC
66 CTTCATTTCCTTCTTTTCCC
* ** * * * *
43888 TTTTGTTCTCAAATTGCAAGATGCTTTTTTTTTCTTTTTTCCTTTGTCCTCAAAGAGCAGGACAC
1 TTTAGTTCTCAAAGAGCAGGACGC-CTTTTTCTCTTTTTTCCTTTGTCCTCAAAGAGCAGGACAC
* *
43953 ACTTCA-TTCTTTCTTTTTCC
65 ACTTCATTTCCTTCTTTTCCC
*
43973 TTCTAGTTCTCAAAGAGCAGGACGCACTTTATTCTCTTTTTTCCTTTGTCCTCAAAAAGCAGGAC
1 TT-TAGTTCTCAAAGAGCAGGACGC-CTTT-TTCTCTTTTTTCCTTTGTCCTCAAAGAGCAGGAC
* *
44038 ACATTTAATTTCC-T-TTTT-CC
63 ACACTTCATTTCCTTCTTTTCCC
* * * * * * * * *
44058 TTT-GTCTTTAAAAG-GCAAGATGCATTTTATTTCATTTTTTCCTTAGTCCCCAAGGAGCAGGAC
1 TTTAGT-TCTCAAAGAGCAGGACGCCTTTT-TCTC-TTTTTTCCTTTGTCCTCAAAGAGCAGGAC
* *
44121 -CTATTTCA-TT-CTCCTTTT-CC
63 AC-ACTTCATTTCCTTCTTTTCCC
* *
44141 -TTAATCCTCAAAGAGCAGGACGCC
1 TTTAGTTCTCAAAGAGCAGGACGCC
44165 GCCTTCCTTT
Statistics
Matches: 216, Mismatches: 47, Indels: 28
0.74 0.16 0.10
Matches are distributed among these distances:
81 2 0.01
82 16 0.07
83 71 0.33
84 7 0.03
85 22 0.10
86 56 0.26
87 39 0.18
88 3 0.01
ACGTcount: A:0.21, C:0.26, G:0.12, T:0.40
Consensus pattern (85 bp):
TTTAGTTCTCAAAGAGCAGGACGCCTTTTTCTCTTTTTTCCTTTGTCCTCAAAGAGCAGGACACA
CTTCATTTCCTTCTTTTCCC
Found at i:44117 original size:83 final size:84
Alignment explanation
Indices: 43845--44142 Score: 275
Period size: 83 Copynumber: 3.5 Consensus size: 84
43835 CTCCTCTCCC
* * * * **
43845 TTGTCCTCAAAGAGCATGACACATTTCATTTCCTTCTTTTCCCTT-TTGTTCTCAAATTGCAAGA
1 TTGTCCTCAAAGAGCAGGACACATTTAATTTCC-T-TTTT-CCTTCTAGTTCTAAAAGAGCAAGA
* *
43909 TGCTTTTTTTTTCTTTTTTCCT
63 TGCATTTTATTTCTTTTTTCCT
* * * * * *
43931 TTGTCCTCAAAGAGCAGGACACACTTCATTCTTTCTTTTTCCTTCTAGTTCTCAAAGAGCAGGAC
1 TTGTCCTCAAAGAGCAGGACACA-TTTAAT-TTCCTTTTTCCTTCTAGTTCTAAAAGAGCAAGAT
*
43996 GCACTTTATTCTCTTTTTTCCT
64 GCATTTTATT-TCTTTTTTCCT
* *
44018 TTGTCCTCAAAAAGCAGGACACATTTAATTTCCTTTTTCCTT-T-GTCTTTAAAAG-GCAAGATG
1 TTGTCCTCAAAGAGCAGGACACATTTAATTTCCTTTTTCCTTCTAGT-TCTAAAAGAGCAAGATG
44080 CATTTTATTTCATTTTTTCCT
65 CATTTTATTTC-TTTTTTCCT
* * * *
44101 TAGTCCCCAAGGAGCAGGAC-CTATTTCATTCTCC-TTTTCCTT
1 TTGTCCTCAAAGAGCAGGACAC-ATTTAATT-TCCTTTTTCCTT
44143 AATCCTCAAA
Statistics
Matches: 177, Mismatches: 27, Indels: 19
0.79 0.12 0.09
Matches are distributed among these distances:
82 3 0.02
83 56 0.32
84 10 0.06
85 16 0.09
86 52 0.29
87 37 0.21
88 3 0.02
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.44
Consensus pattern (84 bp):
TTGTCCTCAAAGAGCAGGACACATTTAATTTCCTTTTTCCTTCTAGTTCTAAAAGAGCAAGATGC
ATTTTATTTCTTTTTTCCT
Found at i:44802 original size:20 final size:19
Alignment explanation
Indices: 44777--44845 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 19
44767 TTTACCCAGA
44777 TGTATCGATACATTGTTCAT
1 TGTATCGATACATTGTT-AT
44797 TGTATCGATACA-----A-
1 TGTATCGATACATTGTTAT
44810 TGTATCGATACATTGTTTAT
1 TGTATCGATACATTG-TTAT
*
44830 TGTATCGATATATTGT
1 TGTATCGATACATTGT
44846 ATCGATACAT
Statistics
Matches: 41, Mismatches: 1, Indels: 15
0.72 0.02 0.26
Matches are distributed among these distances:
13 12 0.29
14 1 0.02
19 2 0.05
20 26 0.63
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.45
Consensus pattern (19 bp):
TGTATCGATACATTGTTAT
Found at i:44815 original size:13 final size:13
Alignment explanation
Indices: 44797--44821 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44787 CATTGTTCAT
44797 TGTATCGATACAA
1 TGTATCGATACAA
44810 TGTATCGATACA
1 TGTATCGATACA
44822 TTGTTTATTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:44817 original size:33 final size:33
Alignment explanation
Indices: 44776--44856 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
44766 TTTTACCCAG
44776 ATGTATCGATACATTGTTCATTGTATCGATACA
1 ATGTATCGATACATTGTTCATTGTATCGATACA
* *
44809 ATGTATCGATACATTGTTTATTGTATCGATATA
1 ATGTATCGATACATTGTTCATTGTATCGATACA
*
44842 TTGTATCGATACATT
1 ATGTATCGATACATT
44857 CTGAGTTTAC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.43
Consensus pattern (33 bp):
ATGTATCGATACATTGTTCATTGTATCGATACA
Found at i:44845 original size:13 final size:13
Alignment explanation
Indices: 44827--44852 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44817 ATACATTGTT
44827 TATTGTATCGATA
1 TATTGTATCGATA
44840 TATTGTATCGATA
1 TATTGTATCGATA
44853 CATTCTGAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
TATTGTATCGATA
Found at i:44885 original size:29 final size:29
Alignment explanation
Indices: 44843--44934 Score: 94
Period size: 29 Copynumber: 3.5 Consensus size: 29
44833 ATCGATATAT
*
44843 TGTATCGATACATTCTGAGTTTACCTAGA
1 TGTATCGACACATTCTGAGTTTACCTAGA
*
44872 TGTATTGACACA-T-T---TTT---TA-A
1 TGTATCGACACATTCTGAGTTTACCTAGA
*
44892 TGTATCGATACATTCTGAGTTTACCTAGA
1 TGTATCGACACATTCTGAGTTTACCTAGA
44921 TGTATCGACACATT
1 TGTATCGACACATT
44935 TTTCAATGTA
Statistics
Matches: 49, Mismatches: 5, Indels: 18
0.68 0.07 0.25
Matches are distributed among these distances:
20 11 0.22
21 3 0.06
22 1 0.02
24 3 0.06
25 3 0.06
27 1 0.02
28 3 0.06
29 24 0.49
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.40
Consensus pattern (29 bp):
TGTATCGACACATTCTGAGTTTACCTAGA
Found at i:44900 original size:49 final size:49
Alignment explanation
Indices: 44843--44955 Score: 208
Period size: 49 Copynumber: 2.3 Consensus size: 49
44833 ATCGATATAT
* *
44843 TGTATCGATACATTCTGAGTTTACCTAGATGTATTGACACATTTTTTAA
1 TGTATCGATACATTCTGAGTTTACCTAGATGTATCGACACATTTTTCAA
44892 TGTATCGATACATTCTGAGTTTACCTAGATGTATCGACACATTTTTCAA
1 TGTATCGATACATTCTGAGTTTACCTAGATGTATCGACACATTTTTCAA
44941 TGTATCGATACATTC
1 TGTATCGATACATTC
44956 AGGTATTTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 62 1.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (49 bp):
TGTATCGATACATTCTGAGTTTACCTAGATGTATCGACACATTTTTCAA
Found at i:45974 original size:13 final size:13
Alignment explanation
Indices: 45956--45981 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
45946 CAATTTTTTG
45956 TGTATCGATACAT
1 TGTATCGATACAT
45969 TGTATCGATACAT
1 TGTATCGATACAT
45982 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:45996 original size:32 final size:33
Alignment explanation
Indices: 45936--45999 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
45926 TACAAGCCAA
** *
45936 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
45969 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
46000 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:51617 original size:13 final size:13
Alignment explanation
Indices: 51599--51624 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
51589 CAATTTTTTG
51599 TGTATCGATACAT
1 TGTATCGATACAT
51612 TGTATCGATACAT
1 TGTATCGATACAT
51625 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:51639 original size:32 final size:33
Alignment explanation
Indices: 51579--51642 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
51569 TACAAGCCAA
** *
51579 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
51612 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
51643 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:54375 original size:79 final size:77
Alignment explanation
Indices: 54137--54484 Score: 258
Period size: 78 Copynumber: 4.4 Consensus size: 77
54127 CAAAACATCA
* * * *
54137 ATTTTTCATAATCGGGGATACTCCAATCCCATTA-TTTCAGAGGGGATACTCCAACCCCAGCTTT
1 ATTTTCCATAATCGGGGATACTCCAACCCCGTTATTTTCA-AGGGGATACTCCAACCCCA-ATTT
**
54201 ATTTCTAAAATATTG
64 ATTTC-AAAATACCG
* ** * ** * **
54216 A-TTTCTCACAATTAGAGATACTCCAACCCCG-TATTTTGGTA-GGGATACTCTAACCCCGGCTT
1 ATTTTC-CATAATCGGGGATACTCCAACCCCGTTATTTT-CAAGGGGATACTCCAACCCC-AATT
* *
54278 TATTTCTAAAGCT-TCG
63 TATTTC-AAA-ATACCG
*
54294 ATTTTCCACAATCGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCCAATTTAA
1 ATTTTCCATAATCGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCCAATTT-A
*
54359 TTTTCAAAATGCCG
65 -TTTCAAAATACCG
* * * ** * * *
54373 ATTTTCAATAATC-AGGATGCTCCAACCTTGTTGTTTTCGAGGGGATACTCCAACCCCGATTTTA
1 ATTTTCCATAATCGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCC-AATTTA
* *
54437 TTTTCAGAACACCG
65 -TTTCAAAATACCG
* *
54451 ATTTTTCATAATCAGGGGATACTCCAGCCCCGTT
1 ATTTTCCATAATC-GGGGATACTCCAACCCCGTT
54485 GTCATCTCCA
Statistics
Matches: 213, Mismatches: 42, Indels: 27
0.76 0.15 0.10
Matches are distributed among these distances:
78 124 0.58
79 71 0.33
80 18 0.08
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.32
Consensus pattern (77 bp):
ATTTTCCATAATCGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCCAATTTAT
TTCAAAATACCG
Found at i:54418 original size:157 final size:156
Alignment explanation
Indices: 54099--54484 Score: 390
Period size: 157 Copynumber: 2.4 Consensus size: 156
54089 TTTTCATCTC
** * * * *
54099 AGGGATACTCTAACTGCGGTTTTGTTTCCAAAACATCAATTTTTCATAATCGGGGATACTCCAAT
1 AGGGATACTCTAACCCCGGTTTTATTT-CTAAACATCGATTTTTCATAATCGGGGATACTCCAAC
* * ** *
54164 CCCATTATTTCAGAGGGGATACTCCAACCCCAGCTTTATTTCTAAAATATTGATTTCTCACAATT
65 CCCGTTATTTCAGAGGGGATACTCCAACCCCAGATTTATTTCTAAAATACCGATTTCTCACAATC
*
54229 AGAGATACTCCAACCCCGTATTTTGGT
130 AGAGATACTCCAACCCCGTATTTTCGT
* * * *
54256 AGGGATACTCTAACCCCGGCTTTATTTCTAAAGCTTCGATTTTCCACAATCGGGGATACTCCAAC
1 AGGGATACTCTAACCCCGGTTTTATTTCTAAA-CATCGATTTTTCATAATCGGGGATACTCCAAC
* *
54321 CCCGTTATTTTCA-AGGGGATACTCCAACCCCA-ATTTAATTT-TCAAAATGCCGATTT-TCAAT
65 CCCGTTA-TTTCAGAGGGGATACTCCAACCCCAGATTT-ATTTCT-AAAATACCGATTTCTC-AC
* ** *
54382 AATCAG-GATGCTCCAACCTTGTTGTTTTCG-
126 AATCAGAGATACTCCAACCCCG-TATTTTCGT
* * *
54412 AGGGGATACTCCAACCCCGATTTTATTT-TCAGAACACCGATTTTTCATAATCAGGGGATACTCC
1 A-GGGATACTCTAACCCCGGTTTTATTTCT-A-AACATCGATTTTTCATAATC-GGGGATACTCC
*
54476 AGCCCCGTT
62 AACCCCGTT
54485 GTCATCTCCA
Statistics
Matches: 189, Mismatches: 30, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
156 24 0.13
157 139 0.74
158 26 0.14
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (156 bp):
AGGGATACTCTAACCCCGGTTTTATTTCTAAACATCGATTTTTCATAATCGGGGATACTCCAACC
CCGTTATTTCAGAGGGGATACTCCAACCCCAGATTTATTTCTAAAATACCGATTTCTCACAATCA
GAGATACTCCAACCCCGTATTTTCGT
Found at i:59988 original size:45 final size:45
Alignment explanation
Indices: 59924--60015 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
59914 AGGTAGTGTT
59924 TACATCCATTTGCTCAATTTGGAAGTCAAAACTTGCTACTAACCC
1 TACATCCATTTGCTCAATTTGGAAGTCAAAACTTGCTACTAACCC
*
59969 TACATCCATTTGCTCAATTTGGAAGTCAAAACTTGCTGCTAACCC
1 TACATCCATTTGCTCAATTTGGAAGTCAAAACTTGCTACTAACCC
60014 TA
1 TA
60016 GCATTATCTG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (45 bp):
TACATCCATTTGCTCAATTTGGAAGTCAAAACTTGCTACTAACCC
Found at i:63353 original size:16 final size:17
Alignment explanation
Indices: 63322--63357 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
63312 GCTAACCAAA
63322 TTAAAATTAAATTTGAT
1 TTAAAATTAAATTTGAT
*
63339 TTAAAATT-GATTTGAT
1 TTAAAATTAAATTTGAT
63355 TTA
1 TTA
63358 TGTGGGCCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (17 bp):
TTAAAATTAAATTTGAT
Found at i:67650 original size:20 final size:20
Alignment explanation
Indices: 67619--67665 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
67609 ATATTTTTTT
*
67619 AATTCAATA-AAAATA-ATA
1 AATTAAATATAAAATATATA
*
67637 CATTAAATATAAAATATATA
1 AATTAAATATAAAATATATA
67657 AATTAAATA
1 AATTAAATA
67666 ATTTCTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 7 0.29
19 6 0.25
20 11 0.46
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (20 bp):
AATTAAATATAAAATATATA
Found at i:68129 original size:24 final size:22
Alignment explanation
Indices: 68090--68146 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
68080 CTGTAAACAT
68090 ATTTTAAA-AAAATAATCATAA
1 ATTTTAAATAAAATAATCATAA
**
68111 ATTTTTAAATAAAATTAATTTTAA
1 A-TTTTAAATAAAA-TAATCATAA
*
68135 ATTATAAATAAA
1 ATTTTAAATAAA
68147 TAAAATATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 1 0.03
22 7 0.23
23 14 0.47
24 8 0.27
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
ATTTTAAATAAAATAATCATAA
Done.