Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3446
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: 214122
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1114 original size:40 final size:38
Alignment explanation
Indices: 1036--1213 Score: 173
Period size: 39 Copynumber: 4.6 Consensus size: 38
1026 ATGATGTCCG
* * * *
1036 GGCT-AGTCCGAAGGC-TTTGTGCTAAGTGACCATATCC
1 GGCTAAGTCCGAAGGCATTTGTGC-GAGTTACTAAATCC
* *
1073 GGACTAAGATCCGAAGGCATTTGTGCGAGATACTAATTCC
1 GG-CTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAATCC
* *
1113 GGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAATCC
1 -GGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAATCC
*
1152 GGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CC
1 GGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AATCC
*
1191 GGGCTATGTCCTGAAGGCATTTG
1 -GGCTAAGTCC-GAAGGCATTTG
1214 AACGAGTAGC
Statistics
Matches: 117, Mismatches: 15, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
37 2 0.02
38 8 0.07
39 57 0.49
40 41 0.35
41 9 0.08
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (38 bp):
GGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAATCC
Found at i:3567 original size:39 final size:40
Alignment explanation
Indices: 3376--3637 Score: 282
Period size: 40 Copynumber: 6.6 Consensus size: 40
3366 TTGAATGCTG
* * * * * *
3376 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
** * *
3416 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
* * * *
3455 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 -TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
*
3496 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
*
3536 TCCGGGTTAAGTCCCG-AGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
*
3575 TCCGGGTTAAGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
3614 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
3638 TGAACGAGGA
Statistics
Matches: 196, Mismatches: 20, Indels: 13
0.86 0.09 0.06
Matches are distributed among these distances:
39 75 0.38
40 110 0.56
41 11 0.06
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:3597 original size:79 final size:78
Alignment explanation
Indices: 3429--3637 Score: 267
Period size: 79 Copynumber: 2.6 Consensus size: 78
3419 GGACTAAGAT
* * * * *
3429 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTA
1 CCGAAGGCA-TTGTGCGAGTTATAAA-TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTA
3494 AATCCGGGTTAAGTC
64 AATCCGGGTTAAGTC
* *
3509 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCG-AGGCATTCGTGCGAGTTATTA
1 CCGAAGGCATT-GTGCGAGTTA-TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTA
3573 AATCCGGGTTAAGTC
64 AATCCGGGTTAAGTC
* * * *
3588 CCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 CCGAAGGCATTGTGCGAGTTA-TAAATCCGGGTTAAGTCCCGAAGGCATT
3638 TGAACGAGGA
Statistics
Matches: 114, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
78 26 0.23
79 52 0.46
80 33 0.29
81 3 0.03
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (78 bp):
CCGAAGGCATTGTGCGAGTTATAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAAA
TCCGGGTTAAGTC
Found at i:3657 original size:79 final size:79
Alignment explanation
Indices: 3429--3672 Score: 219
Period size: 79 Copynumber: 3.1 Consensus size: 79
3419 GGACTAAGAT
* * * * * * * **
3429 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGAT-AC
1 CCGAAGGCATTCGTGCGAGTTACTAAA-ACCGGGCTAAGTCCCG-AGGCATTCGAACGAG-TGAC
3492 TAAATCCGGGTTAAGTC
63 TAAATCCGGGTTAAGTC
* * * ** * *
3509 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAGGCATTCGTGCGAGTTATTAA
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAGGCATTCGAACGAGTGACTAA
3574 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
* * *
3588 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCT
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCG-AGGCATTCGAACGAGTGA-CT
* *
3651 ATATCC-GGTTAAATC
64 AAATCCGGGTTAAGTC
3666 CCGAAGG
1 CCGAAGG
3673 TACGTGATTT
Statistics
Matches: 141, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
78 43 0.30
79 60 0.43
80 35 0.25
81 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAGGCATTCGAACGAGTGACTAA
ATCCGGGTTAAGTC
Found at i:13061 original size:29 final size:29
Alignment explanation
Indices: 13026--13099 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
13016 GTTGTGAGAT
* *
13026 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
* *
13055 TGGCACTAAGTGTGCGAGTTTAAAGTACG
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
13084 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
13100 TGGTTGATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 5 0.12
29 35 0.88
ACGTcount: A:0.24, C:0.16, G:0.34, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:19231 original size:24 final size:24
Alignment explanation
Indices: 19204--19255 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
19194 TTTAGCTATC
*
19204 ATCTCCTTATTTTAAGTGAAAAGA
1 ATCTCCTTATTCTAAGTGAAAAGA
19228 ATCTCCTTATTCTAAGTGAAAAGA
1 ATCTCCTTATTCTAAGTGAAAAGA
19252 ATCT
1 ATCT
19256 TGGTTGACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37
Consensus pattern (24 bp):
ATCTCCTTATTCTAAGTGAAAAGA
Found at i:23179 original size:25 final size:25
Alignment explanation
Indices: 23137--23187 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
23127 GAGTATTTTA
23137 TTAATATAATATTAAA-TTAATTATT
1 TTAATATAATATTAAATTTAA-TATT
*
23162 TTAATATTAA-ATTTAATTTAATATT
1 TTAATA-TAATATTAAATTTAATATT
23187 T
1 T
23188 ATCAAGATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
TTAATATAATATTAAATTTAATATT
Found at i:32583 original size:26 final size:26
Alignment explanation
Indices: 32553--32602 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
32543 AAATTTATTG
32553 AAATGA-TCGTTATAC-CCTTATGAGGT
1 AAATGACT-GTTATACTCC-TATGAGGT
32579 AAATGACTGTTATACTCCTATGAG
1 AAATGACTGTTATACTCCTATGAG
32603 ATGTGTGACT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 19 0.86
27 3 0.14
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (26 bp):
AAATGACTGTTATACTCCTATGAGGT
Found at i:40275 original size:6 final size:6
Alignment explanation
Indices: 40266--40407 Score: 94
Period size: 6 Copynumber: 22.8 Consensus size: 6
40256 AACTAGAACT
*
40266 AGAATC AGAATC AGAATC AGAATC AGGTGAT- AGAATC AGAATC AGAATC
1 AGAATC AGAATC AGAATC AGAATC A-G-AATC AGAATC AGAATC AGAATC
* * * * *
40315 AGTATC AGGTAAT- AGAATC AAAATC AAAATC AGTATC AGGTAA-C AAAATC
1 AGAATC A-G-AATC AGAATC AGAATC AGAATC AGAATC A-G-AATC AGAATC
* * *
40365 AAAATC AGAATC AGTATC AGGTAA-C AGAATC AAAAATC AGAAT
1 AGAATC AGAATC AGAATC A-G-AATC AGAATC -AGAATC AGAAT
40408 GTGAATGCAA
Statistics
Matches: 109, Mismatches: 14, Indels: 26
0.73 0.09 0.17
Matches are distributed among these distances:
5 9 0.08
6 79 0.72
7 15 0.14
8 6 0.06
ACGTcount: A:0.50, C:0.14, G:0.16, T:0.20
Consensus pattern (6 bp):
AGAATC
Found at i:40302 original size:31 final size:31
Alignment explanation
Indices: 40265--40407 Score: 205
Period size: 31 Copynumber: 4.6 Consensus size: 31
40255 GAACTAGAAC
* * *
40265 TAGAATCAGAATCAGAATCAGAATCAGGTGA
1 TAGAATCAAAATCAGAATCAGTATCAGGTAA
*
40296 TAGAATCAGAATCAGAATCAGTATCAGGTAA
1 TAGAATCAAAATCAGAATCAGTATCAGGTAA
*
40327 TAGAATCAAAATCAAAATCAGTATCAGGTAA
1 TAGAATCAAAATCAGAATCAGTATCAGGTAA
* *
40358 CAAAATCAAAATCAGAATCAGTATCAGGTAA
1 TAGAATCAAAATCAGAATCAGTATCAGGTAA
*
40389 CAGAATCAAAAATCAGAAT
1 TAGAATC-AAAATCAGAAT
40408 GTGAATGCAA
Statistics
Matches: 103, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
31 92 0.89
32 11 0.11
ACGTcount: A:0.50, C:0.14, G:0.16, T:0.20
Consensus pattern (31 bp):
TAGAATCAAAATCAGAATCAGTATCAGGTAA
Found at i:40346 original size:25 final size:25
Alignment explanation
Indices: 40300--40372 Score: 71
Period size: 25 Copynumber: 2.9 Consensus size: 25
40290 AGGTGATAGA
* **
40300 ATCAGAATCAGAATCAGTATCAGGT
1 ATCAGAATCAAAATCAAAATCAGGT
40325 AAT-AGAATCAAAATCAAAATCA-GT
1 -ATCAGAATCAAAATCAAAATCAGGT
40349 ATCAGGTAA-CAAAATCAAAATCAG
1 ATCA-G-AATCAAAATCAAAATCAG
40373 AATCAGTATC
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
23 2 0.05
24 3 0.08
25 31 0.77
26 4 0.10
ACGTcount: A:0.51, C:0.15, G:0.14, T:0.21
Consensus pattern (25 bp):
ATCAGAATCAAAATCAAAATCAGGT
Found at i:40586 original size:27 final size:26
Alignment explanation
Indices: 40544--40645 Score: 132
Period size: 27 Copynumber: 3.8 Consensus size: 26
40534 GCTCAGTTAT
* *
40544 CAGATATTGTGACAGAGTCACCAGATA
1 CAGATATTGTGGCAGAGCCACCAGA-A
40571 CAGATATTGTGGCAGAGCCACCAGAA
1 CAGATATTGTGGCAGAGCCACCAGAA
*
40597 CAGATATTTGTGGCATAGCCACCAGAAA
1 CAGATA-TTGTGGCAGAGCCACCAG-AA
* *
40625 CAGATAATGTGGCAAAGCCAC
1 CAGATATTGTGGCAGAGCCAC
40646 TTAACAGAAT
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
26 7 0.10
27 53 0.78
28 8 0.12
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.19
Consensus pattern (26 bp):
CAGATATTGTGGCAGAGCCACCAGAA
Found at i:41351 original size:27 final size:27
Alignment explanation
Indices: 41295--41740 Score: 626
Period size: 27 Copynumber: 16.6 Consensus size: 27
41285 GAGGCAAAAT
* * *
41295 GGTAATTTTACCCTACA-AGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
41321 GGTAATTCTACGCTAAAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
*
41348 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
41375 GATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
41402 GATAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
41429 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
41456 GATAATTCTACCCTGCAAGGGTA-TTC
1 GGTAATTCTACCCTACAGGGGTATTTC
41482 TGGTAATTCTACCCTACAGGGGTATTTC
1 -GGTAATTCTACCCTACAGGGGTATTTC
* *
41510 GGTAATTCTACCCTATAGGGGTATTGC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
41537 GATAATTCTACCCTACAGGGGTATTGC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
41564 GATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
41591 GGTAATTCTACCCTATAGGGGTATTGC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
41618 GATAATTTTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
41645 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
41672 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
41699 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
**
41726 AATAATTCTACCCTA
1 GGTAATTCTACCCTA
41741 TATTTTGGTA
Statistics
Matches: 375, Mismatches: 42, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
26 17 0.05
27 355 0.95
28 3 0.01
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.34
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:41771 original size:27 final size:27
Alignment explanation
Indices: 41741--41807 Score: 134
Period size: 27 Copynumber: 2.5 Consensus size: 27
41731 TTCTACCCTA
41741 TATTTTGGTAATTCCACAAATCAGGGG
1 TATTTTGGTAATTCCACAAATCAGGGG
41768 TATTTTGGTAATTCCACAAATCAGGGG
1 TATTTTGGTAATTCCACAAATCAGGGG
41795 TATTTTGGTAATT
1 TATTTTGGTAATT
41808 TTATTGATCG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.39
Consensus pattern (27 bp):
TATTTTGGTAATTCCACAAATCAGGGG
Found at i:41848 original size:27 final size:27
Alignment explanation
Indices: 41758--41931 Score: 107
Period size: 27 Copynumber: 6.4 Consensus size: 27
41748 GTAATTCCAC
* ****
41758 AAATCAGGGGTATTTTGGTAATTCCAC
1 AAATCAAGGGTATTTTGGTAATTTTGT
* *
41785 AAATCAGGGGTATTTTGGTAATTTTAT
1 AAATCAAGGGTATTTTGGTAATTTTGT
** *
41812 TGATCGAGGGTATTTTGGTAATTTTGT
1 AAATCAAGGGTATTTTGGTAATTTTGT
***
41839 AAA-CTAAGGGTATTTCAATAATTTTGT
1 AAATC-AAGGGTATTTTGGTAATTTTGT
* *** *
41866 AAATCGAGGGTAAAATGGTAATTTTAT
1 AAATCAAGGGTATTTTGGTAATTTTGT
* **** *
41893 AAATCGAGGGTAAAACGGTAATTCTGT
1 AAATCAAGGGTATTTTGGTAATTTTGT
*
41920 AAATCGAGGGTA
1 AAATCAAGGGTA
41932 AAATGGTAAT
Statistics
Matches: 120, Mismatches: 25, Indels: 4
0.81 0.17 0.03
Matches are distributed among these distances:
26 1 0.01
27 118 0.98
28 1 0.01
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.36
Consensus pattern (27 bp):
AAATCAAGGGTATTTTGGTAATTTTGT
Found at i:41903 original size:54 final size:54
Alignment explanation
Indices: 41827--41942 Score: 144
Period size: 54 Copynumber: 2.1 Consensus size: 54
41817 GAGGGTATTT
* *** *
41827 TGGTAATTTTGTAAACTAAGGGTATTTCAATAATTTTGTAAATCGAGGGTAAAA
1 TGGTAATTTTATAAACTAAGGGTAAAACAATAATTCTGTAAATCGAGGGTAAAA
* **
41881 TGGTAATTTTATAAA-TCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAA
1 TGGTAATTTTATAAACT-AAGGGTAAAACAATAATTCTGTAAATCGAGGGTAAAA
41935 TGGTAATT
1 TGGTAATT
41943 CTATCTTACA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
53 1 0.02
54 52 0.98
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.34
Consensus pattern (54 bp):
TGGTAATTTTATAAACTAAGGGTAAAACAATAATTCTGTAAATCGAGGGTAAAA
Found at i:41932 original size:27 final size:27
Alignment explanation
Indices: 41857--41944 Score: 140
Period size: 27 Copynumber: 3.3 Consensus size: 27
41847 GGTATTTCAA
*
41857 TAATTTTGTAAATCGAGGGTAAAATGG
1 TAATTCTGTAAATCGAGGGTAAAATGG
* * *
41884 TAATTTTATAAATCGAGGGTAAAACGG
1 TAATTCTGTAAATCGAGGGTAAAATGG
41911 TAATTCTGTAAATCGAGGGTAAAATGG
1 TAATTCTGTAAATCGAGGGTAAAATGG
41938 TAATTCT
1 TAATTCT
41945 ATCTTACAGG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.33
Consensus pattern (27 bp):
TAATTCTGTAAATCGAGGGTAAAATGG
Found at i:41986 original size:27 final size:27
Alignment explanation
Indices: 41956--42147 Score: 210
Period size: 27 Copynumber: 7.1 Consensus size: 27
41946 TCTTACAGGA
*
41956 GTATTTCAGTAATTTTACAAATTGAGG
1 GTATTTCAGTAATTTTACAAATCGAGG
*
41983 GTATTTCAGTAATTTTGCAAAAT-GAGG
1 GTATTTCAGTAATTTTAC-AAATCGAGG
42010 GTATTTCAGTAATTTTACAAATCGAGG
1 GTATTTCAGTAATTTTACAAATCGAGG
* * *
42037 ATATTT-ATGTAATTTTATAAATCGGGG
1 GTATTTCA-GTAATTTTACAAATCGAGG
* *
42064 GTACTTT-GGTAATTTTACAAGTCGAGG
1 GTA-TTTCAGTAATTTTACAAATCGAGG
* * **
42091 GTATTTTAATAATTTTACAGGTCGAGG
1 GTATTTCAGTAATTTTACAAATCGAGG
* * *
42118 GTATTTTAGTAATTTCACAAATCAAGG
1 GTATTTCAGTAATTTTACAAATCGAGG
42145 GTA
1 GTA
42148 ATTTTATAAA
Statistics
Matches: 142, Mismatches: 18, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
26 8 0.06
27 127 0.89
28 7 0.05
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.39
Consensus pattern (27 bp):
GTATTTCAGTAATTTTACAAATCGAGG
Found at i:42178 original size:27 final size:27
Alignment explanation
Indices: 42144--42241 Score: 151
Period size: 27 Copynumber: 3.6 Consensus size: 27
42134 ACAAATCAAG
*
42144 GGTAATTTTATAAACTAGGGGTATTCT
1 GGTAATTTTATAAACTAGGGGTATTTT
* *
42171 GATAATTTTACAAACTAGGGGTATTTT
1 GGTAATTTTATAAACTAGGGGTATTTT
42198 GGTAATTTTATAAACTAGGGGTATTTT
1 GGTAATTTTATAAACTAGGGGTATTTT
* *
42225 GGTAATTTGAGAAACTA
1 GGTAATTTTATAAACTA
42242 AAGTATTCTA
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 64 1.00
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.40
Consensus pattern (27 bp):
GGTAATTTTATAAACTAGGGGTATTTT
Found at i:44879 original size:28 final size:27
Alignment explanation
Indices: 44834--44888 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
44824 TATAATCTTG
44834 AAATTGTATTTGAATGGGCTAAGGCCC
1 AAATTGTATTTGAATGGGCTAAGGCCC
*
44861 AAATTG-ATTCTGTAATGGGCTCAGGCCC
1 AAATTGTATT-TG-AATGGGCTAAGGCCC
44889 GAACTGTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 3 0.12
27 8 0.32
28 14 0.56
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.29
Consensus pattern (27 bp):
AAATTGTATTTGAATGGGCTAAGGCCC
Found at i:48570 original size:43 final size:42
Alignment explanation
Indices: 48427--48570 Score: 155
Period size: 43 Copynumber: 3.4 Consensus size: 42
48417 TACCGAGATG
* * *
48427 TGATTACATGTAAGACCATGTCTAGGACATTGGCATTGTATTG
1 TGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTA-TA
48470 TGATTACATGTAAGACCATGTCTGGGACATTGGCATCGT-TAA
1 TGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT-A
*** * * *
48512 TCGATTTTGTTTAAGACCCTGTCTGGGACAGTGGCATCGATATA
1 T-GATTACATGTAAGACCATGTCTGGGACATTGGCATCG-TATA
*
48556 TGATAACATGTAAGA
1 TGATTACATGTAAGA
48571 TCATATCTAG
Statistics
Matches: 83, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 77 0.93
44 3 0.04
45 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (42 bp):
TGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTATA
Found at i:53539 original size:29 final size:29
Alignment explanation
Indices: 53480--53637 Score: 230
Period size: 29 Copynumber: 5.5 Consensus size: 29
53470 ATAGTAAGTC
* *
53480 CGCACACTTAGTG-TTATATAATAAAACT
1 CGCACACTTAGTGCTTACATAATCAAACT
53508 CGCACACTTAGTGCTTACATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCAAACT
53537 CGCACACTTAGTGCTTACATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCAAACT
53566 CGCACACTTAGTGCTTACATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCAAACT
* * * * *
53595 TGCACACTTAGTGCTATGCA-ATTTAAACC
1 CGCACACTTAGTGCT-TACATAATCAAACT
53624 CGCACACTTAGTGC
1 CGCACACTTAGTGC
53638 CAATCTCATG
Statistics
Matches: 120, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
28 13 0.11
29 104 0.87
30 3 0.03
ACGTcount: A:0.34, C:0.26, G:0.12, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCTTACATAATCAAACT
Found at i:58829 original size:43 final size:43
Alignment explanation
Indices: 58768--58851 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 43
58758 ATTGAATTCG
58768 ATCTCGAACAGCTCGTGGGTAAGCCCTGTACA-ATGTGTCCCTA
1 ATCTCGAACAGCTCGTGGGTAAGCCCTGTA-ATATGTGTCCCTA
*
58811 ATCTCGAACAGCTTGTGGGTAAGCCCTGTAATATGTGTCCC
1 ATCTCGAACAGCTCGTGGGTAAGCCCTGTAATATGTGTCCC
58852 CAAGAAAGGA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
42 1 0.03
43 38 0.97
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (43 bp):
ATCTCGAACAGCTCGTGGGTAAGCCCTGTAATATGTGTCCCTA
Found at i:70216 original size:23 final size:21
Alignment explanation
Indices: 70164--70259 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
70154 CCTGATCAGT
** * *
70164 ATACGACACATAAAGTGCCTA
1 ATACGACACACGAGGTGCCTG
*
70185 AAACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
70206 ATACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
70227 ATACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
70248 AAATACGACACA
1 --ATACGACACA
70260 TAAAGTGCCT
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
21 57 0.85
23 10 0.15
ACGTcount: A:0.36, C:0.27, G:0.23, T:0.14
Consensus pattern (21 bp):
ATACGACACACGAGGTGCCTG
Found at i:70224 original size:42 final size:43
Alignment explanation
Indices: 70164--70269 Score: 142
Period size: 42 Copynumber: 2.5 Consensus size: 43
70154 CCTGATCAGT
*
70164 ATACGACACATAAAGTGCCTAAAACGACACACGAGGTGCCTG-
1 ATACGACACACAAAGTGCCTAAAACGACACACGAGGTGCCTGA
* * * *
70206 ATACGACACACGAGGTGCCTGATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTAAAACGACACACGAGGTGCCTG-A
*
70250 ATACGACACATAAAGTGCCT
1 ATACGACACACAAAGTGCCT
70270 GATCGATAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
42 37 0.69
44 17 0.31
ACGTcount: A:0.36, C:0.26, G:0.23, T:0.15
Consensus pattern (43 bp):
ATACGACACACAAAGTGCCTAAAACGACACACGAGGTGCCTGA
Found at i:70668 original size:15 final size:15
Alignment explanation
Indices: 70643--70700 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
70633 TCATATATAT
70643 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
70659 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
70674 AATAATTTCAATCAA
1 TATAAATTCAATCAA
70689 TATAAATTCAAT
1 TATAAATTCAAT
70701 AAAACATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:70685 original size:30 final size:28
Alignment explanation
Indices: 70646--70704 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 28
70636 TATATATTAT
70646 ATAATTCAATCAATATAAATTCAATCAAA
1 ATAATTCAATCAATATAAATTCAAT-AAA
70675 ATAATTTCAATCAATATAAATTCAATAAA
1 ATAA-TTCAATCAATATAAATTCAATAAA
70704 A
1 A
70705 CATATATTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 8 0.28
30 21 0.72
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (28 bp):
ATAATTCAATCAATATAAATTCAATAAA
Found at i:73844 original size:17 final size:17
Alignment explanation
Indices: 73822--73854 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
73812 TTTGGCCGAA
73822 ACGGGCACATGGGCCCT
1 ACGGGCACATGGGCCCT
73839 ACGGGCACATGGGCCC
1 ACGGGCACATGGGCCC
73855 CACATGGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.36, G:0.36, T:0.09
Consensus pattern (17 bp):
ACGGGCACATGGGCCCT
Found at i:81390 original size:40 final size:40
Alignment explanation
Indices: 81346--81450 Score: 151
Period size: 40 Copynumber: 2.6 Consensus size: 40
81336 GCTACTCGTT
*
81346 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
81386 CAAATGCCTTCGGGACTTAACCAGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
81426 CCAATGCCTTCGGG-CTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
81451 CATCATTCGA
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
39 9 0.16
40 47 0.81
41 2 0.03
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:96937 original size:79 final size:81
Alignment explanation
Indices: 96828--97010 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
96818 TACTCGTTCA
* *
96828 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
96891 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
* **
96908 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
96971 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
96987 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
97011 CATCATTCGA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 58 0.65
80 28 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:97010 original size:40 final size:40
Alignment explanation
Indices: 96807--97010 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
96797 CGGAATTTAA
** *
96807 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
96847 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
96887 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
96926 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
96966 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
97006 CCGGA
1 CCGGA
97011 CATCATTCGA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.23
40 93 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:99638 original size:15 final size:15
Alignment explanation
Indices: 99618--99650 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
99608 CCACGCACAC
99618 TTAGTGCCATGTACT
1 TTAGTGCCATGTACT
99633 TTAGTGCCATGTACT
1 TTAGTGCCATGTACT
99648 TTA
1 TTA
99651 AACCCGCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.42
Consensus pattern (15 bp):
TTAGTGCCATGTACT
Found at i:99666 original size:29 final size:29
Alignment explanation
Indices: 99633--99699 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
99623 GCCATGTACT
*
99633 TTAGTGCCATGTACTTT-AAACCCGCACAC
1 TTAGTGCCATGCA-TTTCAAACCCGCACAC
*
99662 TTAGTGCCATGCATTTCAAGCCCGCACAC
1 TTAGTGCCATGCATTTCAAACCCGCACAC
99691 TTAGTGCCA
1 TTAGTGCCA
99700 ATCTCACAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 3 0.09
29 32 0.91
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.27
Consensus pattern (29 bp):
TTAGTGCCATGCATTTCAAACCCGCACAC
Found at i:103306 original size:42 final size:42
Alignment explanation
Indices: 103224--103325 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 42
103214 TGCCAATAGC
* * **
103224 CTAGCTATGGTCTTACATGAAGTCTCATATCGAGACCATATA
1 CTAGATATGGTCTTACACGAAGTCTCATAAAGAGACCATATA
* *** *
103266 CTAGATATGGTATTACACGAAGTCTCATAAAGATTTCATATC
1 CTAGATATGGTCTTACACGAAGTCTCATAAAGAGACCATATA
*
103308 CCAGATATGGTCTTACAC
1 CTAGATATGGTCTTACAC
103326 ATAGTCTTAT
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (42 bp):
CTAGATATGGTCTTACACGAAGTCTCATAAAGAGACCATATA
Found at i:103950 original size:19 final size:20
Alignment explanation
Indices: 103922--103960 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
103912 TCCCATTATT
103922 TATTTATTTTT-TGTTTTAA
1 TATTTATTTTTATGTTTTAA
*
103941 TATTTGTTTTTATGTTTTAA
1 TATTTATTTTTATGTTTTAA
103961 ATGTATTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.72
Consensus pattern (20 bp):
TATTTATTTTTATGTTTTAA
Found at i:103978 original size:25 final size:23
Alignment explanation
Indices: 103941--103986 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
103931 TTTGTTTTAA
*
103941 TATTTGTTTTTATGTTTTAAATG
1 TATTTGTTTTTATATTTTAAATG
103964 TATTTGATTTATTATATTTTAAA
1 TATTTG-TTT-TTATATTTTAAA
103987 GTTTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 3 0.15
25 11 0.55
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (23 bp):
TATTTGTTTTTATATTTTAAATG
Found at i:108248 original size:14 final size:13
Alignment explanation
Indices: 108214--108245 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
108204 CACTCAAACG
108214 ACAAAATTAAATC
1 ACAAAATTAAATC
108227 ACAAAATTAAATC
1 ACAAAATTAAATC
108240 ACAAAA
1 ACAAAA
108246 ATTTCGATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.66, C:0.16, G:0.00, T:0.19
Consensus pattern (13 bp):
ACAAAATTAAATC
Found at i:109390 original size:30 final size:30
Alignment explanation
Indices: 109356--109421 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 30
109346 TCCTTCCATG
* *
109356 CATTTTTATATTTTTTGTTTTTATTAAT-AT
1 CATTTTTACATTTTTT-TCTTTATTAATAAT
*
109386 CA--TTTACATTTTTTTCTTTATTAGTAAT
1 CATTTTTACATTTTTTTCTTTATTAATAAT
109414 CATTTTTA
1 CATTTTTA
109422 AAAATATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
27 9 0.30
28 15 0.50
30 6 0.20
ACGTcount: A:0.24, C:0.08, G:0.03, T:0.65
Consensus pattern (30 bp):
CATTTTTACATTTTTTTCTTTATTAATAAT
Found at i:109405 original size:27 final size:29
Alignment explanation
Indices: 109360--109418 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
109350 TCCATGCATT
* *
109360 TTTATATTTTTTGTTTTTATTAAT-ATCA
1 TTTACATTTTTTGTCTTTATTAATAATCA
*
109388 TTTACATTTTTT-TCTTTATTAGTAATCA
1 TTTACATTTTTTGTCTTTATTAATAATCA
109416 TTT
1 TTT
109419 TTAAAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 9 0.33
28 18 0.67
ACGTcount: A:0.24, C:0.07, G:0.03, T:0.66
Consensus pattern (29 bp):
TTTACATTTTTTGTCTTTATTAATAATCA
Found at i:109729 original size:15 final size:17
Alignment explanation
Indices: 109711--109742 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
109701 GGACAAAAAC
109711 TATAAT-TAAAC-TTAT
1 TATAATGTAAACATTAT
109726 TATAATGTAAACATTAT
1 TATAATGTAAACATTAT
109743 AAATAAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 5 0.33
17 4 0.27
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (17 bp):
TATAATGTAAACATTAT
Found at i:114244 original size:56 final size:56
Alignment explanation
Indices: 114183--114296 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
114173 TTATATATTA
114183 TTCATCCTAAAAAAAATACTTTCTATATCTACTATTCCGATTTAAGGTCACATATC
1 TTCATCCTAAAAAAAATACTTTCTATATCTACTATTCCGATTTAAGGTCACATATC
114239 TTCATCCTAAAAAAAATACTTTCTATATCTACTATTCCGATTTAAGGTCACATATC
1 TTCATCCTAAAAAAAATACTTTCTATATCTACTATTCCGATTTAAGGTCACATATC
114295 TT
1 TT
114297 TCATTCCAAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.39
Consensus pattern (56 bp):
TTCATCCTAAAAAAAATACTTTCTATATCTACTATTCCGATTTAAGGTCACATATC
Found at i:118856 original size:49 final size:49
Alignment explanation
Indices: 118779--118975 Score: 196
Period size: 49 Copynumber: 4.0 Consensus size: 49
118769 GTAGCCAAAG
* *
118779 CTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAA
1 CTATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAA
* * * *
118828 CTGTCTGGTACACGTAGTAGCCTACACTTAGTACTACACACGCGACCTCA
1 CTATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACC-AA
* ** * * * *
118878 CCATCTAATACACGTAGTAGCTTGCACTTAGTACTACACACGTGATCACAG
1 CTATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGA-C-CAA
* * * ** *
118929 TTTTCGGGTATGCATAGTAGCCTGCACTTAGTACTACACATGCGACC
1 CTATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACC
118976 TCACAATAGA
Statistics
Matches: 118, Mismatches: 27, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
49 43 0.36
50 40 0.34
51 34 0.29
52 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.26
Consensus pattern (49 bp):
CTATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAA
Found at i:118910 original size:50 final size:49
Alignment explanation
Indices: 118793--118919 Score: 173
Period size: 50 Copynumber: 2.6 Consensus size: 49
118783 CTGGTACGCA
* ** **
118793 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACTGTCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAACCATCTAATACACG
* *
118842 TAGTAGCCTACACTTAGTACTACACACGCGACCTCACCATCTAATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACC-AACCATCTAATACACG
*
118892 TAGTAGCTTGCACTTAGTACTACACACG
1 TAGTAGCCTGCACTTAGTACTACACACG
118920 TGATCACAGT
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
49 31 0.46
50 37 0.54
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCAACCATCTAATACACG
Found at i:121167 original size:30 final size:31
Alignment explanation
Indices: 121101--121169 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 31
121091 TAAAGATAAC
*
121101 AAGAAAACC-GAATAAAGAAATCCAAGATAG
1 AAGAAACCCAGAATAAAGAAATCCAAGATAG
*
121131 AA-AAACCCAGAATAAAGAAATGC-AGAATA-
1 AAGAAACCCAGAATAAAGAAATCCAAG-ATAG
121160 AAGAAACCCA
1 AAGAAACCCA
121170 AGATACGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 9 0.26
30 25 0.74
ACGTcount: A:0.61, C:0.16, G:0.14, T:0.09
Consensus pattern (31 bp):
AAGAAACCCAGAATAAAGAAATCCAAGATAG
Found at i:135064 original size:13 final size:13
Alignment explanation
Indices: 135046--135070 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
135036 AAAATAGTTA
135046 TTTTTATATTTTC
1 TTTTTATATTTTC
135059 TTTTTATATTTT
1 TTTTTATATTTT
135071 ATATAAAGTA
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:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTATATTTTC
Found at i:135955 original size:19 final size:18
Alignment explanation
Indices: 135941--135977 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
135931 AATTTTAACT
135941 TTTTTATATTTTTTTAGAA
1 TTTTTATATTTTTTTA-AA
135960 TTTTTATATTTTTTTAAA
1 TTTTTATATTTTTTTAAA
135978 ATATAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (18 bp):
TTTTTATATTTTTTTAAA
Found at i:136040 original size:20 final size:19
Alignment explanation
Indices: 135970--136054 Score: 84
Period size: 19 Copynumber: 4.3 Consensus size: 19
135960 TTTTTATATT
135970 TTTTTAAAATATAAATTTTGAAA
1 TTTTTAAAAT-T--ATTTTG-AA
*
135993 TTTTTATAAA-TATTTTTAA
1 TTTTTA-AAATTATTTTGAA
*
136012 TTTTAAAAATTATTTTGAA
1 TTTTTAAAATTATTTTGAA
136031 TTTTTGAAAATTATTTT-AA
1 TTTTT-AAAATTATTTTGAA
136050 TTTTT
1 TTTTT
136055 TTGTAATTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
18 3 0.05
19 26 0.47
20 16 0.29
22 1 0.02
23 6 0.11
24 3 0.05
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
TTTTTAAAATTATTTTGAA
Found at i:136055 original size:20 final size:20
Alignment explanation
Indices: 135970--136054 Score: 86
Period size: 20 Copynumber: 4.2 Consensus size: 20
135960 TTTTTATATT
*
135970 TTTTTAAAATATAAATTTTGAAA
1 TTTTTAAAA-AT-TATTTTG-AA
* *
135993 TTTTTATAAA-TATTTTTAA
1 TTTTTAAAAATTATTTTGAA
136012 -TTTTAAAAATTATTTTGAA
1 TTTTTAAAAATTATTTTGAA
*
136031 TTTTTGAAAATTATTTT-AA
1 TTTTTAAAAATTATTTTGAA
136050 TTTTT
1 TTTTT
136055 TTGTAATTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
18 8 0.15
19 17 0.31
20 20 0.37
22 1 0.02
23 8 0.15
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.58
Consensus pattern (20 bp):
TTTTTAAAAATTATTTTGAA
Found at i:139002 original size:39 final size:39
Alignment explanation
Indices: 138940--139018 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
138930 CTGGGACATG
* *
138940 TTAGTGTACAGAAGAGTGAATTGCTTCGCGCTGCACTTA
1 TTAGTGTACAGAAAAGTGAATTGCTTCGCGCCGCACTTA
*
138979 TTAGTGTACAGAAAAGTGTATTGCTTCGCGCCGCACTTA
1 TTAGTGTACAGAAAAGTGAATTGCTTCGCGCCGCACTTA
139018 T
1 T
139019 GGGACATGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (39 bp):
TTAGTGTACAGAAAAGTGAATTGCTTCGCGCCGCACTTA
Found at i:140344 original size:25 final size:25
Alignment explanation
Indices: 140316--140504 Score: 103
Period size: 25 Copynumber: 7.6 Consensus size: 25
140306 CATACAACAC
* * *
140316 GCCATAAAGACTTTTCAGATAATTT
1 GCCACAAAGGCTTTACAGATAATTT
* **
140341 GCCATAAAGGCTTTACAGATAACAT
1 GCCACAAAGGCTTTACAGATAATTT
* *
140366 GCCACAAAGGCTTTTA-TGATAATTC
1 GCCACAAAGGC-TTTACAGATAATTT
* * *
140391 ACCACAAAGGCTTTACAGATAACTA
1 GCCACAAAGGCTTTACAGATAATTT
* * * * *
140416 GTCAAAAAGGATTTTA-TGATAATAT
1 GCCACAAAGG-CTTTACAGATAATTT
* * * * *
140441 GTCATAAAGGCTTTATAGATAACTC
1 GCCACAAAGGCTTTACAGATAATTT
* * * * *
140466 GTCATAGAGGCTTTACAGATAACTA
1 GCCACAAAGGCTTTACAGATAATTT
*
140491 GCCACAAAAGCTTT
1 GCCACAAAGGCTTT
140505 TTTTATAATT
Statistics
Matches: 126, Mismatches: 34, Indels: 8
0.75 0.20 0.05
Matches are distributed among these distances:
24 8 0.06
25 110 0.87
26 8 0.06
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.29
Consensus pattern (25 bp):
GCCACAAAGGCTTTACAGATAATTT
Found at i:140387 original size:50 final size:50
Alignment explanation
Indices: 140311--140463 Score: 166
Period size: 50 Copynumber: 3.1 Consensus size: 50
140301 CTTTCCATAC
* * *
140311 AACACGCCATAAAGACTTTTCA-GATAATTTGCCATAAAGGCTTTACAGAT
1 AACATGCCAAAAAGGCTTTT-ATGATAATTTGCCATAAAGGCTTTACAGAT
* ** *
140361 AACATGCCACAAAGGCTTTTATGATAATTCACCACAAAGGCTTTACAGAT
1 AACATGCCAAAAAGGCTTTTATGATAATTTGCCATAAAGGCTTTACAGAT
* * * * *
140411 AAC-TAGTCAAAAAGGATTTTATGATAATATGTCATAAAGGCTTTATAGAT
1 AACAT-GCCAAAAAGGCTTTTATGATAATTTGCCATAAAGGCTTTACAGAT
140461 AAC
1 AAC
140464 TCGTCATAGA
Statistics
Matches: 86, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
49 2 0.02
50 84 0.98
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (50 bp):
AACATGCCAAAAAGGCTTTTATGATAATTTGCCATAAAGGCTTTACAGAT
Found at i:141095 original size:4 final size:4
Alignment explanation
Indices: 141088--141137 Score: 91
Period size: 4 Copynumber: 12.5 Consensus size: 4
141078 CACACACAAC
*
141088 CATA CATA CATA CATA CATA CATA CATA CATA CATG CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
141136 CA
1 CA
141138 ACCATATCTC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.48, C:0.26, G:0.02, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:145434 original size:22 final size:22
Alignment explanation
Indices: 145400--145441 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
145390 GGATAAAGAT
145400 TTTTAAACAATTTAATAATTATC
1 TTTTAAACAATTTAA-AATTATC
*
145423 TTTT-AACTATTTAAAATTA
1 TTTTAAACAATTTAAAATTA
145442 AATTAATAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 9 0.50
23 4 0.22
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTTAAACAATTTAAAATTATC
Found at i:145650 original size:26 final size:26
Alignment explanation
Indices: 145610--145676 Score: 84
Period size: 25 Copynumber: 2.5 Consensus size: 26
145600 AAGTTTGAAA
145610 AAAAAATATTAAAAACTCAT-AAAATTAT
1 AAAAAA-ATTAAAAACT--TGAAAATTAT
145638 AAAAAAATTAAAAACTTGAAAATTAT
1 AAAAAAATTAAAAACTTGAAAATTAT
*
145664 -AGAAAATTAAAAA
1 AAAAAAATTAAAAA
145677 AAATATAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
25 13 0.35
26 8 0.22
27 10 0.27
28 6 0.16
ACGTcount: A:0.67, C:0.04, G:0.03, T:0.25
Consensus pattern (26 bp):
AAAAAAATTAAAAACTTGAAAATTAT
Found at i:145695 original size:35 final size:36
Alignment explanation
Indices: 145630--145704 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 36
145620 AAAAACTCAT
**
145630 AAAATTATAAAAAAATTAAAAACTTGAAAATTATAG
1 AAAATTATAAAAAAATTAAAAACTACAAAATTATAG
*
145666 AAAATTA-AAAAAAATATAAAAAC-ACAAAATTATAT
1 AAAATTATAAAAAAAT-TAAAAACTACAAAATTATAG
145701 AAAA
1 AAAA
145705 AAATTATAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 21 0.60
36 14 0.40
ACGTcount: A:0.69, C:0.04, G:0.03, T:0.24
Consensus pattern (36 bp):
AAAATTATAAAAAAATTAAAAACTACAAAATTATAG
Found at i:152397 original size:32 final size:32
Alignment explanation
Indices: 152361--152455 Score: 78
Period size: 32 Copynumber: 3.2 Consensus size: 32
152351 ACATTTTGTA
152361 AATACTTGCGAACTTAGTGAGTTTTAATACAG
1 AATACTTGCGAACTTAGTGAGTTTTAATACAG
** * ** *
152393 AATACCTTAAG-TCTTTCT-AG-TTT-GT--A-
1 AATA-CTTGCGAACTTAGTGAGTTTTAATACAG
152419 AATACTTGCGAACTTAGTGAGTTTTAATACAG
1 AATACTTGCGAACTTAGTGAGTTTTAATACAG
152451 AATAC
1 AATAC
152456 CTTAAGTCTT
Statistics
Matches: 43, Mismatches: 12, Indels: 16
0.61 0.17 0.23
Matches are distributed among these distances:
25 4 0.09
26 8 0.19
27 3 0.07
28 3 0.07
29 2 0.05
30 3 0.07
31 3 0.07
32 13 0.30
33 4 0.09
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.37
Consensus pattern (32 bp):
AATACTTGCGAACTTAGTGAGTTTTAATACAG
Found at i:152445 original size:58 final size:58
Alignment explanation
Indices: 152355--152472 Score: 236
Period size: 58 Copynumber: 2.0 Consensus size: 58
152345 GAACAAACAT
152355 TTTGTAAATACTTGCGAACTTAGTGAGTTTTAATACAGAATACCTTAAGTCTTTCTAG
1 TTTGTAAATACTTGCGAACTTAGTGAGTTTTAATACAGAATACCTTAAGTCTTTCTAG
152413 TTTGTAAATACTTGCGAACTTAGTGAGTTTTAATACAGAATACCTTAAGTCTTTCTAG
1 TTTGTAAATACTTGCGAACTTAGTGAGTTTTAATACAGAATACCTTAAGTCTTTCTAG
152471 TT
1 TT
152473 AAGTTCCTTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.41
Consensus pattern (58 bp):
TTTGTAAATACTTGCGAACTTAGTGAGTTTTAATACAGAATACCTTAAGTCTTTCTAG
Found at i:153622 original size:23 final size:23
Alignment explanation
Indices: 153596--153640 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
153586 TCACTGAATA
* *
153596 TGCCACATAGGCATTACAAAATT
1 TGCCACAGAGGCAATACAAAATT
153619 TGCCACAGAGGCAATACAAAAT
1 TGCCACAGAGGCAATACAAAAT
153641 ACGCCTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.20
Consensus pattern (23 bp):
TGCCACAGAGGCAATACAAAATT
Found at i:171053 original size:35 final size:35
Alignment explanation
Indices: 171014--171085 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
171004 TGCCATGAGG
171014 TGAGTGTAAGTATGTGAGTGTTTAAGGGTGACAAA
1 TGAGTGTAAGTATGTGAGTGTTTAAGGGTGACAAA
171049 TGAGTGTAAGTATGTGAGTGTTTAAGGGTGACAAA
1 TGAGTGTAAGTATGTGAGTGTTTAAGGGTGACAAA
171084 TG
1 TG
171086 GCTCGAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.31, C:0.03, G:0.35, T:0.32
Consensus pattern (35 bp):
TGAGTGTAAGTATGTGAGTGTTTAAGGGTGACAAA
Found at i:179768 original size:42 final size:42
Alignment explanation
Indices: 179716--179810 Score: 127
Period size: 42 Copynumber: 2.3 Consensus size: 42
179706 TGAGACTTCA
* * * * * *
179716 TGTAAGACCATGTCTGGGACATGGCTTTGATATGATATTTCG
1 TGTAAGACCATGTCTGAGACATGGCATCGATACGAGATTCCG
*
179758 TGTAATACCATGTCTGAGACATGGCATCGATACGAGATTCCG
1 TGTAAGACCATGTCTGAGACATGGCATCGATACGAGATTCCG
179800 TGTAAGACCAT
1 TGTAAGACCAT
179811 AGTTGGGCTA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (42 bp):
TGTAAGACCATGTCTGAGACATGGCATCGATACGAGATTCCG
Found at i:182242 original size:37 final size:37
Alignment explanation
Indices: 182201--182271 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
182191 CTATAGTGCA
*
182201 AAGTATATGGTTATTTGATATGTGAACGAAAATGAAT
1 AAGTATATGGTTATTTGATATGTGAACAAAAATGAAT
*
182238 AAGTATATGGTTATTTGATATGTGTACAAAAATG
1 AAGTATATGGTTATTTGATATGTGAACAAAAATG
182272 TTCAAAAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.39, C:0.03, G:0.21, T:0.37
Consensus pattern (37 bp):
AAGTATATGGTTATTTGATATGTGAACAAAAATGAAT
Found at i:184283 original size:46 final size:44
Alignment explanation
Indices: 184208--184321 Score: 147
Period size: 46 Copynumber: 2.5 Consensus size: 44
184198 GGGTCATTTG
* ** * *
184208 TGTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCTTCAAGA
1 TGTGCCAGTGTAAGACATGTCTGAAACATGCATCGGCTACAAAA
184252 TGTAAGCCAGTGTAAGACATGTCTGAAACATGCATCGGCTACAAAA
1 TGT--GCCAGTGTAAGACATGTCTGAAACATGCATCGGCTACAAAA
*
184298 TGTGTCAGTGTAAGACCATGTCTG
1 TGTGCCAGTGTAAGA-CATGTCTG
184322 GGACATAGAA
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
44 14 0.23
45 8 0.13
46 39 0.64
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.26
Consensus pattern (44 bp):
TGTGCCAGTGTAAGACATGTCTGAAACATGCATCGGCTACAAAA
Found at i:191638 original size:46 final size:45
Alignment explanation
Indices: 191481--191654 Score: 188
Period size: 46 Copynumber: 3.8 Consensus size: 45
191471 TCATTTGTGT
* **
191481 GCTAGTGTAAGACATGTCTGAGACATGCATTGGCCATATTATGAGA
1 GCTAGTGTAAGACATGTCTGAGACATGCATCGGCC-TAAGATGAGA
* * * * *
191527 GCTAGTGTAAGACCATGTCTGGGACATGGCATTGGCATTGAGACGAGA
1 GCTAGTGTAAGA-CATGTCTGAGACAT-GCATCGGC-CTAAGATGAGA
*
191575 GCTAGTGTAAAACATGTCTGAGACATGCATCGGCCTCAAGATGTA-A
1 GCTAGTGTAAGACATGTCTGAGACATGCATCGGCCT-AAGATG-AGA
* *
191621 GCCAGTGTAAGACATGTCTGGGACATGCATCGGC
1 GCTAGTGTAAGACATGTCTGAGACATGCATCGGC
191655 TACAAAATGT
Statistics
Matches: 108, Mismatches: 15, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
45 1 0.01
46 55 0.51
47 27 0.25
48 25 0.23
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (45 bp):
GCTAGTGTAAGACATGTCTGAGACATGCATCGGCCTAAGATGAGA
Found at i:191691 original size:45 final size:44
Alignment explanation
Indices: 191578--191692 Score: 126
Period size: 46 Copynumber: 2.5 Consensus size: 44
191568 GACGAGAGCT
* *
191578 AGTGTAAAACATGTCTGAGACATGCATCGGCCTCAAGATGTAAGCC
1 AGTGT-AAACATGTCTGGGACATGCATCGGCCTCAAAATGT-AGCC
*
191624 AGTGTAAGACATGTCTGGGACATGCATCGG-CTACAAAATGT-GTC
1 AGTGTAA-ACATGTCTGGGACATGCATCGGCCT-CAAAATGTAGCC
*
191668 AGTGTACAACCATGTATGGGACATG
1 AGTGTA-AA-CATGTCTGGGACATG
191693 GAATCAGCAC
Statistics
Matches: 61, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
44 9 0.15
45 19 0.31
46 33 0.54
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.23
Consensus pattern (44 bp):
AGTGTAAACATGTCTGGGACATGCATCGGCCTCAAAATGTAGCC
Found at i:199272 original size:86 final size:86
Alignment explanation
Indices: 199127--199296 Score: 277
Period size: 86 Copynumber: 2.0 Consensus size: 86
199117 CTCGACATGA
* * * *
199127 AAATTTTCTCCACGAAGGTTATCCTAACTCTGAAAGATCTTTCCATATCATCTCCATTTTATAGG
1 AAATTTCCTCCACAAAGGTTATCCTAACTCCGAAAAATCTTTCCATATCATCTCCATTTTATAGG
*
199192 AAACATCTACCACCAATATGC
66 AAACATCAACCACCAATATGC
* *
199213 AAATTTCCTCCACAAAGGTTATCTTAACTCCGAAAAATCTTTTCATATCATCTCCATTTTATAGG
1 AAATTTCCTCCACAAAGGTTATCCTAACTCCGAAAAATCTTTCCATATCATCTCCATTTTATAGG
199278 AAACATCAACCACCAATAT
66 AAACATCAACCACCAATAT
199297 AAAACATGAT
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
86 77 1.00
ACGTcount: A:0.35, C:0.25, G:0.08, T:0.32
Consensus pattern (86 bp):
AAATTTCCTCCACAAAGGTTATCCTAACTCCGAAAAATCTTTCCATATCATCTCCATTTTATAGG
AAACATCAACCACCAATATGC
Found at i:207004 original size:11 final size:11
Alignment explanation
Indices: 206990--207042 Score: 65
Period size: 11 Copynumber: 5.0 Consensus size: 11
206980 GTATATCATA
206990 GCATATCATGT
1 GCATATCATGT
* *
207001 GCATCTCAT-A
1 GCATATCATGT
*
207011 ACATATCATGT
1 GCATATCATGT
207022 GCATATCATGT
1 GCATATCATGT
207033 -CATATCATGT
1 GCATATCATGT
207043 ATAACAATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
10 17 0.49
11 18 0.51
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (11 bp):
GCATATCATGT
Found at i:207009 original size:21 final size:21
Alignment explanation
Indices: 206968--207042 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 21
206958 ACCCAACCCA
* * *
206968 AGCATATAATGAGTATATCAT
1 AGCATATCATGTGCATATCAT
*
206989 AGCATATCATGTGCATCTCAT
1 AGCATATCATGTGCATATCAT
*
207010 AACATATCATGTGCATATCAT
1 AGCATATCATGTGCATATCAT
207031 -GTCATATCATGT
1 AG-CATATCATGT
207043 ATAACAATAT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (21 bp):
AGCATATCATGTGCATATCAT
Found at i:207041 original size:10 final size:10
Alignment explanation
Indices: 206982--207042 Score: 61
Period size: 10 Copynumber: 5.9 Consensus size: 10
206972 TATAATGAGT
206982 ATATCATAG-C
1 ATATCAT-GTC
206992 ATATCATGTGC
1 ATATCATGT-C
* **
207003 ATCTCATAAC
1 ATATCATGTC
207013 ATATCATGTGC
1 ATATCATGT-C
207024 ATATCATGTC
1 ATATCATGTC
207034 ATATCATGT
1 ATATCATGT
207043 ATAACAATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
9 1 0.02
10 24 0.57
11 17 0.40
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (10 bp):
ATATCATGTC
Found at i:209214 original size:27 final size:27
Alignment explanation
Indices: 209183--209360 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
209173 TAAATTGTAC
209183 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
209210 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
209236 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
209264 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
209292 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
209319 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
209346 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
209361 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:209297 original size:82 final size:81
Alignment explanation
Indices: 209184--209339 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
209174 AAATTGTACA
* *
209184 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
209248 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
209265 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
209330 TGCGAGTTGA
65 TGCGAATTGA
209340 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:209351 original size:82 final size:81
Alignment explanation
Indices: 209180--209360 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
209170 GATTAAATTG
* *
209180 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
209245 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
209261 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
209325 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
209343 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
209361 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:213821 original size:27 final size:27
Alignment explanation
Indices: 213787--213964 Score: 189
Period size: 27 Copynumber: 6.6 Consensus size: 27
213777 TAAATTGTAC
213787 AGCACTAAGTGT-CGGATTTGACTATGT
1 AGCACTAAGTGTGC-GATTTGACTATGT
* ** *
213814 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
213840 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
213868 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
213896 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
213923 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
213950 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
213965 GACTCAATAT
Statistics
Matches: 128, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
27 104 0.81
28 24 0.19
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:213955 original size:82 final size:82
Alignment explanation
Indices: 213784--213966 Score: 219
Period size: 82 Copynumber: 2.2 Consensus size: 82
213774 GGATAAATTG
* *
213784 TACAGCACTAAGTGT-CGGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTA
1 TACAGCACTAAGTGTGCGGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTA
213848 AGTGTGCGAATTGACCA
66 AGTGTGCGAATTGACCA
* * ** *
213865 TGCGGCACTAAGTGTGC-GAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCAC
1 TACAGCACTAAGTGTGCGGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCAC
* **
213928 TAAGTGTGCGAGTTGATTA
64 TAAGTGTGCGAATTGACCA
* *
213947 TATAGCACTGAGTGTGCGGA
1 TACAGCACTAAGTGTGCGGA
213967 CTCAATATAC
Statistics
Matches: 84, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
81 16 0.19
82 66 0.79
83 2 0.02
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (82 bp):
TACAGCACTAAGTGTGCGGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTA
AGTGTGCGAATTGACCA
Done.