Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
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: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 89 of 199
Found at i:30895897 original size:30 final size:31
Alignment explanation
Indices: 30895858--30895918 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
30895848 GGGAGGGGAG
* *
30895858 GGGAGAGGAGTAAAAGTTTTGGGGGGAAAGT
1 GGGAGAGGAGTAAAAGTTTTGAGGGAAAAGT
30895889 GGGA-AGGAGTAAAAGTTTTGAGGGAAAAGT
1 GGGAGAGGAGTAAAAGTTTTGAGGGAAAAGT
30895919 AAAAAAGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.36, C:0.00, G:0.44, T:0.20
Consensus pattern (31 bp):
GGGAGAGGAGTAAAAGTTTTGAGGGAAAAGT
Found at i:30895981 original size:9 final size:9
Alignment explanation
Indices: 30895967--30896003 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
30895957 TATAGTTTGA
30895967 TATTCGAAT
1 TATTCGAAT
30895976 TATTCGAAT
1 TATTCGAAT
*
30895985 TATTCGAGT
1 TATTCGAAT
30895994 TATTCGAAT
1 TATTCGAAT
30896003 T
1 T
30896004 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:30896615 original size:29 final size:29
Alignment explanation
Indices: 30896594--30896649 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
30896584 ATTATAGTTG
*
30896594 GAATGAAAATAGTAATAAAATTCAAACAT
1 GAATGAAAATAATAATAAAATTCAAACAT
30896623 GAATGAAAATAATAATAAAATTCAAAC
1 GAATGAAAATAATAATAAAATTCAAAC
30896650 TTCTTTATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.61, C:0.07, G:0.09, T:0.23
Consensus pattern (29 bp):
GAATGAAAATAATAATAAAATTCAAACAT
Found at i:30897630 original size:3 final size:3
Alignment explanation
Indices: 30897622--30897652 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
30897612 ATTTAAGGTG
30897622 ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT A
1 ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT A
30897653 GTTGACTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ACT
Found at i:30899480 original size:22 final size:22
Alignment explanation
Indices: 30899455--30899507 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
30899445 AAAATTTCAA
30899455 AAAAAATTATTA-AAA-AAAGTAT
1 AAAAAATTA-TACAAAGAAAGT-T
*
30899477 AAAAAAATATACAAAGAAAGTT
1 AAAAAATTATACAAAGAAAGTT
30899499 AAAAAATTA
1 AAAAAATTA
30899508 AAAACTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 2 0.07
22 20 0.74
23 5 0.19
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.23
Consensus pattern (22 bp):
AAAAAATTATACAAAGAAAGTT
Found at i:30900125 original size:94 final size:93
Alignment explanation
Indices: 30900015--30900201 Score: 313
Period size: 94 Copynumber: 2.0 Consensus size: 93
30900005 GTCCCCTGCA
*
30900015 TGGAGCATTTTCTCTCTAGCCATTTCAACCACCCCAACTTGATTGCTTTTGAGCCCTGCAACCCA
1 TGGAGCATTTTCTCTCTAGCCATTTCAACCACCACAACTTGATTGCTTTTGAGCCCTGCAACCCA
30900080 GGATTCCCGA-GATAATTTTCCCCCTTTAT
66 GGATT-CCGAGGATAA-TTTCCCCCTTTAT
*
30900109 TGGAGCATTTTCTCTCTAGCCATTTCAACCACCACAACTTGATTGCTTTTGAGCCCTGCAACCTA
1 TGGAGCATTTTCTCTCTAGCCATTTCAACCACCACAACTTGATTGCTTTTGAGCCCTGCAACCCA
* *
30900174 GGATTCCTAGGATAATTTCTCCCTTTAT
66 GGATTCCGAGGATAATTTCCCCCTTTAT
30900202 ACCCCGCCTC
Statistics
Matches: 88, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
93 15 0.17
94 73 0.83
ACGTcount: A:0.22, C:0.30, G:0.14, T:0.34
Consensus pattern (93 bp):
TGGAGCATTTTCTCTCTAGCCATTTCAACCACCACAACTTGATTGCTTTTGAGCCCTGCAACCCA
GGATTCCGAGGATAATTTCCCCCTTTAT
Found at i:30902378 original size:29 final size:29
Alignment explanation
Indices: 30902346--30902406 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
30902336 TTTGTGATTA
30902346 AAATTATAATATTGAATAATTGAATAATT
1 AAATTATAATATTGAATAATTGAATAATT
* * ** *
30902375 AAATTGTAATTTTTCATAATTGAGTAATT
1 AAATTATAATATTGAATAATTGAATAATT
30902404 AAA
1 AAA
30902407 ATGTAATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.43
Consensus pattern (29 bp):
AAATTATAATATTGAATAATTGAATAATT
Found at i:30902411 original size:29 final size:29
Alignment explanation
Indices: 30902361--30902416 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
30902351 ATAATATTGA
*
30902361 ATAATTGAATAATTAAATTGTAATTTTTC
1 ATAATTGAATAATTAAAATGTAATTTTTC
*
30902390 ATAATTGAGTAATTAAAATGTAATTTT
1 ATAATTGAATAATTAAAATGTAATTTT
30902417 ACGCATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (29 bp):
ATAATTGAATAATTAAAATGTAATTTTTC
Found at i:30919418 original size:41 final size:41
Alignment explanation
Indices: 30919361--30919443 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
30919351 TGTCGGTAAT
30919361 CTTTCACAAGCAATAGCAAAAACAAAGTAGTAAAGCAACAA
1 CTTTCACAAGCAATAGCAAAAACAAAGTAGTAAAGCAACAA
30919402 CTTTCACAAGCAATAGCAAAAACAAAGTAGTAAAGCAACAA
1 CTTTCACAAGCAATAGCAAAAACAAAGTAGTAAAGCAACAA
30919443 C
1 C
30919444 CTATGTTGCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.53, C:0.20, G:0.12, T:0.14
Consensus pattern (41 bp):
CTTTCACAAGCAATAGCAAAAACAAAGTAGTAAAGCAACAA
Found at i:30926336 original size:21 final size:21
Alignment explanation
Indices: 30926310--30926350 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
30926300 ATCTGCTCAA
* *
30926310 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
30926331 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
30926351 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:30929456 original size:3 final size:3
Alignment explanation
Indices: 30929448--30929472 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
30929438 TTCTGTAGTT
30929448 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
30929473 AATATTGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:30933946 original size:24 final size:24
Alignment explanation
Indices: 30933902--30933947 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
30933892 CACACCAGGG
*
30933902 ATTATATCCAATTTAACAACATTA
1 ATTATATCCAATTTAAAAACATTA
*
30933926 ATTATA-CCTATTGTAAAAACAT
1 ATTATATCCAATT-TAAAAACAT
30933948 GTCTGAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (24 bp):
ATTATATCCAATTTAAAAACATTA
Found at i:30937821 original size:89 final size:90
Alignment explanation
Indices: 30937721--30937885 Score: 219
Period size: 89 Copynumber: 1.8 Consensus size: 90
30937711 TTAGGGCTTG
* * * * *
30937721 AATTTGATTGTGATAATGGT-GGCAATGTGTTCA-TCGTTTAAAAGTATGATTGTGATTAG-TAT
1 AATTTGATTGTGACAATGGTAGGAAAT-TGTGCAGT-GTTTAAAAGTATGACTGTGATCAGTTAT
30937783 ATTGTTTAAAAGTGTGATTTAGACTCA
64 ATTGTTTAAAAGTGTGATTTAGACTCA
* * *
30937810 AATTTGATTGTGACAGTGGTAGTAAATTGTGCAGTGTTTAAAAGTGTGACTGTGATCAGTTATAT
1 AATTTGATTGTGACAATGGTAGGAAATTGTGCAGTGTTTAAAAGTATGACTGTGATCAGTTATAT
30937875 TGTTTAAAAGT
66 TGTTTAAAAGT
30937886 ACGATTGGGG
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
89 44 0.68
90 21 0.32
ACGTcount: A:0.30, C:0.05, G:0.24, T:0.41
Consensus pattern (90 bp):
AATTTGATTGTGACAATGGTAGGAAATTGTGCAGTGTTTAAAAGTATGACTGTGATCAGTTATAT
TGTTTAAAAGTGTGATTTAGACTCA
Found at i:30937920 original size:90 final size:87
Alignment explanation
Indices: 30937826--30938108 Score: 262
Period size: 90 Copynumber: 3.3 Consensus size: 87
30937816 ATTGTGACAG
* *
30937826 TGGTAGTAAATTGTGCAGTGTTTAAAAGTGTGACTGTGATCAGTTATATTGTTTAAAAGTACGAT
1 TGGTAGCAAATTGTGCATTGTTT-AAAG-GTGA-TGTGATCAGTTATATTGTTTAAAAGTACGAT
*
30937891 TGGGGATTGAATTC-AATCATGATAA
63 TTGGGATTGAATTCGAA-CATGATAA
* * * * * *
30937916 TGGTAGCGAATTGTGCATTATTTAAAGGT-ATG-GATGCA--AATAGTGATT---GGTACGATTT
1 TGGTAGCAAATTGTGCATTGTTTAAAGGTGATGTGAT-CAGTTATATTGTTTAAAAGTACGATTT
30937974 GGGATTGAATTCGAACATGATAA
65 GGGATTGAATTCGAACATGATAA
* * * * *
30937997 TGGTAGCAAATTATGCATTGTTTGAAGGCATGGTTGTGATTAGTTATATTGTTTAAAAGTAAGAT
1 TGGTAGCAAATTGTGCATTGTTTAAAGG--T-GATGTGATCAGTTATATTGTTTAAAAGTACGAT
30938062 TTGGGATTGAATAT-GAACATTGAT-A
63 TTGGGATTGAAT-TCGAACA-TGATAA
* *
30938087 TGGTGGCGAATTGTGCATTGTT
1 TGGTAGCAAATTGTGCATTGTT
30938109 GATTCGTTAT
Statistics
Matches: 156, Mismatches: 23, Indels: 28
0.75 0.11 0.14
Matches are distributed among these distances:
81 52 0.33
82 2 0.01
83 1 0.01
84 7 0.04
85 6 0.04
86 7 0.04
87 8 0.05
88 2 0.01
89 4 0.03
90 62 0.40
91 5 0.03
ACGTcount: A:0.31, C:0.06, G:0.26, T:0.37
Consensus pattern (87 bp):
TGGTAGCAAATTGTGCATTGTTTAAAGGTGATGTGATCAGTTATATTGTTTAAAAGTACGATTTG
GGATTGAATTCGAACATGATAA
Found at i:30944116 original size:2 final size:2
Alignment explanation
Indices: 30944109--30944141 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
30944099 CCACATTGAG
30944109 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30944142 CATAGGTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30947441 original size:17 final size:17
Alignment explanation
Indices: 30947408--30947479 Score: 58
Period size: 17 Copynumber: 4.1 Consensus size: 17
30947398 ACATCATTAC
*
30947408 TAATTCAATTGAT-TAAA
1 TAATTCAA-TAATATAAA
30947425 TAATTCAATAATATAAA
1 TAATTCAATAATATAAA
* *
30947442 TAATACAA-AATGTAAAA
1 TAATTCAATAATAT-AAA
*
30947459 TTTAATTTAATAATATAAA
1 --TAATTCAATAATATAAA
30947478 TA
1 TA
30947480 GTATATATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
16 7 0.16
17 24 0.55
19 9 0.20
20 4 0.09
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.38
Consensus pattern (17 bp):
TAATTCAATAATATAAA
Found at i:30948068 original size:31 final size:30
Alignment explanation
Indices: 30947993--30948068 Score: 109
Period size: 30 Copynumber: 2.5 Consensus size: 30
30947983 CCGAATATAA
30947993 TAAATATATATTTTTTATTTTTAAAAATATTT
1 TAAA-ATA-ATTTTTTATTTTTAAAAATATTT
30948025 TAAAATAATTTTTTATTTTT-AAAATATTTT
1 TAAAATAATTTTTTATTTTTAAAAATA-TTT
*
30948055 TAAAATACTTTTTT
1 TAAAATAATTTTTT
30948069 TAATTTTCTA
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
29 6 0.14
30 29 0.69
31 3 0.07
32 4 0.10
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (30 bp):
TAAAATAATTTTTTATTTTTAAAAATATTT
Found at i:30949974 original size:99 final size:101
Alignment explanation
Indices: 30949854--30950047 Score: 230
Period size: 101 Copynumber: 1.9 Consensus size: 101
30949844 ACCAAAATTT
* * *
30949854 TTTTTTATTGAATTTAGTGCCTCCACATGAAGA-GAG-CATTGAAAAATTCAAAAAAAAAAATGT
1 TTTTTTATTGAATTTAGTGCCTCCACATGAAAATGAGACATCGAAAAATTCAAAAAAAAAAATGC
*
30949917 TGCTGCCGCTACATTTGGAGTTGGCACTAGGGGGAA
66 TGCTGCCGCCACATTTGGAGTTGGCACTAGGGGGAA
** * * * ** ** *
30949953 TTTTTTATTGGTTTTGGTGCCTCTACATGAAAATGTGACATCGAAAAATTTTAAATTAAAATTGC
1 TTTTTTATTGAATTTAGTGCCTCCACATGAAAATGAGACATCGAAAAATTCAAAAAAAAAAATGC
* *
30950018 TGGTGTCGCCACATTTGGAGTTGGCACTAG
66 TGCTGCCGCCACATTTGGAGTTGGCACTAG
30950048 AAAAATAAAG
Statistics
Matches: 77, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
99 28 0.36
100 2 0.03
101 47 0.61
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.34
Consensus pattern (101 bp):
TTTTTTATTGAATTTAGTGCCTCCACATGAAAATGAGACATCGAAAAATTCAAAAAAAAAAATGC
TGCTGCCGCCACATTTGGAGTTGGCACTAGGGGGAA
Found at i:30951358 original size:90 final size:90
Alignment explanation
Indices: 30951207--30951370 Score: 224
Period size: 90 Copynumber: 1.8 Consensus size: 90
30951197 TTAAAAGTAT
* * * *
30951207 GATTGTGATTAGTTATATTGTTTAAAAGGGTGATTTAGATTTGATTTTGATTCTGACAATGGTAA
1 GATTGTGATAAGTTATATTGTTCAAAAGGGTGATTTAGATTTGAATTTGATTCTCACAATGGTAA
*
30951272 TAAATTGTGTAGTTTTTAGAAATAC
66 CAAATTGTGTAGTTTTTAGAAATAC
* *
30951297 GATTGTGATAAGTTATATTGTTCAAAAGTGTGATTTGAGA-TTGAATTTGA-TCATCATAATGGT
1 GATTGTGATAAGTTATATTGTTCAAAAGGGTGATTT-AGATTTGAATTTGATTC-TCACAATGGT
*
30951360 AACGAATTGTG
64 AACAAATTGTG
30951371 CATTGTTTAA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
89 2 0.03
90 59 0.92
91 3 0.05
ACGTcount: A:0.32, C:0.04, G:0.22, T:0.42
Consensus pattern (90 bp):
GATTGTGATAAGTTATATTGTTCAAAAGGGTGATTTAGATTTGAATTTGATTCTCACAATGGTAA
CAAATTGTGTAGTTTTTAGAAATAC
Found at i:30952584 original size:18 final size:18
Alignment explanation
Indices: 30952563--30952617 Score: 67
Period size: 18 Copynumber: 3.0 Consensus size: 18
30952553 TTAAAATATA
30952563 TATAAT-TTTTGAAATTTT
1 TATAATATTTTG-AATTTT
30952581 TATAAATATTTTGAATTTT
1 TAT-AATATTTTGAATTTT
* *
30952600 GAAAATATTTTGAATTTT
1 TATAATATTTTGAATTTT
30952618 AGTTGGGAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 18 0.55
19 10 0.30
20 5 0.15
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.56
Consensus pattern (18 bp):
TATAATATTTTGAATTTT
Found at i:30959566 original size:34 final size:34
Alignment explanation
Indices: 30959521--30959610 Score: 126
Period size: 34 Copynumber: 2.6 Consensus size: 34
30959511 ACTTATACAA
*
30959521 ATATCATATCAGAATTTCATATTACCAAAAACAT
1 ATATCATATCAGAATGTCATATTACCAAAAACAT
* * **
30959555 ATATCAGATCAGAATGTCATATTTCCAAATGCAT
1 ATATCATATCAGAATGTCATATTACCAAAAACAT
*
30959589 ATATCATATCAGGATGTCATAT
1 ATATCATATCAGAATGTCATAT
30959611 CAAATCAGAA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (34 bp):
ATATCATATCAGAATGTCATATTACCAAAAACAT
Found at i:30965384 original size:27 final size:27
Alignment explanation
Indices: 30965336--30965486 Score: 144
Period size: 27 Copynumber: 5.6 Consensus size: 27
30965326 AGTACCGAGA
* * *
30965336 CCCTCATAGGGTAAAATAACCGTAATGT
1 CCCT-ATAGGGTAAAATGATCGTAATGC
* * *
30965364 CCCTATAAGGTAAAATGACCGTAATAC
1 CCCTATAGGGTAAAATGATCGTAATGC
* * * *
30965391 CCCTGTAGGGTAAAATGATAGAAAAGC
1 CCCTATAGGGTAAAATGATCGTAATGC
*
30965418 CCCCAT-GGGTAAAATGATCGTAATGC
1 CCCTATAGGGTAAAATGATCGTAATGC
* *
30965444 CCCTGTAGGGTAAAATGATCGTAATAC
1 CCCTATAGGGTAAAATGATCGTAATGC
*
30965471 TCCC-ATAGGGTTAAAT
1 -CCCTATAGGGTAAAAT
30965487 AACCGAAATA
Statistics
Matches: 100, Mismatches: 21, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
26 21 0.21
27 72 0.72
28 7 0.07
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.24
Consensus pattern (27 bp):
CCCTATAGGGTAAAATGATCGTAATGC
Found at i:30965434 original size:26 final size:27
Alignment explanation
Indices: 30965396--30965462 Score: 82
Period size: 26 Copynumber: 2.5 Consensus size: 27
30965386 AATACCCCTG
30965396 TAGGGTAAAATGATAGAAAAGCCCCCA
1 TAGGGTAAAATGATAGAAAAGCCCCCA
* * * **
30965423 T-GGGTAAAATGATCGTAATGCCCCTG
1 TAGGGTAAAATGATAGAAAAGCCCCCA
30965449 TAGGGTAAAATGAT
1 TAGGGTAAAATGAT
30965463 CGTAATACTC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 21 0.62
27 13 0.38
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.22
Consensus pattern (27 bp):
TAGGGTAAAATGATAGAAAAGCCCCCA
Found at i:30965440 original size:53 final size:54
Alignment explanation
Indices: 30965372--30965511 Score: 176
Period size: 53 Copynumber: 2.6 Consensus size: 54
30965362 GTCCCTATAA
30965372 GGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGATAG-AAAAGCCCCCAT-G
1 GGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGATAGTAAAA-CCCCCATAG
* * * * *
30965425 GGTAAAATGATCGTAATGCCCCTGTAGGGTAAAATGATCGTAATACTCCCATAG
1 GGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGATAGTAAAACCCCCATAG
* * * *
30965479 GGTTAAATAACCGAAATACCCCTGTAAGGTAAA
1 GGTAAAATGACCGTAATACCCCTGTAGGGTAAA
30965512 TTGGCTGTAA
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
53 43 0.58
54 31 0.42
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.22
Consensus pattern (54 bp):
GGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGATAGTAAAACCCCCATAG
Found at i:30965626 original size:24 final size:24
Alignment explanation
Indices: 30965561--30965632 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
30965551 CCCACGAGTG
* * * *
30965561 TAAATGATTGATTTGTCCGTAATG
1 TAAATGACTGATTTGTCTGTGATT
*
30965585 TAAATGTCTGATTTGTCTGTGATT
1 TAAATGACTGATTTGTCTGTGATT
*
30965609 TAAATGACTGATTTGTCTGCGATT
1 TAAATGACTGATTTGTCTGTGATT
30965633 GGTATAACTG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.25, C:0.10, G:0.21, T:0.44
Consensus pattern (24 bp):
TAAATGACTGATTTGTCTGTGATT
Found at i:30965642 original size:24 final size:24
Alignment explanation
Indices: 30965592--30965648 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
30965582 ATGTAAATGT
* * *
30965592 CTGATTTGTCTGTGATTTAAATGA
1 CTGATTTGTCTGCGATTGAAATAA
**
30965616 CTGATTTGTCTGCGATTGGTATAA
1 CTGATTTGTCTGCGATTGAAATAA
30965640 CTGATTTGT
1 CTGATTTGT
30965649 ATGACTGATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.21, C:0.11, G:0.23, T:0.46
Consensus pattern (24 bp):
CTGATTTGTCTGCGATTGAAATAA
Found at i:30965876 original size:32 final size:32
Alignment explanation
Indices: 30965833--30965973 Score: 192
Period size: 32 Copynumber: 4.4 Consensus size: 32
30965823 ACGATGCTAT
* *
30965833 TGATGGATTTGTATCGATCATATTACCGTTAC
1 TGATGGCTTTGTGTCGATCATATTACCGTTAC
* * *
30965865 TGATGGCTTTGTGTTGGTCATATTACCGTTAT
1 TGATGGCTTTGTGTCGATCATATTACCGTTAC
30965897 TGATGGCTTTGTGTCGATCATATTACCGTTAC
1 TGATGGCTTTGTGTCGATCATATTACCGTTAC
* * * * *
30965929 TGATGGCTTTATGCCGATCATATCACTGCTAC
1 TGATGGCTTTGTGTCGATCATATTACCGTTAC
30965961 TGATGGCTTTGTG
1 TGATGGCTTTGTG
30965974 CCAATAATAT
Statistics
Matches: 95, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 95 1.00
ACGTcount: A:0.19, C:0.17, G:0.23, T:0.41
Consensus pattern (32 bp):
TGATGGCTTTGTGTCGATCATATTACCGTTAC
Found at i:30971219 original size:324 final size:324
Alignment explanation
Indices: 30970608--30971242 Score: 818
Period size: 324 Copynumber: 2.0 Consensus size: 324
30970598 GGTGTTGCTA
* **
30970608 TTTCTCTTTTATTTTTAATAATAATTTTTGGCCATTTATTTTTCCTTTATTTTTGCAAGTATAGT
1 TTTCTCTTTTATTTTTAATAAT-ATTTTTGGCCATTTATTTTCCCTTTATTTTTGCAAGTATAAC
* * *
30970673 AGTTCCTTCCCCAGGTTCACAAGAAAAATAGGAAGGCAGACATCGTAGTAGGAACCTATAATGGT
65 AATTCCTTCCCCAGGTTCACAAGAAAAATAGGAAGGCAAACATCATAGTAGGAACCTATAATGGT
* * * * *
30970738 CGAGTAGACACAAAATAATGATGTGACATTAGTATTTATAACCCCTCTCAACCACACAATATTCA
130 CGAGTAAACACAAAATAAGGATGTGACATTAGTATTGATAACCCATCTCAACCACACAATAGTCA
* * * *
30970803 TAGTCAATGTGGGTCTATTCTGTAGGCCTTATCTTCACAAGTACTTGTTATTAGTATGTCGGTTC
195 TAGTCAATGTGGGTCTATTCTGTAAGCCTTACCTTCACAAGTACTTGTTATTAGCATGTCGATTC
30970868 ACAATCCTTCTAGCAAAATCAATTTTATTTCTAATTTGAACTT-TATTTACTATTTCACATTGCC
260 ACAATCCTTCTAGCAAAATCAATTTTATTTCTAATTTGAACTTCT-TTTACTATTTCACATTGCC
30970932 T
324 T
*
30970933 TTTCTCTTTTA-TTTTAAT-AT-TTTTTGGTCATTTATTTTCCCTTTCA-TTTTGCAAGTATAAC
1 TTTCTCTTTTATTTTTAATAATATTTTTGGCCATTTATTTTCCCTTT-ATTTTTGCAAGTATAAC
** * *
30970994 AATTCCTCATTCTTCAGGTTTACAAGTAAAAA-AGGAAGGTAAACATCATAGTAGGAACCTATAA
65 AATT-C-C-TTCCCCAGGTTCACAAG-AAAAATAGGAAGGCAAACATCATAGTAGGAACCTATAA
* * * *
30971058 TGGTCGGGTAAACACAGAAA-AAGGATGTGACATTAGTATTGATAATCCATCTCCACCACACTAT
126 TGGTCGAGTAAACACA-AAATAAGGATGTGACATTAGTATTGATAACCCATCTCAACCACACAAT
* * * * * *
30971122 AGTCACT-GTCGATGTTGGTTTATTTTGTAAGTCTTACCTTCACAAGTACTTGTTATTGGCATGT
190 AGTCA-TAGTCAATGTGGGTCTATTCTGTAAGCCTTACCTTCACAAGTACTTGTTATTAGCATGT
* * * **
30971186 TGATTCACAATCTTTCTAGCGAAATTTATTTTATTTCTAATTTGAACTTCTTTTACT
254 CGATTCACAATCCTTCTAGCAAAATCAATTTTATTTCTAATTTGAACTTCTTTTACT
30971243 GTTTTGAAAT
Statistics
Matches: 267, Mismatches: 35, Indels: 17
0.84 0.11 0.05
Matches are distributed among these distances:
321 38 0.14
322 2 0.01
323 3 0.01
324 203 0.76
325 21 0.08
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (324 bp):
TTTCTCTTTTATTTTTAATAATATTTTTGGCCATTTATTTTCCCTTTATTTTTGCAAGTATAACA
ATTCCTTCCCCAGGTTCACAAGAAAAATAGGAAGGCAAACATCATAGTAGGAACCTATAATGGTC
GAGTAAACACAAAATAAGGATGTGACATTAGTATTGATAACCCATCTCAACCACACAATAGTCAT
AGTCAATGTGGGTCTATTCTGTAAGCCTTACCTTCACAAGTACTTGTTATTAGCATGTCGATTCA
CAATCCTTCTAGCAAAATCAATTTTATTTCTAATTTGAACTTCTTTTACTATTTCACATTGCCT
Found at i:30981296 original size:29 final size:29
Alignment explanation
Indices: 30981263--30981319 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
30981253 GACAGCAGAG
30981263 CAGGGGTAAGTTTGAAGATTTTACTATAA
1 CAGGGGTAAGTTTGAAGATTTTACTATAA
30981292 CAGGGGTAAGTTTGAAGATTTTACTATA
1 CAGGGGTAAGTTTGAAGATTTTACTATA
30981320 CTTATTGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.33, C:0.07, G:0.25, T:0.35
Consensus pattern (29 bp):
CAGGGGTAAGTTTGAAGATTTTACTATAA
Found at i:30986509 original size:18 final size:18
Alignment explanation
Indices: 30986468--30986502 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
30986458 GACTTTTTTT
30986468 TCTTCTATGTTCTTTCCA
1 TCTTCTATGTTCTTTCCA
30986486 TCTTCTAATGTT-TTTCC
1 TCTTCT-ATGTTCTTTCC
30986503 TTTTTCTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.11, C:0.26, G:0.06, T:0.57
Consensus pattern (18 bp):
TCTTCTATGTTCTTTCCA
Found at i:30988429 original size:22 final size:22
Alignment explanation
Indices: 30988396--30988441 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
30988386 ACTTATTGCC
*
30988396 ATCGATGTATTATGCTAATATA
1 ATCGATGTATTATGCCAATATA
30988418 ATCGAT-TGATTATGCCAATATA
1 ATCGATGT-ATTATGCCAATATA
30988440 AT
1 AT
30988442 TGAATATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (22 bp):
ATCGATGTATTATGCCAATATA
Found at i:30992795 original size:12 final size:12
Alignment explanation
Indices: 30992778--30992805 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
30992768 GACAAAGTTA
30992778 CAACACTAGGCT
1 CAACACTAGGCT
30992790 CAACACTAGGCT
1 CAACACTAGGCT
30992802 CAAC
1 CAAC
30992806 CCATAAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.36, G:0.14, T:0.14
Consensus pattern (12 bp):
CAACACTAGGCT
Found at i:30997538 original size:21 final size:21
Alignment explanation
Indices: 30997500--30997539 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
30997490 ATCCCTTGCC
* **
30997500 TTATTTTATTGTTTAATTTAT
1 TTATTTTATTATGAAATTTAT
30997521 TTATTTTATTATGAAATTT
1 TTATTTTATTATGAAATTT
30997540 TACTTTAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.68
Consensus pattern (21 bp):
TTATTTTATTATGAAATTTAT
Found at i:30997699 original size:18 final size:19
Alignment explanation
Indices: 30997676--30997723 Score: 73
Period size: 18 Copynumber: 2.6 Consensus size: 19
30997666 TTTTTTCTCA
*
30997676 CTATTGTTATTAT-TTTAT
1 CTATTGTTATTATCATTAT
30997694 CTATTGTTATTATCATTAT
1 CTATTGTTATTATCATTAT
30997713 CTATT-TTATTA
1 CTATTGTTATTA
30997724 CAAATTGCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 19 0.68
19 9 0.32
ACGTcount: A:0.25, C:0.08, G:0.04, T:0.62
Consensus pattern (19 bp):
CTATTGTTATTATCATTAT
Found at i:30997908 original size:12 final size:12
Alignment explanation
Indices: 30997893--30997917 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30997883 TTATCATTGC
30997893 TATTATTTATTT
1 TATTATTTATTT
30997905 TATTATTTATTT
1 TATTATTTATTT
30997917 T
1 T
30997918 TTCCTTTGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TATTATTTATTT
Found at i:31003729 original size:10 final size:10
Alignment explanation
Indices: 31003714--31003743 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
31003704 AGTACATATC
31003714 AATCACATTT
1 AATCACATTT
*
31003724 AATCACATTC
1 AATCACATTT
31003734 AATCACATTT
1 AATCACATTT
31003744 TATGATAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37
Consensus pattern (10 bp):
AATCACATTT
Found at i:31006226 original size:10 final size:10
Alignment explanation
Indices: 31006211--31006240 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
31006201 AGTACATATC
31006211 AATCACATTT
1 AATCACATTT
*
31006221 AATCACATTC
1 AATCACATTT
31006231 AATCACATTT
1 AATCACATTT
31006241 TATGATAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37
Consensus pattern (10 bp):
AATCACATTT
Found at i:31008469 original size:220 final size:224
Alignment explanation
Indices: 31008061--31008472 Score: 602
Period size: 220 Copynumber: 1.8 Consensus size: 224
31008051 AAAACCTGAC
* * *
31008061 CAAATCCTCATATTTCAAACCACTAGAACCACATATACCAACTATCCCCAATGTTAGGACTCTAT
1 CAAATCCTCATATGTCAAACCACTAGAACCACATATACCAACCATCCCCAATGTTAGGAATCTAT
*
31008126 CCCCCATCAAACTCTTCTAATATTCAGTAACCACTATCCCCCCTCAACACACAATCCTTCTTTAC
66 CCCCCATCAAACTCTTCTAATATTCAG--A-CACTATCCCCCCTCAACACACAACCCTTCTTTAC
*
31008191 ACTCGAAACCAACTCAAGCTCGAAAATCATACAAGAAGTACATAAAAAGAAAAGAAAGAAACAAA
128 ACTCGAAACCAACTCAAGCTCGAAAATCATACAAGAAGGACATAAAAAGAAAAGAAAGAAACAAA
31008256 AAAAAAACCTACTTGACTTTGAAGTGAAAGAG
193 AAAAAAACCTACTTGACTTTGAAGTGAAAGAG
* *
31008288 CAAATCCTCAT-TCGTCAAA-CACTAGAACCACATATATCAACCATCTCCAATGTT-GGAAATCT
1 CAAATCCTCATAT-GTCAAACCACTAGAACCACATATACCAACCATCCCCAATGTTAGG-AATCT
* * * * *
31008350 A-GCCCCATCAAACTTTTCTACTATTCAG-CTC-ATCCCCCCTCAACCCACAACCCTTCTTTACA
64 ATCCCCCATCAAACTCTTCTAATATTCAGACACTATCCCCCCTCAACACACAACCCTTCTTTACA
* * *
31008412 CTCGAAACCAACTCAAGCTCGACAATCATACAAGAAGGGCATACAAAGAAAAGAAAGAAAC
129 CTCGAAACCAACTCAAGCTCGAAAATCATACAAGAAGGACATAAAAAGAAAAGAAAGAAAC
31008473 CAAATAATAA
Statistics
Matches: 168, Mismatches: 15, Indels: 11
0.87 0.08 0.06
Matches are distributed among these distances:
220 86 0.51
221 2 0.01
225 26 0.15
226 38 0.23
227 16 0.10
ACGTcount: A:0.40, C:0.30, G:0.09, T:0.21
Consensus pattern (224 bp):
CAAATCCTCATATGTCAAACCACTAGAACCACATATACCAACCATCCCCAATGTTAGGAATCTAT
CCCCCATCAAACTCTTCTAATATTCAGACACTATCCCCCCTCAACACACAACCCTTCTTTACACT
CGAAACCAACTCAAGCTCGAAAATCATACAAGAAGGACATAAAAAGAAAAGAAAGAAACAAAAAA
AAAACCTACTTGACTTTGAAGTGAAAGAG
Found at i:31009195 original size:12 final size:11
Alignment explanation
Indices: 31009168--31009197 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
31009158 ATATATTTTT
31009168 TATTTTTAAAA
1 TATTTTTAAAA
31009179 TATTTTTAAAA
1 TATTTTTAAAA
31009190 TAATTTTT
1 T-ATTTTT
31009198 TTTTATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:31024085 original size:22 final size:22
Alignment explanation
Indices: 31024054--31024095 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
31024044 AGTTTCCATA
*
31024054 TCATATAATAAAAAGACCAACT
1 TCATACAATAAAAAGACCAACT
* *
31024076 TCATACAATAACAAGGCCAA
1 TCATACAATAAAAAGACCAA
31024096 ATTTTTCGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.52, C:0.21, G:0.07, T:0.19
Consensus pattern (22 bp):
TCATACAATAAAAAGACCAACT
Found at i:31029495 original size:37 final size:37
Alignment explanation
Indices: 31029453--31029529 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
31029443 AAATGTTAGT
*
31029453 ATTGTCAAAATTCTTTTATTAAATTAATTATTGTTAC
1 ATTGTCAAAATTCTTTTATTAAATTAATTATTGTGAC
*
31029490 ATTGTCAAAATTCTTTTATTAAATTTATTATTGTGAC
1 ATTGTCAAAATTCTTTTATTAAATTAATTATTGTGAC
31029527 ATT
1 ATT
31029530 TTGACAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.34, C:0.08, G:0.06, T:0.52
Consensus pattern (37 bp):
ATTGTCAAAATTCTTTTATTAAATTAATTATTGTGAC
Found at i:31031727 original size:28 final size:26
Alignment explanation
Indices: 31031674--31031738 Score: 69
Period size: 28 Copynumber: 2.5 Consensus size: 26
31031664 TTTTAAATTT
*
31031674 AAAAAAT-AAAAAATTAAATTCCTAA
1 AAAAAATAAAAAAATTAAATTCATAA
*
31031699 AAAAAATAAAAATAATTTAAATTTATAA
1 AAAAAATAAAAA-AA-TTAAATTCATAA
* *
31031727 AATATATAAAAA
1 AAAAAATAAAAA
31031739 CCAACACCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
25 7 0.21
26 4 0.12
27 2 0.06
28 20 0.61
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (26 bp):
AAAAAATAAAAAAATTAAATTCATAA
Found at i:31035197 original size:24 final size:24
Alignment explanation
Indices: 31035170--31035215 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
31035160 AATTTCAGAC
*
31035170 ATGTTTTTACAATAGG-TATAATTA
1 ATGTTGTTA-AATAGGATATAATTA
*
31035194 ATGTTGTTAAATTGGATATAAT
1 ATGTTGTTAAATAGGATATAAT
31035216 CCCTGGTGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.46
Consensus pattern (24 bp):
ATGTTGTTAAATAGGATATAATTA
Found at i:31035719 original size:6 final size:6
Alignment explanation
Indices: 31035708--31035737 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
31035698 ATAGTAATTA
31035708 TATATT TATATT TATATT TATATT TATATT
1 TATATT TATATT TATATT TATATT TATATT
31035738 AAATCACTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATATT
Found at i:31035888 original size:20 final size:20
Alignment explanation
Indices: 31035863--31035912 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
31035853 TGGCTTAAAA
31035863 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
31035883 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
31035900 GTGGTAGTGGATT
1 TTGGTAGTGGATT
31035913 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:31043036 original size:9 final size:9
Alignment explanation
Indices: 31043018--31043083 Score: 64
Period size: 9 Copynumber: 7.2 Consensus size: 9
31043008 TTTGGTTAAA
31043018 AATTACCCG
1 AATTACCCG
*
31043027 AATTATCCG
1 AATTACCCG
31043036 -ATTGA-CCG
1 AATT-ACCCG
* *
31043044 AATTAACTG
1 AATTACCCG
31043053 AATTACCCG
1 AATTACCCG
31043062 AAAATTACCCG
1 --AATTACCCG
31043073 AATTACCCG
1 AATTACCCG
31043082 AA
1 AA
31043084 AATTACCCAA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
8 7 0.15
9 32 0.67
11 9 0.19
ACGTcount: A:0.38, C:0.26, G:0.12, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:31043075 original size:20 final size:20
Alignment explanation
Indices: 31043052--31043091 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
31043042 CGAATTAACT
31043052 GAATTACCCGAAAATTACCC
1 GAATTACCCGAAAATTACCC
31043072 GAATTACCCGAAAATTACCC
1 GAATTACCCGAAAATTACCC
31043092 AAAAAGTTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.30, G:0.10, T:0.20
Consensus pattern (20 bp):
GAATTACCCGAAAATTACCC
Found at i:31043096 original size:11 final size:11
Alignment explanation
Indices: 31043053--31043095 Score: 65
Period size: 11 Copynumber: 4.2 Consensus size: 11
31043043 GAATTAACTG
31043053 AATTACCCGAA
1 AATTACCCGAA
31043064 AATTACCCG--
1 AATTACCCGAA
31043073 AATTACCCGAA
1 AATTACCCGAA
31043084 AATTACCC-AA
1 AATTACCCGAA
31043094 AA
1 AA
31043096 AGTTCGGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
9 9 0.30
10 4 0.13
11 17 0.57
ACGTcount: A:0.47, C:0.28, G:0.07, T:0.19
Consensus pattern (11 bp):
AATTACCCGAA
Found at i:31045269 original size:14 final size:14
Alignment explanation
Indices: 31045250--31045276 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31045240 GATTCTTAAT
31045250 TATAATTTAACATA
1 TATAATTTAACATA
31045264 TATAATTTAACAT
1 TATAATTTAACAT
31045277 GCTTCGATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (14 bp):
TATAATTTAACATA
Found at i:31045602 original size:18 final size:18
Alignment explanation
Indices: 31045581--31045621 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
31045571 TAATTGATAT
* *
31045581 GGAGGATATATTTGAGGA
1 GGAGGATACATGTGAGGA
*
31045599 GGAGGATACATGTGAGGT
1 GGAGGATACATGTGAGGA
31045617 GGAGG
1 GGAGG
31045622 TGGGTGATAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.02, G:0.46, T:0.22
Consensus pattern (18 bp):
GGAGGATACATGTGAGGA
Found at i:31045650 original size:18 final size:18
Alignment explanation
Indices: 31045581--31045652 Score: 54
Period size: 18 Copynumber: 3.7 Consensus size: 18
31045571 TAATTGATAT
* * *
31045581 GGAGGATATATTTGAGGA
1 GGAGGATACATTGGTGGA
31045599 GGAGGATACATGTGAGGTGGA
1 GGAGGATACAT-T--GGTGGA
*
31045620 GGTGGGTGATACATTGGTGGA
1 -G-GAG-GATACATTGGTGGA
31045641 GGAGGATACATT
1 GGAGGATACATT
31045653 TGAGGCTGGT
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
18 18 0.42
19 3 0.07
20 1 0.02
21 10 0.23
22 1 0.02
23 3 0.07
24 7 0.16
ACGTcount: A:0.28, C:0.04, G:0.43, T:0.25
Consensus pattern (18 bp):
GGAGGATACATTGGTGGA
Found at i:31046596 original size:14 final size:14
Alignment explanation
Indices: 31046558--31046600 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
31046548 CAAAATATAC
31046558 AATATAATTAAA-T
1 AATATAATTAAATT
31046571 AATATAAATTAAATT
1 AATAT-AATTAAATT
*
31046586 AA-ATAATTTAATT
1 AATATAATTAAATT
31046599 AA
1 AA
31046601 CTGTTTACCT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 15 0.56
14 9 0.33
15 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATAATTAAATT
Found at i:31049083 original size:3 final size:3
Alignment explanation
Indices: 31049068--31049192 Score: 135
Period size: 3 Copynumber: 42.0 Consensus size: 3
31049058 TAAAACAATT
* * *
31049068 TAA TAA TAG TAA TAA TAA TAA TAA TAA T-G TAA TAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * ** * **
31049115 TAA TAA TAA GAA TAA GAA TAA TGG TAA TAA TAA TAA TAA TAA TGA TGG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
31049163 TAT TAA TAA TAA TAA TAA TAA CAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
31049193 AATCTTAAAA
Statistics
Matches: 100, Mismatches: 21, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
2 1 0.01
3 99 0.99
ACGTcount: A:0.59, C:0.01, G:0.07, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:31049815 original size:36 final size:36
Alignment explanation
Indices: 31049768--31049855 Score: 167
Period size: 36 Copynumber: 2.4 Consensus size: 36
31049758 GGTTAGGCCG
31049768 AAACGGCGTCGTTTTGGTGCCAGAGTGGCCTGCCCA
1 AAACGGCGTCGTTTTGGTGCCAGAGTGGCCTGCCCA
31049804 AAACGGCGTCGTTTTGGTGCCAGAGTGGCCTGCCCA
1 AAACGGCGTCGTTTTGGTGCCAGAGTGGCCTGCCCA
*
31049840 AAACGGCGCCGTTTTG
1 AAACGGCGTCGTTTTG
31049856 AAGGTCTATT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.17, C:0.27, G:0.33, T:0.23
Consensus pattern (36 bp):
AAACGGCGTCGTTTTGGTGCCAGAGTGGCCTGCCCA
Found at i:31054345 original size:96 final size:98
Alignment explanation
Indices: 31054175--31054358 Score: 275
Period size: 96 Copynumber: 1.9 Consensus size: 98
31054165 GCACCTGCAT
* * *
31054175 TTTTCGTGTAAAAATTTCGATTCCAGAAAAGAGAAAAAAGATACATTTTTACCCAAAAGAATAGG
1 TTTTCGTGTAAAAATTTCAATTCCAGAAAAGAGAAAAAAGACACATTTTGACCCAAAAGAATAGG
*
31054240 TTAGAGAAAGTAGTGTCAAATATCTAGGTCATA
66 TTAGAGAAAGCAGTGTCAAATATCTAGGTCATA
* * *
31054273 TTTTC-TGTAAAAATTTCAATTCCAG-AAAGGGGAAAAA-ACACATATTTGCCCCAAAAGAATAG
1 TTTTCGTGTAAAAATTTCAATTCCAGAAAAGAGAAAAAAGACACAT-TTTGACCCAAAAGAATAG
31054335 GTTAGAGAAAGCAGTGTCAAATAT
65 GTTAGAGAAAGCAGTGTCAAATAT
31054359 TTAGAGGGAT
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
95 5 0.06
96 49 0.63
97 19 0.24
98 5 0.06
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.27
Consensus pattern (98 bp):
TTTTCGTGTAAAAATTTCAATTCCAGAAAAGAGAAAAAAGACACATTTTGACCCAAAAGAATAGG
TTAGAGAAAGCAGTGTCAAATATCTAGGTCATA
Found at i:31057144 original size:6 final size:6
Alignment explanation
Indices: 31057133--31057167 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
31057123 CTTTTCTCGG
* *
31057133 TCCCTA TCCCTA TCCTTA TCTCTA TCCCTA TCCCT
1 TCCCTA TCCCTA TCCCTA TCCCTA TCCCTA TCCCT
31057168 GTGGCGATCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.14, C:0.46, G:0.00, T:0.40
Consensus pattern (6 bp):
TCCCTA
Found at i:31057154 original size:24 final size:24
Alignment explanation
Indices: 31057120--31057167 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
31057110 CACGATCACG
* *
31057120 ATCCTTTTCTCGGTCCCTATCCCT
1 ATCCTTATCTCGATCCCTATCCCT
*
31057144 ATCCTTATCTCTATCCCTATCCCT
1 ATCCTTATCTCGATCCCTATCCCT
31057168 GTGGCGATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.12, C:0.42, G:0.04, T:0.42
Consensus pattern (24 bp):
ATCCTTATCTCGATCCCTATCCCT
Found at i:31062198 original size:20 final size:21
Alignment explanation
Indices: 31062173--31062212 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
31062163 TGAAAACAAA
31062173 AAAATA-TA-TATCTAAAAATT
1 AAAATATTATTAT-TAAAAATT
31062193 AAAATATTATTATTAAAAAT
1 AAAATATTATTATTAAAAAT
31062213 AACTTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 9 0.50
22 3 0.17
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAATATTATTATTAAAAATT
Found at i:31063503 original size:9 final size:9
Alignment explanation
Indices: 31063478--31063518 Score: 66
Period size: 9 Copynumber: 4.7 Consensus size: 9
31063468 TTAAAAAAAA
*
31063478 CGAATTACC
1 CGAATTAAC
31063487 CGAA-TAAC
1 CGAATTAAC
31063495 CGAATTAAC
1 CGAATTAAC
31063504 CGAATTAAC
1 CGAATTAAC
31063513 CGAATT
1 CGAATT
31063519 TCCTCATCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 7 0.23
9 23 0.77
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.22
Consensus pattern (9 bp):
CGAATTAAC
Found at i:31063514 original size:18 final size:17
Alignment explanation
Indices: 31063478--31063518 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
31063468 TTAAAAAAAA
*
31063478 CGAATTACCCGAATAAC
1 CGAATTAACCGAATAAC
31063495 CGAATTAACCGAATTAAC
1 CGAATTAACCGAA-TAAC
31063513 CGAATT
1 CGAATT
31063519 TCCTCATCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.22
Consensus pattern (17 bp):
CGAATTAACCGAATAAC
Found at i:31065598 original size:14 final size:14
Alignment explanation
Indices: 31065579--31065617 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
31065569 TAGACTTTAG
*
31065579 TTTTAGTTTTAGAC
1 TTTTAGTTTTAGAA
31065593 TTTTAGTTTTAGAA
1 TTTTAGTTTTAGAA
*
31065607 TTTTATTTTTA
1 TTTTAGTTTTA
31065618 TTTATTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.23, C:0.03, G:0.10, T:0.64
Consensus pattern (14 bp):
TTTTAGTTTTAGAA
Found at i:31065682 original size:18 final size:18
Alignment explanation
Indices: 31065661--31065703 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
31065651 TTGGGTTGGG
31065661 TAATTGGGTTAAGTTAGA
1 TAATTGGGTTAAGTTAGA
*
31065679 TAATTGGGTTAGGTTAGA
1 TAATTGGGTTAAGTTAGA
31065697 TAATTGG
1 TAATTGG
31065704 ATTTAGGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.30, T:0.40
Consensus pattern (18 bp):
TAATTGGGTTAAGTTAGA
Found at i:31065756 original size:13 final size:15
Alignment explanation
Indices: 31065726--31065763 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
31065716 AGTGGGCCTA
*
31065726 TTTATATATTATATT
1 TTTATTTATTATATT
31065741 TTTATTTATTA-ATT
1 TTTATTTATTATATT
31065755 TTT-TTTATT
1 TTTATTTATT
31065764 TTACCTGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 6 0.27
14 6 0.27
15 10 0.45
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTATTTATTATATT
Found at i:31068803 original size:54 final size:54
Alignment explanation
Indices: 31068745--31068850 Score: 140
Period size: 54 Copynumber: 2.0 Consensus size: 54
31068735 ATTGCGATTT
* *
31068745 TCCTAACAGACTTCCACATTCAGATTGTCTTGACAGACTTCCCAATTACAATCG
1 TCCTAACAGACTTCCACATTCAGATTGTCCTGACAGACCTCCCAATTACAATCG
*** * **
31068799 TCCTAGTGGACTTCCATATTCAGATTGTCCTGATGGACCTCCCAATTACAAT
1 TCCTAACAGACTTCCACATTCAGATTGTCCTGACAGACCTCCCAATTACAAT
31068851 TATCCTTACG
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 44 1.00
ACGTcount: A:0.27, C:0.28, G:0.13, T:0.31
Consensus pattern (54 bp):
TCCTAACAGACTTCCACATTCAGATTGTCCTGACAGACCTCCCAATTACAATCG
Found at i:31068810 original size:27 final size:27
Alignment explanation
Indices: 31068780--31068850 Score: 76
Period size: 27 Copynumber: 2.6 Consensus size: 27
31068770 TGTCTTGACA
31068780 GACTTCCCAATTACAATCGTCCT-AGTG
1 GACTTCCCAATTACAATCGTCCTGA-TG
*
31068807 GACTT-CCATATT-CAGATTGTCCTGATG
1 GACTTCCCA-ATTACA-ATCGTCCTGATG
*
31068834 GACCTCCCAATTACAAT
1 GACTTCCCAATTACAAT
31068851 TATCCTTACG
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
26 5 0.14
27 26 0.70
28 6 0.16
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.31
Consensus pattern (27 bp):
GACTTCCCAATTACAATCGTCCTGATG
Found at i:31068866 original size:54 final size:54
Alignment explanation
Indices: 31068754--31068867 Score: 131
Period size: 54 Copynumber: 2.1 Consensus size: 54
31068744 TTCCTAACAG
* * * * *
31068754 ACTTCCACATTCAGATTGTCTTGACAGACTTCCCAATTACAATCGTCCTAGTGG
1 ACTTCCACATTCAGATTGTCCTGACAGACCTCCCAATTACAATCATCCTAGCGA
* ** *
31068808 ACTTCCATATTCAGATTGTCCTGATGGACCTCCCAATTACAATTATCCTTA-CGA
1 ACTTCCACATTCAGATTGTCCTGACAGACCTCCCAATTACAATCATCC-TAGCGA
31068862 ACTTCC
1 ACTTCC
31068868 CTCAATAGAT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
54 48 0.96
55 2 0.04
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.32
Consensus pattern (54 bp):
ACTTCCACATTCAGATTGTCCTGACAGACCTCCCAATTACAATCATCCTAGCGA
Found at i:31078681 original size:27 final size:27
Alignment explanation
Indices: 31078650--31078715 Score: 107
Period size: 27 Copynumber: 2.4 Consensus size: 27
31078640 AACTTTCCCT
*
31078650 CATTAGATAGTCATTACGGGT-TTCTCA
1 CATTAGATAGCCATTACGGGTCTT-TCA
31078677 CATTAGATAGCCATTACGGGTCTTTCA
1 CATTAGATAGCCATTACGGGTCTTTCA
31078704 CATTAGATAGCC
1 CATTAGATAGCC
31078716 CTTGCGAAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
27 35 0.95
28 2 0.05
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.33
Consensus pattern (27 bp):
CATTAGATAGCCATTACGGGTCTTTCA
Found at i:31078731 original size:27 final size:27
Alignment explanation
Indices: 31078650--31078734 Score: 82
Period size: 27 Copynumber: 3.1 Consensus size: 27
31078640 AACTTTCCCT
* * * *
31078650 CATTAGATAGTCATTACGGGTTTCTCA
1 CATTAGATAGCCATTACGAGTCTATCA
* *
31078677 CATTAGATAGCCATTACGGGTCTTTCA
1 CATTAGATAGCCATTACGAGTCTATCA
* *
31078704 CATTAGATAGCCCTTGCGAAGT-TATCA
1 CATTAGATAGCCATTACG-AGTCTATCA
31078731 CATT
1 CATT
31078735 TACGGTAATG
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
27 48 0.96
28 2 0.04
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (27 bp):
CATTAGATAGCCATTACGAGTCTATCA
Found at i:31080264 original size:18 final size:17
Alignment explanation
Indices: 31080222--31080264 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
31080212 TGTTTAAGTT
*
31080222 TATAATATTTTATATTA
1 TATAATTTTTTATATTA
* *
31080239 TGTTATTTTTATATATTA
1 TATAATTTTT-TATATTA
31080257 TATAATTT
1 TATAATTT
31080265 ATAACACATT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TATAATTTTTTATATTA
Found at i:31081344 original size:9 final size:9
Alignment explanation
Indices: 31081329--31081358 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
31081319 TTATATTTTT
31081329 AAAAAATAA
1 AAAAAATAA
*
31081338 TAAAAATAA
1 AAAAAATAA
31081347 AAAAAATAA
1 AAAAAATAA
31081356 AAA
1 AAA
31081359 TTCTTAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (9 bp):
AAAAAATAA
Found at i:31081348 original size:15 final size:15
Alignment explanation
Indices: 31081328--31081359 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
31081318 TTTATATTTT
31081328 TAAAAAATAATAAAAA
1 TAAAAAA-AATAAAAA
31081344 TAAAAAAAATAAAAA
1 TAAAAAAAATAAAAA
31081359 T
1 T
31081360 TCTTAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (15 bp):
TAAAAAAAATAAAAA
Found at i:31081589 original size:36 final size:36
Alignment explanation
Indices: 31081549--31081622 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
31081539 ATACGATAAC
31081549 AAGATGTTGATTTGACATGCTTAATTTTTTAAATTT
1 AAGATGTTGATTTGACATGCTTAATTTTTTAAATTT
31081585 AAGATGTTGATTTGACATGCTTAATTTTTTAAATTT
1 AAGATGTTGATTTGACATGCTTAATTTTTTAAATTT
31081621 AA
1 AA
31081623 CTCAAACAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.32, C:0.05, G:0.14, T:0.49
Consensus pattern (36 bp):
AAGATGTTGATTTGACATGCTTAATTTTTTAAATTT
Found at i:31083448 original size:27 final size:27
Alignment explanation
Indices: 31083361--31083514 Score: 154
Period size: 27 Copynumber: 5.7 Consensus size: 27
31083351 CCCCAAACTA
* *
31083361 TTATAAAATGACTGTTATG-CCCTCACG
1 TTATAAAATGACTATTATGCCCCT-ATG
** *
31083388 TGGTAAAATGACTATTATG-CCCTCACG
1 TTATAAAATGACTATTATGCCCCT-ATG
**
31083415 TGGTAAAATGACTATTATGCCCCTATG
1 TTATAAAATGACTATTATGCCCCTATG
** *
31083442 TTATAAAATGA-TGGCTATGCCCCAATG
1 TTATAAAATGACT-ATTATGCCCCTATG
31083469 TTATAAAATGACTATTATGCCCCTATG
1 TTATAAAATGACTATTATGCCCCTATG
*
31083496 TTATAAAATGATTA-TATGC
1 TTATAAAATGACTATTATGC
31083515 TTAATGTTAT
Statistics
Matches: 111, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
26 6 0.05
27 100 0.90
28 5 0.05
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (27 bp):
TTATAAAATGACTATTATGCCCCTATG
Found at i:31083832 original size:34 final size:32
Alignment explanation
Indices: 31083788--31083855 Score: 109
Period size: 34 Copynumber: 2.1 Consensus size: 32
31083778 GAACTATTAT
*
31083788 TGTCATTGTAATGGGCTAAGGCCCACACTGATAC
1 TGTCACTGTAATGGGCTAAGGCCCA-ACTGA-AC
31083822 TGTCACTGTAATGGGCTAAGGCCCAACTGAAC
1 TGTCACTGTAATGGGCTAAGGCCCAACTGAAC
31083854 TG
1 TG
31083856 AACTGTTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
32 4 0.12
33 5 0.15
34 24 0.73
ACGTcount: A:0.26, C:0.24, G:0.25, T:0.25
Consensus pattern (32 bp):
TGTCACTGTAATGGGCTAAGGCCCAACTGAAC
Found at i:31090464 original size:20 final size:19
Alignment explanation
Indices: 31090441--31090524 Score: 73
Period size: 21 Copynumber: 4.2 Consensus size: 19
31090431 TTCAAATATT
31090441 AAAAAATTATTAAAAAT-TAG
1 AAAAAA-TA-TAAAAATGTAG
31090461 AAAAAATATAAAAATCGTA-
1 AAAAAATATAAAAAT-GTAG
*
31090480 AAAAAATATTAAAAATTGTAA
1 AAAAAATA-TAAAAA-TGTAG
*
31090501 AAAAAATTATAAAATATATAG
1 AAAAAA-TATAAAA-ATGTAG
31090522 AAA
1 AAA
31090525 TATAAAAATA
Statistics
Matches: 55, Mismatches: 2, Indels: 13
0.79 0.03 0.19
Matches are distributed among these distances:
18 7 0.13
19 10 0.18
20 17 0.31
21 18 0.33
22 3 0.05
ACGTcount: A:0.68, C:0.01, G:0.05, T:0.26
Consensus pattern (19 bp):
AAAAAATATAAAAATGTAG
Found at i:31090474 original size:19 final size:19
Alignment explanation
Indices: 31090440--31090586 Score: 70
Period size: 19 Copynumber: 7.7 Consensus size: 19
31090430 ATTCAAATAT
* *
31090440 TAAAAAATTATTAAAAAT-
1 TAAAAAAATATAAAAAATG
31090458 TAGAAAAAATAT-AAAAATCG
1 TA-AAAAAATATAAAAAAT-G
*
31090478 TAAAAAAATATTAAAAATTG
1 TAAAAAAATA-TAAAAAATG
* *
31090498 TAAAAAAA-ATTATAAAATA
1 TAAAAAAATA-TAAAAAATG
* * *
31090517 TATAGAAATAT-AAAAATA
1 TAAAAAAATATAAAAAATG
*** **
31090535 TAAAATTTTAT-AAAGTTG
1 TAAAAAAATATAAAAAATG
* *
31090553 TAAGAAAATTATACAAAATG
1 TAA-AAAAATATAAAAAATG
*
31090573 TAAAGAAATATAAA
1 TAAAAAAATATAAA
31090587 TTTCTTAAAA
Statistics
Matches: 97, Mismatches: 24, Indels: 15
0.71 0.18 0.11
Matches are distributed among these distances:
18 27 0.28
19 45 0.46
20 20 0.21
21 5 0.05
ACGTcount: A:0.64, C:0.01, G:0.06, T:0.29
Consensus pattern (19 bp):
TAAAAAAATATAAAAAATG
Found at i:31090514 original size:10 final size:10
Alignment explanation
Indices: 31090440--31090514 Score: 55
Period size: 10 Copynumber: 7.5 Consensus size: 10
31090430 ATTCAAATAT
31090440 TAAAAAATTA
1 TAAAAAATTA
*
31090450 TTAAAAATTA
1 TAAAAAATTA
*
31090460 GAAAAAA-TA
1 TAAAAAATTA
**
31090469 T-AAAAATCG
1 TAAAAAATTA
*
31090478 TAAAAAAATA
1 TAAAAAATTA
*
31090488 TTAAAAATTGTA
1 -TAAAAAAT-TA
*
31090500 AAAAAAATTA
1 TAAAAAATTA
31090510 TAAAA
1 TAAAA
31090515 TATATAGAAA
Statistics
Matches: 47, Mismatches: 14, Indels: 8
0.68 0.20 0.12
Matches are distributed among these distances:
8 5 0.11
9 3 0.06
10 25 0.53
11 12 0.26
12 2 0.04
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.27
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:31090783 original size:34 final size:34
Alignment explanation
Indices: 31090743--31090810 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
31090733 TCGTTAAATT
* **
31090743 TTTTTTATGATTTTATAAAATTTTATAATTTTTA
1 TTTTTTACGATTTTATAAAAAATTATAATTTTTA
*
31090777 TTTTTTACGATTTTATAAAAAATTCTAATTTTTA
1 TTTTTTACGATTTTATAAAAAATTATAATTTTTA
31090811 ATAAATTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (34 bp):
TTTTTTACGATTTTATAAAAAATTATAATTTTTA
Found at i:31090822 original size:17 final size:17
Alignment explanation
Indices: 31090786--31090826 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
31090776 ATTTTTTACG
31090786 ATTTTATAAAAAATTCTA
1 ATTTT-TAAAAAATTCTA
* *
31090804 ATTTTTAATAAATTTTA
1 ATTTTTAAAAAATTCTA
31090821 ATTTTT
1 ATTTTT
31090827 TATATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTTAAAAAATTCTA
Found at i:31098681 original size:16 final size:16
Alignment explanation
Indices: 31098651--31098683 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
31098641 CTAAAATTTC
31098651 TAATTCTATTTTTTAA
1 TAATTCTATTTTTTAA
31098667 TAATT-TATTTATTTAA
1 TAATTCTATTT-TTTAA
31098683 T
1 T
31098684 TCTGAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (16 bp):
TAATTCTATTTTTTAA
Found at i:31101027 original size:42 final size:43
Alignment explanation
Indices: 31100927--31101065 Score: 129
Period size: 42 Copynumber: 3.2 Consensus size: 43
31100917 TGTGATCTCG
* ** * * *
31100927 TGTAAGACCACGTCTGGGACGTTGGCATCGATTTGA-GATTTACG
1 TGTAAGACCATGTCTGGGACAATGGCATTGATAT-ATGA-TTACA
* * *
31100971 TGTAAGACCATGTCTGGGACATTGGTATTG-TATATGATTTCA
1 TGTAAGACCATGTCTGGGACAATGGCATTGATATATGATTACA
* * *
31101013 TGTAAGGCCCTGTCTGGGACAATGGCATTGATATTTGATTACA
1 TGTAAGACCATGTCTGGGACAATGGCATTGATATATGATTACA
*
31101056 TGTAAAACCA
1 TGTAAGACCA
31101066 CGTTTGAGAT
Statistics
Matches: 77, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
42 30 0.39
43 21 0.27
44 26 0.34
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACAATGGCATTGATATATGATTACA
Found at i:31104576 original size:2 final size:2
Alignment explanation
Indices: 31104569--31104593 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31104559 AATGAAACAT
31104569 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 T
31104594 CAAACATTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31112619 original size:135 final size:135
Alignment explanation
Indices: 31112351--31112752 Score: 686
Period size: 135 Copynumber: 3.0 Consensus size: 135
31112341 CCTTAATTTA
* * * ** * * *
31112351 ACTTAAAATTTTGTTTTTTTATTCAATCAAATAGCTGGACTTTACCTCCAGGTTGAGTTTGGAAC
1 ACTTAAAGTTTTGTGTTTTTATTCAATCAAATACCTAAAGTTTACTTCAAGGTTGAGTTTGGAAC
* *
31112416 TCAACTTTTC----TAAAAACCTTAAATGGCTTAAAGTAGCCATGTGTAGGAAAATTTATTGCCG
66 TTAATTTTTCTAATTAAAAACCTTAAATGGCTTAAAGTAGCCATGTGTAGGAAAATTTATTGCCG
31112477 TTGTT
131 TTGTT
31112482 ACTTAAAGTTTTGTGTTTTTATTCAATCAAATACCTAAAGTTTACTTCAAGGTTGAGTTTGGAAC
1 ACTTAAAGTTTTGTGTTTTTATTCAATCAAATACCTAAAGTTTACTTCAAGGTTGAGTTTGGAAC
31112547 TTAATTTTTCTAATTAAAAACCTTAAATGGCTTAAAGTAGCCATGTGTAGGAAAATTTATTGCCG
66 TTAATTTTTCTAATTAAAAACCTTAAATGGCTTAAAGTAGCCATGTGTAGGAAAATTTATTGCCG
31112612 TTGTT
131 TTGTT
31112617 ACTTAAAGTTTTGTGTTTTTATTCAATCAAATACCTAAAGTTTACTTCAAGGTTGAGTTTGGAAC
1 ACTTAAAGTTTTGTGTTTTTATTCAATCAAATACCTAAAGTTTACTTCAAGGTTGAGTTTGGAAC
31112682 TTAATTTTTCTAATTAAAAACCTTAAATGGCTTAAAGTAGCCATGTGTAGGAAAATTTATTGCCG
66 TTAATTTTTCTAATTAAAAACCTTAAATGGCTTAAAGTAGCCATGTGTAGGAAAATTTATTGCCG
31112747 TTGTT
131 TTGTT
31112752 A
1 A
31112753 GTTAGCACCT
Statistics
Matches: 257, Mismatches: 10, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
131 65 0.25
135 192 0.75
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (135 bp):
ACTTAAAGTTTTGTGTTTTTATTCAATCAAATACCTAAAGTTTACTTCAAGGTTGAGTTTGGAAC
TTAATTTTTCTAATTAAAAACCTTAAATGGCTTAAAGTAGCCATGTGTAGGAAAATTTATTGCCG
TTGTT
Found at i:31122813 original size:9 final size:9
Alignment explanation
Indices: 31122799--31122830 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
31122789 AACTTGGTGC
31122799 ATTTTGTTT
1 ATTTTGTTT
31122808 ATTTTGTTT
1 ATTTTGTTT
31122817 ATTTTGTTT
1 ATTTTGTTT
31122826 ATTTT
1 ATTTT
31122831 TAATATTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.78
Consensus pattern (9 bp):
ATTTTGTTT
Found at i:31122911 original size:23 final size:23
Alignment explanation
Indices: 31122881--31122932 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
31122871 TGCAACTTGG
31122881 TTTCATAATAATAGCTA-ATATGC
1 TTTCATAATAATAGCTATA-ATGC
*
31122904 TTTCATAATGATAGCTATAATGC
1 TTTCATAATAATAGCTATAATGC
31122927 TTTCAT
1 TTTCAT
31122933 CTTTTTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (23 bp):
TTTCATAATAATAGCTATAATGC
Found at i:31127268 original size:9 final size:9
Alignment explanation
Indices: 31127254--31127285 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
31127244 AACTTGGTGC
31127254 ATTTTGTTT
1 ATTTTGTTT
31127263 ATTTTGTTT
1 ATTTTGTTT
31127272 ATTTTGTTT
1 ATTTTGTTT
31127281 ATTTT
1 ATTTT
31127286 TAATATTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.78
Consensus pattern (9 bp):
ATTTTGTTT
Found at i:31127366 original size:23 final size:23
Alignment explanation
Indices: 31127336--31127387 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
31127326 TGCAACTTGG
31127336 TTTCATAATAATAGCTA-ATATGC
1 TTTCATAATAATAGCTATA-ATGC
*
31127359 TTTCATAATGATAGCTATAATGC
1 TTTCATAATAATAGCTATAATGC
31127382 TTTCAT
1 TTTCAT
31127388 CTTTTTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (23 bp):
TTTCATAATAATAGCTATAATGC
Found at i:31129129 original size:24 final size:22
Alignment explanation
Indices: 31129095--31129139 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
31129085 TGTAATAATT
*
31129095 TCATTTTTAATTTTCATGTTTC
1 TCATTTTTAATTTCCATGTTTC
31129117 TCATCTTTCTAATTTCCATGTTT
1 TCAT-TTT-TAATTTCCATGTTT
31129140 ATAGTCATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 3 0.15
24 13 0.65
ACGTcount: A:0.18, C:0.18, G:0.04, T:0.60
Consensus pattern (22 bp):
TCATTTTTAATTTCCATGTTTC
Found at i:31132329 original size:22 final size:25
Alignment explanation
Indices: 31132281--31132332 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 25
31132271 AAGAGGAGAA
*
31132281 AAAGAAAGAGAAATGATGAAAACAC
1 AAAGAAAGAGAAATGATAAAAACAC
*
31132306 AAAGAAA-A-AAATGA-AAAAATAC
1 AAAGAAAGAGAAATGATAAAAACAC
31132328 AAAGA
1 AAAGA
31132333 GGCGGAGATG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 11 0.44
23 6 0.24
24 1 0.04
25 7 0.28
ACGTcount: A:0.71, C:0.06, G:0.15, T:0.08
Consensus pattern (25 bp):
AAAGAAAGAGAAATGATAAAAACAC
Found at i:31132424 original size:21 final size:22
Alignment explanation
Indices: 31132400--31132446 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
31132390 AAAGAATATG
*
31132400 AAGAGAAATAAG-AGAAGAAGA
1 AAGAGAAAGAAGTAGAAGAAGA
* *
31132421 AAGA-AAAGAAGTATAAGGAGA
1 AAGAGAAAGAAGTAGAAGAAGA
31132442 AAGAG
1 AAGAG
31132447 GTTGAGGGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.64, C:0.00, G:0.30, T:0.06
Consensus pattern (22 bp):
AAGAGAAAGAAGTAGAAGAAGA
Found at i:31139255 original size:5 final size:5
Alignment explanation
Indices: 31139245--31139269 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
31139235 TAAGCAATGC
31139245 TATTT TATTT TATTT TATTT TATTT
1 TATTT TATTT TATTT TATTT TATTT
31139270 GGATTGAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TATTT
Found at i:31141409 original size:21 final size:22
Alignment explanation
Indices: 31141385--31141444 Score: 70
Period size: 21 Copynumber: 2.7 Consensus size: 22
31141375 TTAATATATA
31141385 AACAAAAATTAAATTAAATTT-
1 AACAAAAATTAAATTAAATTTG
*
31141406 AACAAAAATTAACA-TGAATTTG
1 AACAAAAATTAA-ATTAAATTTG
*
31141428 AACTAAAAATTATATTA
1 AAC-AAAAATTAAATTA
31141445 TTAACATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
21 18 0.56
22 5 0.16
23 9 0.28
ACGTcount: A:0.58, C:0.07, G:0.03, T:0.32
Consensus pattern (22 bp):
AACAAAAATTAAATTAAATTTG
Found at i:31144383 original size:21 final size:23
Alignment explanation
Indices: 31144358--31144410 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 23
31144348 TGGGTTTAAA
31144358 AATTTTAATTTTAATTGA-A-TT
1 AATTTTAATTTTAATTGAGATTT
* *
31144379 AATTTTAAATTTAGTTGAGATTT
1 AATTTTAATTTTAATTGAGATTT
*
31144402 AATTATAAT
1 AATTTTAAT
31144411 CTAAAATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 16 0.62
22 1 0.04
23 9 0.35
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.53
Consensus pattern (23 bp):
AATTTTAATTTTAATTGAGATTT
Found at i:31146470 original size:13 final size:14
Alignment explanation
Indices: 31146452--31146480 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
31146442 AAGAGAAGAT
31146452 AATATTT-TATAAA
1 AATATTTATATAAA
31146465 AATATTTATATAAA
1 AATATTTATATAAA
31146479 AA
1 AA
31146481 CATGAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AATATTTATATAAA
Found at i:31152234 original size:38 final size:38
Alignment explanation
Indices: 31152181--31152369 Score: 245
Period size: 38 Copynumber: 5.0 Consensus size: 38
31152171 AATTTTCAAT
* *
31152181 ACACCGGCACAAAGCCTGCTAGACACATAGCTCGAATA
1 ACACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATA
* * * **
31152219 AAACCGGTACAAAGCCTGTTAGGCATGTAGCCCGAATA
1 ACACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATA
* * * *
31152257 TCACCGGTACAAAGCCTGCTAGGCACATAACCTGAATA
1 ACACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATA
* *
31152295 TCACC-GCACAAAGCCTGCTAGGCACATAGCTCGAATA
1 ACACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATA
*
31152332 ACACTGGCACAAAGCCTGCTAGGCACATAGCCCGAATA
1 ACACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATA
31152370 TCATTACGTT
Statistics
Matches: 129, Mismatches: 21, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
37 31 0.24
38 98 0.76
ACGTcount: A:0.34, C:0.30, G:0.20, T:0.16
Consensus pattern (38 bp):
ACACCGGCACAAAGCCTGCTAGGCACATAGCCCGAATA
Found at i:31152344 original size:75 final size:76
Alignment explanation
Indices: 31152181--31152372 Score: 235
Period size: 75 Copynumber: 2.5 Consensus size: 76
31152171 AATTTTCAAT
* * ** * * *
31152181 ACACCGGCACAAAGCCTGCTAGACACAT-AGCTCGAATAAAACCGGTACAAAGCCTGTTAGGCAT
1 ACACCGGCACAAAGCCTGCTAGGCACATAACCT-GAATATCACCGGCACAAAGCCTGCTAGGCAC
*
31152245 GTAGCCCGAATA
65 ATAGCCCGAATA
* *
31152257 TCACCGGTACAAAGCCTGCTAGGCACATAACCTGAATATCACC-GCACAAAGCCTGCTAGGCACA
1 ACACCGGCACAAAGCCTGCTAGGCACATAACCTGAATATCACCGGCACAAAGCCTGCTAGGCACA
*
31152321 TAGCTCGAATA
66 TAGCCCGAATA
* * *
31152332 ACACTGGCACAAAGCCTGCTAGGCACATAGCCCGAATATCA
1 ACACCGGCACAAAGCCTGCTAGGCACATAACCTGAATATCA
31152373 TTACGTTTCT
Statistics
Matches: 99, Mismatches: 16, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
75 63 0.64
76 33 0.33
77 3 0.03
ACGTcount: A:0.34, C:0.30, G:0.20, T:0.16
Consensus pattern (76 bp):
ACACCGGCACAAAGCCTGCTAGGCACATAACCTGAATATCACCGGCACAAAGCCTGCTAGGCACA
TAGCCCGAATA
Found at i:31154317 original size:29 final size:29
Alignment explanation
Indices: 31154265--31154386 Score: 120
Period size: 29 Copynumber: 4.2 Consensus size: 29
31154255 TAGTAAGCCA
* *
31154265 TGTGGTAAACCGTGTGGGTCACACGGCCG
1 TGTGGTTAACCGTGTGGGTCACACGACCG
* * * *
31154294 TGTAGTTAGCCGTGTGGGTTACACAACCG
1 TGTGGTTAACCGTGTGGGTCACACGACCG
* *
31154323 TGTGG-CAACCCGTGTGGGTCACACGACCA
1 TGTGGTTAA-CCGTGTGGGTCACACGACCG
* * * *
31154352 TGTGGTTAACCTTGTAGGTTACACGACTG
1 TGTGGTTAACCGTGTGGGTCACACGACCG
31154381 TGTGGT
1 TGTGGT
31154387 AGGTTGTGTG
Statistics
Matches: 73, Mismatches: 18, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
28 1 0.01
29 70 0.96
30 2 0.03
ACGTcount: A:0.19, C:0.22, G:0.33, T:0.26
Consensus pattern (29 bp):
TGTGGTTAACCGTGTGGGTCACACGACCG
Found at i:31154336 original size:58 final size:58
Alignment explanation
Indices: 31154265--31154385 Score: 152
Period size: 58 Copynumber: 2.1 Consensus size: 58
31154255 TAGTAAGCCA
* * * * *
31154265 TGTGGTAAACCGTGTGGGTCACACGGCCGTGTAGTTAGCCGTGTGGGTTACACAACCG
1 TGTGGCAAACCGTGTGGGTCACACGACCATGTAGTTAACCGTGTAGGTTACACAACCG
* * * * *
31154323 TGTGGCAACCCGTGTGGGTCACACGACCATGTGGTTAACCTTGTAGGTTACACGACTG
1 TGTGGCAAACCGTGTGGGTCACACGACCATGTAGTTAACCGTGTAGGTTACACAACCG
31154381 TGTGG
1 TGTGG
31154386 TAGGTTGTGT
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.19, C:0.22, G:0.33, T:0.26
Consensus pattern (58 bp):
TGTGGCAAACCGTGTGGGTCACACGACCATGTAGTTAACCGTGTAGGTTACACAACCG
Found at i:31158252 original size:3 final size:3
Alignment explanation
Indices: 31158244--31158304 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
31158234 TTCATCCTTC
31158244 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
31158292 TTA TTA TTA TTA T
1 TTA TTA TTA TTA T
31158305 AAATTGTTTT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:31159781 original size:3 final size:3
Alignment explanation
Indices: 31159773--31159799 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
31159763 TTTTAAGCCT
31159773 ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
31159800 GTGAGTCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:31161117 original size:16 final size:15
Alignment explanation
Indices: 31161068--31161106 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
31161058 TTTCCTGGTG
* *
31161068 ATCACATTCCCAGCA
1 ATCACATTCCAAGAA
31161083 ATCACATTCCAAGAA
1 ATCACATTCCAAGAA
31161098 ATCACATTC
1 ATCACATTC
31161107 TATTGAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.38, C:0.33, G:0.05, T:0.23
Consensus pattern (15 bp):
ATCACATTCCAAGAA
Found at i:31162279 original size:5 final size:5
Alignment explanation
Indices: 31162269--31162320 Score: 68
Period size: 5 Copynumber: 10.4 Consensus size: 5
31162259 TAACTATCCC
* * * *
31162269 TTCTT TTCTT TTCTT TTCTT TTCCT TTCCT TTCCT TTCTT TTCCT TTCTT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT
31162319 TT
1 TT
31162321 ACAATTATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 43 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (5 bp):
TTCTT
Found at i:31162284 original size:10 final size:10
Alignment explanation
Indices: 31162273--31162320 Score: 78
Period size: 10 Copynumber: 4.8 Consensus size: 10
31162263 TATCCCTTCT
*
31162273 TTTCTTTTCT
1 TTTCTTTTCC
31162283 TTTCTTTTCC
1 TTTCTTTTCC
*
31162293 TTTCCTTTCC
1 TTTCTTTTCC
31162303 TTTCTTTTCC
1 TTTCTTTTCC
31162313 TTTCTTTT
1 TTTCTTTT
31162321 ACAATTATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 35 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTCTTTTCC
Found at i:31162289 original size:15 final size:15
Alignment explanation
Indices: 31162269--31162320 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
31162259 TAACTATCCC
*
31162269 TTCTTTTCTTTTCTT
1 TTCTTTTCTTTTCCT
*
31162284 TTCTTTTCCTTTCCT
1 TTCTTTTCTTTTCCT
*
31162299 TTCCTTTCTTTTCCT
1 TTCTTTTCTTTTCCT
31162314 TTCTTTT
1 TTCTTTT
31162321 ACAATTATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (15 bp):
TTCTTTTCTTTTCCT
Found at i:31163220 original size:60 final size:60
Alignment explanation
Indices: 31163114--31163229 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 60
31163104 GTTTTTTTGA
* * ** *
31163114 AATTTTTAGAATTGGAACTAAATTGATAAATTTTGTAAATGTTGAGGGCTAAATTTATTG
1 AATTTTTAGAATTGGAACTAAAATGACAAATTTTGTAAATACTGAGGACTAAATTTATTG
* * *
31163174 AATTTTTA-AGATTTGAATTAAAATGACAAATTTTGTAAATACTGAGGATTAAATTT
1 AATTTTTAGA-ATTGGAACTAAAATGACAAATTTTGTAAATACTGAGGACTAAATTT
31163230 GTTTAGTATT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
59 1 0.02
60 46 0.98
ACGTcount: A:0.40, C:0.03, G:0.16, T:0.41
Consensus pattern (60 bp):
AATTTTTAGAATTGGAACTAAAATGACAAATTTTGTAAATACTGAGGACTAAATTTATTG
Found at i:31163246 original size:60 final size:59
Alignment explanation
Indices: 31163114--31163247 Score: 142
Period size: 60 Copynumber: 2.2 Consensus size: 59
31163104 GTTTTTTTGA
* * * ** *
31163114 AATTTTTAGAATTGGAACTAAATTGATAAATTTTGTAAATGTTGAGGGCTAAATTTATTG
1 AATTTTTAG-ATTTGAACTAAAATGACAAATTTTGTAAATACTGAGGACTAAATTTATTG
* * * *
31163174 AATTTTTAAGATTTGAATTAAAATGACAAATTTTGTAAATACTGAGGATTAAATTTGTTT
1 AATTTTT-AGATTTGAACTAAAATGACAAATTTTGTAAATACTGAGGACTAAATTTATTG
*
31163234 AGTATTTTAGATTT
1 AAT-TTTTAGATTT
31163248 AGGGTCAAAT
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
60 55 0.90
61 6 0.10
ACGTcount: A:0.37, C:0.03, G:0.16, T:0.44
Consensus pattern (59 bp):
AATTTTTAGATTTGAACTAAAATGACAAATTTTGTAAATACTGAGGACTAAATTTATTG
Found at i:31164897 original size:18 final size:17
Alignment explanation
Indices: 31164865--31164898 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
31164855 GGTTCTGTTT
*
31164865 CTTTTTTTTTTCTTTCC
1 CTTTTTTTGTTCTTTCC
31164882 CTTTTCTTTGTTCTTTC
1 CTTTT-TTTGTTCTTTC
31164899 GTTTCTTGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.00, C:0.24, G:0.03, T:0.74
Consensus pattern (17 bp):
CTTTTTTTGTTCTTTCC
Found at i:31165702 original size:21 final size:21
Alignment explanation
Indices: 31165673--31165721 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
31165663 AATTAATATG
31165673 TATTGATACAATATGTATGATC
1 TATT-ATACAATATGTATGATC
* * * *
31165695 TGTTATACGATTTGTCTGATC
1 TATTATACAATATGTATGATC
31165716 TATTAT
1 TATTAT
31165722 TCATCAAGCA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (21 bp):
TATTATACAATATGTATGATC
Found at i:31167219 original size:29 final size:30
Alignment explanation
Indices: 31167183--31167257 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 30
31167173 GTGTTACAAA
31167183 AAAATTTATATATAAAATT-ACATAAAA-T
1 AAAATTTATATATAAAATTAACATAAAACT
* * *
31167211 CAAAATTTATGTATATAATTACACATTAAACT
1 -AAAATTTATATATAAAATTA-ACATAAAACT
31167243 AAAATTTATATATAA
1 AAAATTTATATATAA
31167258 TTTTGATATT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
29 17 0.45
31 20 0.53
32 1 0.03
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.37
Consensus pattern (30 bp):
AAAATTTATATATAAAATTAACATAAAACT
Found at i:31167247 original size:31 final size:28
Alignment explanation
Indices: 31167183--31167259 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 28
31167173 GTGTTACAAA
*
31167183 AAAATTTATATATAAAATTACATAAAATC
1 AAAATTTAT-TATATAATTACATAAAATC
*
31167212 AAAATTTATGTATATAATTACACATTAAA-C
1 AAAATTTAT-TATATAATT--ACATAAAATC
31167242 TAAAATTTA-TATATAATT
1 -AAAATTTATTATATAATT
31167260 TTGATATTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
29 26 0.62
30 1 0.02
31 15 0.36
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.39
Consensus pattern (28 bp):
AAAATTTATTATATAATTACATAAAATC
Found at i:31168020 original size:18 final size:18
Alignment explanation
Indices: 31167999--31168439 Score: 94
Period size: 18 Copynumber: 24.6 Consensus size: 18
31167989 GAAAGTATTT
* *
31167999 TTTTTTAAAATACGAGAA
1 TTTTTGAAAACACGAGAA
31168017 TTTTTGAAAACACGAGAA
1 TTTTTGAAAACACGAGAA
*
31168035 --TTTGTAAACACGA-ATA
1 TTTTTGAAAACACGAGA-A
* *
31168051 TTTTAG-AAACACGAAAA
1 TTTTTGAAAACACGAGAA
*
31168068 TTTTTGGAAAAAAACGA-AA
1 TTTTT-G-AAAACACGAGAA
* * *
31168087 TTTTCTTAAAACACGACACTTTT
1 TTTT-TGAAAACACGAGA----A
*
31168110 TTTTTG-AAACACGGGAA
1 TTTTTGAAAACACGAGAA
* * *
31168127 TTTTT-AAAACAAGACATT
1 TTTTTGAAAACACGAGA-A
31168145 TTTTTG-AAACA--A-AA
1 TTTTTGAAAACACGAGAA
* *
31168159 TTTTTTCTTAAAA-A--AAAA
1 --TTTT-TGAAAACACGAGAA
* *
31168177 ATTTT--AAATACGAGAA
1 TTTTTGAAAACACGAGAA
*
31168193 TTTTT-AAAACACGAAAA
1 TTTTTGAAAACACGAGAA
*
31168210 TTTTT-AAAACACGGAAATA
1 TTTTTGAAAACAC-GAGA-A
*
31168229 TTTTTTTTTAAAACACGA-AA
1 ---TTTTTGAAAACACGAGAA
*
31168249 TTTTTTTTTTTGAAAACAAGA-AA
1 ----T-TTTT-GAAAACACGAGAA
* *
31168272 ATTTTG-AAACACTAGAA
1 TTTTTGAAAACACGAGAA
31168289 -TTTTGAAAACACGA-AGA
1 TTTTTGAAAACACGAGA-A
*
31168306 TTTTTG-AAACATGAGAA
1 TTTTTGAAAACACGAGAA
*
31168323 TTTTT-AAAAGCACGAGGA
1 TTTTTGAAAA-CACGAGAA
* *
31168341 TTATTGAAAGCACGA-AGA
1 TTTTTGAAAACACGAGA-A
* * *
31168359 TTTAT-AAAAAACGACAA
1 TTTTTGAAAACACGAGAA
*
31168376 TTTTTG-AAATACGAGAAA
1 TTTTTGAAAACACGAG-AA
* * *
31168394 TTTTTTAAAA-GCGAAAA
1 TTTTTGAAAACACGAGAA
* *
31168411 TTTTTTCAAAACACGAAAA
1 -TTTTTGAAAACACGAGAA
*
31168430 CTTTTGAAAA
1 TTTTTGAAAA
31168440 ACGCGAAATT
Statistics
Matches: 324, Mismatches: 50, Indels: 98
0.69 0.11 0.21
Matches are distributed among these distances:
13 3 0.01
14 1 0.00
15 3 0.01
16 40 0.12
17 97 0.30
18 105 0.32
19 20 0.06
20 9 0.03
21 13 0.04
22 12 0.04
23 21 0.06
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (18 bp):
TTTTTGAAAACACGAGAA
Found at i:31168038 original size:16 final size:16
Alignment explanation
Indices: 31168005--31168070 Score: 53
Period size: 16 Copynumber: 3.9 Consensus size: 16
31167995 ATTTTTTTTT
*
31168005 AAAATACGAGAATTTTTG
1 AAAACACGAGAA--TTTG
31168023 AAAACACGAGAATTTG
1 AAAACACGAGAATTTG
* *
31168039 TAAACACGA-ATATTTT
1 AAAACACGAGA-ATTTG
*
31168055 AGAAACACGAAAATTT
1 A-AAACACGAGAATTT
31168071 TTGGAAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
15 1 0.02
16 16 0.39
17 12 0.29
18 12 0.29
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.27
Consensus pattern (16 bp):
AAAACACGAGAATTTG
Found at i:31168211 original size:17 final size:17
Alignment explanation
Indices: 31168173--31168439 Score: 117
Period size: 17 Copynumber: 14.8 Consensus size: 17
31168163 TTCTTAAAAA
* *
31168173 AAAAATTTT-AAATACG
1 AAAATTTTTAAAACACG
*
31168189 AGAATTTTTAAAACACG
1 AAAATTTTTAAAACACG
31168206 AAAATTTTTAAAACACGG
1 AAAATTTTTAAAACAC-G
31168224 AAATATTTTTTTTTAAAACACG
1 AAA-A----TTTTTAAAACACG
* *
31168246 AAATTTTTTTTTTTGAAAACAAG
1 AAA-----ATTTTT-AAAACACG
* *
31168269 AAAA-TTTTGAAACACT
1 AAAATTTTTAAAACACG
* *
31168285 AGAATTTTGAAAACACG
1 AAAATTTTTAAAACACG
* * *
31168302 AAGATTTTTGAAACATG
1 AAAATTTTTAAAACACG
*
31168319 AGAATTTTTAAAAGCACG
1 AAAATTTTTAAAA-CACG
** * *
31168337 AGGATTATTGAAAGCACG
1 AAAATT-TTTAAAACACG
* * *
31168355 AAGATTTATAAAAAACG
1 AAAATTTTTAAAACACG
* * *
31168372 ACAATTTTTGAAATACG
1 AAAATTTTTAAAACACG
*
31168389 AGAAATTTTTTAAAA-GCG
1 A-AAA-TTTTTAAAACACG
31168407 AAAATTTTTTCAAAACACG
1 AAAA-TTTTT-AAAACACG
*
31168426 AAAACTTTTGAAAA
1 AAAA-TTTTTAAAA
31168440 ACGCGAAATT
Statistics
Matches: 190, Mismatches: 42, Indels: 36
0.71 0.16 0.13
Matches are distributed among these distances:
16 15 0.08
17 85 0.45
18 34 0.18
19 24 0.13
22 9 0.05
23 22 0.12
26 1 0.01
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.32
Consensus pattern (17 bp):
AAAATTTTTAAAACACG
Found at i:31168248 original size:22 final size:22
Alignment explanation
Indices: 31168210--31168276 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 22
31168200 AACACGAAAA
31168210 TTTTTAAAACACGGAAATATTTT
1 TTTTTAAAACAC-GAAATATTTT
*
31168233 TTTTTAAAACACGAAATTTTTT
1 TTTTTAAAACACGAAATATTTT
*
31168255 TTTTTGAAAACAAGAAA-ATTTT
1 TTTTT-AAAACACGAAATATTTT
31168277 GAAACACTAG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
22 18 0.45
23 22 0.55
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.45
Consensus pattern (22 bp):
TTTTTAAAACACGAAATATTTT
Found at i:31168290 original size:16 final size:16
Alignment explanation
Indices: 31168271--31168326 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
31168261 AAAACAAGAA
31168271 AATTTTGAAACACTAG
1 AATTTTGAAACACTAG
*
31168287 AATTTTGAAAACACGAAG
1 AATTTTG-AAACAC-TAG
*
31168305 ATTTTTGAAACA-TGAG
1 AATTTTGAAACACT-AG
31168321 AATTTT
1 AATTTT
31168327 TAAAAGCACG
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
16 14 0.42
17 11 0.33
18 8 0.24
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (16 bp):
AATTTTGAAACACTAG
Found at i:31168446 original size:19 final size:19
Alignment explanation
Indices: 31168400--31168447 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
31168390 GAAATTTTTT
* **
31168400 AAAA-GCGAAAATTTTTTC
1 AAAACGCGAAAACTTTTGA
*
31168418 AAAACACGAAAACTTTTGA
1 AAAACGCGAAAACTTTTGA
31168437 AAAACGCGAAA
1 AAAACGCGAAA
31168448 TTCGAAAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 4 0.17
19 20 0.83
ACGTcount: A:0.52, C:0.15, G:0.12, T:0.21
Consensus pattern (19 bp):
AAAACGCGAAAACTTTTGA
Found at i:31168493 original size:18 final size:17
Alignment explanation
Indices: 31168445--31168494 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
31168435 GAAAAACGCG
31168445 AAATTCGAAAATTTCTA
1 AAATTCGAAAATTTCTA
* * *
31168462 AAATACGAGTAATTTTTA
1 AAATTCGA-AAATTTCTA
31168480 AAGATTCGAAAATTT
1 AA-ATTCGAAAATTT
31168495 GAAACAAGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 7 0.27
18 14 0.54
19 5 0.19
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (17 bp):
AAATTCGAAAATTTCTA
Found at i:31177993 original size:18 final size:18
Alignment explanation
Indices: 31177972--31178413 Score: 103
Period size: 18 Copynumber: 24.6 Consensus size: 18
31177962 CGAAAGTTTT
* *
31177972 TTTTTTAAAATACGAGAA
1 TTTTTGAAAACACGAGAA
31177990 TTTTTGAAAACACGAGAA
1 TTTTTGAAAACACGAGAA
*
31178008 --TTTGTAAACACGA-ATA
1 TTTTTGAAAACACGAGA-A
* *
31178024 TTTTAG-AAACACGAAAA
1 TTTTTGAAAACACGAGAA
*
31178041 TTTTTGGAAAAAAACGA-AA
1 TTTTT-G-AAAACACGAGAA
* * *
31178060 TTTTCTTAAAACACGACACTTTT
1 TTTT-TGAAAACACGAGA----A
*
31178083 TTTTTG-AAACACGGGAA
1 TTTTTGAAAACACGAGAA
* * *
31178100 TTTTT-AAAACAAGACATT
1 TTTTTGAAAACACGAGA-A
31178118 TTTTTG-AAACA--A-AA
1 TTTTTGAAAACACGAGAA
* *
31178132 TTTTTTCTTAAAA-A--AAAA
1 --TTTT-TGAAAACACGAGAA
* *
31178150 ATTTT--AAATACGAGAA
1 TTTTTGAAAACACGAGAA
*
31178166 TTTTT-AAAACACGAAAA
1 TTTTTGAAAACACGAGAA
*
31178183 TTTTT-AAAACACGGAAATA
1 TTTTTGAAAACAC-GAGA-A
*
31178202 TTTTTTTTTAAAACACGA-AA
1 ---TTTTTGAAAACACGAGAA
* *
31178222 TTTTTTTTTTGAAAACAAGAAAA
1 ----T-TTTTGAAAACACGAGAA
*
31178245 TTTTTG-AAACACTAGAA
1 TTTTTGAAAACACGAGAA
31178262 -TTTTGAAAACACGA-AGA
1 TTTTTGAAAACACGAGA-A
*
31178279 TTTTTG-AAACATGAGAA
1 TTTTTGAAAACACGAGAA
*
31178296 TTTTT-AAAAGCACGAGGA
1 TTTTTGAAAA-CACGAGAA
* *
31178314 TTATTGAAAGCACGA-AGA
1 TTTTTGAAAACACGAGA-A
* * *
31178332 TTTAT-AAAAAACGACAA
1 TTTTTGAAAACACGAGAA
*
31178349 TTTTTG-AAATACGAGAAA
1 TTTTTGAAAACACGAG-AA
* * *
31178367 TTTTT-TAAACGCGAAAA
1 TTTTTGAAAACACGAGAA
** *
31178384 TTTTTTTCAAACACGAAAA
1 -TTTTTGAAAACACGAGAA
*
31178403 CTTTTGAAAAC
1 TTTTTGAAAAC
31178414 GCGAAAATTC
Statistics
Matches: 325, Mismatches: 51, Indels: 96
0.69 0.11 0.20
Matches are distributed among these distances:
13 3 0.01
14 1 0.00
15 3 0.01
16 34 0.10
17 102 0.31
18 105 0.32
19 22 0.07
20 9 0.03
21 13 0.04
22 20 0.06
23 13 0.04
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (18 bp):
TTTTTGAAAACACGAGAA
Found at i:31178011 original size:16 final size:16
Alignment explanation
Indices: 31177978--31178043 Score: 53
Period size: 16 Copynumber: 3.9 Consensus size: 16
31177968 TTTTTTTTTT
*
31177978 AAAATACGAGAATTTTTG
1 AAAACACGAGAA--TTTG
31177996 AAAACACGAGAATTTG
1 AAAACACGAGAATTTG
* *
31178012 TAAACACGA-ATATTTT
1 AAAACACGAGA-ATTTG
*
31178028 AGAAACACGAAAATTT
1 A-AAACACGAGAATTT
31178044 TTGGAAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
15 1 0.02
16 16 0.39
17 12 0.29
18 12 0.29
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.27
Consensus pattern (16 bp):
AAAACACGAGAATTTG
Found at i:31178184 original size:17 final size:17
Alignment explanation
Indices: 31178146--31178422 Score: 142
Period size: 17 Copynumber: 15.4 Consensus size: 17
31178136 TTCTTAAAAA
* *
31178146 AAAAATTTT-AAATACG
1 AAAATTTTTAAAACACG
*
31178162 AGAATTTTTAAAACACG
1 AAAATTTTTAAAACACG
31178179 AAAATTTTTAAAACACGG
1 AAAATTTTTAAAACAC-G
31178197 AAATATTTTTTTTTAAAACACG
1 AAA-A----TTTTTAAAACACG
* *
31178219 AAATTTTTTTTTTGAAAACAAG
1 AAA----ATTTTT-AAAACACG
* *
31178241 AAAATTTTTGAAACACT
1 AAAATTTTTAAAACACG
* *
31178258 AGAATTTTGAAAACACG
1 AAAATTTTTAAAACACG
* * *
31178275 AAGATTTTTGAAACATG
1 AAAATTTTTAAAACACG
*
31178292 AGAATTTTTAAAAGCACG
1 AAAATTTTTAAAA-CACG
** * *
31178310 AGGATTATTGAAAGCACG
1 AAAATT-TTTAAAACACG
* * *
31178328 AAGATTTATAAAAAACG
1 AAAATTTTTAAAACACG
* * *
31178345 ACAATTTTTGAAATACG
1 AAAATTTTTAAAACACG
* *
31178362 AGAAATTTTTTAAACGCG
1 A-AAATTTTTAAAACACG
*
31178380 AAAATTTTTTTCAAACACG
1 AAAA--TTTTTAAAACACG
* *
31178399 AAAACTTTTGAAAACGCG
1 AAAA-TTTTTAAAACACG
31178417 AAAATT
1 AAAATT
31178423 CGAAAATTTC
Statistics
Matches: 199, Mismatches: 46, Indels: 31
0.72 0.17 0.11
Matches are distributed among these distances:
16 7 0.04
17 86 0.43
18 53 0.27
19 21 0.11
21 5 0.03
22 14 0.07
23 12 0.06
25 1 0.01
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.32
Consensus pattern (17 bp):
AAAATTTTTAAAACACG
Done.