Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010841.1 Kokia drynarioides strain JFW-HI SEQ_125808, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 268051
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 19 characters in sequence are not A, C, G, or T
Found at i:4812 original size:75 final size:75
Alignment explanation
Indices: 4690--4903 Score: 304
Period size: 75 Copynumber: 2.9 Consensus size: 75
4680 ATTCCATCAA
* * * * * **
4690 CTCCTCCTTCAACTTATCCCAAGCTTGTTTAGGAGTCTCACAGGGGTGAGCTACTGCTGCCTTAC
1 CTCCTCCTTCAGCTTATCCAAAGCTTGTTTGGGAGTCTCACAAGGGTGAGTTGTTGCTGCCTTAC
*
4755 CTTGGAACTC
66 CTTGGAACCC
* * *
4765 CTCCTCCTTCAGCTTATCCAAAGCTTGTTTGGGAGTCTCCCAAGGGTGAGTTGTTTCTACCTTAC
1 CTCCTCCTTCAGCTTATCCAAAGCTTGTTTGGGAGTCTCACAAGGGTGAGTTGTTGCTGCCTTAC
4830 CTTGGAACCC
66 CTTGGAACCC
*
4840 CTCCTCCTTCAGCTTATCGCAAA-CTTGTTTGGGAGTCTCACAAAGGTGAGTTGTTGCTGCCTTA
1 CTCCTCCTTCAGCTTATC-CAAAGCTTGTTTGGGAGTCTCACAAGGGTGAGTTGTTGCTGCCTTA
4904 ACAAACAGCC
Statistics
Matches: 123, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
75 119 0.97
76 4 0.03
ACGTcount: A:0.18, C:0.29, G:0.21, T:0.33
Consensus pattern (75 bp):
CTCCTCCTTCAGCTTATCCAAAGCTTGTTTGGGAGTCTCACAAGGGTGAGTTGTTGCTGCCTTAC
CTTGGAACCC
Found at i:5931 original size:75 final size:75
Alignment explanation
Indices: 5798--6008 Score: 325
Period size: 75 Copynumber: 2.8 Consensus size: 75
5788 ACCCCATCAA
* **
5798 CTCCTCCTTCAGCTTATCCCAAACTTGTTTGGGAGTCTCAC-AGGGATGAGCTACTGCTGCCATA
1 CTCCTCCTTCAGCTTATCCCAAACTTGTTTGGGAGTCTCACAAGGG-TGAGTTGTTGCTGCCATA
5862 CCTTGGAACTC
65 CCTTGGAACTC
* * *
5873 CTCCTCCTTTAGCTTATCCCAAGCTTGTTTGGGAGTCTCACAAGGGTGAGTTGTTGCTGCCTTAC
1 CTCCTCCTTCAGCTTATCCCAAACTTGTTTGGGAGTCTCACAAGGGTGAGTTGTTGCTGCCATAC
5938 CTTGGAACTC
66 CTTGGAACTC
* * *
5948 CTCCGCCTTCAGCTTATGCCAAACTTGTTTGGGAGTCTCATAAGGGTGAGTTGTTGCTGCC
1 CTCCTCCTTCAGCTTATCCCAAACTTGTTTGGGAGTCTCACAAGGGTGAGTTGTTGCTGCC
6009 TTAACAAGCA
Statistics
Matches: 124, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
75 120 0.97
76 4 0.03
ACGTcount: A:0.18, C:0.27, G:0.23, T:0.32
Consensus pattern (75 bp):
CTCCTCCTTCAGCTTATCCCAAACTTGTTTGGGAGTCTCACAAGGGTGAGTTGTTGCTGCCATAC
CTTGGAACTC
Found at i:8650 original size:12 final size:12
Alignment explanation
Indices: 8633--8657 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8623 TGTGTACACC
8633 TATTTTCCATTT
1 TATTTTCCATTT
8645 TATTTTCCATTT
1 TATTTTCCATTT
8657 T
1 T
8658 CTACTCTTAC
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:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (12 bp):
TATTTTCCATTT
Found at i:11457 original size:18 final size:18
Alignment explanation
Indices: 11434--11476 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
11424 GTTCAATGTG
11434 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
11452 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
11470 TAATTAA
1 TAATTAA
11477 AAATTATTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:13226 original size:22 final size:22
Alignment explanation
Indices: 13191--13234 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
13181 TTAGTTGTGG
* *
13191 ATTTAGTTACTTTTATTCTCTA
1 ATTTAATTACTTTTAGTCTCTA
*
13213 ATTTAATTATTTTTAGTCTCTA
1 ATTTAATTACTTTTAGTCTCTA
13235 TTTTTTTGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.25, C:0.11, G:0.05, T:0.59
Consensus pattern (22 bp):
ATTTAATTACTTTTAGTCTCTA
Found at i:25855 original size:3 final size:3
Alignment explanation
Indices: 25847--25881 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
25837 AAGAGTGAAA
*
25847 GAT GAT GAT GAT GTT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
25882 AGAAACAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
GAT
Found at i:32102 original size:22 final size:21
Alignment explanation
Indices: 32076--32130 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
32066 TTCTTTATAT
*
32076 ATTTTTTAAAAAAAATTTAAA
1 ATTTTTTAAAAAAAAATTAAA
32097 ATTTTTTAAAAAAAAATTAAA
1 ATTTTTTAAAAAAAAATTAAA
32118 ATTTTTTAAAAAA
1 ATTTTTTAAAAAA
32131 TATATAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTTTTTAAAAAAAAATTAAA
Found at i:32143 original size:21 final size:20
Alignment explanation
Indices: 32076--32143 Score: 84
Period size: 21 Copynumber: 3.4 Consensus size: 20
32066 TTCTTTATAT
*
32076 ATTTTTTAAAAAAAATTTAAA
1 ATTTTTT-AAAAAAATATAAA
*
32097 ATTTTTTAAAAAAAAATTAAA
1 ATTTTTTAAAAAAATA-TAAA
*
32118 ATTTTTT-AAAAAATATATA
1 ATTTTTTAAAAAAATATAAA
32137 ATTTTTT
1 ATTTTTT
32144 GTTATGAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
19 10 0.24
20 14 0.33
21 18 0.43
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTTTTTAAAAAAATATAAA
Found at i:34789 original size:37 final size:37
Alignment explanation
Indices: 34739--34853 Score: 162
Period size: 37 Copynumber: 3.1 Consensus size: 37
34729 TACATCTACA
*
34739 TATTCGGGCTTTGTGCTTAGTAGACTTCGTGCTGGTG
1 TATTCGGGCTTTGTGCCTAGTAGACTTCGTGCTGGTG
*
34776 TATTCGGGCTTTGTGCCTAGTAGGA-TTCGTG-TCGTTG
1 TATTCGGGCTTTGTGCCTAGTA-GACTTCGTGCT-GGTG
* *
34813 TATTCGGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTG
1 TATTCGGGCTTTGTGCCTAGTAGACTTCGTGCTGGTG
34850 TATT
1 TATT
34854 TATTGGGCTT
Statistics
Matches: 69, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
36 2 0.03
37 65 0.94
38 2 0.03
ACGTcount: A:0.10, C:0.17, G:0.32, T:0.40
Consensus pattern (37 bp):
TATTCGGGCTTTGTGCCTAGTAGACTTCGTGCTGGTG
Found at i:34878 original size:40 final size:40
Alignment explanation
Indices: 34742--35004 Score: 214
Period size: 40 Copynumber: 6.7 Consensus size: 40
34732 ATCTACATAT
* * * * *
34742 TCGGGCTTTGTGCTTAGTAGACTTCGTGCTGGTGTA--T-
1 TCGGGCTTAGTGCCTAGCAGGCTTCGTGCCGGTGTATTTA
* * * * *
34779 TCGGGCTTTGTGCCTAGTAGGATTCGTGTCGTTGTA--T-
1 TCGGGCTTAGTGCCTAGCAGGCTTCGTGCCGGTGTATTTA
* *
34816 TCGGGCTTTGTGCCTAGTAGGCTTCGTGCCGGTGTATTTA
1 TCGGGCTTAGTGCCTAGCAGGCTTCGTGCCGGTGTATTTA
* * *
34856 TTGGGCTTAGTACCTAGCAGGCTTCATGCCGGTGTATTTA
1 TCGGGCTTAGTGCCTAGCAGGCTTCGTGCCGGTGTATTTA
* ** *
34896 TCGGGCTTAATGCCTAATAGGCTTCGTACCGGTGTATTTA
1 TCGGGCTTAGTGCCTAGCAGGCTTCGTGCCGGTGTATTTA
* * * * *
34936 TCGAGCTTAGTGCGTAGCACGCTTTGTGCCGGTGTATACTA
1 TCGGGCTTAGTGCCTAGCAGGCTTCGTGCCGGTGTAT-TTA
* * * * *
34977 TCAGGCTTTGAGCCTAGCAAGTTTCGTG
1 TCGGGCTTAGTGCCTAGCAGGCTTCGTG
35005 TCGATGCTAT
Statistics
Matches: 184, Mismatches: 38, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
37 64 0.35
39 1 0.01
40 97 0.53
41 22 0.12
ACGTcount: A:0.15, C:0.19, G:0.30, T:0.36
Consensus pattern (40 bp):
TCGGGCTTAGTGCCTAGCAGGCTTCGTGCCGGTGTATTTA
Found at i:35250 original size:40 final size:40
Alignment explanation
Indices: 35195--35276 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
35185 TTAGGGATGT
*
35195 TATGTCTACTTACAATTTATTACCCTTATATTTCAATGAG
1 TATGTCTACTTACAATTTATTACCCTAATATTTCAATGAG
35235 TATGTCTACTTACAATTTATTACCCTAATATTTCAATGAG
1 TATGTCTACTTACAATTTATTACCCTAATATTTCAATGAG
35275 TA
1 TA
35277 AGTAAGGGTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.44
Consensus pattern (40 bp):
TATGTCTACTTACAATTTATTACCCTAATATTTCAATGAG
Found at i:42350 original size:15 final size:15
Alignment explanation
Indices: 42332--42376 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
42322 TTCACTATTA
*
42332 TGTCTTTTGTGTTTT
1 TGTCTTTCGTGTTTT
*
42347 TGTCTATCGTGTTTT
1 TGTCTTTCGTGTTTT
* *
42362 TATCTTTCATGTTTT
1 TGTCTTTCGTGTTTT
42377 GCATGCATAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.07, C:0.11, G:0.16, T:0.67
Consensus pattern (15 bp):
TGTCTTTCGTGTTTT
Found at i:45195 original size:23 final size:22
Alignment explanation
Indices: 45167--45238 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 22
45157 ACGGTCAATT
45167 TCGGGTCGTGTTTGGTCAACGGG
1 TCGGGTCG-GTTTGGTCAACGGG
* *
45190 TCGGGTCAGGTTCGATCAACGGG
1 TCGGGTC-GGTTTGGTCAACGGG
* * *
45213 TCGAGTTGAGTTTGGTCAATGGG
1 TCGGGTCG-GTTTGGTCAACGGG
45236 TCG
1 TCG
45239 AGTCAATCAA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
22 1 0.03
23 38 0.95
24 1 0.03
ACGTcount: A:0.14, C:0.17, G:0.40, T:0.29
Consensus pattern (22 bp):
TCGGGTCGGTTTGGTCAACGGG
Found at i:51305 original size:13 final size:14
Alignment explanation
Indices: 51276--51305 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
51266 TTCAGTACAT
51276 TGACATTTAACTTC
1 TGACATTTAACTTC
51290 TGACATTTAA-TTC
1 TGACATTTAACTTC
51303 TGA
1 TGA
51306 TTGCATTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.43
Consensus pattern (14 bp):
TGACATTTAACTTC
Found at i:61772 original size:13 final size:14
Alignment explanation
Indices: 61743--61772 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
61733 TTCAATACAT
61743 TGACATTTAACTTC
1 TGACATTTAACTTC
61757 TGACATTTAA-TTC
1 TGACATTTAACTTC
61770 TGA
1 TGA
61773 TTGCATTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.43
Consensus pattern (14 bp):
TGACATTTAACTTC
Found at i:62721 original size:26 final size:26
Alignment explanation
Indices: 62691--62743 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
62681 ATGGAATGCG
62691 AAGTATGTTTAAGATTGTACAAGCAT
1 AAGTATGTTTAAGATTGTACAAGCAT
62717 AAGTATGTTTAAGATTGTACAAGCAT
1 AAGTATGTTTAAGATTGTACAAGCAT
62743 A
1 A
62744 TGTGTATCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.34
Consensus pattern (26 bp):
AAGTATGTTTAAGATTGTACAAGCAT
Found at i:78975 original size:16 final size:17
Alignment explanation
Indices: 78956--78997 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
78946 TATTTAAGCC
78956 TAAACATTATTAAA-TA
1 TAAACATTATTAAATTA
*
78972 TAAATATTA-TAAATTA
1 TAAACATTATTAAATTA
*
78988 TAAAGATTAT
1 TAAACATTAT
78998 AGAAAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
TAAACATTATTAAATTA
Found at i:79142 original size:19 final size:19
Alignment explanation
Indices: 79100--79151 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
79090 TAAAAATATT
*
79100 AATATTATAAATAA--TTAT
1 AATATTATAAA-AACTTTAA
79118 AATATTATAAAAACTTTAA
1 AATATTATAAAAACTTTAA
*
79137 AATATTACAAAAACT
1 AATATTATAAAAACT
79152 ATGAACAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 2 0.07
18 11 0.37
19 17 0.57
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.37
Consensus pattern (19 bp):
AATATTATAAAAACTTTAA
Found at i:79248 original size:27 final size:27
Alignment explanation
Indices: 79218--79280 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
79208 TTAAAAGGTT
79218 ATAATTTTTAAAATATAAAAAATATCG
1 ATAATTTTTAAAATATAAAAAATATCG
79245 ATAATTTTTAAAATATAAAAAATATCG
1 ATAATTTTTAAAATATAAAAAATATCG
79272 ATAATTTTT
1 ATAATTTTT
79281 GATATTTTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.41
Consensus pattern (27 bp):
ATAATTTTTAAAATATAAAAAATATCG
Found at i:79508 original size:11 final size:10
Alignment explanation
Indices: 79489--79617 Score: 55
Period size: 9 Copynumber: 13.6 Consensus size: 10
79479 AGACTAGTAA
*
79489 TTATTATTTAT
1 TTATAATTT-T
79500 TTATAATTTT
1 TTATAATTTT
79510 TT-TAATTTT
1 TTATAATTTT
* *
79519 TGAGTAA-TGT
1 TTA-TAATTTT
* *
79529 TAATAA-TAT
1 TTATAATTTT
79538 TTAT-ATTTT
1 TTATAATTTT
79547 TCTATAA-TTT
1 T-TATAATTTT
* *
79557 TTA-AAATAT
1 TTATAATTTT
79566 TTAT-A-TTT
1 TTATAATTTT
* *
79574 TAATAA-GTT
1 TTATAATTTT
79583 TTATAATTTT
1 TTATAATTTT
79593 TTAATAA-TTT
1 TT-ATAATTTT
79603 TTAT-ATTTT
1 TTATAATTTT
*
79612 TAATAA
1 TTATAA
79618 ATTCTTAGAA
Statistics
Matches: 92, Mismatches: 14, Indels: 25
0.70 0.11 0.19
Matches are distributed among these distances:
8 9 0.10
9 43 0.47
10 24 0.26
11 16 0.17
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (10 bp):
TTATAATTTT
Found at i:79593 original size:9 final size:9
Alignment explanation
Indices: 79499--79613 Score: 90
Period size: 9 Copynumber: 12.4 Consensus size: 9
79489 TTATTATTTA
79499 TTTATAATT
1 TTTATAATT
*
79508 TTTTTAATT
1 TTTATAATT
*
79517 TTTGAGTAATG
1 TTT-A-TAATT
* *
79528 TTAATAATA
1 TTTATAATT
*
79537 TTTATATTT
1 TTTATAATT
79546 TTCTATAATT
1 TT-TATAATT
* *
79556 TTTAAAATA
1 TTTATAATT
79565 TTTAT-ATT
1 TTTATAATT
* *
79573 TTAATAAGT
1 TTTATAATT
79582 TTTATAATTT
1 TTTATAA-TT
79592 TTTAATAATT
1 TTT-ATAATT
79602 TTTAT-ATT
1 TTTATAATT
79610 TTTA
1 TTTA
79614 ATAAATTCTT
Statistics
Matches: 83, Mismatches: 17, Indels: 13
0.73 0.15 0.12
Matches are distributed among these distances:
8 13 0.16
9 42 0.51
10 18 0.22
11 10 0.12
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (9 bp):
TTTATAATT
Found at i:79611 original size:18 final size:18
Alignment explanation
Indices: 79553--79617 Score: 80
Period size: 20 Copynumber: 3.6 Consensus size: 18
79543 TTTTTCTATA
*
79553 ATTTTTAA-AATATTTAT
1 ATTTTTAATAATTTTTAT
*
79570 A-TTTTAATAAGTTTTAT
1 ATTTTTAATAATTTTTAT
79587 AATTTTTTAATAATTTTTAT
1 -A-TTTTTAATAATTTTTAT
79607 ATTTTTAATAA
1 ATTTTTAATAA
79618 ATTCTTAGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
16 6 0.15
17 8 0.20
18 11 0.27
19 1 0.02
20 15 0.37
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
ATTTTTAATAATTTTTAT
Found at i:95209 original size:22 final size:21
Alignment explanation
Indices: 95171--95212 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
95161 TTGAATATGA
*
95171 TTTTATTTTAATAATTTTTAT
1 TTTTATTTCAATAATTTTTAT
95192 TTTTATTTCATATAATTTTTA
1 TTTTATTTCA-ATAATTTTTA
95213 ATAATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTTATTTCAATAATTTTTAT
Found at i:95281 original size:13 final size:13
Alignment explanation
Indices: 95246--95280 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
95236 ATAATTGATC
95246 AAATGGAAAATAG
1 AAATGGAAAATAG
95259 AAATGGAAAATAG
1 AAATGGAAAATAG
95272 AAAT-GAAAA
1 AAATGGAAAA
95281 ACAGATGACC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 5 0.23
13 17 0.77
ACGTcount: A:0.66, C:0.00, G:0.20, T:0.14
Consensus pattern (13 bp):
AAATGGAAAATAG
Found at i:107522 original size:22 final size:23
Alignment explanation
Indices: 107492--107549 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
107482 TAAAGTGGAC
107492 CATGCAAATTAAATTAATTAAAG-
1 CATG-AAATTAAATTAATTAAAGA
* * *
107515 CATGAAATTATATTATTTAATGTA
1 CATGAAATTAAATTAATTAAAG-A
107539 CATGAAATTAA
1 CATGAAATTAA
107550 TTCAGCCCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 15 0.52
23 4 0.14
24 10 0.34
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.36
Consensus pattern (23 bp):
CATGAAATTAAATTAATTAAAGA
Found at i:109534 original size:17 final size:19
Alignment explanation
Indices: 109509--109554 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 19
109499 AAACGAATAG
109509 TAATAAAATAGGA-AAA-T
1 TAATAAAATAGGATAAAGT
* *
109526 TAATTAAATTGGATAAAGT
1 TAATAAAATAGGATAAAGT
109545 TAATGAAAAT
1 TAAT-AAAAT
109555 CTAAAACTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 11 0.48
18 3 0.13
19 5 0.22
20 4 0.17
ACGTcount: A:0.57, C:0.00, G:0.13, T:0.30
Consensus pattern (19 bp):
TAATAAAATAGGATAAAGT
Found at i:110536 original size:20 final size:20
Alignment explanation
Indices: 110488--110540 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
110478 TCTTTTTTTT
*
110488 TTTTATTTAAAAATCACTAC
1 TTTTATTTAAAAATCACAAC
*
110508 TTTT-CTTAAAAATCA-AAGC
1 TTTTATTTAAAAATCACAA-C
110527 TTTTATTTAAAAAT
1 TTTTATTTAAAAAT
110541 AGTTAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 1 0.04
19 15 0.54
20 12 0.43
ACGTcount: A:0.42, C:0.11, G:0.02, T:0.45
Consensus pattern (20 bp):
TTTTATTTAAAAATCACAAC
Found at i:110619 original size:21 final size:20
Alignment explanation
Indices: 110595--110642 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
110585 TTAAAATGAC
*
110595 TAAAAATAGATTTTTATTTTT
1 TAAAAATA-AATTTTATTTTT
* *
110616 TAAAATCTAAATTTTCTTTTT
1 TAAAA-ATAAATTTTATTTTT
110637 TAAAAA
1 TAAAAA
110643 ATCACTACTT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (20 bp):
TAAAAATAAATTTTATTTTT
Found at i:110655 original size:20 final size:20
Alignment explanation
Indices: 110632--110682 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
110622 CTAAATTTTC
**
110632 TTTTTTAAAAAATCACTACT
1 TTTTTTAAAAAATCAAAACT
110652 TTTTTTAAAAAATCAAAACT
1 TTTTTTAAAAAATCAAAACT
*
110672 TTATTTAAAAA
1 TTTTTTAAAAA
110683 TTTAAACTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (20 bp):
TTTTTTAAAAAATCAAAACT
Found at i:110755 original size:113 final size:110
Alignment explanation
Indices: 110547--110789 Score: 312
Period size: 113 Copynumber: 2.2 Consensus size: 110
110537 AAATAGTTAA
*
110547 AAAAAATTCAAAACTTTATTTAAAAAAATTAAATTTTTTTAAAATGACTAAAAATAGATTTTTAT
1 AAAAAA-TCAAAACTTTATTTAAAAAAATTAAATTTTTTTAAAATGACTAAAAACAGATTTTTAT
******** *
110612 TTTTTAAAATCTAAATTTTCTTTTTTAAAAAATCACTACTTTTTTT
65 TTTTTAAAATCTAAATTTAAAAAAAAAAAAAATCAATACTTTTTTT
*
110658 AAAAAATCAAAACTTTATTT-AAAAATTTAAACTTTTTCCTTTAAAATGACTAAAAACAGATTTT
1 AAAAAATCAAAACTTTATTTAAAAAAATTAAA--TTTT--TTTAAAATGACTAAAAACAGATTTT
110722 TATTTTTTAAAATCT-AATTTAAAAAAAAAAAAAACTCAATACTTTTTTT
62 TATTTTTTAAAATCTAAATTTAAAAAAAAAAAAAA-TCAATACTTTTTTT
110771 -AAAAATCAAAACTTTATTT
1 AAAAAATCAAAACTTTATTT
110790 TGAAATAGTT
Statistics
Matches: 116, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
109 10 0.09
110 14 0.12
111 10 0.09
112 30 0.26
113 52 0.45
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.43
Consensus pattern (110 bp):
AAAAAATCAAAACTTTATTTAAAAAAATTAAATTTTTTTAAAATGACTAAAAACAGATTTTTATT
TTTTAAAATCTAAATTTAAAAAAAAAAAAAATCAATACTTTTTTT
Found at i:110779 original size:19 final size:21
Alignment explanation
Indices: 110751--110790 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
110741 TAAAAAAAAA
*
110751 AAAAACTCAATACTTT-TTTT
1 AAAAACTCAAAACTTTATTTT
110771 AAAAA-TCAAAACTTTATTTT
1 AAAAACTCAAAACTTTATTTT
110791 GAAATAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (21 bp):
AAAAACTCAAAACTTTATTTT
Found at i:111759 original size:42 final size:42
Alignment explanation
Indices: 111666--112354 Score: 701
Period size: 42 Copynumber: 16.4 Consensus size: 42
111656 TCACATATGA
* * * * *
111666 GCCTCTGAATGCAATGAAAAGTAAACGGTCTTTGCACACTT-G
1 GCCTCTAAATGCAATGAAAAGTAAATGGAC-CTCCACACTTAG
*
111708 TGCCTCTAAATGCAATGAAAAGTAAATGGACCACCACACTTAG
1 -GCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACTTAG
* * * *
111751 GTCTCTAAATGC-GTGAAAAGTAAATGG-CCTTCACACCTAG
1 GCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACTTAG
** * * *
111791 GCCTCTAAATGCAATGAAAAGTAAATAAATCTCCACACCTAA
1 GCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACTTAG
* * * * *
111833 GCCTTTAAATGCAATGAAAAGTAAATGAACCTCCTCACCTGG
1 GCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACTTAG
* * * *
111875 GCCTCTAAATGCGATGAAAAGTAAATGGATCTCCACACCTGG
1 GCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACTTAG
* * *
111917 GCCTCTAAATGCGATGAAAAGTAAATGAACATCCACA-TCTAG
1 GCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACT-TAG
* * *
111959 GCCTTTAAATGCAATGAAAAGTAAATGGACCTCCACACGTGG
1 GCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACTTAG
* *
112001 GCCTCTAAATGCAATGAAAAGTAAATGGACCTCCATACTTGG
1 GCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACTTAG
* *
112043 GCCTTTAAATGCAATGAAAAGTAAATGAACCTCCACACTTAG
1 GCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACTTAG
* * * *
112085 GCCTCTAAATGCGATGAAAAGTAAATGGATCTCCATACTTGG
1 GCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACTTAG
* ** * * * *
112127 GCTTCTAAATGGGATGAAAAGTATATGGACCTTCACACCTGG
1 GCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACTTAG
** * *
112169 GCCTCTAAATGGGATGAAAAGTAAATGGACCTTCACACCTCA-
1 GCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACA-CTTAG
* * * ** * * *
112211 GCTTTTTAATGTGATAAAAAGTAAATGGACCACCATACTT-G
1 GCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACTTAG
**
112252 AGCCTCTAAATGTGATGAAAAGTAAATGGACCTCCACACTT-G
1 -GCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACTTAG
* *
112294 AGCCTTTAAATGCAATGAAAAGTAAATAGACCTCCACACTT-G
1 -GCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACTTAG
*
112336 AGCCTCTAAGTGCAATGAA
1 -GCCTCTAAATGCAATGAA
112355 TGCTTTCCTT
Statistics
Matches: 552, Mismatches: 86, Indels: 17
0.84 0.13 0.03
Matches are distributed among these distances:
40 21 0.04
41 28 0.05
42 474 0.86
43 29 0.05
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.24
Consensus pattern (42 bp):
GCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACTTAG
Found at i:118604 original size:4 final size:4
Alignment explanation
Indices: 118595--118640 Score: 65
Period size: 4 Copynumber: 11.5 Consensus size: 4
118585 TGAATAAACA
* * *
118595 AATG AATG AATG AGTG AATG GATG AATG AATG AATG TATG AATG AA
1 AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG AA
118641 ATTAGGGTAC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.46, C:0.00, G:0.28, T:0.26
Consensus pattern (4 bp):
AATG
Found at i:123239 original size:17 final size:19
Alignment explanation
Indices: 123214--123259 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 19
123204 AAACGAATAG
123214 TAATAAAATAGGA-AAA-T
1 TAATAAAATAGGATAAAGT
* *
123231 TAATTAAATTGGATAAAGT
1 TAATAAAATAGGATAAAGT
123250 TAATGAAAAT
1 TAAT-AAAAT
123260 CTAAAACTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 11 0.48
18 3 0.13
19 5 0.22
20 4 0.17
ACGTcount: A:0.57, C:0.00, G:0.13, T:0.30
Consensus pattern (19 bp):
TAATAAAATAGGATAAAGT
Found at i:123469 original size:16 final size:16
Alignment explanation
Indices: 123448--123479 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
123438 AAGCATAAAT
123448 ATAAATAAACATGAAA
1 ATAAATAAACATGAAA
123464 ATAAATAAACATGAAA
1 ATAAATAAACATGAAA
123480 TAAGAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (16 bp):
ATAAATAAACATGAAA
Found at i:124344 original size:159 final size:154
Alignment explanation
Indices: 124032--124489 Score: 489
Period size: 154 Copynumber: 3.0 Consensus size: 154
124022 AATCAAAAGT
* *
124032 TTTCTTCTTTTTTTTTTTAACAAAATCACTATTTTTATTAAAAAATCAAAGCTTTTATTTCGAAA
1 TTTCTT-TTTTTTTTTTTAACAAAATCACTACTTTTATTAAAAAATCAAAGCTTTTATCTCGAAA
*
124097 TAGTTAAAAAAATCAAAATTTATTTAAAAAATTTAAAGTTTTTCCTTTAAAATGATTAAAAAGCA
65 TAGTTAAAAAAATCAAAATTTATTTAAAAAATTTAAACTTTTTCCTTTAAAATGATTAAAAAGCA
124162 TATTTTAATTTTAAAAAATCTAAAC
130 TATTTTAATTTTAAAAAATCTAAAC
* * * *
124187 TTTCTTTTTTTTTTTTTTACGAAAATCATTACTTTTCTT-AAAAATTAAAGCTTTTATCTCGAAA
1 TTTCTTTTTTTTTTTTTAAC-AAAATCACTACTTTTATTAAAAAATCAAAGCTTTTATCTCGAAA
* *
124251 TAGTTAACAAAAAAAATCAAAACTTTGTTTAAAAAAATTTAAACTTTTTCCTTTAAAATGATTCA
65 TAGTT----AAAAAAATCAAAA-TTTATTT-AAAAAATTTAAACTTTTTCCTTTAAAATGATTAA
* *
124316 AAA-CATATTTTTATTTTTAAAAATCTAAA-
124 AAAGCATATTTTAATTTTAAAAAATCTAAAC
* * * * *
124345 ---C-----TTTTTTTTAA-AAAATTACTA-TTTTTTTAAAAAATCAAAAC-TTTATTTCGATAT
1 TTTCTTTTTTTTTTTTTAACAAAATCACTACTTTTATTAAAAAATCAAAGCTTTTATCTCGAAAT
* * * * * **
124399 AGTT-AAAAAATTAAATCTTTGTTT-AAAAATTTAAACTTTTTTCTTTAAAATGACTAAAAAATA
66 AGTTAAAAAAATCAAA-ATTTATTTAAAAAATTTAAACTTTTTCCTTTAAAATGATTAAAAAGCA
* * *
124462 GATTTTTATTTTTAAAAATCTAAAC
130 TATTTTAATTTTAAAAAATCTAAAC
124487 TTT
1 TTT
124490 ATTTAAAAAA
Statistics
Matches: 263, Mismatches: 26, Indels: 38
0.80 0.08 0.12
Matches are distributed among these distances:
140 33 0.13
141 24 0.09
142 17 0.06
147 21 0.08
148 18 0.07
150 9 0.03
154 41 0.16
155 22 0.08
158 13 0.05
159 30 0.11
160 35 0.13
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (154 bp):
TTTCTTTTTTTTTTTTTAACAAAATCACTACTTTTATTAAAAAATCAAAGCTTTTATCTCGAAAT
AGTTAAAAAAATCAAAATTTATTTAAAAAATTTAAACTTTTTCCTTTAAAATGATTAAAAAGCAT
ATTTTAATTTTAAAAAATCTAAAC
Found at i:124352 original size:20 final size:21
Alignment explanation
Indices: 124329--124388 Score: 74
Period size: 19 Copynumber: 3.0 Consensus size: 21
124319 CATATTTTTA
124329 TTTTT-AAAAATCTAAACTTT
1 TTTTTAAAAAATCTAAACTTT
124349 TTTTTAAAAAAT-T--ACTATT
1 TTTTTAAAAAATCTAAACT-TT
*
124368 TTTTTAAAAAATCAAAACTTT
1 TTTTTAAAAAATCTAAACTTT
124389 ATTTCGATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
18 3 0.09
19 14 0.41
20 6 0.18
21 8 0.24
22 3 0.09
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.48
Consensus pattern (21 bp):
TTTTTAAAAAATCTAAACTTT
Found at i:126541 original size:21 final size:22
Alignment explanation
Indices: 126494--126553 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
126484 AGCTGTGCAG
***
126494 ATTTCTACCGATACCTTTACTA
1 ATTTCTACCGATACAAGTACTA
126516 A-TTCTACCGATACAAGTA-TA
1 ATTTCTACCGATACAAGTACTA
*
126536 ATTTCTACCAATACAAGT
1 ATTTCTACCGATACAAGT
126554 CATGCAACTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 3 0.09
21 29 0.88
22 1 0.03
ACGTcount: A:0.35, C:0.23, G:0.07, T:0.35
Consensus pattern (22 bp):
ATTTCTACCGATACAAGTACTA
Found at i:127420 original size:51 final size:51
Alignment explanation
Indices: 127356--127548 Score: 208
Period size: 51 Copynumber: 3.8 Consensus size: 51
127346 CCGTATAGGA
* * * *
127356 ATTCA-TATACTCACGATGACACTGAGTCATCGGACTTTTAATTCGTTATGG
1 ATTCATTA-ACTCACGATGACACTTAGTCATCAGACCTTTAATTCGTAATGG
* * *
127407 ATTCATTAACTCACGATGACACTTAGTCATTAGACCTTTAATTTGTCATGG
1 ATTCATTAACTCACGATGACACTTAGTCATCAGACCTTTAATTCGTAATGG
* * * * * * * *
127458 ATTTATTTACTCATGATGGCACTTAGTCATCGGACCTTTAATCCATAAAGG
1 ATTCATTAACTCACGATGACACTTAGTCATCAGACCTTTAATTCGTAATGG
* *
127509 ATTCATTTACTCATGATGACACTTAGTCATCAGACTCTTT
1 ATTCATTAACTCACGATGACACTTAGTCATCAGAC-CTTT
127549 TGTTTATAGC
Statistics
Matches: 120, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
51 114 0.95
52 6 0.05
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (51 bp):
ATTCATTAACTCACGATGACACTTAGTCATCAGACCTTTAATTCGTAATGG
Found at i:127492 original size:102 final size:103
Alignment explanation
Indices: 127363--127548 Score: 266
Period size: 102 Copynumber: 1.8 Consensus size: 103
127353 GGAATTCATA
* * * * *
127363 TACTCACGATGACACTGAGTCATCGGACTTTTAATTCGTTATGGATTCATTAACTCACGATGACA
1 TACTCACGATGACACTGAGTCATCGGACCTTTAATCCATAAAGGATTCATTAACTCACGATGACA
*
127428 CTTAGTCATTAGAC-CTTTAATTTGTCATGGATTTATT
66 CTTAGTCATCAGACTCTTTAATTTGTCATGGATTTATT
* * * * *
127465 TACTCATGATGGCACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTTACTCATGATGACA
1 TACTCACGATGACACTGAGTCATCGGACCTTTAATCCATAAAGGATTCATTAACTCACGATGACA
127530 CTTAGTCATCAGACTCTTT
66 CTTAGTCATCAGACTCTTT
127549 TGTTTATAGC
Statistics
Matches: 72, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
102 68 0.94
103 4 0.06
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (103 bp):
TACTCACGATGACACTGAGTCATCGGACCTTTAATCCATAAAGGATTCATTAACTCACGATGACA
CTTAGTCATCAGACTCTTTAATTTGTCATGGATTTATT
Found at i:131184 original size:51 final size:51
Alignment explanation
Indices: 131097--131289 Score: 242
Period size: 51 Copynumber: 3.8 Consensus size: 51
131087 CCGTATAAGA
* * * ** *
131097 ATTCATATACTCATGGTGACACTGAGTCATTGGACCTTTAATTCATCATGG
1 ATTCATTTACTCATGATGACACTTAGTCATCAGACCTTTAATTCGTCATGG
* * *
131148 ATTCATTTACCCACGATGACACTTAATCATCAGACCTTTAATTCGTCATGG
1 ATTCATTTACTCATGATGACACTTAGTCATCAGACCTTTAATTCGTCATGG
* * * * * *
131199 ATTCATTTACTCATGAGGACACTTTGTCATCGGACCTTTAATCCGTAAAGG
1 ATTCATTTACTCATGATGACACTTAGTCATCAGACCTTTAATTCGTCATGG
131250 ATTCATTTACTCATGATGACACTTAGTCATCAGACTCTTT
1 ATTCATTTACTCATGATGACACTTAGTCATCAGAC-CTTT
131290 CGTTTATAGC
Statistics
Matches: 120, Mismatches: 21, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
51 116 0.97
52 4 0.03
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (51 bp):
ATTCATTTACTCATGATGACACTTAGTCATCAGACCTTTAATTCGTCATGG
Found at i:133768 original size:27 final size:28
Alignment explanation
Indices: 133738--133790 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
133728 AGCCCCTAAT
133738 GTTTGTTTGG-TCACTTTGGCCCTTATG
1 GTTTGTTTGGCTCACTTTGGCCCTTATG
* *
133765 GTTTTTTTGGCTTACTTTGGCCCTTA
1 GTTTGTTTGGCTCACTTTGGCCCTTA
133791 ACCTTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.08, C:0.19, G:0.23, T:0.51
Consensus pattern (28 bp):
GTTTGTTTGGCTCACTTTGGCCCTTATG
Found at i:133979 original size:14 final size:13
Alignment explanation
Indices: 133960--134010 Score: 52
Period size: 12 Copynumber: 4.0 Consensus size: 13
133950 ATTAATTATT
133960 TTTTTAAAATATAA
1 TTTTTAAAATAT-A
*
133974 TTTTTAAAAAATA
1 TTTTTAAAATATA
*
133987 -TTTTAAAAT-TT
1 TTTTTAAAATATA
*
133998 TTTTTTAAATATA
1 TTTTTAAAATATA
134011 AAATTATAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
11 1 0.03
12 16 0.53
13 2 0.07
14 11 0.37
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TTTTTAAAATATA
Found at i:134072 original size:6 final size:6
Alignment explanation
Indices: 134061--134097 Score: 56
Period size: 6 Copynumber: 6.0 Consensus size: 6
134051 TTTCTGCTCT
*
134061 CCTTCC CCTTCC CTCTTCC CCTTCC CCTTCT CCTTCC
1 CCTTCC CCTTCC C-CTTCC CCTTCC CCTTCC CCTTCC
134098 AAAAAATGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (6 bp):
CCTTCC
Found at i:134080 original size:13 final size:12
Alignment explanation
Indices: 134061--134097 Score: 56
Period size: 13 Copynumber: 3.0 Consensus size: 12
134051 TTTCTGCTCT
134061 CCTTCCCCTTCC
1 CCTTCCCCTTCC
134073 CTCTTCCCCTTCC
1 C-CTTCCCCTTCC
*
134086 CCTTCTCCTTCC
1 CCTTCCCCTTCC
134098 AAAAAATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (12 bp):
CCTTCCCCTTCC
Found at i:137277 original size:2 final size:2
Alignment explanation
Indices: 137270--137303 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
137260 TAGATCATCT
137270 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
137304 CACAATTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:138344 original size:59 final size:62
Alignment explanation
Indices: 138263--138379 Score: 159
Period size: 62 Copynumber: 1.9 Consensus size: 62
138253 ATCACTTTAA
* * * * *
138263 TATTAAATTAATATAATATTTATC-A-AG-ATAAATATTAGATTAAATTTAATGTTAAATCT
1 TATTAAAATAATAAAATATTTATCTACAGAATAAACATTAAATTAAATTTAATATTAAATCT
*
138322 TATTAAAATAATAAAATGTTTATCTACAGAATAAACATTAAATTAAATTTAATATTAA
1 TATTAAAATAATAAAATATTTATCTACAGAATAAACATTAAATTAAATTTAATATTAA
138380 GATACTCACT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
59 21 0.43
60 1 0.02
61 2 0.04
62 25 0.51
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.41
Consensus pattern (62 bp):
TATTAAAATAATAAAATATTTATCTACAGAATAAACATTAAATTAAATTTAATATTAAATCT
Found at i:139029 original size:37 final size:37
Alignment explanation
Indices: 138983--139058 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
138973 TTTTTTGATG
138983 AAACAAGAGTTTAAGGAATAAAATAGGAAAACAATGA
1 AAACAAGAGTTTAAGGAATAAAATAGGAAAACAATGA
*
139020 AAACAAGAGTTTAAGGACTAAAATAGGAAAACAATGA
1 AAACAAGAGTTTAAGGAATAAAATAGGAAAACAATGA
139057 AA
1 AA
139059 TTGCTTGTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.59, C:0.07, G:0.18, T:0.16
Consensus pattern (37 bp):
AAACAAGAGTTTAAGGAATAAAATAGGAAAACAATGA
Found at i:142235 original size:15 final size:15
Alignment explanation
Indices: 142215--142246 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
142205 GAATTTACAC
*
142215 ATAAAATGAAAACAA
1 ATAAAATGAAAAAAA
142230 ATAAAATGAAAAAAA
1 ATAAAATGAAAAAAA
142245 AT
1 AT
142247 GTGGTCACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.75, C:0.03, G:0.06, T:0.16
Consensus pattern (15 bp):
ATAAAATGAAAAAAA
Found at i:142883 original size:3 final size:3
Alignment explanation
Indices: 142875--142934 Score: 61
Period size: 3 Copynumber: 20.0 Consensus size: 3
142865 CGGGGCAACA
* * *
142875 TCT TCT TCT TTT TCT TCCT TC- TCT TCT TTT TGT TCT TCT T-T TCTT
1 TCT TCT TCT TCT TCT T-CT TCT TCT TCT TCT TCT TCT TCT TCT TC-T
142920 TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT
142935 ACCTCAATAC
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
2 4 0.08
3 38 0.79
4 6 0.12
ACGTcount: A:0.00, C:0.28, G:0.02, T:0.70
Consensus pattern (3 bp):
TCT
Found at i:142901 original size:18 final size:17
Alignment explanation
Indices: 142878--142931 Score: 72
Period size: 18 Copynumber: 3.1 Consensus size: 17
142868 GGCAACATCT
142878 TCTTCTTTTTCTTCCTTC
1 TCTTCTTTTTCTT-CTTC
*
142896 TCTTCTTTTTGTTCTTC
1 TCTTCTTTTTCTTCTTC
*
142913 TTTTCTTTCTTCTTCTTC
1 TCTTCTTT-TTCTTCTTC
142931 T
1 T
142932 TCTACCTCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
17 11 0.34
18 21 0.66
ACGTcount: A:0.00, C:0.28, G:0.02, T:0.70
Consensus pattern (17 bp):
TCTTCTTTTTCTTCTTC
Found at i:142901 original size:21 final size:21
Alignment explanation
Indices: 142875--142933 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
142865 CGGGGCAACA
142875 TCTTCTTCTTTTTCTTCCTTC
1 TCTTCTTCTTTTTCTTCCTTC
*
142896 TCTTCTT-TTTGTTCTT-CTTT
1 TCTTCTTCTTT-TTCTTCCTTC
*
142916 TCTTTCTTCTTCTTCTTC
1 TC-TTCTTCTTTTTCTTC
142934 TACCTCAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
20 8 0.25
21 22 0.69
22 2 0.06
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.69
Consensus pattern (21 bp):
TCTTCTTCTTTTTCTTCCTTC
Found at i:148855 original size:18 final size:18
Alignment explanation
Indices: 148834--148883 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
148824 CATTCGAACC
*
148834 TGTGGTTGCATCTGAGTA
1 TGTGATTGCATCTGAGTA
* * * *
148852 TGTGACTACATCTGATTT
1 TGTGATTGCATCTGAGTA
148870 TGTGATTGCATCTG
1 TGTGATTGCATCTG
148884 GTCAAGCTGT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.18, C:0.14, G:0.26, T:0.42
Consensus pattern (18 bp):
TGTGATTGCATCTGAGTA
Found at i:173774 original size:17 final size:17
Alignment explanation
Indices: 173751--173875 Score: 126
Period size: 17 Copynumber: 7.2 Consensus size: 17
173741 ACCAAACCCT
173751 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
173769 -TTAAATTTATTTTTAAA
1 TTTAAATTTA-TTTTAAA
*
173786 TTTAAATTTATTCTAAA
1 TTTAAATTTATTTTAAA
* *
173803 CTTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
** *
173820 TTTAAATTTAAATTAAG
1 TTTAAATTTATTTTAAA
* *
173837 TTTAAATTTACTTGTAAT
1 TTTAAATTTA-TTTTAAA
* *
173855 TTTAAAATTACTTTAAA
1 TTTAAATTTATTTTAAA
173872 TTTA
1 TTTA
173876 TTAAAAGTCC
Statistics
Matches: 87, Mismatches: 17, Indels: 7
0.78 0.15 0.06
Matches are distributed among these distances:
17 60 0.69
18 27 0.31
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:173789 original size:6 final size:6
Alignment explanation
Indices: 173751--173846 Score: 69
Period size: 6 Copynumber: 16.7 Consensus size: 6
173741 ACCAAACCCT
* **
173751 TTTAAA TTT-AT TTTAAGA -TTAAA TTTATT TTTAAA TTTAAA TTT--A
1 TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* ** *
173796 TTCTAAA CTTAAA TTT-GT TTTAAA TTTAAA TTTAAA -TTAAG TTTAAA
1 TT-TAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
173843 TTTA
1 TTTA
173847 CTTGTAATTT
Statistics
Matches: 68, Mismatches: 14, Indels: 16
0.69 0.14 0.16
Matches are distributed among these distances:
4 3 0.04
5 13 0.19
6 50 0.74
7 2 0.03
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:173790 original size:35 final size:35
Alignment explanation
Indices: 173751--173870 Score: 127
Period size: 35 Copynumber: 3.5 Consensus size: 35
173741 ACCAAACCCT
*
173751 TTTAAATTTATTTTAAGATTAAATTTATTTTTAAA
1 TTTAAATTTATTTTAAGATTAAATTTACTTTTAAA
* *
173786 TTTAAATTTATTCTAA-ACTTAAATTT-GTTTTAAA
1 TTTAAATTTATTTTAAGA-TTAAATTTACTTTTAAA
** * * *
173820 TTTAAATTTAAATTAAGTTTAAATTTACTTGTAAT
1 TTTAAATTTATTTTAAGATTAAATTTACTTTTAAA
* *
173855 TTTAAAATTACTTTAA
1 TTTAAATTTATTTTAA
173871 ATTTATTAAA
Statistics
Matches: 70, Mismatches: 12, Indels: 6
0.80 0.14 0.07
Matches are distributed among these distances:
34 29 0.41
35 41 0.59
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (35 bp):
TTTAAATTTATTTTAAGATTAAATTTACTTTTAAA
Found at i:173825 original size:23 final size:23
Alignment explanation
Indices: 173799--173846 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
173789 AAATTTATTC
*
173799 TAAACTTAAATT-TGTTTTAAATT
1 TAAACTTAAATTAAG-TTTAAATT
*
173822 TAAATTTAAATTAAGTTTAAATT
1 TAAACTTAAATTAAGTTTAAATT
173845 TA
1 TA
173847 CTTGTAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (23 bp):
TAAACTTAAATTAAGTTTAAATT
Found at i:175628 original size:29 final size:29
Alignment explanation
Indices: 175592--176018 Score: 279
Period size: 29 Copynumber: 14.7 Consensus size: 29
175582 GACCTTTAAA
175592 TTTCCAAAAATT-CATTTTTTACCCCGAAC
1 TTTCCAAAAATTCCA-TTTTTACCCCGAAC
* *
175621 TTTTCAAAAATTACCA-TTTCACCCTCGAA-
1 TTTCCAAAAATT-CCATTTTTACCC-CGAAC
* *
175650 TTTTC-AAAATTCCATTTTTTACCTCGAAC
1 TTTCCAAAAATTCCA-TTTTTACCCCGAAC
* * ** *
175679 TTTTCAAAAACTACCA-TTTTA-CCTTAAA
1 TTTCCAAAAA-TTCCATTTTTACCCCGAAC
* **
175707 TTTCCAAAAATTCCA-TTTGACCCTAAAC
1 TTTCCAAAAATTCCATTTTTACCCCGAAC
** *
175735 TTTCCAAAAATTAAAATTTTACCCTCGAA-
1 TTTCCAAAAATTCCATTTTTACCC-CGAAC
* **
175764 TGTCCCTAAATTCCATTTTTACCCCCGAAC
1 TTTCCAAAAATTCCATTTTTA-CCCCGAAC
*
175794 TTTCCAAAAATTACCA-TTTTACTCACGAA-
1 TTTCCAAAAATT-CCATTTTTAC-CCCGAAC
* *
175823 TTTCTAAAAATTCCATTTTTGACCCCAAAC
1 TTTCCAAAAATTCCATTTTT-ACCCCGAAC
*
175853 TTTCCAAAAATTACCA--TTTACCCTCG-AG
1 TTTCCAAAAATT-CCATTTTTACCC-CGAAC
** *
175881 TTTCCAAAAATTTAATTTTTAGCCTCGAAC
1 TTTCCAAAAATTCCATTTTTA-CCCCGAAC
* *
175911 TTTCCAAAAATTACCA-TTTTACCCCCAAA
1 TTTCCAAAAATT-CCATTTTTACCCCGAAC
* * *
175940 TTTCTAAAAATTTCATTTTTGACCTCGAAC
1 TTTCCAAAAATTCCATTTTT-ACCCCGAAC
** ** * *
175970 TTTCCAAAAATTATAAATTTACCCCTAAA
1 TTTCCAAAAATTCCATTTTTACCCCGAAC
* *
175999 TTCCCAAAAATTTCATTTTT
1 TTTCCAAAAATTCCATTTTT
176019 GTTCCTAATT
Statistics
Matches: 309, Mismatches: 62, Indels: 54
0.73 0.15 0.13
Matches are distributed among these distances:
27 12 0.04
28 62 0.20
29 136 0.44
30 86 0.28
31 13 0.04
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.37
Consensus pattern (29 bp):
TTTCCAAAAATTCCATTTTTACCCCGAAC
Found at i:175801 original size:59 final size:58
Alignment explanation
Indices: 175559--176018 Score: 439
Period size: 59 Copynumber: 7.9 Consensus size: 58
175549 AAAGGTCCCT
* * * **
175559 GAACTGTCCAAAAATTA-CATTATGACCTTTAAATTTCCAAAAATT-CATTTTTTACCCC
1 GAACTTTCCAAAAATTACCATT-TTACCCTCGAATTTCCAAAAATTCCA-TTTTTACCCC
* * * *
175617 GAACTTTTCAAAAATTACCATTTCACCCTCGAATTTTC-AAAATTCCATTTTTTACCTC
1 GAACTTTCCAAAAATTACCATTTTACCCTCGAATTTCCAAAAATTCCA-TTTTTACCCC
* * ** * *
175675 GAACTTTTCAAAAACTACCATTTTA-CCTTAAATTTCCAAAAATTCCA-TTTGACCCT
1 GAACTTTCCAAAAATTACCATTTTACCCTCGAATTTCCAAAAATTCCATTTTTACCCC
* ** * **
175731 AAACTTTCCAAAAATTAAAATTTTACCCTCGAATGTCCCTAAATTCCATTTTTACCCCC
1 GAACTTTCCAAAAATTACCATTTTACCCTCGAATTTCCAAAAATTCCATTTTTA-CCCC
* * *
175790 GAACTTTCCAAAAATTACCATTTTACTCACGAATTTCTAAAAATTCCATTTTTGACCCC
1 GAACTTTCCAAAAATTACCATTTTACCCTCGAATTTCCAAAAATTCCATTTTT-ACCCC
* * ** *
175849 AAACTTTCCAAAAATTACCA-TTTACCCTCGAGTTTCCAAAAATTTAATTTTTAGCCTC
1 GAACTTTCCAAAAATTACCATTTTACCCTCGAATTTCCAAAAATTCCATTTTTA-CCCC
* * * * *
175907 GAACTTTCCAAAAATTACCATTTTACCCCCAAATTTCTAAAAATTTCATTTTTGACCTC
1 GAACTTTCCAAAAATTACCATTTTACCCTCGAATTTCCAAAAATTCCATTTTT-ACCCC
** * * * *
175966 GAACTTTCCAAAAATTATAAATTTACCC-CTAAATTCCCAAAAATTTCATTTTT
1 GAACTTTCCAAAAATTACCATTTTACCCTC-GAATTTCCAAAAATTCCATTTTT
176019 GTTCCTAATT
Statistics
Matches: 335, Mismatches: 56, Indels: 21
0.81 0.14 0.05
Matches are distributed among these distances:
56 26 0.08
57 33 0.10
58 123 0.37
59 151 0.45
60 2 0.01
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.37
Consensus pattern (58 bp):
GAACTTTCCAAAAATTACCATTTTACCCTCGAATTTCCAAAAATTCCATTTTTACCCC
Found at i:183626 original size:17 final size:17
Alignment explanation
Indices: 183580--183620 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
183570 CTTGATATTC
183580 AAAAAAATAATTTGCCT
1 AAAAAAATAATTTGCCT
*
183597 AAAAAAATAATTTTCCT
1 AAAAAAATAATTTGCCT
183614 AAAAAAA
1 AAAAAAA
183621 ATATTTGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.61, C:0.10, G:0.02, T:0.27
Consensus pattern (17 bp):
AAAAAAATAATTTGCCT
Found at i:184763 original size:49 final size:49
Alignment explanation
Indices: 184691--184804 Score: 210
Period size: 49 Copynumber: 2.3 Consensus size: 49
184681 ACCAAATTCG
184691 TCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGATGCGGTCA
1 TCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGATGCGGTCA
184740 TCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGATGCGGTCA
1 TCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGATGCGGTCA
* *
184789 TCTTCTTAATGAGATA
1 TCTTCCTGATGAGATA
184805 TTGAGAAGAA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 63 1.00
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.25
Consensus pattern (49 bp):
TCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGATGCGGTCA
Found at i:184984 original size:258 final size:258
Alignment explanation
Indices: 184527--185021 Score: 719
Period size: 258 Copynumber: 1.9 Consensus size: 258
184517 ACAACGAGTA
* * * * *
184527 GTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGAAACCAAGCTCAATATGAGCAA
1 GTCATCTTCCTAATGAGATACAGAGAAGAAGACCAAATCAATGAAACCAAGCTCAATAGGAGCAA
* * * *
184592 AACTTCGAAGCCCAGCTTCCTGATGAGGTACTGAGAAGCAGGTTAAAGCAATAAAATGGTCAGCT
66 AACTTCGAAGCCCAACTTCCTGATGAGATACTGAGAAGCAAGTCAAAGCAATAAAATGGTCAGCT
* * *
184657 TCCTGATGAGATACTGAGAAATGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTG
131 TCCTAATGAGATACTGAGAAATGGACCAAATTCGTCTTCCTGATCAGATACAAAGAAGCGGATTG
*
184722 AAACAAGTGATGCGGTCATCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGATGCG
196 AAACAAGCGATGCGGTCATCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGATGCG
* ** *
184785 GTCATCTTCTTAATGAGATATTGAGAAGAAGGCCAAATCAAT-AAAGCCAAGCTCAA-AGGGAGC
1 GTCATCTTCCTAATGAGATACAGAGAAGAAGACCAAATCAATGAAA-CCAAGCTCAATA-GGAGC
* * *
184848 AAATCTTC-AAGCCCTAACTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGGTTA
64 AAAACTTCGAAGCCC-AACTTCCTGATGAGATACTGAGAAGCAAGTCAAAGCAATAAAATGGTCA
*
184912 GCTTCCTAATGAGATACTGAGAAGTGGACCAAATTCGTCCTT-CTGATCAGATACAAAGAAGCGG
128 GCTTCCTAATGAGATACTGAGAAATGGACCAAATTCGT-CTTCCTGATCAGATACAAAGAAGCGG
* *
184976 ATTGAAACAAGCGATGCGGTCATCTTTCTGATGAGATACTGAGAAG
192 ATTGAAACAAGCGATGCGGTCATCTTCCTGATGAGATACAGAGAAG
185022 TAGACCAAAT
Statistics
Matches: 210, Mismatches: 23, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
257 10 0.05
258 197 0.94
259 3 0.01
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (258 bp):
GTCATCTTCCTAATGAGATACAGAGAAGAAGACCAAATCAATGAAACCAAGCTCAATAGGAGCAA
AACTTCGAAGCCCAACTTCCTGATGAGATACTGAGAAGCAAGTCAAAGCAATAAAATGGTCAGCT
TCCTAATGAGATACTGAGAAATGGACCAAATTCGTCTTCCTGATCAGATACAAAGAAGCGGATTG
AAACAAGCGATGCGGTCATCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGATGCG
Found at i:185021 original size:209 final size:208
Alignment explanation
Indices: 184740--185260 Score: 717
Period size: 209 Copynumber: 2.5 Consensus size: 208
184730 GATGCGGTCA
* *
184740 TCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGATGCGGTCATC-TTCTTAATGAGAT
1 TCTTCCTGATGAGATACAAAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTTC-TGATGAGAT
* * *
184804 ATTGAGAAGAAGGCCAAATCAATAAAGCCAAGCTCAAAGGGAGCAAATCTTC-AAGCCCTAACTT
65 ACTGAGAAGTAGGCCAAATCAATAAAGCC-AGCTCAAAGGGAGCAAATCTTCGAA-CCCCAACTT
*
184868 CCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGGTTAGCTTCCTAATGAGATACTGAG
128 CCCGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGGTTAGCTTCCTAATGAGATACTGAG
184933 AAGTGGACCAAATTCG
193 AAGTGGACCAAATTCG
* *
184949 TCCTT-CTGATCAGATACAAAGAAGCGGATTGAAACAAGCGATGCGGTCATCTTTCTGATGAGAT
1 T-CTTCCTGATGAGATACAAAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTTCTGATGAGAT
* * ** ** * **
185013 ACTGAGAAGTAGACCAAATCAATGAAGTCGGGCTCAAAATGAGCGAATCTTCGAACCCCAGTTTC
65 ACTGAGAAGTAGGCCAAATCAATAAAG-CCAGCTCAAAGGGAGCAAATCTTCGAACCCCAACTTC
* * *
185078 CCGATGAGATATTGAGAGGCAAGTCGAAGCAATAAAATGGTTAGCTTCCTAATGAGATATTGAGA
129 CCGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGGTTAGCTTCCTAATGAGATACTGAGA
185143 AGTGGACCAAATTCG
194 AGTGGACCAAATTCG
* * * *
185158 TCTTCCTGATGAAATACAAAGAAGCGGATTGAAACAAATGATGCGGTCATCTTCCTGATGAGATG
1 TCTTCCTGATGAGATACAAAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTTCTGATGAGATA
* *
185223 CTAAGAAGTAGGTCAAATCAATGAAA-CCAGACTCAAAG
66 CTGAGAAGTAGGCCAAATCAAT-AAAGCCAG-CTCAAAG
185261 ACTACAGTGA
Statistics
Matches: 272, Mismatches: 33, Indels: 14
0.85 0.10 0.04
Matches are distributed among these distances:
208 5 0.02
209 256 0.94
210 11 0.04
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (208 bp):
TCTTCCTGATGAGATACAAAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTTCTGATGAGATA
CTGAGAAGTAGGCCAAATCAATAAAGCCAGCTCAAAGGGAGCAAATCTTCGAACCCCAACTTCCC
GATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGGTTAGCTTCCTAATGAGATACTGAGAAG
TGGACCAAATTCG
Found at i:185596 original size:6 final size:6
Alignment explanation
Indices: 185587--185701 Score: 102
Period size: 6 Copynumber: 20.2 Consensus size: 6
185577 ATTTATTTTC
*
185587 AAATTT AAATTT --ATTCT AAATTT AAATTT -ATTTT AAATTT AAATTT
1 AAATTT AAATTT AAATT-T AAATTT AAATTT AAATTT AAATTT AAATTT
* * *
185633 AAATTT --ATTT AATTTT AAATTT AAA-TT AAGTTT AAATTT -ACTTGT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATT-T
* *
185678 AAATTT AAAATT -ATTTT AAATTT A
1 AAATTT AAATTT AAATTT AAATTT A
185702 TTAAAAGTCC
Statistics
Matches: 87, Mismatches: 12, Indels: 20
0.73 0.10 0.17
Matches are distributed among these distances:
4 7 0.08
5 15 0.17
6 59 0.68
7 6 0.07
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (6 bp):
AAATTT
Found at i:185609 original size:17 final size:17
Alignment explanation
Indices: 185572--185701 Score: 125
Period size: 17 Copynumber: 7.2 Consensus size: 17
185562 ACCAAACCCT
*
185572 TTTAGATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
*
185590 TTTAAATTTATTCTAAA
1 TTTAAATTTATTTTAAA
185607 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
185624 TTTAAATTTAAATTTATTTAAT
1 TTTAAATTT--A--T-TTTAAA
** *
185646 TTTAAATTTAAATTAAG
1 TTTAAATTTATTTTAAA
*
185663 TTTAAATTTACTTGTAAA
1 TTTAAATTTA-TTTTAAA
*
185681 TTTAAAATTATTTTAAA
1 TTTAAATTTATTTTAAA
185698 TTTA
1 TTTA
185702 TTAAAAGTCC
Statistics
Matches: 93, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
17 52 0.56
18 24 0.26
19 1 0.01
20 1 0.01
21 1 0.01
22 14 0.15
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:185613 original size:23 final size:22
Alignment explanation
Indices: 185603--185672 Score: 104
Period size: 23 Copynumber: 3.1 Consensus size: 22
185593 AAATTTATTC
185603 TAAATTTAAATTTATTTTAAATT
1 TAAATTTAAATTTA-TTTAAATT
*
185626 TAAATTTAAATTTATTTAATTT
1 TAAATTTAAATTTATTTAAATT
*
185648 TAAATTTAAATTAAGTTTAAATT
1 TAAATTTAAATTTA-TTTAAATT
185671 TA
1 TA
185673 CTTGTAAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
22 20 0.47
23 23 0.53
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (22 bp):
TAAATTTAAATTTATTTAAATT
Found at i:185621 original size:11 final size:11
Alignment explanation
Indices: 185607--185703 Score: 71
Period size: 11 Copynumber: 9.1 Consensus size: 11
185597 TTATTCTAAA
185607 TTTAAATTTAT
1 TTTAAATTTAT
*
185618 TTTAAATTTAAA
1 TTTAAATTT-AT
185630 TTTAAATTTA-
1 TTTAAATTTAT
* *
185640 TTTAATTTTAAA
1 TTTAAATTT-AT
* *
185652 TTTAAATTAAG
1 TTTAAATTTAT
185663 TTTAAATTTACT
1 TTTAAATTTA-T
*
185675 TGTAAATTTA-
1 TTTAAATTTAT
185685 ---AAA-TTAT
1 TTTAAATTTAT
185692 TTTAAATTTAT
1 TTTAAATTTAT
185703 T
1 T
185704 AAAAGTCCCA
Statistics
Matches: 69, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
6 3 0.04
7 3 0.04
10 11 0.16
11 26 0.38
12 26 0.38
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:185649 original size:22 final size:22
Alignment explanation
Indices: 185595--185659 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
185585 TCAAATTTAA
*
185595 ATTT-ATTCTAAATTTAAATTT
1 ATTTAATTTTAAATTTAAATTT
*
185616 ATTTTAAATTTAAATTTAAATTT
1 A-TTTAATTTTAAATTTAAATTT
185639 ATTTAATTTTAAATTTAAATT
1 ATTTAATTTTAAATTTAAATT
185660 AAGTTTAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
21 1 0.03
22 22 0.56
23 16 0.41
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTAATTTTAAATTTAAATTT
Found at i:185681 original size:45 final size:45
Alignment explanation
Indices: 185587--185701 Score: 135
Period size: 45 Copynumber: 2.5 Consensus size: 45
185577 ATTTATTTTC
* * *
185587 AAATTTAAATTTATTCTAAATTTAAATTTATTTTAAATTTAAATTT
1 AAATTT-AATTTATTTTAAATTTAAATTAAGTTTAAATTTAAATTT
*
185633 AAATTT-ATTTAATTTTAAATTTAAATTAAGTTTAAATTT-ACTTGT
1 AAATTTAATTT-ATTTTAAATTTAAATTAAGTTTAAATTTAAATT-T
*
185678 AAATTTAAAATTATTTTAAATTTA
1 AAATTT-AATTTATTTTAAATTTA
185702 TTAAAAGTCC
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
44 7 0.12
45 32 0.53
46 18 0.30
47 3 0.05
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (45 bp):
AAATTTAATTTATTTTAAATTTAAATTAAGTTTAAATTTAAATTT
Found at i:187605 original size:29 final size:28
Alignment explanation
Indices: 187525--187663 Score: 99
Period size: 30 Copynumber: 4.8 Consensus size: 28
187515 TGACCTCTAG
* *
187525 ATTTCCAAAAATTACATTTTTTACCCTCGA
1 ATTTCAAAAAATTACA-TTTTTA-CCTTGA
187555 ACTTCTC-AAAAATTACCA-TTTTACCTATGA
1 A-TT-TCAAAAAATTA-CATTTTTACCT-TGA
*
187585 ATTTCCAAAAAATT-CATTTTTTACCCTGA
1 ATTT-CAAAAAATTACA-TTTTTACCTTGA
* *
187614 TTTTTC-AAAAATTACCA-TTTTACCCTCGA
1 -ATTTCAAAAAATTA-CATTTTTA-CCTTGA
187643 ATTTCAAAAAATTACATTTTT
1 ATTTCAAAAAATTACATTTTT
187664 GACCCTAAAC
Statistics
Matches: 89, Mismatches: 6, Indels: 29
0.72 0.05 0.23
Matches are distributed among these distances:
28 21 0.24
29 26 0.29
30 28 0.31
31 10 0.11
32 4 0.04
ACGTcount: A:0.35, C:0.21, G:0.03, T:0.41
Consensus pattern (28 bp):
ATTTCAAAAAATTACATTTTTACCTTGA
Found at i:187771 original size:59 final size:57
Alignment explanation
Indices: 187525--188013 Score: 502
Period size: 59 Copynumber: 8.4 Consensus size: 57
187515 TGACCTCTAG
* * **
187525 ATTTCCAAAAATTACATTTTTTACCCTCGAAC-TTCTCAAAAATTACCATTTTACCTATGA
1 ATTTCCAAAAATTCCA-TTTTTACCCT-AAACTTTC-CAAAAATTACCATTTTACC-CCGA
* * *
187585 ATTTCCAAAAAATT-CATTTTTTACCCT-GATTTTTCAAAAATTACCATTTTACCCTCGA
1 ATTTCC-AAAAATTCCA-TTTTTACCCTAAACTTTCCAAAAATTACCATTTTACCC-CGA
* *
187643 ATTTCAAAAAATTACATTTTTGACCCTAAACTTTCC-AAAATTACCATTTTACCCCTGA
1 ATTTCCAAAAATTCCATTTTT-ACCCTAAACTTTCCAAAAATTACCATTTTACCCC-GA
* * * * *
187701 GTGTCCCAAAATTCCATTTTTATCCCTAAACTTTACAAAAATTACCATTTTACCCACTA
1 ATTTCCAAAAATTCCATTTTTA-CCCTAAACTTTCCAAAAATTACCATTTTACCC-CGA
* * *
187760 ATGTCCTAAAATTCCATTTTTACCCTCAAATTTTCCAAAAATTACCATTTTACCCTCGA
1 ATTTCCAAAAATTCCATTTTTACCCT-AAACTTTCCAAAAATTACCATTTTACCC-CGA
** * *
187819 ATTTTTAAAATTTCAATTTTTGACCCTAAACTTTCCAAAAATTACCATTTTACCCTCGA
1 ATTTCCAAAAATTCCATTTTT-ACCCTAAACTTTCCAAAAATTACCATTTTACCC-CGA
* ** * *
187878 GTTTCCAAAAATTCCATTTTTAGCCCCGAACTTTCCAAAAGTTACCATTTTACCCTTGA
1 ATTTCCAAAAATTCCATTTTTA-CCCTAAACTTTCCAAAAATTACCATTTTACCC-CGA
* * * *
187937 ATTT-CTAAAATTCCATTTTTTCCCTTTAACTTTCCAAAAGTTACCATTTTACCCCGA
1 ATTTCCAAAAATTCCATTTTTACCC-TAAACTTTCCAAAAATTACCATTTTACCCCGA
*
187994 ATTTCCAAAAATTTCATTTT
1 ATTTCCAAAAATTCCATTTT
188014 GGTTCTCGAT
Statistics
Matches: 368, Mismatches: 46, Indels: 32
0.83 0.10 0.07
Matches are distributed among these distances:
57 23 0.06
58 142 0.39
59 171 0.46
60 25 0.07
61 7 0.02
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.39
Consensus pattern (57 bp):
ATTTCCAAAAATTCCATTTTTACCCTAAACTTTCCAAAAATTACCATTTTACCCCGA
Found at i:195753 original size:42 final size:42
Alignment explanation
Indices: 195671--195782 Score: 109
Period size: 42 Copynumber: 2.6 Consensus size: 42
195661 AAGCATGAAG
* ***
195671 ATAT-ATTAAAGGAAGACTTATGTCTCGGGATGAAAATGAGA
1 ATATGATTAAAGGAAGACTTATGACTCAAAATGAAAATGAGA
* * *
195712 ATATGATTAAAGGAAGACTCATGACTCAAAATGAGAGTGAGA
1 ATATGATTAAAGGAAGACTTATGACTCAAAATGAAAATGAGA
* * *
195754 TTATGTTTAAAAAGGAAGATTTATGACTC
1 ATATGATT--AAAGGAAGACTTATGACTC
195783 GGTAAAGCAT
Statistics
Matches: 57, Mismatches: 11, Indels: 3
0.80 0.15 0.04
Matches are distributed among these distances:
41 4 0.07
42 36 0.63
44 17 0.30
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (42 bp):
ATATGATTAAAGGAAGACTTATGACTCAAAATGAAAATGAGA
Found at i:195831 original size:40 final size:40
Alignment explanation
Indices: 195764--195840 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
195754 TTATGTTTAA
* * *
195764 AAAGGAAGATTTATGACTCGGTAAAGCATAAGATTGTAAT
1 AAAGGAAGACTTATGAATCCGTAAAGCATAAGATTGTAAT
* *
195804 AAAGGAAGACTTGTGAATCCGTGAAGCATAAGATTGT
1 AAAGGAAGACTTATGAATCCGTAAAGCATAAGATTGT
195841 CTAAAAAAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.40, C:0.09, G:0.25, T:0.26
Consensus pattern (40 bp):
AAAGGAAGACTTATGAATCCGTAAAGCATAAGATTGTAAT
Found at i:205990 original size:15 final size:15
Alignment explanation
Indices: 205971--206019 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
205961 GATCAATTCA
205971 AAAAATAAAAAAATT
1 AAAAATAAAAAAATT
* *
205986 TAAAATAAATCAAATT
1 AAAAATAAA-AAAATT
*
206002 AAAAATATAAAAATT
1 AAAAATAAAAAAATT
206017 AAA
1 AAA
206020 TTTATAACTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
15 16 0.57
16 12 0.43
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAAATAAAAAAATT
Found at i:208793 original size:31 final size:31
Alignment explanation
Indices: 208753--208825 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
208743 TAGTAAAGTG
*
208753 GTCACTGAATTATTTAAAAAATTTTATTTAA
1 GTCATTGAATTATTTAAAAAATTTTATTTAA
* *
208784 GTCATTGAATTATTTAAATATTTTTATTTAA
1 GTCATTGAATTATTTAAAAAATTTTATTTAA
* *
208815 ATCATTAAATT
1 GTCATTGAATT
208826 GTTAATTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.49
Consensus pattern (31 bp):
GTCATTGAATTATTTAAAAAATTTTATTTAA
Found at i:216252 original size:2 final size:2
Alignment explanation
Indices: 216245--216275 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
216235 TCAATATTAA
216245 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
216276 AGGGTGTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:219531 original size:5 final size:5
Alignment explanation
Indices: 219523--219585 Score: 65
Period size: 5 Copynumber: 11.6 Consensus size: 5
219513 TTATATTATT
219523 TTTTA TTTTA TTTTAA TATTTA TTTTA TTTTAA TATTTA TTTTA TTTTA
1 TTTTA TTTTA TTTT-A T-TTTA TTTTA TTTT-A T-TTTA TTTTA TTTTA
219572 TATATT- TTTTA TTT
1 T-T-TTA TTTTA TTT
219586 ATTGAAATTT
Statistics
Matches: 51, Mismatches: 0, Indels: 14
0.78 0.00 0.22
Matches are distributed among these distances:
4 2 0.04
5 31 0.61
6 10 0.20
7 8 0.16
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:219533 original size:12 final size:12
Alignment explanation
Indices: 219512--219588 Score: 54
Period size: 12 Copynumber: 6.5 Consensus size: 12
219502 TTTAGATTCG
*
219512 TTTATATTATTT
1 TTTATTTTATTT
219524 TTTATTTTA-TT
1 TTTATTTTATTT
*
219535 TTAATATTTA--T
1 TTTAT-TTTATTT
* *
219546 TTTATTTTAATA
1 TTTATTTTATTT
219558 TTTATTTTATTT
1 TTTATTTTATTT
*
219570 TATATATTTT-TTA
1 T-T-TATTTTATTT
219583 TTTATT
1 TTTATT
219589 GAAATTTTTA
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
10 4 0.08
11 15 0.28
12 24 0.45
13 4 0.08
14 6 0.11
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTATTTTATTT
Found at i:219544 original size:17 final size:17
Alignment explanation
Indices: 219524--219578 Score: 101
Period size: 17 Copynumber: 3.2 Consensus size: 17
219514 TATATTATTT
219524 TTTATTTTATTTTAATA
1 TTTATTTTATTTTAATA
219541 TTTATTTTATTTTAATA
1 TTTATTTTATTTTAATA
219558 TTTATTTTATTTTATATA
1 TTTATTTTATTTTA-ATA
219576 TTT
1 TTT
219579 TTTATTTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 31 0.84
18 6 0.16
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTATTTTATTTTAATA
Found at i:219588 original size:29 final size:30
Alignment explanation
Indices: 219512--219588 Score: 79
Period size: 34 Copynumber: 2.5 Consensus size: 30
219502 TTTAGATTCG
*
219512 TTTATATTATTT-TTTATTTTATTTTAATA
1 TTTATTTTATTTATTTATTTTATTTTAATA
219541 TTTATTTTATTTTAATATTTATTTTATTTT-ATA
1 TTTATTTTA--TT--TATTTATTTTATTTTAATA
219574 TATT-TTTTATTTATT
1 T-TTATTTTATTTATT
219589 GAAATTTTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
29 12 0.29
31 4 0.10
33 10 0.24
34 15 0.37
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (30 bp):
TTTATTTTATTTATTTATTTTATTTTAATA
Found at i:236216 original size:22 final size:22
Alignment explanation
Indices: 236174--236216 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
236164 ATTCATGAAC
*
236174 TAAATGAATAAATAAATACAAG
1 TAAATGAATAAATAAACACAAG
*
236196 TAAATGCAATCAAT-AACACAA
1 TAAATG-AATAAATAAACACAA
236217 TTTTAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.60, C:0.12, G:0.07, T:0.21
Consensus pattern (22 bp):
TAAATGAATAAATAAACACAAG
Found at i:236417 original size:15 final size:15
Alignment explanation
Indices: 236397--236433 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
236387 AAGAAAAAAA
* *
236397 AAATAAATGACATAC
1 AAATAAATAACAAAC
236412 AAATAAATAACAAAC
1 AAATAAATAACAAAC
236427 AAATAAA
1 AAATAAA
236434 ATATAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.70, C:0.11, G:0.03, T:0.16
Consensus pattern (15 bp):
AAATAAATAACAAAC
Found at i:236722 original size:21 final size:21
Alignment explanation
Indices: 236689--236729 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
236679 TACGAATTAA
*
236689 AAACAAAAACAAAATTAAATT
1 AAACAAAAACAAAATAAAATT
* *
236710 AAACTAAATCAAAATAAAAT
1 AAACAAAAACAAAATAAAAT
236730 AAAAATTACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.20
Consensus pattern (21 bp):
AAACAAAAACAAAATAAAATT
Found at i:238463 original size:102 final size:102
Alignment explanation
Indices: 238283--238887 Score: 427
Period size: 102 Copynumber: 5.9 Consensus size: 102
238273 ATTAGGTTTG
* * * * *
238283 TAACTTCACTCCATTCCACTACAACTTCAGAGAGATTGAGATCCGTTACGGTTAGTTTTAATTCG
1 TAACTTCACTCCATTCCATTACAACTTCAGGGAGATTGAGATCTGCTACGATTAGTTTTAATTCG
238348 CCCCTCTGCAACTTTAAGGG-TATAAGATTTGATATTA
66 CCCCTCTGCAACTTT-AGGGATATAAGATTTGATATTA
** ** * * *
238385 TTGCTTCACTCCATTCCATTGTAACTTCAGGGAGATTGAGAACTGCTATGTTTAGTTTTAATAT-
1 TAACTTCACTCCATTCCATTACAACTTCAGGGAGATTGAGATCTGCTACGATTAGTTTTAAT-TC
* * * *
238449 GCCCCTCTGTAACTTTAGGGATATAGGATTTGGTGTTA
65 GCCCCTCTGCAACTTTAGGGATATAAGATTTGATATTA
* *
238487 TAACTTCACTCTATTTCATTACAACTTCAGGGAGATTGAGATCTGCTACGATTAGTTTTAATTCG
1 TAACTTCACTCCATTCCATTACAACTTCAGGGAGATTGAGATCTGCTACGATTAGTTTTAATTCG
* * ** * * * *
238552 TCTCTC-AAATACTTTAGGGGTATAGGATTTGGTGTTA
66 CCCCTCTGCA-ACTTTAGGGATATAAGATTTGATATTA
* * * * ** * * * * * *
238589 TAAATTCATTCCATTCTACTGTAACTTTAGGGACATTGATATCTGCTACGGTTAGTTTTAATCCA
1 TAACTTCACTCCATTCCATTACAACTTCAGGGAGATTGAGATCTGCTACGATTAGTTTTAATTCG
* * *
238654 CCCCTTTGCAACTTTAATAACTTTAGAGG-TATAGGATTCTG-TATTG
66 CCCCTCTG---C------AACTTTAG-GGATATAAGATT-TGATATTA
* * * * * * * *
238700 TAACATCACTCCATTCCACTGCAACTTTAGGGAGATTGAGATCTACTACGGTTAGTTTTAATCCA
1 TAACTTCACTCCATTCCATTACAACTTCAGGGAGATTGAGATCTGCTACGATTAGTTTTAATTCG
* * * * *
238765 CCCCTCTGCAACTTTAGAGG-TGTAGGATTTGGTGTTG
66 CCCCTCTGCAACTTTAG-GGATATAAGATTTGATATTA
*** * * * * *
238802 TAACTTCACTCCATTCTGCTGCAACTTCAGGGAGATTAAGATCTGTTAC--TTA-TTTTACTCCG
1 TAACTTCACTCCATTCCATTACAACTTCAGGGAGATTGAGATCTGCTACGATTAGTTTTAATTCG
** *
238864 CCCCTCTGTTACTTTAGGGGTATA
66 CCCCTCTGCAACTTTAGGGATATA
238888 GGAGTTGTTG
Statistics
Matches: 412, Mismatches: 73, Indels: 39
0.79 0.14 0.07
Matches are distributed among these distances:
98 2 0.00
99 26 0.06
100 3 0.01
101 8 0.02
102 283 0.69
103 1 0.00
108 1 0.00
111 83 0.20
112 5 0.01
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (102 bp):
TAACTTCACTCCATTCCATTACAACTTCAGGGAGATTGAGATCTGCTACGATTAGTTTTAATTCG
CCCCTCTGCAACTTTAGGGATATAAGATTTGATATTA
Found at i:238646 original size:204 final size:203
Alignment explanation
Indices: 238268--238890 Score: 493
Period size: 213 Copynumber: 3.0 Consensus size: 203
238258 CTTCAGGAAG
* *
238268 ATAGGATTAGGTTTGTAACTTCACTCCATTCCACTACAACTTCAGAGAGATTGAGATCCGTTACG
1 ATAGGATTAGGTTTATAACTTCACTCCATTCCACTACAACTTCAGAGAGATTGAGATCCGCTACG
* ** ***
238333 GTTAGTTTTAATTCGCCCCTCTGCAACTTTAAGGGTATAAGATTTGATATTATTGCTTCACTCCA
66 ATTAGTTTTAATTCGCCCCTCTAAAACTTTAAGGGTATAAGATTTGATATTATAAATTCACTCCA
* * * *
238398 TTCCATTGTAACTTCAGGGAGATTGAGAACTGCTATGTTTAGTTTTAATATGCCCCTCTGTAACT
131 TTCCACTGTAACTTCAGGGACATTGAGAACTGCTACGGTTAGTTTTAATATGCCCCTCTGTAACT
238463 TTAGGGAT
196 TTAGGGAT
* * * * * *
238471 ATAGGATTTGGTGTTATAACTTCACTCTATTTCATTACAACTTCAGGGAGATTGAGATCTGCTAC
1 ATAGGATTAGGT-TTATAACTTCACTCCATTCCACTACAACTTCAGAGAGATTGAGATCCGCTAC
* * * * * * *
238536 GATTAGTTTTAATTCGTCTCTC-AAATACTTTAGGGGTATAGGATTTGGTGTTATAAATTCATTC
65 GATTAGTTTTAATTCGCCCCTCTAAA-ACTTTAAGGGTATAAGATTTGATATTATAAATTCACTC
* * * * **
238600 CATTCTACTGTAACTTTAGGGACATTGATATCTGCTACGGTTAGTTTTAATCCACCCCTTTGCAA
129 CATTCCACTGTAACTTCAGGGACATTGAGAACTGCTACGGTTAGTTTTAAT--A------TGCCC
* *
238665 CTTTAATAACTTTAGAGG-T
186 CTCT-GTAACTTTAG-GGAT
** * * * * * **
238684 ATAGGATTCTGTATTGTAACATCACTCCATTCCACTGCAACTTTAGGGAGATTGAGATCTACTAC
1 ATAGGATTAGGT-TTATAACTTCACTCCATTCCACTACAACTTCAGAGAGATTGAGATCCGCTAC
* * * ** * * * * * *
238749 GGTTAGTTTTAATCCACCCCTCTGCAACTTT-AGAGGTGTAGGATTTGGTGTTGTAACTTCACTC
65 GATTAGTTTTAATTCGCCCCTCTAAAACTTTAAG-GGTATAAGATTTGATATTATAAATTCACTC
** * * * * * * ** *
238813 CATTCTGCTGCAACTTCAGGGAGATTAAGATCTGTTAC--TTA-TTTTACTCCGCCCCTCTGTTA
129 CATTCCACTGTAACTTCAGGGACATTGAGAACTGCTACGGTTAGTTTTAATATGCCCCTCTGTAA
*
238875 CTTTAGGGGT
194 CTTTAGGGAT
238885 ATAGGA
1 ATAGGA
238891 GTTGTTGTTT
Statistics
Matches: 334, Mismatches: 71, Indels: 32
0.76 0.16 0.07
Matches are distributed among these distances:
200 2 0.01
201 15 0.04
202 5 0.01
203 12 0.04
204 137 0.41
206 1 0.00
210 6 0.02
211 3 0.01
212 7 0.02
213 143 0.43
214 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (203 bp):
ATAGGATTAGGTTTATAACTTCACTCCATTCCACTACAACTTCAGAGAGATTGAGATCCGCTACG
ATTAGTTTTAATTCGCCCCTCTAAAACTTTAAGGGTATAAGATTTGATATTATAAATTCACTCCA
TTCCACTGTAACTTCAGGGACATTGAGAACTGCTACGGTTAGTTTTAATATGCCCCTCTGTAACT
TTAGGGAT
Found at i:238756 original size:111 final size:111
Alignment explanation
Indices: 238562--238780 Score: 316
Period size: 111 Copynumber: 2.0 Consensus size: 111
238552 TCTCTCAAAT
* * * * *
238562 ACTTTAGGGGTATAGGATTTGGTGTTATAAATTCATTCCATTCTACTGTAACTTTAGGGACATTG
1 ACTTTAGAGGTATAGGATTTGGTATTATAAATTCACTCCATTCCACTGCAACTTTAGGGACATTG
* * *
238627 ATATCTGCTACGGTTAGTTTTAATCCACCCCTTTGCAACTTTAATA
66 AGATCTACTACGGTTAGTTTTAATCCACCCCTCTGCAACTTTAATA
* *
238673 ACTTTAGAGGTATAGGATTCT-GTATTGTAACA-TCACTCCATTCCACTGCAACTTTAGGGAGAT
1 ACTTTAGAGGTATAGGATT-TGGTATTATAA-ATTCACTCCATTCCACTGCAACTTTAGGGACAT
238736 TGAGATCTACTACGGTTAGTTTTAATCCACCCCTCTGCAACTTTA
64 TGAGATCTACTACGGTTAGTTTTAATCCACCCCTCTGCAACTTTA
238781 GAGGTGTAGG
Statistics
Matches: 96, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
111 94 0.98
112 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (111 bp):
ACTTTAGAGGTATAGGATTTGGTATTATAAATTCACTCCATTCCACTGCAACTTTAGGGACATTG
AGATCTACTACGGTTAGTTTTAATCCACCCCTCTGCAACTTTAATA
Found at i:240265 original size:102 final size:102
Alignment explanation
Indices: 239726--240286 Score: 625
Period size: 102 Copynumber: 5.6 Consensus size: 102
239716 ATTCAAGAAG
* * * * **
239726 ATAGGATTTGGGTTTGTAACTTCAGTCCATTCCACT-TCAACTTTATGGAGATTGAGATCCACTA
1 ATAGGATTTGGTTTTGTAACTTCACTCCATTCCACTGT-AACTTCAAGGAGATTGAGATCTGCTA
* * * *
239790 CGATTATTTTTAATCTGCCCCTCTACAACTTTATGGGT
65 CGGTTAGTTTTAATCCGCCCCTCTACAACTTTAGGGGT
* * ** * * *
239828 AT-GGATTTGATGTTGTCGCTTCACTCCATTCCACTATAACTTCAGGGAGATTGAGATCTACTAC
1 ATAGGATTTGGTTTTGTAACTTCACTCCATTCCACTGTAACTTCAAGGAGATTGAGATCTGCTAC
* *
239892 -G--A--TTTAATACGCCCCTCTACAAGTTTA-GGGT
66 GGTTAGTTTTAATCCGCCCCTCTACAACTTTAGGGGT
* * * * **
239923 ATAGGATTTAGTGTTATAACTTCACTTCATTCCACTACAACTTCAAGGAGATTGAGATCTGCTAC
1 ATAGGATTTGGTTTTGTAACTTCACTCCATTCCACTGTAACTTCAAGGAGATTGAGATCTGCTAC
* * * *
239988 GGTTAGTTTTAATCCGCCCTTTTATAACTTTAAGGGT
66 GGTTAGTTTTAATCCGCCCCTCTACAACTTTAGGGGT
* * * * *
240025 ATAGGATTTGGTATTGTAACTTCACTCCATTCCACTGCAACTTCAAGGAGATTGAGATTTGTTAT
1 ATAGGATTTGGTTTTGTAACTTCACTCCATTCCACTGTAACTTCAAGGAGATTGAGATCTGCTAC
*
240090 GGTTAGTTTTAATCTGCCCCTCTACAACTTTAGGGGT
66 GGTTAGTTTTAATCCGCCCCTCTACAACTTTAGGGGT
* * *
240127 ATAGGATTTGGTTTTGTAACTTCACTCCATTTCACTGTAACTTTAGGGAGATTGAGATCTGCTAC
1 ATAGGATTTGGTTTTGTAACTTCACTCCATTCCACTGTAACTTCAAGGAGATTGAGATCTGCTAC
* * * **
240192 GGTTAGTTTAAACCCACCCCTCTGTAACTTTAGGGGT
66 GGTTAGTTTTAATCCGCCCCTCTACAACTTTAGGGGT
* * * * *
240229 ATTGGATTTGGTTTTGTAACTTCACTTCATTCCACTGTAATTTTATGGAGATTGAGAT
1 ATAGGATTTGGTTTTGTAACTTCACTCCATTCCACTGTAACTTCAAGGAGATTGAGAT
240287 TTGTTATTTG
Statistics
Matches: 392, Mismatches: 59, Indels: 16
0.84 0.13 0.03
Matches are distributed among these distances:
95 6 0.02
96 75 0.19
97 1 0.00
98 1 0.00
99 1 0.00
101 71 0.18
102 237 0.60
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (102 bp):
ATAGGATTTGGTTTTGTAACTTCACTCCATTCCACTGTAACTTCAAGGAGATTGAGATCTGCTAC
GGTTAGTTTTAATCCGCCCCTCTACAACTTTAGGGGT
Found at i:240906 original size:20 final size:20
Alignment explanation
Indices: 240881--240928 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
240871 TTTAAAAATA
*
240881 TCAAACATCAGTCAAAGATG
1 TCAAACATCAGTAAAAGATG
**
240901 TCAAACATTGGTAAAAGATG
1 TCAAACATCAGTAAAAGATG
*
240921 ACAAACAT
1 TCAAACAT
240929 TAAACAATGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.21
Consensus pattern (20 bp):
TCAAACATCAGTAAAAGATG
Found at i:240964 original size:20 final size:20
Alignment explanation
Indices: 240939--240995 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
240929 TAAACAATGG
* * *
240939 TAAAAAATTGGAAATATTGA
1 TAAAAAATAGCAAATATCGA
*
240959 TAAAAAATAGCAAATGTCGA
1 TAAAAAATAGCAAATATCGA
*
240979 TAAAAAATAACAAATAT
1 TAAAAAATAGCAAATAT
240996 TAATCAAGAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.60, C:0.05, G:0.11, T:0.25
Consensus pattern (20 bp):
TAAAAAATAGCAAATATCGA
Found at i:253839 original size:96 final size:96
Alignment explanation
Indices: 253675--253866 Score: 348
Period size: 96 Copynumber: 2.0 Consensus size: 96
253665 GAGATAATTT
*
253675 TGAGCTTTGTACCCACAGTAAGTCGTGAGGCGGAGATAGAGATAAAAATTCTTTGTAAAGATGAG
1 TGAGCTTTGTACCCACAGTAAGTCGTGAGGCGGAGATAGAGATAAAAATTCTTCGTAAAGATGAG
253740 TGCCAGGGACCATCCTCGCACCCACCTCGTC
66 TGCCAGGGACCATCCTCGCACCCACCTCGTC
* *
253771 TGAGCTTTGTACCCACATTAAGTCGTGAGGCGGAGATAGAGATAAAAATTCTTCGTAAAGATGGG
1 TGAGCTTTGTACCCACAGTAAGTCGTGAGGCGGAGATAGAGATAAAAATTCTTCGTAAAGATGAG
*
253836 TGCCAGGGAGCATCCTCGCACCCACCTCGTC
66 TGCCAGGGACCATCCTCGCACCCACCTCGTC
253867 CAATTAATAT
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
96 92 1.00
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.23
Consensus pattern (96 bp):
TGAGCTTTGTACCCACAGTAAGTCGTGAGGCGGAGATAGAGATAAAAATTCTTCGTAAAGATGAG
TGCCAGGGACCATCCTCGCACCCACCTCGTC
Found at i:254385 original size:27 final size:27
Alignment explanation
Indices: 254354--254407 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
254344 TTATTAGGAG
254354 AGTAATTATATTTT-TTCGAAATTACAA
1 AGTAATTATATTTTCTT-GAAATTACAA
*
254381 AGTAATTATATTTTCTTGGAATTACAA
1 AGTAATTATATTTTCTTGAAATTACAA
254408 TTCTCTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 23 0.92
28 2 0.08
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.44
Consensus pattern (27 bp):
AGTAATTATATTTTCTTGAAATTACAA
Found at i:255298 original size:17 final size:18
Alignment explanation
Indices: 255278--255314 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
255268 CATAAGTTAA
255278 AATA-ATATGAAA-TTTAT
1 AATATATAT-AAATTTTAT
255295 AATATATATAAATTTTAT
1 AATATATATAAATTTTAT
255313 AA
1 AA
255315 GAAAAAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (18 bp):
AATATATATAAATTTTAT
Found at i:265200 original size:30 final size:29
Alignment explanation
Indices: 265145--265533 Score: 218
Period size: 30 Copynumber: 13.2 Consensus size: 29
265135 TAAAAATCAT
* * *
265145 ATTTTGACCCCAAACTTTT-CAAAATTAC
1 ATTTTCACCCTAAAATTTTCCAAAATTAC
**
265173 AAATTCACCCTAAAATTTTTCCAAAATTAC
1 ATTTTCACCCTAAAA-TTTTCCAAAATTAC
* *
265203 ATTTTTACCCCT-AAACTTTCCAAAATTAC
1 ATTTTCA-CCCTAAAATTTTCCAAAATTAC
* **
265232 ATTTTCACCCCAAAACTTTTCCAAAAGCAC
1 ATTTTCACCCTAAAA-TTTTCCAAAATTAC
* *
265262 ATTTTTACCCTTAAAA--TTCCTAAAATCAC
1 ATTTTCACCC-TAAAATTTTCC-AAAATTAC
*
265291 ATTTT-AACCTCAAAACTTTTCCAAAATTAC
1 ATTTTCACCCT-AAAA-TTTTCCAAAATTAC
* * *
265321 ATTTTTACCCCTAAACTTTTCCAAAATCAC
1 ATTTTCA-CCCTAAAATTTTCCAAAATTAC
* * * * *
265351 ATTTTGATCCC-AAAACTTCCCAAAATCAT
1 ATTTTCA-CCCTAAAATTTTCCAAAATTAC
* * *
265380 ATTTTCACCCCCAAACTTTTCCAAAATCAC
1 ATTTTCA-CCCTAAAATTTTCCAAAATTAC
* * * * *
265410 ATTTTAACCATCAAACTTTTCCAAAATCAT
1 ATTTTCACCCT-AAAATTTTCCAAAATTAC
* * * * *
265440 AGTTTGACCCCTAAACTTTCCCAAAATCAC
1 ATTTTCA-CCCTAAAATTTTCCAAAATTAC
* * *
265470 ATTTTGA-TCTCAAAACTTTCCCAAAATTAC
1 ATTTTCACCCT-AAAA-TTTTCCAAAATTAC
* * * *
265500 ATTTTTAACCTTAAATTCTCCAAAACTT-C
1 ATTTTCACCCTAAAATTTTCCAAAA-TTAC
265529 ATTTT
1 ATTTT
265534 TCAACCCCAT
Statistics
Matches: 289, Mismatches: 52, Indels: 39
0.76 0.14 0.10
Matches are distributed among these distances:
27 1 0.00
28 26 0.09
29 80 0.28
30 158 0.55
31 21 0.07
32 3 0.01
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.35
Consensus pattern (29 bp):
ATTTTCACCCTAAAATTTTCCAAAATTAC
Found at i:265325 original size:89 final size:87
Alignment explanation
Indices: 265127--265509 Score: 367
Period size: 89 Copynumber: 4.3 Consensus size: 87
265117 AGAGGTCTCT
** * * * * ** *
265127 AAACTTTTTAAAAATCATATTTTGACCCCAAACTTTT-CAAAATTACAAATTCACCCTAAAATTT
1 AAACTTTTCCAAAATTACATTTTAACCCCAAACTTTTCCAAAATCACATTTTGACCCTAAAA--T
* * * *
265191 TTCCAAAATTACATTTTTACCCCT
64 TCCCAAAATCACATTTTAACCCCA
* * *
265215 AAAC-TTTCCAAAATTACATTTTCACCCCAAAACTTTTCCAAAAGCACATTTTTACCCTTAAAAT
1 AAACTTTTCCAAAATTACATTTTAACCCC-AAACTTTTCCAAAATCACATTTTGACCC-TAAAAT
* *
265279 TCCTAAAATCACATTTTAACCTCA
64 TCCCAAAATCACATTTTAACCCCA
*
265303 AAACTTTTCCAAAATTACATTTTTACCCCTAAACTTTTCCAAAATCACATTTTGATCCC-AAAAC
1 AAACTTTTCCAAAATTACATTTTAACCCC-AAACTTTTCCAAAATCACATTTTGA-CCCTAAAA-
* * *
265367 TTCCCAAAATCATATTTTCACCCCC
63 TTCCCAAAATCACATTTTAACCCCA
* * * * *
265392 AAACTTTTCCAAAATCACATTTTAACCATCAAACTTTTCCAAAATCATAGTTTGACCCCTAAACT
1 AAACTTTTCCAAAATTACATTTTAACC-CCAAACTTTTCCAAAATCACATTTTGA-CCCTAAA-A
* * *
265457 TTCCCAAAATCACATTTTGATCTCA
63 TTCCCAAAATCACATTTTAACCCCA
*
265482 AAACTTTCCCAAAATTACATTTTTAACC
1 AAACTTTTCCAAAATTACA-TTTTAACC
265510 TTAAATTCTC
Statistics
Matches: 246, Mismatches: 39, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
87 19 0.08
88 39 0.16
89 131 0.53
90 49 0.20
91 8 0.03
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.34
Consensus pattern (87 bp):
AAACTTTTCCAAAATTACATTTTAACCCCAAACTTTTCCAAAATCACATTTTGACCCTAAAATTC
CCAAAATCACATTTTAACCCCA
Found at i:265522 original size:89 final size:89
Alignment explanation
Indices: 265193--265524 Score: 373
Period size: 89 Copynumber: 3.7 Consensus size: 89
265183 TAAAATTTTT
* * * * * * *
265193 CCAAAATTACATTTTTACCCCTAAAC-TTTCCAAAATTACATTTTCACCCCAAAACTTTTCCAAA
1 CCAAAATCACATTTTAACCTCAAAACTTTTCCAAAATTACATTTTTAACCCTAAACTTTTCCAAA
* * * *
265257 AGCACATTTTTACCCTTAAAATTC
66 ATCACATTTTGACCCCTAAACTTC
* *
265281 CTAAAATCACATTTTAACCTCAAAACTTTTCCAAAATTACATTTTTACCCCTAAACTTTTCCAAA
1 CCAAAATCACATTTTAACCTCAAAACTTTTCCAAAATTACATTTTTAACCCTAAACTTTTCCAAA
* *
265346 ATCACATTTTGATCCCAAAACTTC
66 ATCACATTTTGACCCCTAAACTTC
* * * * * *
265370 CCAAAATCATATTTTCACCCCCAAACTTTTCCAAAATCACA-TTTTAACCATCAAACTTTTCCAA
1 CCAAAATCACATTTTAACCTCAAAACTTTTCCAAAATTACATTTTTAACCCT-AAACTTTTCCAA
* *
265434 AATCATAGTTTGACCCCTAAACTTTC
65 AATCACATTTTGACCCCTAAAC-TTC
* * * * *
265460 CCAAAATCACATTTTGATCTCAAAACTTTCCCAAAATTACATTTTTAACCTTAAA-TTCTCCAAA
1 CCAAAATCACATTTTAACCTCAAAACTTTTCCAAAATTACATTTTTAACCCTAAACTTTTCCAAA
265524 A
66 A
265525 CTTCATTTTT
Statistics
Matches: 206, Mismatches: 34, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
88 29 0.14
89 128 0.62
90 40 0.19
91 9 0.04
ACGTcount: A:0.37, C:0.28, G:0.02, T:0.34
Consensus pattern (89 bp):
CCAAAATCACATTTTAACCTCAAAACTTTTCCAAAATTACATTTTTAACCCTAAACTTTTCCAAA
ATCACATTTTGACCCCTAAACTTC
Found at i:265533 original size:59 final size:59
Alignment explanation
Indices: 265127--265524 Score: 387
Period size: 59 Copynumber: 6.7 Consensus size: 59
265117 AGAGGTCTCT
** * * * * ** *
265127 AAACTTTTTAAAAATCATATTTTGACCCC-AAACTTTTCAAAATTACAAATTCACC-CTA
1 AAACTTTTCCAAAATCACATTTTTACCCCTAAACTTTCCAAAATCACATTTTAACCTC-A
* * * * *
265185 AAATTTTTCCAAAATTACATTTTTACCCCTAAACTTTCCAAAATTACATTTTCACCCCA
1 AAACTTTTCCAAAATCACATTTTTACCCCTAAACTTTCCAAAATCACATTTTAACCTCA
* * *
265244 AAACTTTTCCAAAAGCACATTTTTACCCTTAAA-ATTCCTAAAATCACATTTTAACCTCA
1 AAACTTTTCCAAAATCACATTTTTACCCCTAAACTTTCC-AAAATCACATTTTAACCTCA
* *
265303 AAACTTTTCCAAAATTACATTTTTACCCCTAAACTTTTCCAAAATCACATTTTGATCC-CA
1 AAACTTTTCCAAAATCACATTTTTACCCCTAAAC-TTTCCAAAATCACATTTT-AACCTCA
* * * *
265363 AAAC-TTCCCAAAATCATATTTTCACCCCCAAACTTTTCCAAAATCACATTTTAACCATC-
1 AAACTTTTCCAAAATCACATTTTTACCCCTAAAC-TTTCCAAAATCACATTTTAACC-TCA
* * * * *
265422 AAACTTTTCCAAAATCATAGTTTGACCCCTAAACTTTCCCAAAATCACATTTTGATCTCA
1 AAACTTTTCCAAAATCACATTTTTACCCCTAAACTTT-CCAAAATCACATTTTAACCTCA
* * * *
265482 AAACTTTCCCAAAATTACATTTTTAACCTTAAA-TTCTCCAAAA
1 AAACTTTTCCAAAATCACATTTTTACCCCTAAACTT-TCCAAAA
265525 CTTCATTTTT
Statistics
Matches: 287, Mismatches: 41, Indels: 23
0.82 0.12 0.07
Matches are distributed among these distances:
58 30 0.10
59 160 0.56
60 90 0.31
61 7 0.02
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.34
Consensus pattern (59 bp):
AAACTTTTCCAAAATCACATTTTTACCCCTAAACTTTCCAAAATCACATTTTAACCTCA
Found at i:267344 original size:59 final size:59
Alignment explanation
Indices: 267248--267570 Score: 353
Period size: 59 Copynumber: 5.4 Consensus size: 59
267238 ACATTCGAGA
* * * * *
267248 GTAAAATGGTAATTTTTTGGAAGTATCAAGGTCAAAAATGAGAATTTTGGAAGTTCGGGG
1 GTAAAATGGTAA-TTTTTGGAAGTTTCGAGGTTAAAAATGAGATTTTTGGAAGTTTGGGG
* * * * *
267308 GTAAAATTGAAATTTTTGGAAGTTTCGATGTTAAAAATGGGATTTTTGGAAGTTTGAGG
1 GTAAAATGGTAATTTTTGGAAGTTTCGAGGTTAAAAATGAGATTTTTGGAAGTTTGGGG
* * * *
267367 GTAAAATGGTAATTTTTGGAAGGTTC-AGGGTTAAAAAATGGGATTTTAGAAAGTTTGGGG
1 GTAAAATGGTAATTTTTGGAAGTTTCGA-GGTT-AAAAATGAGATTTTTGGAAGTTTGGGG
* * * * ** * * *
267427 GTAAAATGGTATTTTTTAGAAGATTCGGGGGCAAAAATGGGATTTTTTGAAGTTTAGGG
1 GTAAAATGGTAATTTTTGGAAGTTTCGAGGTTAAAAATGAGATTTTTGGAAGTTTGGGG
* * *
267486 GTAAAATGGTAATTTTTTGAAGGTTT-GGGGTTAAAAATGAGATTTTTGGAAGTTTAGGG
1 GTAAAATGGTAATTTTTGGAA-GTTTCGAGGTTAAAAATGAGATTTTTGGAAGTTTGGGG
267545 GTAAAATGGTAATTTTTGGACAGTTT
1 GTAAAATGGTAATTTTTGGA-AGTTT
267571 AAAGACCTCC
Statistics
Matches: 223, Mismatches: 35, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
58 1 0.00
59 159 0.71
60 63 0.28
ACGTcount: A:0.32, C:0.02, G:0.29, T:0.36
Consensus pattern (59 bp):
GTAAAATGGTAATTTTTGGAAGTTTCGAGGTTAAAAATGAGATTTTTGGAAGTTTGGGG
Found at i:267353 original size:30 final size:30
Alignment explanation
Indices: 267261--267570 Score: 196
Period size: 29 Copynumber: 10.4 Consensus size: 30
267251 AAATGGTAAT
* * *
267261 TTTTTGGAAGTATC-AAGGTCAAAAATGAGA
1 TTTTTGGAAGTTTCGAGGGT-AAAAATGGGA
* * * **
267291 ATTTTGGAAG-TTCGGGGGTAAAATTGAAA
1 TTTTTGGAAGTTTCGAGGGTAAAAATGGGA
* *
267320 TTTTTGGAAGTTTCGATGTTAAAAATGGGA
1 TTTTTGGAAGTTTCGAGGGTAAAAATGGGA
*
267350 TTTTTGGAAGTTT-GAGGGT-AAAATGGTAA
1 TTTTTGGAAGTTTCGAGGGTAAAAATGG-GA
*
267379 TTTTTGGAAGGTTC-AGGGTTAAAAAATGGGA
1 TTTTTGGAAGTTTCGAGGG-T-AAAAATGGGA
* * * *
267410 TTTTAGAAAGTTT-GGGGGT-AAAATGGTA
1 TTTTTGGAAGTTTCGAGGGTAAAAATGGGA
* * * *
267438 TTTTTTAGAAGATTCGGGGGCAAAAATGGGA
1 -TTTTTGGAAGTTTCGAGGGTAAAAATGGGA
* * *
267469 TTTTTTGAAGTTTAG-GGGT-AAAATGGTAA
1 TTTTTGGAAGTTTCGAGGGTAAAAATGG-GA
* *
267498 TTTTTTGAAGGTTT-G-GGGTTAAAAATGAGA
1 TTTTTGGAA-GTTTCGAGGG-TAAAAATGGGA
* *
267528 TTTTTGGAAGTTTAG-GGGT-AAAATGGTAA
1 TTTTTGGAAGTTTCGAGGGTAAAAATGG-GA
267557 TTTTTGGACAGTTT
1 TTTTTGGA-AGTTT
267571 AAAGACCTCC
Statistics
Matches: 223, Mismatches: 39, Indels: 36
0.75 0.13 0.12
Matches are distributed among these distances:
28 28 0.13
29 80 0.36
30 80 0.36
31 28 0.13
32 7 0.03
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.36
Consensus pattern (30 bp):
TTTTTGGAAGTTTCGAGGGTAAAAATGGGA
Found at i:267375 original size:119 final size:119
Alignment explanation
Indices: 267248--267570 Score: 386
Period size: 119 Copynumber: 2.7 Consensus size: 119
267238 ACATTCGAGA
* * *
267248 GTAAAATGGTAATTTTTTGGAA-GTATCAAGGTCAAAAATGAGAATTTTGGAAGTTCGGGGGTAA
1 GTAAAATGGTAATTTTTTGGAAGGT-TCAGGGTAAAAAATGAGAATTTTGGAAGTTTGGGGGTAA
* * * **
267312 AATTGAAATTTTTGGAAGTTTCGATGTTAAAAATGGGATTTTTGGAAGTTT-GAGG
65 AATGGTAATTTTTGGAAGTTTCGAGGGCAAAAATGGGATTTTTGGAAGTTTAG-GG
* *
267367 GTAAAATGGTAA-TTTTTGGAAGGTTCAGGGTTAAAAAATG-GGATTTTAGAAAGTTTGGGGGTA
1 GTAAAATGGTAATTTTTTGGAAGGTTCAGGG-TAAAAAATGAGAATTTT-GGAAGTTTGGGGGTA
* * * * *
267430 AAATGGTATTTTTTAGAAGATTCGGGGGCAAAAATGGGATTTTTTGAAGTTTAGGG
64 AAATGGTAATTTTTGGAAGTTTCGAGGGCAAAAATGGGATTTTTGGAAGTTTAGGG
** * * *
267486 GTAAAATGGTAATTTTTT-GAAGGTTTGGGGTTAAAAATGAGATTTTTGGAAGTTTAGGGGTAAA
1 GTAAAATGGTAATTTTTTGGAAGGTTCAGGGTAAAAAATGAGAATTTTGGAAGTTTGGGGGTAAA
267550 ATGGTAATTTTTGGACAGTTT
66 ATGGTAATTTTTGGA-AGTTT
267571 AAAGACCTCC
Statistics
Matches: 172, Mismatches: 25, Indels: 14
0.82 0.12 0.07
Matches are distributed among these distances:
118 56 0.33
119 110 0.64
120 6 0.03
ACGTcount: A:0.32, C:0.02, G:0.29, T:0.36
Consensus pattern (119 bp):
GTAAAATGGTAATTTTTTGGAAGGTTCAGGGTAAAAAATGAGAATTTTGGAAGTTTGGGGGTAAA
ATGGTAATTTTTGGAAGTTTCGAGGGCAAAAATGGGATTTTTGGAAGTTTAGGG
Found at i:267571 original size:30 final size:28
Alignment explanation
Indices: 267282--267571 Score: 192
Period size: 30 Copynumber: 9.8 Consensus size: 28
267272 ATCAAGGTCA
**
267282 AAAATGAGAA-TTTTGGAAGTTCGGGGGT
1 AAAATG-GAATTTTTGGAAGTTTAGGGGT
* * * *
267310 AAAATTGAAATTTTTGGAAGTTTCGATGTT
1 AAAA-TGGAATTTTTGGAAGTTTAG-GGGT
*
267340 AAAAATGGGATTTTTGGAAGTTT-GAGGGT
1 -AAAATGGAATTTTTGGAAGTTTAG-GGGT
* *
267369 AAAATGGTAATTTTTGGAAGGTTCAGGGTT
1 AAAATGG-AATTTTTGGAA-GTTTAGGGGT
* * * *
267399 AAAAAATGGGATTTTAGAAAGTTTGGGGGT
1 --AAAATGGAATTTTTGGAAGTTTAGGGGT
* * ** *
267429 AAAATGGTATTTTTTAGAAGATTCGGGGGCA
1 AAAATGG-AATTTTTGGAAG-TTTAGGGG-T
* *
267460 AAAATGGGATTTTTTGAAGTTTAGGGGT
1 AAAATGGAATTTTTGGAAGTTTAGGGGT
*
267488 AAAATGGTAATTTTTTGAAGGTTT-GGGGTT
1 AAAATGG-AATTTTTGGAA-GTTTAGGGG-T
267518 AAAAAT-GAGATTTTTGGAAGTTTAGGGGT
1 -AAAATGGA-ATTTTTGGAAGTTTAGGGGT
267547 AAAATGGTAATTTTTGGACAGTTTA
1 AAAATGG-AATTTTTGGA-AGTTTA
267572 AAGACCTCCC
Statistics
Matches: 208, Mismatches: 33, Indels: 40
0.74 0.12 0.14
Matches are distributed among these distances:
28 32 0.15
29 71 0.34
30 73 0.35
31 25 0.12
32 7 0.03
ACGTcount: A:0.32, C:0.02, G:0.30, T:0.36
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAGTTTAGGGGT
Done.