Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015470.1 Corchorus capsularis cultivar CVL-1 contig15491, 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: 200050
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:4086 original size:24 final size:24
Alignment explanation
Indices: 4059--4107 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
4049 TATAACTGTC
4059 TATGAAAAATTGAAAATAATGGAT
1 TATGAAAAATTGAAAATAATGGAT
*
4083 TATGAAAAATTGAAAATCATGGAT
1 TATGAAAAATTGAAAATAATGGAT
4107 T
1 T
4108 GATGTGAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.51, C:0.02, G:0.16, T:0.31
Consensus pattern (24 bp):
TATGAAAAATTGAAAATAATGGAT
Found at i:4373 original size:25 final size:23
Alignment explanation
Indices: 4345--4396 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
4335 CAGTCCAAAC
* *
4345 TATATACATAATATTTTTTGTTAAT
1 TATAT-CATAAAATTTATT-TTAAT
*
4370 TATATGATAAAATTTATTTTAAT
1 TATATCATAAAATTTATTTTAAT
4393 TATA
1 TATA
4397 CAATTCGATC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 9 0.38
24 10 0.42
25 5 0.21
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (23 bp):
TATATCATAAAATTTATTTTAAT
Found at i:16399 original size:33 final size:31
Alignment explanation
Indices: 16320--16416 Score: 97
Period size: 32 Copynumber: 3.0 Consensus size: 31
16310 GTTATTTTGG
*
16320 CACCATGGTCGGTCGCAATCCGCGCGCGACC
1 CACCATGGCCGGTCGCAATCCGCGCGCGACC
* * *
16351 CAGCCATGGCGGGTCGCTATCCG-GTCGTGACC
1 CA-CCATGGCCGGTCGCAATCCGCG-CGCGACC
* *
16383 AACACCATGGCCGGTCGCAATCCGCACGCAACC
1 --CACCATGGCCGGTCGCAATCCGCGCGCGACC
16416 C
1 C
16417 GGCTTTGTTC
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
31 4 0.08
32 23 0.44
33 23 0.44
34 2 0.04
ACGTcount: A:0.19, C:0.40, G:0.28, T:0.13
Consensus pattern (31 bp):
CACCATGGCCGGTCGCAATCCGCGCGCGACC
Found at i:17439 original size:22 final size:22
Alignment explanation
Indices: 17414--17460 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
17404 CGAAAAAACC
17414 CAAACCCGAAAAAACCCGAACT
1 CAAACCCGAAAAAACCCGAACT
* * *
17436 CAAACCTGAAAAAACCTGAATT
1 CAAACCCGAAAAAACCCGAACT
17458 CAA
1 CAA
17461 TACAAATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.51, C:0.30, G:0.09, T:0.11
Consensus pattern (22 bp):
CAAACCCGAAAAAACCCGAACT
Found at i:17682 original size:32 final size:32
Alignment explanation
Indices: 17639--17750 Score: 127
Period size: 32 Copynumber: 3.5 Consensus size: 32
17629 TCAATCCGAG
*
17639 CCCGAAACCGAATTAACCTGACCCAAAATTAA
1 CCCGAACCCGAATTAACCTGACCCAAAATTAA
* * * * *
17671 TCCGAACCCGAATCAACATGACTCAAATTTAA
1 CCCGAACCCGAATTAACCTGACCCAAAATTAA
* *
17703 CCCGAACCCGAATTATCCCGACCC-AAATTCAA
1 CCCGAACCCGAATTAACCTGACCCAAAATT-AA
*
17735 CCCGAACCCGACTTAA
1 CCCGAACCCGAATTAA
17751 ATCCGAACCT
Statistics
Matches: 64, Mismatches: 15, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
31 4 0.06
32 60 0.94
ACGTcount: A:0.38, C:0.35, G:0.10, T:0.17
Consensus pattern (32 bp):
CCCGAACCCGAATTAACCTGACCCAAAATTAA
Found at i:17738 original size:16 final size:15
Alignment explanation
Indices: 17649--17739 Score: 56
Period size: 16 Copynumber: 5.7 Consensus size: 15
17639 CCCGAAACCG
*
17649 AATTAACCTGACCCAA
1 AATTAACCCGACCC-A
* *
17665 AATTAATCCGAACCCG
1 AATTAACCCG-ACCCA
* ** *
17681 AATCAACATGACTCA
1 AATTAACCCGACCCA
*
17696 AATTTAACCCGAACCCG
1 AA-TTAACCCG-ACCCA
*
17713 AATTATCCCGACCCA
1 AATTAACCCGACCCA
17728 AATTCAACCCGA
1 AATT-AACCCGA
17740 ACCCGACTTA
Statistics
Matches: 54, Mismatches: 17, Indels: 8
0.68 0.22 0.10
Matches are distributed among these distances:
15 13 0.24
16 32 0.59
17 9 0.17
ACGTcount: A:0.40, C:0.33, G:0.09, T:0.19
Consensus pattern (15 bp):
AATTAACCCGACCCA
Found at i:24394 original size:13 final size:13
Alignment explanation
Indices: 24376--24402 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
24366 CCACTTGACA
24376 ACATTAAAATTAT
1 ACATTAAAATTAT
24389 ACATTAAAATTAT
1 ACATTAAAATTAT
24402 A
1 A
24403 TTCATTGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (13 bp):
ACATTAAAATTAT
Found at i:25126 original size:23 final size:23
Alignment explanation
Indices: 25099--25142 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
25089 TAATACAATT
* *
25099 AATTTCACCAAAAAGAAAATTAG
1 AATTTAACCAAAAACAAAATTAG
*
25122 AATTTAACCCAAAACAAAATT
1 AATTTAACCAAAAACAAAATT
25143 TTTATACAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.57, C:0.16, G:0.05, T:0.23
Consensus pattern (23 bp):
AATTTAACCAAAAACAAAATTAG
Found at i:36558 original size:27 final size:27
Alignment explanation
Indices: 36517--36574 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
36507 GGACCAAAAG
* * *
36517 CAAGTGGCCTTTAATAGTCAGCAGGCC
1 CAAGTAGCCTATAATAGTCAACAGGCC
36544 CAAGTAGCCTATAATAGTCAACAGGCC
1 CAAGTAGCCTATAATAGTCAACAGGCC
36571 CAAG
1 CAAG
36575 GAAGCCTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.26, G:0.22, T:0.19
Consensus pattern (27 bp):
CAAGTAGCCTATAATAGTCAACAGGCC
Found at i:36791 original size:130 final size:130
Alignment explanation
Indices: 36535--36809 Score: 345
Period size: 130 Copynumber: 2.1 Consensus size: 130
36525 CTTTAATAGT
* *
36535 CAGCAGGCCCAAGTAGCCTATAATAGTCAACAGGCCCAAGGAAGCCTTACCCTTGAATAATCAAA
1 CAGCAGGCCCAAGTAGCCTATAATAGTCAACAGACCCAAGGAAGCCTTACCCTCG-A-AATCAAA
* * * * * * **
36600 ATTAAACTTTGATCGCATTTGTTGGGAGGGTTTTAATTTCCATGCTCCTGGTCTAAAAGAGATTA
64 ATTAAACCTTGATCACATTTGTTAGGAGGGCTTTAACTTCCACGCTCCCAGTCTAAAAGAGATTA
36665 GG
129 GG
* * * * *
36667 CAGCAGACCCAAGTGGCCTATAATTGTCAGCATACCCAAGGAAGCCTTACCCTCG-AATCAAAAT
1 CAGCAGGCCCAAGTAGCCTATAATAGTCAACAGACCCAAGGAAGCCTTACCCTCGAAATCAAAAT
* *
36731 TAAACCCTTGATCATATTTGTTAGGAGGGCTTTAACTTCCACGCTCCCAGTCTGAAAGAGATTAG
66 TAAA-CCTTGATCACATTTGTTAGGAGGGCTTTAACTTCCACGCTCCCAGTCTAAAAGAGATTAG
*
36796 T
130 G
*
36797 TAGCAGGCCCAAG
1 CAGCAGGCCCAAG
36810 GAAGTCTTAT
Statistics
Matches: 122, Mismatches: 20, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
129 13 0.11
130 61 0.50
132 48 0.39
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.25
Consensus pattern (130 bp):
CAGCAGGCCCAAGTAGCCTATAATAGTCAACAGACCCAAGGAAGCCTTACCCTCGAAATCAAAAT
TAAACCTTGATCACATTTGTTAGGAGGGCTTTAACTTCCACGCTCCCAGTCTAAAAGAGATTAGG
Found at i:37046 original size:252 final size:250
Alignment explanation
Indices: 36718--37266 Score: 886
Period size: 252 Copynumber: 2.2 Consensus size: 250
36708 AAGCCTTACC
*
36718 CTCGAATCAAAATTAAACCCTTGATCATATTTGTTAGG-AGGGCTTTAACTTCCACGCTCCCAGT
1 CTCGAATCAAAATTAAACCCTTAATCATATTTGTT-GGAAGGGCTTTAACTTCCACGCTCCCAGT
* * **
36782 CTGAAAGAGATTAGTTAGCAGGCCCAAGGAAGTCTTATCCTTGAATAATCTTGAATCAAAATTAA
65 CTGAAAGAGATTAGTTAGCAGGCCCAAGAAAGCCTTATCCTCAAATAATCTTGAATCAAAATTAA
36847 ACCCTTGATATATTTGTTAGGAGGGCTTTAATTTCCACGCTCCCAGACTGAAAGAGATTAGTCAG
130 ACCCTTGATATATTTGTTAGGAGGGCTTTAATTTCCACGCTCCCAGACTGAAAGAGATTAGTCAG
* *
36912 CAAGCCCAAGTGGCCTATAATAGTTAACAGGCCCAAGGAAACTCTACCCTT-GAATAAT
195 CAAGCCCAAGTGGCCTATAATAATTAACAGGCCCAAAGAAA--CTA-CCTTCGAATAAT
*
36970 CTCGAATCAAAATTAAACCCTTAATCGTATTTGTTGGAAGGGCTTTAACTTCCACGCTCCCAGTC
1 CTCGAATCAAAATTAAACCCTTAATCATATTTGTTGGAAGGGCTTTAACTTCCACGCTCCCAGTC
*
37035 TGAAAGAGATTAGTTAGCAGGCCCAAGAAAGCCTTATCCTCAAATAATCTTGAATTAAAATTAAA
66 TGAAAGAGATTAGTTAGCAGGCCCAAGAAAGCCTTATCCTCAAATAATCTTGAATCAAAATTAAA
* * ** *
37100 CCCTTGATATATTTGTTGGGAGGGTTTTAATTTCCACGCTCCCAGTGTGAAAGAGATTAGTCAGT
131 CCCTTGATATATTTGTTAGGAGGGCTTTAATTTCCACGCTCCCAGACTGAAAGAGATTAGTCAGC
* *
37165 AGGCCCAAGTGGCCTATAATAATTAATAGGCCCAAAGAAACTACCTTCGAATAAT
196 AAGCCCAAGTGGCCTATAATAATTAACAGGCCCAAAGAAACTACCTTCGAATAAT
* *
37220 CTCGAATCAAAATTAGACCCTTAATCATATTTGTTGGAAGGACTTTA
1 CTCGAATCAAAATTAAACCCTTAATCATATTTGTTGGAAGGGCTTTA
37267 TTTTTCACGC
Statistics
Matches: 276, Mismatches: 19, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
249 4 0.01
250 54 0.20
251 2 0.01
252 216 0.78
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (250 bp):
CTCGAATCAAAATTAAACCCTTAATCATATTTGTTGGAAGGGCTTTAACTTCCACGCTCCCAGTC
TGAAAGAGATTAGTTAGCAGGCCCAAGAAAGCCTTATCCTCAAATAATCTTGAATCAAAATTAAA
CCCTTGATATATTTGTTAGGAGGGCTTTAATTTCCACGCTCCCAGACTGAAAGAGATTAGTCAGC
AAGCCCAAGTGGCCTATAATAATTAACAGGCCCAAAGAAACTACCTTCGAATAAT
Found at i:37059 original size:140 final size:139
Alignment explanation
Indices: 36793--37061 Score: 407
Period size: 140 Copynumber: 1.9 Consensus size: 139
36783 TGAAAGAGAT
* * * * *
36793 TAGTTAGCAGGCCCAAGGAAGTCTTATCCTTGAATAATCTTGAATCAAAATTAAACCCTTGATAT
1 TAGTTAACAGGCCCAAGGAACTCTTACCCTTGAATAATCTCGAATCAAAATTAAACCCTTAATAT
*
36858 ATTTGTTAGGAGGGCTTTAATTTCCACGCTCCCAGACTGAAAGAGATTAGTCAGCAAGCCCAAGT
66 ATTTGTTAGGAGGGCTTTAACTTCCACGCTCCCAGACTGAAAGAGATTAGTCAGCAAGCCCAAGT
36923 GGCCTATAA
131 GGCCTATAA
36932 TAGTTAACAGGCCCAAGGAAACTC-TACCCTTGAATAATCTCGAATCAAAATTAAACCCTTAATC
1 TAGTTAACAGGCCCAAGG-AACTCTTACCCTTGAATAATCTCGAATCAAAATTAAACCCTTAAT-
* * * *
36996 GTATTTGTT-GGAAGGGCTTTAACTTCCACGCTCCCAGTCTGAAAGAGATTAGTTAGCAGGCCCA
64 ATATTTGTTAGG-AGGGCTTTAACTTCCACGCTCCCAGACTGAAAGAGATTAGTCAGCAAGCCCA
37060 AG
128 AG
37062 AAAGCCTTAT
Statistics
Matches: 117, Mismatches: 10, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
139 55 0.47
140 62 0.53
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (139 bp):
TAGTTAACAGGCCCAAGGAACTCTTACCCTTGAATAATCTCGAATCAAAATTAAACCCTTAATAT
ATTTGTTAGGAGGGCTTTAACTTCCACGCTCCCAGACTGAAAGAGATTAGTCAGCAAGCCCAAGT
GGCCTATAA
Found at i:37154 original size:112 final size:113
Alignment explanation
Indices: 36964--37173 Score: 323
Period size: 112 Copynumber: 1.9 Consensus size: 113
36954 TCTACCCTTG
*
36964 AATAATCTCGAATCAAAATTAAACCCTTAATCGTATTTGTTGGAAGGGCTTTAACTTCCACGCTC
1 AATAATCTCGAATCAAAATTAAACCCTTAATCATATTTGTTGGAAGGGCTTTAACTTCCACGCTC
*
37029 CCAGTCTGAAAGAGATTAGTTAGCAGGCCCAAGAAAGCCTTATCCTCA
66 CCAGTCTGAAAGAGATTAGTCAGCAGGCCCAAGAAAGCCTTATCCTCA
* * * * * *
37077 AATAATCTTGAATTAAAATTAAACCCTTGAT-ATATTTGTTGGGAGGGTTTTAATTTCCACGCTC
1 AATAATCTCGAATCAAAATTAAACCCTTAATCATATTTGTTGGAAGGGCTTTAACTTCCACGCTC
* *
37141 CCAGTGTGAAAGAGATTAGTCAGTAGGCCCAAG
66 CCAGTCTGAAAGAGATTAGTCAGCAGGCCCAAG
37174 TGGCCTATAA
Statistics
Matches: 87, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
112 59 0.68
113 28 0.32
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.30
Consensus pattern (113 bp):
AATAATCTCGAATCAAAATTAAACCCTTAATCATATTTGTTGGAAGGGCTTTAACTTCCACGCTC
CCAGTCTGAAAGAGATTAGTCAGCAGGCCCAAGAAAGCCTTATCCTCA
Found at i:43892 original size:22 final size:22
Alignment explanation
Indices: 43858--43914 Score: 84
Period size: 21 Copynumber: 2.7 Consensus size: 22
43848 AATGTAAGTT
43858 TATTTTTTT-CTTTTC-AAAAC
1 TATTTTTTTACTTTTCAAAAAC
43878 TACTTTTTTTAC-TTTCAAAAAC
1 TA-TTTTTTTACTTTTCAAAAAC
43900 TATTTTTTTACTTTT
1 TATTTTTTTACTTTT
43915 TATTTTCCAC
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
20 2 0.06
21 20 0.61
22 11 0.33
ACGTcount: A:0.25, C:0.14, G:0.00, T:0.61
Consensus pattern (22 bp):
TATTTTTTTACTTTTCAAAAAC
Found at i:44351 original size:13 final size:13
Alignment explanation
Indices: 44335--44360 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44325 AAAGTCAAAC
44335 ATAAAATCTGAGA
1 ATAAAATCTGAGA
44348 ATAAAATCTGAGA
1 ATAAAATCTGAGA
44361 GCTCATCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.15, T:0.23
Consensus pattern (13 bp):
ATAAAATCTGAGA
Found at i:45141 original size:89 final size:89
Alignment explanation
Indices: 45036--45204 Score: 311
Period size: 89 Copynumber: 1.9 Consensus size: 89
45026 ATTCTTTTAG
*
45036 TAGAGAGTAGAGACACATGGAACTCATAACTTTCTTGAATTGTGCACCCGTTTAGAGATTTACTT
1 TAGAGAGCAGAGACACATGGAACTCATAACTTTCTTGAATTGTGCACCCGTTTAGAGATTTACTT
45101 GTGCACTTTGCAAATCTTTGTCAA
66 GTGCACTTTGCAAATCTTTGTCAA
45125 TAGAGAGCAGAGACACATGGAACTCATAACTTTCTTGAATTGTGCACCCGTTTAGAGATTTACTT
1 TAGAGAGCAGAGACACATGGAACTCATAACTTTCTTGAATTGTGCACCCGTTTAGAGATTTACTT
**
45190 GTGCTTTTTGCAAAT
66 GTGCACTTTGCAAAT
45205 ATATTATAAA
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 77 1.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.34
Consensus pattern (89 bp):
TAGAGAGCAGAGACACATGGAACTCATAACTTTCTTGAATTGTGCACCCGTTTAGAGATTTACTT
GTGCACTTTGCAAATCTTTGTCAA
Found at i:45869 original size:180 final size:176
Alignment explanation
Indices: 45523--45870 Score: 414
Period size: 180 Copynumber: 2.0 Consensus size: 176
45513 TTATTCTATG
* *
45523 ATCTACAACTTTTATGAAGGACTCAAAAACTAAATTTAATGTTTCAAGTATAAAAAATGTTTCCA
1 ATCTACAACTTTTATGAAGGACTCAAAAACTAAATTTAATGTTTAAAGTAAAAAAAATGTTTCCA
* * * * *
45588 ACAAATTAGTTGTTTCGATTAACGGGAATGGACGGTCCACTTAATATTACTTAACTTTTGCTTCG
66 ACAAATTAGTTGTTTCGATGAACGAGAATGGACGGTCCACTTAATATTACATAACTTTTGCTCCA
* *
45653 GATATCTGATTGAGATGATTCAAGTGTCTCTTAAAAGGTTGTCATT
131 GATATCTGATTGAGATAATTCAAGTATCTCTTAAAAGGTTGTCATT
* *
45699 ATCTACAACTTTTATGAAGGACTCAAAAGCTAAGTTTAATGTTTAAACTGTTTTAAAAAAAAT-T
1 ATCTACAACTTTTATGAAGGACTCAAAAACTAAATTTAATGTTTAAA--G---TAAAAAAAATGT
* * * * * * *
45763 CTTACGAA-GAATTAGTTGTTT-GGTGAGCGAGAATGTACGGTCTACTTAATATTACATAATTTT
61 -TT-CCAACAAATTAGTTGTTTCGATGAACGAGAATGGACGGTCCACTTAATATTACATAACTTT
* * * *
45826 TGCTCCATATATTTTATTGAGATAATTTAAGTATCTCTTAAAAGG
124 TGCTCCAGATATCTGATTGAGATAATTCAAGTATCTCTTAAAAGG
45871 CTGTTCCATG
Statistics
Matches: 143, Mismatches: 22, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
176 44 0.31
178 1 0.01
180 72 0.50
181 23 0.16
182 3 0.02
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (176 bp):
ATCTACAACTTTTATGAAGGACTCAAAAACTAAATTTAATGTTTAAAGTAAAAAAAATGTTTCCA
ACAAATTAGTTGTTTCGATGAACGAGAATGGACGGTCCACTTAATATTACATAACTTTTGCTCCA
GATATCTGATTGAGATAATTCAAGTATCTCTTAAAAGGTTGTCATT
Found at i:47309 original size:31 final size:31
Alignment explanation
Indices: 47253--47412 Score: 169
Period size: 31 Copynumber: 5.1 Consensus size: 31
47243 ACGGTGTCCG
* * * *
47253 ACGTGGCATGCCACATGCACGAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* *
47284 ATGTGTCACGCCACGTGTACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* *
47315 ACGTGTCATGCCACGTGTACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
** * *
47346 ACGTGGCACATCACGTGTACAAATAAAGTGTC
1 ACGTGGCACGCCACGTGTACCAA-AAAGTGAC
* *
47378 ACGTGGCATGCCACATGTA-CAGAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCA-AAAAGTGAC
47409 ACGT
1 ACGT
47413 CACATGCCAC
Statistics
Matches: 107, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
31 84 0.79
32 23 0.21
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.18
Consensus pattern (31 bp):
ACGTGGCACGCCACGTGTACCAAAAAGTGAC
Found at i:47319 original size:19 final size:19
Alignment explanation
Indices: 47295--47350 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
47285 TGTGTCACGC
47295 CACGTGTACCAAAAAGTGA
1 CACGTGTACCAAAAAGTGA
*
47314 CACGTGT--C----A-TGC
1 CACGTGTACCAAAAAGTGA
47326 CACGTGTACCAAAAAGTGA
1 CACGTGTACCAAAAAGTGA
47345 CACGTG
1 CACGTG
47351 GCACATCACG
Statistics
Matches: 28, Mismatches: 2, Indels: 14
0.64 0.05 0.32
Matches are distributed among these distances:
12 9 0.32
13 1 0.04
14 1 0.04
17 1 0.04
18 1 0.04
19 15 0.54
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.18
Consensus pattern (19 bp):
CACGTGTACCAAAAAGTGA
Found at i:47361 original size:62 final size:63
Alignment explanation
Indices: 47253--47412 Score: 207
Period size: 62 Copynumber: 2.6 Consensus size: 63
47243 ACGGTGTCCG
* * * * * *
47253 ACGTGGCATGCCACATGCACGAAAAAGTGACATGTGTCACGCCACGTGTACCAA-AAAGTGAC
1 ACGTGGCATGCCACATGTACCAAAAAGTGACACGTGGCACACCACGTGTACAAATAAAGTGAC
* * * *
47315 ACGTGTCATGCCACGTGTACCAAAAAGTGACACGTGGCACATCACGTGTACAAATAAAGTGTC
1 ACGTGGCATGCCACATGTACCAAAAAGTGACACGTGGCACACCACGTGTACAAATAAAGTGAC
47378 ACGTGGCATGCCACATGTA-CAGAAAAGTGACACGT
1 ACGTGGCATGCCACATGTACCA-AAAAGTGACACGT
47413 CACATGCCAC
Statistics
Matches: 84, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
62 47 0.56
63 37 0.44
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.18
Consensus pattern (63 bp):
ACGTGGCATGCCACATGTACCAAAAAGTGACACGTGGCACACCACGTGTACAAATAAAGTGAC
Found at i:47419 original size:31 final size:30
Alignment explanation
Indices: 47253--47432 Score: 166
Period size: 31 Copynumber: 5.8 Consensus size: 30
47243 ACGGTGTCCG
* * *
47253 ACGTGGCATGCCACATGCACGAAAAAGTGAC
1 ACGTGACATGCCACGTGTAC-AAAAAGTGAC
* * *
47284 ATGTGTCACGCCACGTGTACCAAAAAGTGAC
1 ACGTGACATGCCACGTGTA-CAAAAAGTGAC
*
47315 ACGTGTCATGCCACGTGTACCAAAAAGTGAC
1 ACGTGACATGCCACGTGTA-CAAAAAGTGAC
*
47346 ACGTGGCACAT--CACGTGTACAAATAAAGTGTC
1 ACGT-G-ACATGCCACGTGTAC-AA-AAAGTGAC
* *
47378 ACGTGGCATGCCACATGTACAGAAAAGTGAC
1 ACGTGACATGCCACGTGTACA-AAAAGTGAC
* *
47409 ACGTCACATGCCACGTGCACAAAA
1 ACGTGACATGCCACGTGTACAAAA
47433 GGATGCGTGC
Statistics
Matches: 125, Mismatches: 16, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
30 7 0.06
31 93 0.74
32 22 0.18
33 3 0.02
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.17
Consensus pattern (30 bp):
ACGTGACATGCCACGTGTACAAAAAGTGAC
Found at i:47424 original size:63 final size:62
Alignment explanation
Indices: 47253--47432 Score: 197
Period size: 63 Copynumber: 2.9 Consensus size: 62
47243 ACGGTGTCCG
* * ** * *
47253 ACGTGGCATGCCACATGCAC-GAAAAAGTGACATGTGTCACGCCACGTGTACCAAAAAGTGAC
1 ACGTGGCATGCCACATGTACAG-AAAAGTGACACGTCACATGCCACGTGTACAAAAAAGTGAC
* * *
47315 ACGTGTCATGCCACGTGTACCA-AAAAGTGACACGTGGCACAT--CACGTGTACAAATAAAGTGT
1 ACGTGGCATGCCACATGTA-CAGAAAAGTGACACGT--CACATGCCACGTGTACAAA-AAAGTGA
47377 C
62 C
*
47378 ACGTGGCATGCCACATGTACAGAAAAGTGACACGTCACATGCCACGTGCACAAAA
1 ACGTGGCATGCCACATGTACAGAAAAGTGACACGTCACATGCCACGTGTACAAAA
47433 GGATGCGTGC
Statistics
Matches: 98, Mismatches: 12, Indels: 16
0.78 0.10 0.13
Matches are distributed among these distances:
61 5 0.05
62 42 0.43
63 49 0.50
64 2 0.02
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.17
Consensus pattern (62 bp):
ACGTGGCATGCCACATGTACAGAAAAGTGACACGTCACATGCCACGTGTACAAAAAAGTGAC
Found at i:51588 original size:15 final size:15
Alignment explanation
Indices: 51568--51604 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
51558 ATCTGAAATA
*
51568 CTTCAGGTATTGATT
1 CTTCAGATATTGATT
*
51583 CTTCAGATCTTGATT
1 CTTCAGATATTGATT
51598 CTTCAGA
1 CTTCAGA
51605 GTTTTCTGCT
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:0.22, C:0.19, G:0.16, T:0.43
Consensus pattern (15 bp):
CTTCAGATATTGATT
Found at i:51616 original size:15 final size:16
Alignment explanation
Indices: 51598--51627 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
51588 GATCTTGATT
51598 CTTCAGAG-TTTTCTG
1 CTTCAGAGCTTTTCTG
51613 CTTCAGAGCTTTTCT
1 CTTCAGAGCTTTTCT
51628 ACCTTCTGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.47
Consensus pattern (16 bp):
CTTCAGAGCTTTTCTG
Found at i:52844 original size:17 final size:17
Alignment explanation
Indices: 52822--52861 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
52812 TTTTTATTAT
**
52822 TAAAAAATAAATTTCAA
1 TAAAAAATAAATTAAAA
*
52839 TAAAAAATATATTAAAA
1 TAAAAAATAAATTAAAA
52856 TAAAAA
1 TAAAAA
52862 TATTAAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (17 bp):
TAAAAAATAAATTAAAA
Found at i:52866 original size:14 final size:15
Alignment explanation
Indices: 52842--52870 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
52832 ATTTCAATAA
52842 AAAATATATTAAAAT
1 AAAATATATTAAAAT
52857 AAAA-ATATTAAAAT
1 AAAATATATTAAAAT
52871 TTTATGCCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAAATATATTAAAAT
Found at i:55598 original size:25 final size:26
Alignment explanation
Indices: 55564--55615 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
55554 GGCATCAGAC
*
55564 ATGAAATGCGGCGCAAC-ACAACACA
1 ATGAAATGCGGCGCAACAACAAAACA
* *
55589 ATGAGATGCGGTGCAACAACAAAACA
1 ATGAAATGCGGCGCAACAACAAAACA
55615 A
1 A
55616 GCCTAACACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.10
Consensus pattern (26 bp):
ATGAAATGCGGCGCAACAACAAAACA
Found at i:55876 original size:27 final size:27
Alignment explanation
Indices: 55808--55878 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
55798 TGCTAAATTG
55808 CCGCAACTAGCCAAAATTACAAAAACC
1 CCGCAACTAGCCAAAATTACAAAAACC
* * *
55835 CCGTAACTAGCCAAAATTGCAAGAACC
1 CCGCAACTAGCCAAAATTACAAAAACC
* * *
55862 CTGCAACAAGACAAAAT
1 CCGCAACTAGCCAAAAT
55879 CACCAAGGCA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.46, C:0.30, G:0.11, T:0.13
Consensus pattern (27 bp):
CCGCAACTAGCCAAAATTACAAAAACC
Found at i:56570 original size:22 final size:23
Alignment explanation
Indices: 56545--56592 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
56535 AATATGTAAA
*
56545 ATATTTTAT-TAAATTAA-AATAT
1 ATATTATATGTAAA-TAAGAATAT
56567 ATA-TATATGTAAATAAGAATAT
1 ATATTATATGTAAATAAGAATAT
56589 ATAT
1 ATAT
56593 ATGTAAGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (23 bp):
ATATTATATGTAAATAAGAATAT
Found at i:56634 original size:20 final size:19
Alignment explanation
Indices: 56605--56657 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
56595 GTAAGAATTT
56605 TATTTTAATATATAATATA
1 TATTTTAATATATAATATA
*
56624 TATTATTAATATGTAATATA
1 TATT-TTAATATATAATATA
*
56644 TATGTGTAATATAT
1 TAT-TTTAATATAT
56658 TCAAACCGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 4 0.14
20 24 0.83
21 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (19 bp):
TATTTTAATATATAATATA
Found at i:61234 original size:20 final size:21
Alignment explanation
Indices: 61209--61249 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
61199 GAATTGTGGC
61209 ATTGTG-AAATTGATTTTGGG
1 ATTGTGAAAATTGATTTTGGG
*
61229 ATTGTGAAAATTGGTTTTGGG
1 ATTGTGAAAATTGATTTTGGG
61250 GACTTTGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (21 bp):
ATTGTGAAAATTGATTTTGGG
Found at i:73831 original size:2 final size:2
Alignment explanation
Indices: 73826--73850 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
73816 TTTGTTATGA
73826 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 A
73851 AAAGTACGAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:73914 original size:31 final size:31
Alignment explanation
Indices: 73879--73944 Score: 107
Period size: 31 Copynumber: 2.1 Consensus size: 31
73869 AACTTTATGT
*
73879 TTTCCGATTGTACCCTTATTTTT-AAAATATA
1 TTTCCAATTGTACCCTT-TTTTTAAAAATATA
73910 TTTCCAATTGTACCCTTTTTTTAAAAATATA
1 TTTCCAATTGTACCCTTTTTTTAAAAATATA
73941 TTTC
1 TTTC
73945 TAAATTGCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
30 5 0.15
31 28 0.85
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.50
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTTTTTTAAAAATATA
Found at i:74162 original size:37 final size:38
Alignment explanation
Indices: 74089--74162 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 38
74079 TTATTTAATT
* * * *
74089 ATTTTGCCTTTTGTCTTTGTTTCCGATCGTTGTATTTA
1 ATTTTGCCTTTTGTCTTCGTCTCCGAACGTTCTATTTA
*
74127 ATTTTGCTTTTTGTCTTCGTCTCC-AACGTTCTATTT
1 ATTTTGCCTTTTGTCTTCGTCTCCGAACGTTCTATTT
74163 GGGCTTAGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
37 10 0.32
38 21 0.68
ACGTcount: A:0.11, C:0.19, G:0.14, T:0.57
Consensus pattern (38 bp):
ATTTTGCCTTTTGTCTTCGTCTCCGAACGTTCTATTTA
Found at i:74248 original size:22 final size:22
Alignment explanation
Indices: 74220--74340 Score: 111
Period size: 22 Copynumber: 5.5 Consensus size: 22
74210 TGGTCCAATT
74220 TCAAAATTTCA-AAACGAGGTTA
1 TCAAAATTTCATAAA-GAGGTTA
* * * *
74242 TCAAAATTACATAATGTGATTA
1 TCAAAATTTCATAAAGAGGTTA
* * *
74264 TCAAAGTTTCATAGAG-GAGTCA
1 TCAAAATTTCATAAAGAG-GTTA
* * *
74286 ACAAAATTTGATAGAGAGGTTA
1 TCAAAATTTCATAAAGAGGTTA
74308 TCAAAATTTCATAAAGAGGTTA
1 TCAAAATTTCATAAAGAGGTTA
*
74330 TCAAATTTTCA
1 TCAAAATTTCA
74341 AAGTGTATGA
Statistics
Matches: 78, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
21 1 0.01
22 74 0.95
23 3 0.04
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (22 bp):
TCAAAATTTCATAAAGAGGTTA
Found at i:74516 original size:22 final size:22
Alignment explanation
Indices: 74491--74609 Score: 95
Period size: 22 Copynumber: 5.4 Consensus size: 22
74481 AGTTTAGTTT
74491 TCAAAATTTCATAAGAGGGTTA
1 TCAAAATTTCATAAGAGGGTTA
* *
74513 TCAAAATTTCAT-AGTA-TGTAGA
1 TCAAAATTTCATAAG-AGGGT-TA
*
74535 TCAAAATTTCATAAG-GAGATTA
1 TCAAAATTTCATAAGAG-GGTTA
*
74557 ACAAAATTTCATAATGA-GGTTA
1 TCAAAATTTCATAA-GAGGGTTA
** *
74579 TCAAAAAATCAT-AGGGAGGTTA
1 TCAAAATTTCATAAGAG-GGTTA
74601 TCAAAATTT
1 TCAAAATTT
74610 GTCGTTATCA
Statistics
Matches: 75, Mismatches: 13, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
20 1 0.01
21 5 0.07
22 65 0.87
23 4 0.05
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.32
Consensus pattern (22 bp):
TCAAAATTTCATAAGAGGGTTA
Found at i:74527 original size:44 final size:44
Alignment explanation
Indices: 74491--74609 Score: 125
Period size: 44 Copynumber: 2.7 Consensus size: 44
74481 AGTTTAGTTT
*
74491 TCAAAATTTCATAA-GAGGGTTATCAAAATTTCATAGTATGTAGA
1 TCAAAATTTCATAAGGA-GATTATCAAAATTTCATAGTATGTAGA
* * * *
74535 TCAAAATTTCATAAGGAGATTAACAAAATTTCATAATGAGGT-TA
1 TCAAAATTTCATAAGGAGATTATCAAAATTTCATAGT-ATGTAGA
** * *
74579 TCAAAAAATCATAGGGAGGTTATCAAAATTT
1 TCAAAATTTCATAAGGAGATTATCAAAATTT
74610 GTCGTTATCA
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 58 0.92
45 5 0.08
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.32
Consensus pattern (44 bp):
TCAAAATTTCATAAGGAGATTATCAAAATTTCATAGTATGTAGA
Found at i:74723 original size:23 final size:23
Alignment explanation
Indices: 74614--74715 Score: 134
Period size: 23 Copynumber: 4.4 Consensus size: 23
74604 AAATTTGTCG
* * *
74614 TTATCAAGATTTTCATAAGGAG-G
1 TTATCAAAATTTT-ATAGGGAGAT
74637 TTATCAAAATTTTATAGGGAGAT
1 TTATCAAAATTTTATAGGGAGAT
*
74660 TTATCAAAATTTTGTAGGGAGAT
1 TTATCAAAATTTTATAGGGAGAT
*
74683 TTATCAAAAATTTTATAGGAAGAT
1 TTATC-AAAATTTTATAGGGAGAT
74707 TTATCAAAA
1 TTATCAAAA
74716 CTCCATAGCG
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
22 7 0.10
23 43 0.61
24 21 0.30
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.37
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGAT
Found at i:74754 original size:22 final size:22
Alignment explanation
Indices: 74729--74788 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
74719 CATAGCGAGG
74729 TTATCACAATTTCATAGTGTGA
1 TTATCACAATTTCATAGTGTGA
*
74751 TTATCA-AATTTTCAGAGTGTGA
1 TTATCACAA-TTTCATAGTGTGA
*
74773 TTACTGACAA-TTCATA
1 TTA-TCACAATTTCATA
74789 TGGAGGTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
21 2 0.06
22 26 0.81
23 2 0.06
24 2 0.06
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (22 bp):
TTATCACAATTTCATAGTGTGA
Found at i:74840 original size:22 final size:22
Alignment explanation
Indices: 74783--74952 Score: 89
Period size: 22 Copynumber: 7.7 Consensus size: 22
74773 TTACTGACAA
**
74783 TTCATATGGAGGTT-TTTAAAT
1 TTCATATGGAGGTTATCAAAAT
** * *
74804 TCTCATAACGTGGTTATCAATAT
1 T-TCATATGGAGGTTATCAAAAT
* *
74827 ATCATATGGAGGTTATCAACAT
1 TTCATATGGAGGTTATCAAAAT
**
74849 CTT-ATAGTGTTGGTTATCAAAAT
1 -TTCATA-TGGAGGTTATCAAAAT
* *
74872 TTCATTTGGAAGTTATCAAAAT
1 TTCATATGGAGGTTATCAAAAT
74894 TTCATA-GTGAGGTCT-TCAAAAT
1 TTCATATG-GAGGT-TATCAAAAT
* * * *
74916 TCCTTA-GAAAGGTTAACAAAAT
1 TTCATATG-GAGGTTATCAAAAT
* *
74938 TTCATAAGAAGGTTA
1 TTCATATGGAGGTTA
74953 AAAAAAATTT
Statistics
Matches: 112, Mismatches: 28, Indels: 17
0.71 0.18 0.11
Matches are distributed among these distances:
21 3 0.03
22 87 0.78
23 22 0.20
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (22 bp):
TTCATATGGAGGTTATCAAAAT
Found at i:74901 original size:45 final size:45
Alignment explanation
Indices: 74814--74902 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 45
74804 TCTCATAACG
* * *
74814 TGGTTATCAATATATCATATGGAGGTTATCAACATCTTATAGTGT
1 TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTTATAGTGT
* *
74859 TGGTTATCAAAATTTCATTTGGAAGTTATCAAAAT-TTCATAGTG
1 TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTT-ATAGTG
74903 AGGTCTTCAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
44 2 0.05
45 36 0.95
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTTATAGTGT
Found at i:74953 original size:22 final size:22
Alignment explanation
Indices: 74923--74973 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
74913 AATTCCTTAG
*
74923 AAAGGTT-AACAAAATTTCATAA
1 AAAGGTTAAAAAAAATTT-ATAA
*
74945 GAAGGTTAAAAAAAATTTATAA
1 AAAGGTTAAAAAAAATTTATAA
74967 AAAGGTT
1 AAAGGTT
74974 CTTGAAATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.55, C:0.04, G:0.14, T:0.27
Consensus pattern (22 bp):
AAAGGTTAAAAAAAATTTATAA
Found at i:75075 original size:62 final size:62
Alignment explanation
Indices: 75001--75129 Score: 213
Period size: 62 Copynumber: 2.1 Consensus size: 62
74991 TCGTTATTAA
*
75001 AATTTCACAGGAAGGTTATCAAAATTTCATAAGGAAGCCATAAAAAATAGTGTAATTATCAT
1 AATTTCACAGGAAGGTTATCAAAATTTCATAAGGAAGCCATAAAAAATAGTATAATTATCAT
* * * *
75063 AATTTCATAGGAAGTTTATCAAAATTTCATAAGGACGTCATAAAAAATAGTATAATTATCAT
1 AATTTCACAGGAAGGTTATCAAAATTTCATAAGGAAGCCATAAAAAATAGTATAATTATCAT
75125 AATTT
1 AATTT
75130 TTAATTTAAT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (62 bp):
AATTTCACAGGAAGGTTATCAAAATTTCATAAGGAAGCCATAAAAAATAGTATAATTATCAT
Found at i:76303 original size:11 final size:11
Alignment explanation
Indices: 76289--76326 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
76279 ATTCATAACA
76289 AATTTATAATT
1 AATTTATAATT
76300 AATTTATAATT
1 AATTTATAATT
76311 -ATTTGATAATT
1 AATTT-ATAATT
*
76322 TATTT
1 AATTT
76327 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:76975 original size:26 final size:26
Alignment explanation
Indices: 76946--77013 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
76936 TTCCTTCATT
76946 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
76972 TTAATAATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
76998 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
77014 AAACTAAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.54, C:0.10, G:0.01, T:0.34
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:77037 original size:52 final size:51
Alignment explanation
Indices: 76946--77063 Score: 122
Period size: 52 Copynumber: 2.4 Consensus size: 51
76936 TTCCTTCATT
* *
76946 TTAATCATAAACTAATTAAATACTAATTAATAATAAACTAATTAGATACTAA
1 TTAAACATAAACTAATTAAATACTAATTAATAATAAACTAATTA-AAACTAA
* * *
76998 TTAAACATAAACTAA-TAAACTAAGTAATT-TTAATTAACTAATTAAAACTAA
1 TTAAACATAAACTAATTAAA-T-ACTAATTAATAATAAACTAATTAAAACTAA
77049 -T---CATAAACTAATTAA
1 TTAAACATAAACTAATTAA
77064 TATTAAAATA
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
47 10 0.17
48 3 0.05
50 1 0.02
51 10 0.17
52 28 0.48
53 6 0.10
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (51 bp):
TTAAACATAAACTAATTAAATACTAATTAATAATAAACTAATTAAAACTAA
Found at i:82314 original size:26 final size:26
Alignment explanation
Indices: 82265--82314 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
82255 GAATCTCGTG
* * *
82265 AATGGAGAAAACTTTTTTTTTTAGGA
1 AATGGAGAAAACTATTGTTGTTAGGA
82291 AATGGAGAAAACTATTGTTGTTAG
1 AATGGAGAAAACTATTGTTGTTAG
82315 AACTTTACCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.38
Consensus pattern (26 bp):
AATGGAGAAAACTATTGTTGTTAGGA
Found at i:86589 original size:24 final size:24
Alignment explanation
Indices: 86561--86608 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
86551 AAATTAACTC
86561 CAAGACTTCTCAAATTCAAAACAT
1 CAAGACTTCTCAAATTCAAAACAT
*
86585 CAAGACTTCTCAAATTTAAAACAT
1 CAAGACTTCTCAAATTCAAAACAT
86609 TTTACTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.46, C:0.23, G:0.04, T:0.27
Consensus pattern (24 bp):
CAAGACTTCTCAAATTCAAAACAT
Found at i:87102 original size:28 final size:28
Alignment explanation
Indices: 87062--87117 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
87052 TCGTTCCAAA
87062 CCCAATTACAAGGTACCCAAACCTAATG
1 CCCAATTACAAGGTACCCAAACCTAATG
87090 CCCAATTACAAGGTACCCAAACCTAATG
1 CCCAATTACAAGGTACCCAAACCTAATG
87118 TAATCGGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.32, G:0.11, T:0.18
Consensus pattern (28 bp):
CCCAATTACAAGGTACCCAAACCTAATG
Found at i:89334 original size:13 final size:14
Alignment explanation
Indices: 89310--89341 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
89300 ACCCTAAATG
89310 TCAATATTTTTTTA
1 TCAATATTTTTTTA
89324 TCAAT-TTTTTTTA
1 TCAATATTTTTTTA
89337 T-AATA
1 TCAATA
89342 ACAATAAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.18
13 9 0.53
14 5 0.29
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (14 bp):
TCAATATTTTTTTA
Found at i:91658 original size:21 final size:21
Alignment explanation
Indices: 91634--91674 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
91624 ATTTTTGTTC
*
91634 TTAAAGAATGTAGTT-TTAAAT
1 TTAAA-AATATAGTTCTTAAAT
91655 TTAAAAATATAGTTCTTAAA
1 TTAAAAATATAGTTCTTAAA
91675 AAATAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.46, C:0.02, G:0.10, T:0.41
Consensus pattern (21 bp):
TTAAAAATATAGTTCTTAAAT
Found at i:93698 original size:51 final size:52
Alignment explanation
Indices: 93606--93714 Score: 193
Period size: 51 Copynumber: 2.1 Consensus size: 52
93596 TTTATTTTTT
*
93606 GCTACAAAATTGAGGGTCATATATTACATTTATATTATAATCATAAGGGTGAG
1 GCTACAAAATTGAGGGTCA-ATATTACATTTATATTATAATCATAAGGATGAG
93659 GCTACAAAATTGAGGGTC-ATATTACATTTATATTATAATCATAAGGATGAG
1 GCTACAAAATTGAGGGTCAATATTACATTTATATTATAATCATAAGGATGAG
93710 GCTAC
1 GCTAC
93715 GAGTACTAAC
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
51 37 0.67
53 18 0.33
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (52 bp):
GCTACAAAATTGAGGGTCAATATTACATTTATATTATAATCATAAGGATGAG
Found at i:99158 original size:45 final size:45
Alignment explanation
Indices: 99107--99195 Score: 178
Period size: 45 Copynumber: 2.0 Consensus size: 45
99097 TTAGGGCTCT
99107 GCCCTCCCTTTTTTACCAAAAAAAGGTGGTAAATATACCAAAGGA
1 GCCCTCCCTTTTTTACCAAAAAAAGGTGGTAAATATACCAAAGGA
99152 GCCCTCCCTTTTTTACCAAAAAAAGGTGGTAAATATACCAAAGG
1 GCCCTCCCTTTTTTACCAAAAAAAGGTGGTAAATATACCAAAGG
99196 TGGAAAGGGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (45 bp):
GCCCTCCCTTTTTTACCAAAAAAAGGTGGTAAATATACCAAAGGA
Found at i:123442 original size:3 final size:3
Alignment explanation
Indices: 123436--123461 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
123426 ATTGGTCTTT
123436 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
123462 TAATTTGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:130142 original size:18 final size:19
Alignment explanation
Indices: 130121--130162 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
130111 TAAAAAAAAA
*
130121 AATTTACTCTTCT-TTTTT
1 AATTTACTATTCTATTTTT
* *
130139 AATTTTCTATTTTATTTTT
1 AATTTACTATTCTATTTTT
130158 AATTT
1 AATTT
130163 TATTTTTCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (19 bp):
AATTTACTATTCTATTTTT
Found at i:133821 original size:169 final size:164
Alignment explanation
Indices: 133542--134029 Score: 532
Period size: 169 Copynumber: 2.9 Consensus size: 164
133532 AAATAAACAT
* * * ** * * * *
133542 GTGGAATTACTAAAAGATCGCCACCCCGGATTAATGAGGAGCGAGAGAACTAATTTTTTTCGTCT
1 GTGGAACTAATAAAAGATCCCCACCAAGGATTGATGATGAGCAAGAGAA-TTATTTTTTTCGTCT
* * * *
133607 GTTCCGACTTGGCAGATTACTTAAATGTCTTAACTTTTAATTCTTGAGAGGATTAAATAACTAGA
65 TTTCCTACTTGGCAGATTACTTAAATGTCCTAATTTTTAATTCTTGAGAGGATTAAATAACTA-A
* *
133672 CTTTTTGGTCATTTCTCAATTGACTTTAATAATAGAGTA
129 CTTTTTGGTCATTTCTCAATTGAC-TT--GAATAGAATA
* * * * ** ** *
133711 GTGGAATTATTAAAAGATCCCTACCAAGGCTT-ACTTTTGGAGTTAGAGAAATT-TTTTTTTGGT
1 GTGGAACTAATAAAAGATCCCCACCAAGGATTGA-TGAT-GAGCAAGAG-AATTATTTTTTTCGT
* * *
133774 CTTTTCCTACTTGGTAGATTACTTAAATGTCCTAATTTTTGATTCTTGA-AGGGATTAAATAAAT
63 CTTTTCCTACTTGGCAGATTACTTAAATGTCCTAATTTTTAATTCTTGAGA-GGATTAAATAACT
* * * *
133838 AATCTTTTTGCTAATTTCTTAATGGACTTGAATAGAATA
127 AA-CTTTTTGGTCATTTCTCAATTGACTTGAATAGAATA
* *
133877 GTGGAACTAATAAAAGATCCCCATCAAGGATTGATGATGAGCAAGAGAATTAATTTTTTCGTCTT
1 GTGGAACTAATAAAAGATCCCCACCAAGGATTGATGATGAGCAAGAGAATTATTTTTTTCGTCTT
* * *
133942 TACCTACTTGGCAGATTACTTAAATGTCCTAATTTTTAACTCTTGAGGGGATTAAATAACTAAAC
66 TTCCTACTTGGCAGATTACTTAAATGTCCTAATTTTTAATTCTTGAGAGGATTAAATAACT-AAC
134007 TTTTTGGTCATTTCTCAATTGAC
130 TTTTTGGTCATTTCTCAATTGAC
134030 AAATGACTCA
Statistics
Matches: 263, Mismatches: 47, Indels: 22
0.79 0.14 0.07
Matches are distributed among these distances:
164 4 0.02
165 92 0.35
166 39 0.15
167 1 0.00
168 5 0.02
169 112 0.43
170 8 0.03
171 2 0.01
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (164 bp):
GTGGAACTAATAAAAGATCCCCACCAAGGATTGATGATGAGCAAGAGAATTATTTTTTTCGTCTT
TTCCTACTTGGCAGATTACTTAAATGTCCTAATTTTTAATTCTTGAGAGGATTAAATAACTAACT
TTTTGGTCATTTCTCAATTGACTTGAATAGAATA
Found at i:135021 original size:26 final size:27
Alignment explanation
Indices: 134965--135021 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 27
134955 ACGTGGATTT
**
134965 TCTTTCAATAATTTCCCAATAACTGGG
1 TCTTTCAATAATTTCCCAATAACTGAA
*
134992 TCTTT-AATAA-TTCTCCAATAATTGAA
1 TCTTTCAATAATTTC-CCAATAACTGAA
135018 TCTT
1 TCTT
135022 CTTTGAAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 3 0.12
26 18 0.69
27 5 0.19
ACGTcount: A:0.32, C:0.19, G:0.07, T:0.42
Consensus pattern (27 bp):
TCTTTCAATAATTTCCCAATAACTGAA
Found at i:140593 original size:17 final size:16
Alignment explanation
Indices: 140566--140597 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
140556 ATTCTTTTTG
140566 TTTGAATTGGTTTCTC
1 TTTGAATTGGTTTCTC
140582 TTTGATATTGGTTTCT
1 TTTGA-ATTGGTTTCT
140598 TCAACTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.12, C:0.09, G:0.19, T:0.59
Consensus pattern (16 bp):
TTTGAATTGGTTTCTC
Found at i:141876 original size:29 final size:29
Alignment explanation
Indices: 141842--141898 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
141832 ATCTTAAATA
*
141842 TGGACATTATTATGTCACTTCAAATATTG
1 TGGACATTATTATGCCACTTCAAATATTG
141871 TGGACATTATTATGCCACTTCAAATATT
1 TGGACATTATTATGCCACTTCAAATATT
141899 TTGAAAACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (29 bp):
TGGACATTATTATGCCACTTCAAATATTG
Found at i:148970 original size:21 final size:20
Alignment explanation
Indices: 148944--148990 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
148934 AGAAATGGGG
* *
148944 TTTTTTATTTTTTTTTTATTT
1 TTTTTTATTTATTTATT-TTT
148965 TTTTTTATTTATTTATTTTT
1 TTTTTTATTTATTTATTTTT
148985 TTTTTT
1 TTTTTT
148991 GTCATTTGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (20 bp):
TTTTTTATTTATTTATTTTT
Found at i:148997 original size:19 final size:18
Alignment explanation
Indices: 148944--148988 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
148934 AGAAATGGGG
*
148944 TTTTTTATTT-TTTTTTTA
1 TTTTTT-TTTATTTATTTA
148962 TTTTTTTTTATTTATTTA
1 TTTTTTTTTATTTATTTA
148980 TTTTTTTTT
1 TTTTTTTTT
148989 TTGTCATTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 3 0.12
18 22 0.88
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (18 bp):
TTTTTTTTTATTTATTTA
Found at i:157966 original size:28 final size:28
Alignment explanation
Indices: 157913--157969 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
157903 TCGATCTATT
*
157913 TAATATCATATAATTTTCAATTCACATG
1 TAATATCATATAATTTTCAATCCACATG
157941 TAATATCATATAATTTT-AGATCCACATG
1 TAATATCATATAATTTTCA-ATCCACATG
157969 T
1 T
157970 CCGATTAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 1 0.04
28 26 0.96
ACGTcount: A:0.39, C:0.14, G:0.05, T:0.42
Consensus pattern (28 bp):
TAATATCATATAATTTTCAATCCACATG
Found at i:165922 original size:18 final size:18
Alignment explanation
Indices: 165891--165925 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
165881 GTTATTAATA
* *
165891 ATAAATAATTTTATTATC
1 ATAAAAAATATTATTATC
165909 ATAAAAAATATTATTAT
1 ATAAAAAATATTATTAT
165926 TTATATTAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
ATAAAAAATATTATTATC
Found at i:171157 original size:17 final size:17
Alignment explanation
Indices: 171131--171178 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
171121 AACCCTGATG
*
171131 ATCACCGGTGATCTTGC
1 ATCACTGGTGATCTTGC
*
171148 ATCACTGGTGATCTTGG
1 ATCACTGGTGATCTTGC
*
171165 ATCACTAGTGATCT
1 ATCACTGGTGATCT
171179 GAGGGGTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (17 bp):
ATCACTGGTGATCTTGC
Found at i:174542 original size:25 final size:25
Alignment explanation
Indices: 174511--174558 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
174501 TACTTAAGAA
174511 AAGAACATTGAAATAAGTATCCAGC
1 AAGAACATTGAAATAAGTATCCAGC
174536 AAGAACATTGAAATAAGTATCCA
1 AAGAACATTGAAATAAGTATCCA
174559 AAAGCAGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.21
Consensus pattern (25 bp):
AAGAACATTGAAATAAGTATCCAGC
Found at i:177043 original size:29 final size:29
Alignment explanation
Indices: 177010--177069 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
177000 ATATTTATCT
* *
177010 TATAATGAGTAGTTTTTTTCTAAAATTGG
1 TATAATGAGTAGTTTTTATCTAAAATGGG
*
177039 TATAATGGGTAGTTTTTATCTAAAATGGG
1 TATAATGAGTAGTTTTTATCTAAAATGGG
177068 TA
1 TA
177070 GTTTTTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.32, C:0.03, G:0.20, T:0.45
Consensus pattern (29 bp):
TATAATGAGTAGTTTTTATCTAAAATGGG
Found at i:179860 original size:1 final size:1
Alignment explanation
Indices: 179849--179879 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
179839 TTACTTGAAC
*
179849 TTTTGTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
179880 GTGGCAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:180462 original size:44 final size:45
Alignment explanation
Indices: 180410--180495 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
180400 TAGATTAGCC
*
180410 TCAAACCTTTCCAGATTTG-GTGTAAAAGAGGTGCTAGATCCGCG
1 TCAAACCTTTCCAGATTTGTGTGTAAAACAGGTGCTAGATCCGCG
* * *
180454 TCAAACCTTTTCAGATTTGTTTGTAAGACAGGTGCTAGATCC
1 TCAAACCTTTCCAGATTTGTGTGTAAAACAGGTGCTAGATCC
180496 AGCTTTGTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.49
45 19 0.51
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (45 bp):
TCAAACCTTTCCAGATTTGTGTGTAAAACAGGTGCTAGATCCGCG
Found at i:182131 original size:14 final size:13
Alignment explanation
Indices: 182113--182138 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
182103 TCCAAGTGGT
182113 TTTTTTTTTAAAA
1 TTTTTTTTTAAAA
182126 TTTTTTTTTAAAA
1 TTTTTTTTTAAAA
182139 AACCCCTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTTTTTTAAAA
Found at i:188471 original size:25 final size:25
Alignment explanation
Indices: 188443--188496 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
188433 ACCGAAATCT
*
188443 TTTCCTTCTCCTAACAAGTAAAGGA
1 TTTCCTTCTCCTAACAAGAAAAGGA
*
188468 TTTCCTTTTCCTAACAAGAAAAGGA
1 TTTCCTTCTCCTAACAAGAAAAGGA
188493 TTTC
1 TTTC
188497 GGTTCCTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.35
Consensus pattern (25 bp):
TTTCCTTCTCCTAACAAGAAAAGGA
Found at i:196126 original size:203 final size:203
Alignment explanation
Indices: 195765--196147 Score: 565
Period size: 203 Copynumber: 1.9 Consensus size: 203
195755 AATTATACAA
* *
195765 TGGAGTTTAGCAGACTACACAAGCCGTTCCTAAAGGGTGATATGTGTTTCCTAGAAACTAAATTG
1 TGGAGTTTAGCAGACTACACAAGCCGATCCTAAAGGGTGACATGTGTTT-CTAGAAACTAAATTG
* * *
195830 AAAATTTTAAAACTTAATTAATTAAAAAAATAGACATGTGTCAACTCTACAACCTGCTTGTGGAG
65 AAAATTTTAAAACTTAAATAATTAAAAAAATAGACATGTGTCAACTCCACAACCCGCTTGTGGAG
* *
195895 TCCAAAATTTACACCGTCAATATATCATATAATCA-CCTCATAATAATAAGGGTTTATATATGAT
130 TCCAAAATTTACACCGCCAATATATCATATAATCACCCTAATAATAATAAGGGTTTATATATGAT
195959 CACCTGCGG
195 CACCTGCGG
* * ** *
195968 TGGAGTTTAGCAGACTACACAAGCGGATCCTGAAGGGTGACATGTGTCCTT-TAGGGACTAGATT
1 TGGAGTTTAGCAGACTACACAAGCCGATCCTAAAGGGTGACATGTGT--TTCTAGAAACTAAATT
*
196032 G-AAATATTTAAAACTTAAATAATTCAAAAAATAGACATGTGTCAACTCCACAACCCGCTTGTGG
64 GAAAAT-TTTAAAACTTAAATAATTAAAAAAATAGACATGTGTCAACTCCACAACCCGCTTGTGG
** *
196096 AGTCCAAAATTTACACCGCCGGTGTATCATATAATCACCCTAATAATAATAA
128 AGTCCAAAATTTACACCGCCAATATATCATATAATCACCCTAATAATAATAA
196148 AAAATAAATA
Statistics
Matches: 160, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
202 4 0.03
203 141 0.88
204 13 0.08
205 2 0.01
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (203 bp):
TGGAGTTTAGCAGACTACACAAGCCGATCCTAAAGGGTGACATGTGTTTCTAGAAACTAAATTGA
AAATTTTAAAACTTAAATAATTAAAAAAATAGACATGTGTCAACTCCACAACCCGCTTGTGGAGT
CCAAAATTTACACCGCCAATATATCATATAATCACCCTAATAATAATAAGGGTTTATATATGATC
ACCTGCGG
Found at i:196383 original size:26 final size:26
Alignment explanation
Indices: 196347--196402 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
196337 AGCGAGAATA
196347 ATTTAATTATAATTAATGATTTTGAT
1 ATTTAATTATAATTAATGATTTTGAT
196373 ATTTAATTATAATTAATGATTTTGAT
1 ATTTAATTATAATTAATGATTTTGAT
196399 ATTT
1 ATTT
196403 CGTATGCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (26 bp):
ATTTAATTATAATTAATGATTTTGAT
Done.