Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017791.1 Corchorus olitorius cultivar O-4 contig17824, 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: 220146
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:145 original size:2 final size:2
Alignment explanation
Indices: 76--126 Score: 59
Period size: 2 Copynumber: 25.5 Consensus size: 2
66 TTTTTAACGT
* * *
76 TA TA TA TA TA TA TA TA TA TA T- TCA GA AA TA TA AA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA
118 TA TA TA TA T
1 TA TA TA TA T
127 TTAATTATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:4216 original size:20 final size:21
Alignment explanation
Indices: 4177--4219 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
4167 ATAGTTGAAT
4177 TTTTGCATGGCACCTTTTGCA
1 TTTTGCATGGCACCTTTTGCA
*
4198 TTTTGCATGGCA-TTTTTGCA
1 TTTTGCATGGCACCTTTTGCA
4218 TT
1 TT
4220 CATCCTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.14, C:0.19, G:0.19, T:0.49
Consensus pattern (21 bp):
TTTTGCATGGCACCTTTTGCA
Found at i:4424 original size:37 final size:37
Alignment explanation
Indices: 4383--4456 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
4373 TTGCATTTGA
*
4383 TATTATTCATTACTATTATTTATTTCCATGTCATACC
1 TATTATTCATTACTATTATTTAGTTCCATGTCATACC
*
4420 TATTATTTATTACTATTATTTAGTTCCATGTCATACC
1 TATTATTCATTACTATTATTTAGTTCCATGTCATACC
4457 GTCCTTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.27, C:0.18, G:0.04, T:0.51
Consensus pattern (37 bp):
TATTATTCATTACTATTATTTAGTTCCATGTCATACC
Found at i:8201 original size:27 final size:27
Alignment explanation
Indices: 8153--8211 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
8143 TTACCAAAAA
* * *
8153 TACCCGTGATGGACAAATTTACTATGT
1 TACCCCTGATGGACAAAATTACGATGT
* * *
8180 TACCCCTGATTGATAAAATTACGATTT
1 TACCCCTGATGGACAAAATTACGATGT
8207 TACCC
1 TACCC
8212 ATATAATGAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.34
Consensus pattern (27 bp):
TACCCCTGATGGACAAAATTACGATGT
Found at i:13805 original size:23 final size:23
Alignment explanation
Indices: 13773--13819 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
13763 TCCAAATTTC
*
13773 TCTTTATTTTCCTTATATCTTTT
1 TCTTTATTTTCCTCATATCTTTT
* *
13796 TCTTTTTTTTCCTCATATTTTTT
1 TCTTTATTTTCCTCATATCTTTT
13819 T
1 T
13820 TCCTTTCTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.72
Consensus pattern (23 bp):
TCTTTATTTTCCTCATATCTTTT
Found at i:13835 original size:21 final size:20
Alignment explanation
Indices: 13811--13862 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
13801 TTTTTCCTCA
*
13811 TATTTTTTTTCCTTTCTATTT
1 TATTTTTTTTCATTT-TATTT
*
13832 TATTTTTTATTTATTTTATTT
1 TATTTTTT-TTCATTTTATTT
*
13853 AATTTTTTTT
1 TATTTTTTTT
13863 AAAACTTTGG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.07
21 20 0.74
22 5 0.19
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (20 bp):
TATTTTTTTTCATTTTATTT
Found at i:13943 original size:34 final size:35
Alignment explanation
Indices: 13904--13981 Score: 88
Period size: 34 Copynumber: 2.2 Consensus size: 35
13894 AAGCCTAGCA
* *
13904 CGCTGGGCCATGTGCTGGCT-GACACGCTGGGCC-G
1 CGCTGGCCCACGTGCTGGCTAG-CACGCTGGGCCTG
* *
13938 CGCTGGCCCGCGTGCTGGCTAGCAGGCTGGGCCTG
1 CGCTGGCCCACGTGCTGGCTAGCACGCTGGGCCTG
13973 CGCCTGGCC
1 CG-CTGGCC
13982 AGCCCATTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
34 27 0.73
35 4 0.11
36 6 0.16
ACGTcount: A:0.06, C:0.36, G:0.41, T:0.17
Consensus pattern (35 bp):
CGCTGGCCCACGTGCTGGCTAGCACGCTGGGCCTG
Found at i:17475 original size:17 final size:16
Alignment explanation
Indices: 17421--17471 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
17411 ATCACCCCCC
*
17421 AGATCACTAGTGATCTA
1 AGATCACCAGTGATC-A
17438 AGATCACCAGTGATGCA
1 AGATCACCAGTGAT-CA
*
17455 AGATCACCGGTGATCA
1 AGATCACCAGTGATCA
17471 A
1 A
17472 AGATTACATG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 3 0.10
17 27 0.87
18 1 0.03
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (16 bp):
AGATCACCAGTGATCA
Found at i:18073 original size:21 final size:21
Alignment explanation
Indices: 18048--18257 Score: 171
Period size: 21 Copynumber: 10.3 Consensus size: 21
18038 GGTAAGAGAA
18048 CAGTAAAATGA-TAATAGTAAT
1 CAGTAAAA-GAGTAATAGTAAT
18069 CAGTAAAAGAGTAA-AGAATAAT
1 CAGTAAAAGAGTAATAG--TAAT
*
18091 TAGTAAAAGAGTAATAGTAAT
1 CAGTAAAAGAGTAATAGTAAT
18112 CAGT-AAAGAGTAA-AG----
1 CAGTAAAAGAGTAATAGTAAT
* *
18127 -AGTAAAAGAGTAATAATAGT
1 CAGTAAAAGAGTAATAGTAAT
*
18147 CAGT-AAAGAGTAAAGAGTAAT
1 CAGTAAAAGAGT-AATAGTAAT
* * *
18168 CAAT-GAAGAGTCATAGTAAT
1 CAGTAAAAGAGTAATAGTAAT
18188 CAGTAAAAGAGTAAATAGTGAA-
1 CAGTAAAAGAGT-AATAGT-AAT
18210 CAGTAAAATGA-TAATAGTAAT
1 CAGTAAAA-GAGTAATAGTAAT
18231 CAGT-AAAGAGTAA-ATGATAAT
1 CAGTAAAAGAGTAATA-G-TAAT
18252 CAGTAA
1 CAGTAA
18258 TTAAAGTTCA
Statistics
Matches: 155, Mismatches: 13, Indels: 41
0.74 0.06 0.20
Matches are distributed among these distances:
14 3 0.02
15 9 0.06
16 1 0.01
19 5 0.03
20 39 0.25
21 60 0.39
22 32 0.21
23 6 0.04
ACGTcount: A:0.53, C:0.05, G:0.20, T:0.23
Consensus pattern (21 bp):
CAGTAAAAGAGTAATAGTAAT
Found at i:18084 original size:7 final size:7
Alignment explanation
Indices: 18074--18166 Score: 57
Period size: 7 Copynumber: 13.3 Consensus size: 7
18064 GTAATCAGTA
18074 AAAGAGT
1 AAAGAGT
*
18081 AAAGAAT
1 AAAGAGT
**
18088 AATTAGT
1 AAAGAGT
18095 AAAAGAGT
1 -AAAGAGT
*
18103 -AATAGT
1 AAAGAGT
**
18109 AATCAGT
1 AAAGAGT
18116 AAAGAGT
1 AAAGAGT
18123 AAAGAGT
1 AAAGAGT
18130 AAAAGAGT
1 -AAAGAGT
18138 AATA-A-T
1 AA-AGAGT
***
18144 AGTCAGT
1 AAAGAGT
18151 AAAGAGT
1 AAAGAGT
18158 AAAGAGT
1 AAAGAGT
18165 AA
1 AA
18167 TCAATGAAGA
Statistics
Matches: 64, Mismatches: 16, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
6 8 0.12
7 43 0.67
8 13 0.20
ACGTcount: A:0.56, C:0.02, G:0.22, T:0.20
Consensus pattern (7 bp):
AAAGAGT
Found at i:18118 original size:35 final size:35
Alignment explanation
Indices: 18078--18166 Score: 124
Period size: 35 Copynumber: 2.5 Consensus size: 35
18068 TCAGTAAAAG
** *
18078 AGTAAAGAATAATTAGTAAAAGAGTAATAGTAATC
1 AGTAAAGAATAAAGAGTAAAAGAGTAATAATAATC
* *
18113 AGTAAAGAGTAAAGAGTAAAAGAGTAATAATAGTC
1 AGTAAAGAATAAAGAGTAAAAGAGTAATAATAATC
*
18148 AGTAAAGAGTAAAGAGTAA
1 AGTAAAGAATAAAGAGTAA
18167 TCAATGAAGA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 49 1.00
ACGTcount: A:0.55, C:0.02, G:0.21, T:0.21
Consensus pattern (35 bp):
AGTAAAGAATAAAGAGTAAAAGAGTAATAATAATC
Found at i:18397 original size:26 final size:28
Alignment explanation
Indices: 18357--18421 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 28
18347 CCAGAAAAAA
18357 AAAAAG-GTAAGAAAA-TGGTAATAAGT
1 AAAAAGAGTAAGAAAATTGGTAATAAGT
* *
18383 AAAAAGAGTAA-AAAATTGGTTATCAGT
1 AAAAAGAGTAAGAAAATTGGTAATAAGT
18410 AAAAAGAGTAAG
1 AAAAAGAGTAAG
18422 GGTAATCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 10 0.29
27 24 0.71
ACGTcount: A:0.57, C:0.02, G:0.22, T:0.20
Consensus pattern (28 bp):
AAAAAGAGTAAGAAAATTGGTAATAAGT
Found at i:19357 original size:22 final size:20
Alignment explanation
Indices: 19315--19382 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 20
19305 AGTTTCTCAC
19315 AATTTCATAGGTAATTATCAA
1 AATTTCATAGGT-ATTATCAA
*
19336 AATTTCATAGCGTGGTTATCAA
1 AATTTCATAG-GT-ATTATCAA
* *
19358 AATTTAATAGGTTTTATCAA
1 AATTTCATAGGTATTATCAA
19378 AATTT
1 AATTT
19383 ATAAAAAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
20 12 0.29
21 12 0.29
22 18 0.43
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (20 bp):
AATTTCATAGGTATTATCAA
Found at i:19672 original size:13 final size:13
Alignment explanation
Indices: 19653--19688 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
19643 TTCAAATTTA
19653 ATAAAATTTTATT
1 ATAAAATTTTATT
* *
19666 TTAAAATTTAATT
1 ATAAAATTTTATT
19679 ATAAAATTTT
1 ATAAAATTTT
19689 TCAATTTTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
ATAAAATTTTATT
Found at i:23754 original size:22 final size:22
Alignment explanation
Indices: 23698--23976 Score: 141
Period size: 22 Copynumber: 12.6 Consensus size: 22
23688 TTGATAGTTT
*
23698 GGTTATCAAAATTATATAGGGA
1 GGTTATCAAAATTTTATAGGGA
* ** * *
23720 GGTGATCTTAATTTTATAGTGT
1 GGTTATCAAAATTTTATAGGGA
* *
23742 GGTTATCAAAATTTAATA-GTA
1 GGTTATCAAAATTTTATAGGGA
* * *
23763 TGATTTTCAAAATTTCATAGGGA
1 -GGTTATCAAAATTTTATAGGGA
** * *** * *
23786 CATTAACAAAATTCCGTAAGAA
1 GGTTATCAAAATTTTATAGGGA
* * *
23808 TGTTATCAAAAATTCATAGGGA
1 GGTTATCAAAATTTTATAGGGA
* *
23830 GGTTATAAAAATTTCATAGGGTA
1 GGTTATCAAAATTTTATAGGG-A
* * *
23853 -GTTATCAAAATTTCATAAGGT
1 GGTTATCAAAATTTTATAGGGA
* * *
23874 GGTTATCGAAATTTCATAAGGA
1 GGTTATCAAAATTTTATAGGGA
* * **
23896 GATTATCAAAATTTCA-AAAGA
1 GGTTATCAAAATTTTATAGGGA
* **
23917 GGGTTATCAAAATTTTACAAAGA
1 -GGTTATCAAAATTTTATAGGGA
**
23940 GGTTTATCAAAATTTTATAATGA
1 GG-TTATCAAAATTTTATAGGGA
*
23963 GGTTATCACAATTT
1 GGTTATCAAAATTT
23977 GATCTAGTGA
Statistics
Matches: 202, Mismatches: 48, Indels: 14
0.77 0.18 0.05
Matches are distributed among these distances:
21 4 0.02
22 170 0.84
23 28 0.14
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.35
Consensus pattern (22 bp):
GGTTATCAAAATTTTATAGGGA
Found at i:23841 original size:66 final size:66
Alignment explanation
Indices: 23771--23911 Score: 160
Period size: 66 Copynumber: 2.1 Consensus size: 66
23761 TATGATTTTC
* * *
23771 AAAATTTCATAGGG-ACATTAACAAAATTCCGTAAGAAT-GTTATCAAAAATTCATAGGGAGGTT
1 AAAATTTCATAGGGTA-ATTAACAAAATTCCATAAG-ATGGTTATCAAAAATTCATAAGGAGATT
23834 ATA
64 ATA
* * * * * *
23837 AAAATTTCATAGGGTAGTTATCAAAATTTCATAAGGTGGTTATCGAAATTTCATAAGGAGATTAT
1 AAAATTTCATAGGGTAATTAACAAAATTCCATAAGATGGTTATCAAAAATTCATAAGGAGATTAT
*
23902 C
66 A
23903 AAAATTTCA
1 AAAATTTCA
23912 AAAGAGGGTT
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
65 1 0.02
66 61 0.97
67 1 0.02
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (66 bp):
AAAATTTCATAGGGTAATTAACAAAATTCCATAAGATGGTTATCAAAAATTCATAAGGAGATTAT
A
Found at i:23923 original size:66 final size:65
Alignment explanation
Indices: 23809--23976 Score: 176
Period size: 66 Copynumber: 2.5 Consensus size: 65
23799 CCGTAAGAAT
* * * * * * *
23809 GTTATCAAAAATTCATAGGGAGGTTATAAAAATTTCATAGGGTAGTTATCAAAATTTCATAAGGT
1 GTTATCAAAATTTCATAAGGAGGTTATCAAAATTTCAAAGGG-AGTTATCAAAATTTCACAAAGA
23874 G
65 G
* * *
23875 GTTATCGAAATTTCATAAGGAGATTATCAAAATTTCAAAAGAGG-GTTATCAAAATTTTACAAAG
1 GTTATCAAAATTTCATAAGGAGGTTATCAAAATTTC-AAAG-GGAGTTATCAAAATTTCACAAAG
23939 AG
64 AG
* * *
23941 GTTTATCAAAATTTTATAATGAGGTTATCACAATTT
1 G-TTATCAAAATTTCATAAGGAGGTTATCAAAATTT
23977 GATCTAGTGA
Statistics
Matches: 84, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
66 50 0.60
67 32 0.38
68 2 0.02
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (65 bp):
GTTATCAAAATTTCATAAGGAGGTTATCAAAATTTCAAAGGGAGTTATCAAAATTTCACAAAGAG
Found at i:24271 original size:22 final size:20
Alignment explanation
Indices: 24218--24259 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
24208 TAATATCCTT
*
24218 ATAACTATTTTCTTTTTACC
1 ATAACTATTTTATTTTTACC
24238 ATAACTATTTTATTTTTACC
1 ATAACTATTTTATTTTTACC
24258 AT
1 AT
24260 TTTACTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.55
Consensus pattern (20 bp):
ATAACTATTTTATTTTTACC
Found at i:26267 original size:35 final size:36
Alignment explanation
Indices: 26221--26294 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 36
26211 TGGCACCACA
*
26221 TTAATCCTCAATTTGGCCTTTTAGTAATTT-CCCTT
1 TTAATCCTCAATTTGGCCTTTTAGCAATTTGCCCTT
*
26256 TTAATCCTCAATTTGGCCTTTTAGCAATTTGGCCTT
1 TTAATCCTCAATTTGGCCTTTTAGCAATTTGCCCTT
26292 TTA
1 TTA
26295 GTATATATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 29 0.81
36 7 0.19
ACGTcount: A:0.20, C:0.22, G:0.11, T:0.47
Consensus pattern (36 bp):
TTAATCCTCAATTTGGCCTTTTAGCAATTTGCCCTT
Found at i:26277 original size:20 final size:20
Alignment explanation
Indices: 26221--26278 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
26211 TGGCACCACA
26221 TTAATCCTCAATTTGGCCTT
1 TTAATCCTCAATTTGGCCTT
* *
26241 TT-A--GT-AATTT-CCCTT
1 TTAATCCTCAATTTGGCCTT
26256 TTAATCCTCAATTTGGCCTT
1 TTAATCCTCAATTTGGCCTT
26276 TTA
1 TTA
26279 GCAATTTGGC
Statistics
Matches: 29, Mismatches: 4, Indels: 10
0.67 0.09 0.23
Matches are distributed among these distances:
15 6 0.21
16 6 0.21
17 1 0.03
18 1 0.03
19 6 0.21
20 9 0.31
ACGTcount: A:0.21, C:0.22, G:0.09, T:0.48
Consensus pattern (20 bp):
TTAATCCTCAATTTGGCCTT
Found at i:26285 original size:16 final size:16
Alignment explanation
Indices: 26264--26295 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
26254 TTTTAATCCT
26264 CAATTTGGCCTTTTAG
1 CAATTTGGCCTTTTAG
26280 CAATTTGGCCTTTTAG
1 CAATTTGGCCTTTTAG
26296 TATATATATT
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:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (16 bp):
CAATTTGGCCTTTTAG
Found at i:27788 original size:16 final size:17
Alignment explanation
Indices: 27756--27800 Score: 74
Period size: 16 Copynumber: 2.7 Consensus size: 17
27746 AATTTTGGAT
27756 ACCCGAACCCGAAAATG
1 ACCCGAACCCGAAAATG
*
27773 ACCCAAACCC-AAAATG
1 ACCCGAACCCGAAAATG
27789 ACCCGAACCCGA
1 ACCCGAACCCGA
27801 TCAACCCGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.42, C:0.40, G:0.13, T:0.04
Consensus pattern (17 bp):
ACCCGAACCCGAAAATG
Found at i:28611 original size:17 final size:18
Alignment explanation
Indices: 28584--28617 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
28574 TTTTGATTCT
*
28584 TATATAATATATGTATAC
1 TATATAATATATATATAC
28602 TATA-AATATATATATA
1 TATATAATATATATATA
28618 TTTTTTTAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (18 bp):
TATATAATATATATATAC
Found at i:28872 original size:23 final size:25
Alignment explanation
Indices: 28831--28878 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
28821 GACATGACCT
28831 AAATATATATACTATATATTTGTAC
1 AAATATATATACTATATATTTGTAC
28856 AAATATATATA-TA-ATATTTGTAC
1 AAATATATATACTATATATTTGTAC
28879 CGATTAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 10 0.43
24 2 0.09
25 11 0.48
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (25 bp):
AAATATATATACTATATATTTGTAC
Found at i:31551 original size:28 final size:28
Alignment explanation
Indices: 31510--31584 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 28
31500 TTAAGATGTC
** *
31510 AAAATTACTGTTTTGCCCTTGGTCAGCT
1 AAAATTACAATTTTGCCCTTGGTCAACT
* * * *
31538 AAAATTACCATTTTACCCCTGGTTAACT
1 AAAATTACAATTTTGCCCTTGGTCAACT
31566 -AAATTACAATTTTGCCCTT
1 AAAATTACAATTTTGCCCTT
31585 AAATGCCGGA
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
27 16 0.42
28 22 0.58
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.39
Consensus pattern (28 bp):
AAAATTACAATTTTGCCCTTGGTCAACT
Found at i:35591 original size:51 final size:51
Alignment explanation
Indices: 35510--35622 Score: 172
Period size: 51 Copynumber: 2.2 Consensus size: 51
35500 TCTATGAGAG
* *
35510 GGTGTGTGTGATATGAGGATCAGAATCAGTAGAGAGCCATGAGAAGAATCT
1 GGTGAGTGTGATATGAGGATCAGAATCAGTAGAGAGACATGAGAAGAATCT
* * *
35561 GGTGAGTGTGATATGAGGATGAGAATCAGTAGAGGGAGATGAGAAGAATCT
1 GGTGAGTGTGATATGAGGATCAGAATCAGTAGAGAGACATGAGAAGAATCT
*
35612 GGTGCGTGTGA
1 GGTGAGTGTGA
35623 GGTTGTTGTG
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.32, C:0.07, G:0.38, T:0.23
Consensus pattern (51 bp):
GGTGAGTGTGATATGAGGATCAGAATCAGTAGAGAGACATGAGAAGAATCT
Found at i:37271 original size:22 final size:24
Alignment explanation
Indices: 37246--37291 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
37236 TGTATTCATT
* *
37246 AAATAGTTTTATTAT-TAT-TATA
1 AAATAATTCTATTATATATATATA
37268 AAATAATTCTATTATATATATATA
1 AAATAATTCTATTATATATATATA
37292 TATATATACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 13 0.65
23 3 0.15
24 4 0.20
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (24 bp):
AAATAATTCTATTATATATATATA
Found at i:38269 original size:108 final size:110
Alignment explanation
Indices: 38080--38289 Score: 343
Period size: 108 Copynumber: 1.9 Consensus size: 110
38070 GATCAACTTG
* *
38080 TTATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACATATACCAAACAATACA
1 TTATTATTAAGTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATACA
*
38145 AAATGCAATGAACTATTGGATTT-AA-AAAAAATACAAGTACCTA
66 AAAGGCAATGAACTATTGGATTTAAAGAAAAAATACAAGTACCTA
* * *
38188 TTATTATTAAGTGTGTTGTTTATTCAATTGAATCTATTAAATAATCACACATACCAAACAATACA
1 TTATTATTAAGTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATACA
*
38253 AAGGGCAATGAACTATTGGATTTAAAGAAAAAATACA
66 AAAGGCAATGAACTATTGGATTTAAAGAAAAAATACA
38290 TGCACCAAAT
Statistics
Matches: 93, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
108 81 0.87
109 2 0.02
110 10 0.11
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.32
Consensus pattern (110 bp):
TTATTATTAAGTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATACA
AAAGGCAATGAACTATTGGATTTAAAGAAAAAATACAAGTACCTA
Found at i:39753 original size:20 final size:21
Alignment explanation
Indices: 39723--39762 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
39713 CCAGCTGTGG
*
39723 CAAATTAGATCCGTGGCAAAA
1 CAAATTAGATCAGTGGCAAAA
39744 CAAA-TAGATCAGTGGCAAA
1 CAAATTAGATCAGTGGCAAA
39763 TCATTAGCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.45, C:0.17, G:0.20, T:0.17
Consensus pattern (21 bp):
CAAATTAGATCAGTGGCAAAA
Found at i:40472 original size:2 final size:2
Alignment explanation
Indices: 40465--40505 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
40455 TGTCAATCAA
* * *
40465 TG TG TG TG TG TG TG TC TG TG TG TG TG TG TC TA TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
40506 TTGTTTGTGA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.02, C:0.05, G:0.41, T:0.51
Consensus pattern (2 bp):
TG
Found at i:40486 original size:14 final size:14
Alignment explanation
Indices: 40467--40505 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
40457 TCAATCAATG
40467 TGTGTGTGTGTGTC
1 TGTGTGTGTGTGTC
40481 TGTGTGTGTGTGTC
1 TGTGTGTGTGTGTC
*
40495 TATGTGTGTGT
1 TGTGTGTGTGT
40506 TTGTTTGTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.03, C:0.05, G:0.41, T:0.51
Consensus pattern (14 bp):
TGTGTGTGTGTGTC
Found at i:40514 original size:14 final size:14
Alignment explanation
Indices: 40467--40514 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
40457 TCAATCAATG
*
40467 TGTGTGTGTGTGTC
1 TGTGTGTGTGTGTT
40481 TGTGTGTGTGTGTCT
1 TGTGTGTGTGTGT-T
*
40496 ATGTGTGTGTTTGTT
1 -TGTGTGTGTGTGTT
40511 TGTG
1 TGTG
40515 AGGGAGAGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 17 0.57
15 1 0.03
16 12 0.40
ACGTcount: A:0.02, C:0.04, G:0.40, T:0.54
Consensus pattern (14 bp):
TGTGTGTGTGTGTT
Found at i:43619 original size:21 final size:21
Alignment explanation
Indices: 43559--43623 Score: 76
Period size: 26 Copynumber: 2.9 Consensus size: 21
43549 TGAGATGATA
43559 TAATATTCCATCAAACAATTG
1 TAATATTCCATCAAACAATTG
*
43580 TAATACACAATTTCATCAAACAATTG
1 TAAT-----ATTCCATCAAACAATTG
43606 TAATATTCCATCAAACAA
1 TAATATTCCATCAAACAA
43624 GTGAAACCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
21 17 0.46
26 20 0.54
ACGTcount: A:0.46, C:0.20, G:0.03, T:0.31
Consensus pattern (21 bp):
TAATATTCCATCAAACAATTG
Found at i:44608 original size:21 final size:21
Alignment explanation
Indices: 44548--44612 Score: 76
Period size: 26 Copynumber: 2.9 Consensus size: 21
44538 TGAGATGATA
44548 TAATATTCCATCAAACAATTG
1 TAATATTCCATCAAACAATTG
*
44569 TAATACACAATTTCATCAAACAATTG
1 TAAT-----ATTCCATCAAACAATTG
44595 TAATATTCCATCAAACAA
1 TAATATTCCATCAAACAA
44613 GTGAAACCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
21 17 0.46
26 20 0.54
ACGTcount: A:0.46, C:0.20, G:0.03, T:0.31
Consensus pattern (21 bp):
TAATATTCCATCAAACAATTG
Found at i:51166 original size:137 final size:137
Alignment explanation
Indices: 50905--51153 Score: 480
Period size: 137 Copynumber: 1.8 Consensus size: 137
50895 CTAGTATAAA
50905 TAAAGAGTTTTTCAATAGAGTTTTGTATGCTTGGAGAAAAGATGTAGTATAAGGGTTAGATTTGG
1 TAAAGAGTTTTTCAATAGAGTTTTGTATGCTTGGAGAAAAGATGTAGTATAAGGGTTAGATTTGG
*
50970 TGGCGACACCCCATAGGACAAAAGGATGGTCCTCATGGGTGTGTGTGACTGTGCGTGTGTGTGTG
66 TGGAGACACCCCATAGGACAAAAGGATGGTCCTCATGGGTGTGTGTGACTGTGCGTGTGTGTGTG
51035 TGTGTGT
131 TGTGTGT
51042 TAAAGAGTTTTTCAATAGAGTTTTGTATGCTTGGAGAAAAGATGTAGTATAAGGGTTAGATTTGG
1 TAAAGAGTTTTTCAATAGAGTTTTGTATGCTTGGAGAAAAGATGTAGTATAAGGGTTAGATTTGG
*
51107 TGGAGACACCCCATAGGACAAAAGGATGGTTCTCATGGGTGTGTGTG
66 TGGAGACACCCCATAGGACAAAAGGATGGTCCTCATGGGTGTGTGTG
51154 TGTGTGTTTG
Statistics
Matches: 110, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
137 110 1.00
ACGTcount: A:0.27, C:0.10, G:0.32, T:0.32
Consensus pattern (137 bp):
TAAAGAGTTTTTCAATAGAGTTTTGTATGCTTGGAGAAAAGATGTAGTATAAGGGTTAGATTTGG
TGGAGACACCCCATAGGACAAAAGGATGGTCCTCATGGGTGTGTGTGACTGTGCGTGTGTGTGTG
TGTGTGT
Found at i:61655 original size:19 final size:18
Alignment explanation
Indices: 61622--61657 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
61612 TGGAAATACT
61622 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
61640 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
61658 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:63263 original size:168 final size:167
Alignment explanation
Indices: 62985--63494 Score: 752
Period size: 168 Copynumber: 3.0 Consensus size: 167
62975 TTATTGCAAA
*
62985 GATATTAATGTAGAGATTTTT-GAAGGGGAAATCGGCAATAAATCCGTGGAAGCTGATTTGGTGG
1 GATATTAATGTAGAG-TTTTTCGAAGGGGAAATCGGCAATAAATCCGTGGAAGTTGATTTGGTGG
* *
63049 TGAATATTTTGAATTCAAATAGGAGTGATGTTGCTAATGGAGATTTGGTTATTTATGATAGCATT
65 TGAATAATTTGAATTCAATTAGGAGTGATGTTGCTAATGGAGATTTGGTTATTTATGATAGCATT
* * *
63114 GACTCTAGAAAAGAGGAGTTTGTTGCAGAATCTATTGAT
130 GACTCTTGTAAAGAGGA-TTTGTTGCAGAATCTAATGAT
*
63153 GATATTAATGTAGAGTTTTTCGAAGGGGAAATCGGCAATAAATCCGTCGAAGTTGATTTGGTGGT
1 GATATTAATGTAGAGTTTTTCGAAGGGGAAATCGGCAATAAATCCGTGGAAGTTGATTTGGTGGT
* * *
63218 GAATAGTTTGAATTCAATTAGGAGCGATGTTGCTAATGGAGATTTGGTTATTTATGATTGCATTG
66 GAATAATTTGAATTCAATTAGGAGTGATGTTGCTAATGGAGATTTGGTTATTTATGATAGCATTG
* *
63283 ACTCTTTTAAAGAGGAATTTGTTGCAGAATCTAATGAA
131 ACTCTTGTAAAGAGG-ATTTGTTGCAGAATCTAATGAT
* * * ** *
63321 GATATTAATGTAGAGATTTTCGAAGGGGAAATTGGCAATATATCTATGGACGTTGATTTGGTGGT
1 GATATTAATGTAGAGTTTTTCGAAGGGGAAATCGGCAATAAATCCGTGGAAGTTGATTTGGTGGT
* * * * * *
63386 GAATAATTTGAATTCATTTAGGAGTGACGTTGCTAATGGAAATTTGGCTAATTATGATACCATTG
66 GAATAATTTGAATTCAATTAGGAGTGATGTTGCTAATGGAGATTTGGTTATTTATGATAGCATTG
*
63451 ACTCTTGTAAAGAGGTATTTGTTGCATAATCTAATGAT
131 ACTCTTGTAAAGAGG-ATTTGTTGCAGAATCTAATGAT
63489 GATATT
1 GATATT
63495 CAGGGCTTAG
Statistics
Matches: 309, Mismatches: 31, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
167 5 0.02
168 303 0.98
169 1 0.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (167 bp):
GATATTAATGTAGAGTTTTTCGAAGGGGAAATCGGCAATAAATCCGTGGAAGTTGATTTGGTGGT
GAATAATTTGAATTCAATTAGGAGTGATGTTGCTAATGGAGATTTGGTTATTTATGATAGCATTG
ACTCTTGTAAAGAGGATTTGTTGCAGAATCTAATGAT
Found at i:65892 original size:213 final size:213
Alignment explanation
Indices: 65525--66167 Score: 1146
Period size: 213 Copynumber: 3.0 Consensus size: 213
65515 TAATTTGTTC
65525 TATCTTTTATTTTTATTTCGTTTGATCTTCTCTTTTCCTT-GATTTCAGGTAGTGTATGACAAGG
1 TATCTTTTATTTTTATTTCGTTTGATCTTCTCTTTT-CTTGGATTTCAGGTAGTGTATGACAAGG
* *
65589 GAAACCACTGATTCTACTGCTCTTATTTCGTACATCCCTGAAATTGAGAAACTCTGCAAATTCAA
65 GCAACCACTGATTCTACTGCTCTTATTCCGTACATCCCTGAAATTGAGAAACTCTGCAAATTCAA
* *
65654 TCGACACAAACAAAACTTGAAAAGCAAAAAAAAAAAGAAATCATGGCTGAAGAACAAGTTGTTGA
130 TCGACACAAACAAAACTTGAAAAGCAAAGACAAAAAGAAATCATGGCTGAAGAACAAGTTGTTGA
65719 TACCAAACCTGTGGGAGAT
195 TACCAAACCTGTGGGAGAT
65738 TATCTTTTATTTTTATTTCGTTTGATCTTCTCTTTTCTTGGATTTCAGGTAGTGTATGACAAGGG
1 TATCTTTTATTTTTATTTCGTTTGATCTTCTCTTTTCTTGGATTTCAGGTAGTGTATGACAAGGG
* *
65803 CAACCACTGATT-TCACTGCTCTTATTCCGTACATCCCTCAAATTGAGAAACTCTGCAGATTCAA
66 CAACCACTGATTCT-ACTGCTCTTATTCCGTACATCCCTGAAATTGAGAAACTCTGCAAATTCAA
* *
65867 TCGACACAAACAAATCTTGAAAAGCAAAGACAAAAAGAAATCATGGCTGAAGAACAAGTTATTGA
130 TCGACACAAACAAAACTTGAAAAGCAAAGACAAAAAGAAATCATGGCTGAAGAACAAGTTGTTGA
65932 TACCAAACCTGTGGGAGAT
195 TACCAAACCTGTGGGAGAT
65951 TATCTTTTATTTTTATTTCGTTTGATCTTCTCTTTTCTTGGATTTCAGGTAGTGTATGACAAGGG
1 TATCTTTTATTTTTATTTCGTTTGATCTTCTCTTTTCTTGGATTTCAGGTAGTGTATGACAAGGG
66016 CAACCACTGATTCTACTGCTCTTATTCCGTACATCCCTGAAATTGAGAAACTCTGCAAATTCAAT
66 CAACCACTGATTCTACTGCTCTTATTCCGTACATCCCTGAAATTGAGAAACTCTGCAAATTCAAT
* * *
66081 CGAATACAGACAAAACTTGAAAAACAAAGACAAAAAGAAATCATGGCTGAAGAACAAGTTGTTGA
131 CG-ACACAAACAAAACTTGAAAAGCAAAGACAAAAAGAAATCATGGCTGAAGAACAAGTTGTTGA
66146 TACCAAACCTGTGGGAGAT
195 TACCAAACCTGTGGGAGAT
66165 TAT
1 TAT
66168 GCTATCCTGA
Statistics
Matches: 411, Mismatches: 15, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
212 4 0.01
213 327 0.80
214 80 0.19
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Consensus pattern (213 bp):
TATCTTTTATTTTTATTTCGTTTGATCTTCTCTTTTCTTGGATTTCAGGTAGTGTATGACAAGGG
CAACCACTGATTCTACTGCTCTTATTCCGTACATCCCTGAAATTGAGAAACTCTGCAAATTCAAT
CGACACAAACAAAACTTGAAAAGCAAAGACAAAAAGAAATCATGGCTGAAGAACAAGTTGTTGAT
ACCAAACCTGTGGGAGAT
Found at i:69768 original size:19 final size:18
Alignment explanation
Indices: 69744--69779 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
69734 TGAAGATTTA
69744 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
69763 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
69780 ATTGTTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:71290 original size:6 final size:7
Alignment explanation
Indices: 71264--71288 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
71254 TTGTGTATTA
71264 TTTTTCT
1 TTTTTCT
71271 TTTTTCT
1 TTTTTCT
71278 TTTTTCT
1 TTTTTCT
71285 TTTT
1 TTTT
71289 CTATTTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:73739 original size:30 final size:28
Alignment explanation
Indices: 73686--73742 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 28
73676 GACTTCAACA
*
73686 AATAGATAATAAATAATGGAAATAGATG
1 AATAGATAATAAATAAGGGAAATAGATG
*
73714 AATAGATGATAGAATTAAGGGAAATAGAT
1 AATAGATAATA-AA-TAAGGGAAATAGAT
73743 TAAATAGAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 10 0.40
29 2 0.08
30 13 0.52
ACGTcount: A:0.54, C:0.00, G:0.21, T:0.25
Consensus pattern (28 bp):
AATAGATAATAAATAAGGGAAATAGATG
Found at i:74175 original size:50 final size:50
Alignment explanation
Indices: 74102--74400 Score: 492
Period size: 50 Copynumber: 6.0 Consensus size: 50
74092 GCATGATGCT
* *
74102 TTGCCACATAGATGTGGGCTTTGTA-TTGCCACATAGATGTAGACTTTGTA
1 TTGCCACATAGATGTGGGCTTTG-AGTTGCCACATAGATGTGGGCTTTGTA
* * * *
74152 TTGCCACATAGATGTGGGTTTTGTGTTGCCACATAGGTGTGGGCTTTGCA
1 TTGCCACATAGATGTGGGCTTTGAGTTGCCACATAGATGTGGGCTTTGTA
74202 TTGCCACATAGATGTGGGCTTTGAGTTGCCACATAGATGTGGGCTTTGTA
1 TTGCCACATAGATGTGGGCTTTGAGTTGCCACATAGATGTGGGCTTTGTA
*
74252 TTGCCACATAGATGTGGGCTTTGAGTTGCCAGATAGATGTGGGCTTTGTA
1 TTGCCACATAGATGTGGGCTTTGAGTTGCCACATAGATGTGGGCTTTGTA
*
74302 TTGCCACATAGATGTGGGCTTTGAGTTGCCACATAGATGTGGGCTTTGCA
1 TTGCCACATAGATGTGGGCTTTGAGTTGCCACATAGATGTGGGCTTTGTA
* *
74352 TTGCCACATAGATGTGGGTTTTGAGTTGCCATATAGATGTGGGCTTTGT
1 TTGCCACATAGATGTGGGCTTTGAGTTGCCACATAGATGTGGGCTTTGT
74401 GTTGAACCAT
Statistics
Matches: 232, Mismatches: 16, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
50 232 1.00
ACGTcount: A:0.20, C:0.15, G:0.30, T:0.35
Consensus pattern (50 bp):
TTGCCACATAGATGTGGGCTTTGAGTTGCCACATAGATGTGGGCTTTGTA
Found at i:74404 original size:25 final size:25
Alignment explanation
Indices: 74102--74400 Score: 444
Period size: 25 Copynumber: 12.0 Consensus size: 25
74092 GCATGATGCT
74102 TTGCCACATAGATGTGGGCTTTGTA
1 TTGCCACATAGATGTGGGCTTTGTA
* *
74127 TTGCCACATAGATGTAGACTTTGTA
1 TTGCCACATAGATGTGGGCTTTGTA
* *
74152 TTGCCACATAGATGTGGGTTTTGTG
1 TTGCCACATAGATGTGGGCTTTGTA
* *
74177 TTGCCACATAGGTGTGGGCTTTGCA
1 TTGCCACATAGATGTGGGCTTTGTA
74202 TTGCCACATAGATGTGGGCTTTG-A
1 TTGCCACATAGATGTGGGCTTTGTA
74226 GTTGCCACATAGATGTGGGCTTTGTA
1 -TTGCCACATAGATGTGGGCTTTGTA
74252 TTGCCACATAGATGTGGGCTTTG-A
1 TTGCCACATAGATGTGGGCTTTGTA
*
74276 GTTGCCAGATAGATGTGGGCTTTGTA
1 -TTGCCACATAGATGTGGGCTTTGTA
74302 TTGCCACATAGATGTGGGCTTTG-A
1 TTGCCACATAGATGTGGGCTTTGTA
*
74326 GTTGCCACATAGATGTGGGCTTTGCA
1 -TTGCCACATAGATGTGGGCTTTGTA
*
74352 TTGCCACATAGATGTGGGTTTTG-A
1 TTGCCACATAGATGTGGGCTTTGTA
*
74376 GTTGCCATATAGATGTGGGCTTTGT
1 -TTGCCACATAGATGTGGGCTTTGT
74401 GTTGAACCAT
Statistics
Matches: 250, Mismatches: 16, Indels: 15
0.89 0.06 0.05
Matches are distributed among these distances:
24 4 0.02
25 243 0.97
26 3 0.01
ACGTcount: A:0.20, C:0.15, G:0.30, T:0.35
Consensus pattern (25 bp):
TTGCCACATAGATGTGGGCTTTGTA
Found at i:77186 original size:17 final size:17
Alignment explanation
Indices: 77153--77185 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
77143 CTCCTCTTGC
*
77153 ATGAAAACACTTCTTTT
1 ATGAAAACAATTCTTTT
77170 ATGAAAACAATT-TTTT
1 ATGAAAACAATTCTTTT
77186 TTTAACTACC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.42
Consensus pattern (17 bp):
ATGAAAACAATTCTTTT
Found at i:82163 original size:16 final size:14
Alignment explanation
Indices: 82126--82169 Score: 54
Period size: 16 Copynumber: 3.0 Consensus size: 14
82116 TATCTATTTA
82126 TTTT-CTTTGCATTG
1 TTTTGCTTTG-ATTG
82140 TTTTGCTTTGATTG
1 TTTTGCTTTGATTG
82154 ATTATTGCTTTGATTG
1 -TT-TTGCTTTGATTG
82170 CTTGCTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 8 0.30
15 7 0.26
16 12 0.44
ACGTcount: A:0.11, C:0.09, G:0.18, T:0.61
Consensus pattern (14 bp):
TTTTGCTTTGATTG
Found at i:93553 original size:13 final size:13
Alignment explanation
Indices: 93535--93561 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
93525 TCTCCTACCG
93535 GTCGTTAACATTA
1 GTCGTTAACATTA
93548 GTCGTTAACATTA
1 GTCGTTAACATTA
93561 G
1 G
93562 AGGAGCAAAT
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:0.30, C:0.15, G:0.19, T:0.37
Consensus pattern (13 bp):
GTCGTTAACATTA
Found at i:94763 original size:25 final size:25
Alignment explanation
Indices: 94729--94777 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
94719 CCAAACAATC
94729 TTGAGCACTCTCACTCGGTCTCTAT
1 TTGAGCACTCTCACTCGGTCTCTAT
*
94754 TTGAGCACTCTCGCTCGGTCTCTA
1 TTGAGCACTCTCACTCGGTCTCTA
94778 CAAACTAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.14, C:0.33, G:0.18, T:0.35
Consensus pattern (25 bp):
TTGAGCACTCTCACTCGGTCTCTAT
Found at i:95129 original size:7 final size:7
Alignment explanation
Indices: 95096--95120 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
95086 AATTCCATCA
95096 AATCTTC
1 AATCTTC
95103 AATCTTC
1 AATCTTC
95110 AATCTTC
1 AATCTTC
95117 AATC
1 AATC
95121 AATCTTCAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.28, G:0.00, T:0.40
Consensus pattern (7 bp):
AATCTTC
Found at i:95689 original size:25 final size:25
Alignment explanation
Indices: 95653--95701 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
95643 CCAAACAATC
95653 TTGAGCACTCTCGCTCGGTCTCTAT
1 TTGAGCACTCTCGCTCGGTCTCTAT
*
95678 TTGAGCATTCTCGCTCGGTCTCTA
1 TTGAGCACTCTCGCTCGGTCTCTA
95702 CAAACTAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.12, C:0.31, G:0.20, T:0.37
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCGGTCTCTAT
Found at i:97014 original size:6 final size:6
Alignment explanation
Indices: 97003--97047 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
96993 TGGAAGTACG
* * * *
97003 AAGAAA AAGAAA AAAAAA AAGAAG AAGAAG AAGAAG AAGAAA AAG
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAG
97048 TCCCCGATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:97033 original size:9 final size:9
Alignment explanation
Indices: 97002--97047 Score: 56
Period size: 9 Copynumber: 5.1 Consensus size: 9
96992 ATGGAAGTAC
97002 GAAGAAAAA
1 GAAGAAAAA
*
97011 GAAAAAAAA
1 GAAGAAAAA
* *
97020 AAAGAAGAA
1 GAAGAAAAA
*
97029 GAAGAAGAA
1 GAAGAAAAA
97038 GAAGAAAAA
1 GAAGAAAAA
97047 G
1 G
97048 TCCCCGATCA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (9 bp):
GAAGAAAAA
Found at i:97811 original size:67 final size:67
Alignment explanation
Indices: 97703--97835 Score: 257
Period size: 67 Copynumber: 2.0 Consensus size: 67
97693 AATTATAAAC
*
97703 CATTTGATGTGATGGTACGGATAAGAAGGAAACGTGATTCCCCTTATTGGTTCCAAAGCTTAGTT
1 CATTTGATGTGATGGTACGGATAAGAAGGAAACGTGATTCCCCTCATTGGTTCCAAAGCTTAGTT
97768 GA
66 GA
97770 CATTTGATGTGATGGTACGGATAAGAAGGAAACGTGATTCCCCTCATTGGTTCCAAAGCTTAGTT
1 CATTTGATGTGATGGTACGGATAAGAAGGAAACGTGATTCCCCTCATTGGTTCCAAAGCTTAGTT
97835 G
66 G
97836 GGGATGGATA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.31
Consensus pattern (67 bp):
CATTTGATGTGATGGTACGGATAAGAAGGAAACGTGATTCCCCTCATTGGTTCCAAAGCTTAGTT
GA
Found at i:98286 original size:19 final size:19
Alignment explanation
Indices: 98229--98287 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
98219 CAAATCTAAG
*
98229 CTTCTCTTCAAATTAAAAA
1 CTTCTCTTCAAATCAAAAA
** *
98248 CTAT-TCGAACAAATC-TAAA
1 CT-TCTC-TTCAAATCAAAAA
98267 CTTCTCTTCAAATCAAAAA
1 CTTCTCTTCAAATCAAAAA
98286 CT
1 CT
98288 ACAGTCTCCT
Statistics
Matches: 29, Mismatches: 7, Indels: 8
0.66 0.16 0.18
Matches are distributed among these distances:
18 7 0.24
19 16 0.55
20 6 0.21
ACGTcount: A:0.42, C:0.24, G:0.02, T:0.32
Consensus pattern (19 bp):
CTTCTCTTCAAATCAAAAA
Found at i:101498 original size:1 final size:1
Alignment explanation
Indices: 101492--101520 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
101482 AAGATAAAGT
101492 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
101521 CTGCCTGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:105975 original size:19 final size:19
Alignment explanation
Indices: 105951--105988 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
105941 GTACCCACCT
*
105951 CCCCTCTATTTGGTACCCG
1 CCCCTCTATTCGGTACCCG
105970 CCCCTCTATTCGGTACCCG
1 CCCCTCTATTCGGTACCCG
105989 TGTTTCCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.11, C:0.45, G:0.16, T:0.29
Consensus pattern (19 bp):
CCCCTCTATTCGGTACCCG
Found at i:115579 original size:37 final size:37
Alignment explanation
Indices: 115528--115602 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
115518 TTAGTCATTA
*
115528 TTTATTTTGCTTAGGAGAGATTTATTCATTATTGGAG
1 TTTATTTTGCTTAGGAAAGATTTATTCATTATTGGAG
* *
115565 TTTATTTTGTTTAGGAAAGATTTATTCCTTATTGGAG
1 TTTATTTTGCTTAGGAAAGATTTATTCATTATTGGAG
115602 T
1 T
115603 GGAAGGAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.24, C:0.05, G:0.20, T:0.51
Consensus pattern (37 bp):
TTTATTTTGCTTAGGAAAGATTTATTCATTATTGGAG
Found at i:117347 original size:19 final size:19
Alignment explanation
Indices: 117289--117350 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
117279 ACAATTATTT
*
117289 ATAAAGTTATGTCTATATGG
1 ATAAAGTTATGTTTATAT-G
* *
117309 A-AAGAGATATGTATT-GATG
1 ATAA-AGTTATGT-TTATATG
117328 ATAAAGTTATGTTTATATG
1 ATAAAGTTATGTTTATATG
117347 ATAA
1 ATAA
117351 GACATGTGTG
Statistics
Matches: 33, Mismatches: 5, Indels: 9
0.70 0.11 0.19
Matches are distributed among these distances:
18 2 0.06
19 18 0.55
20 12 0.36
21 1 0.03
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.39
Consensus pattern (19 bp):
ATAAAGTTATGTTTATATG
Found at i:119605 original size:23 final size:23
Alignment explanation
Indices: 119557--119605 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
119547 TTATGAATCG
**
119557 AAAAAAATTGAGATTTGTTTCAC
1 AAAAAAATTGAGATTTGTGACAC
*
119580 AAAAAAATTTGAGATTTG-GACTC
1 AAAAAAA-TTGAGATTTGTGACAC
119603 AAA
1 AAA
119606 TCGAAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.31
Consensus pattern (23 bp):
AAAAAAATTGAGATTTGTGACAC
Found at i:125641 original size:6 final size:6
Alignment explanation
Indices: 125603--125637 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
125593 GTCAACTTGG
*
125603 GTGAGA GTGAGA GTGAGA GTGAGA GTGAGT GTGAG
1 GTGAGA GTGAGA GTGAGA GTGAGA GTGAGA GTGAG
125638 TGTGTTTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.51, T:0.20
Consensus pattern (6 bp):
GTGAGA
Found at i:126835 original size:21 final size:21
Alignment explanation
Indices: 126794--126841 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
126784 AACATATAAA
126794 ATTATTAAAAAATCTACTAAG
1 ATTATTAAAAAATCTACTAAG
* *
126815 CTTATTAAAAGATCTTA-TAAG
1 ATTATTAAAAAATC-TACTAAG
126836 ATTATT
1 ATTATT
126842 TTTAAAAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.40
Consensus pattern (21 bp):
ATTATTAAAAAATCTACTAAG
Found at i:127419 original size:12 final size:12
Alignment explanation
Indices: 127397--127432 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
127387 ATCAATCTAT
127397 TTTTAATTTTATC
1 TTTT-ATTTTATC
127410 TTTTATTTTATC
1 TTTTATTTTATC
*
127422 ATTTATTTTAT
1 TTTTATTTTAT
127433 TTATGGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 18 0.82
13 4 0.18
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTTATTTTATC
Found at i:132709 original size:15 final size:15
Alignment explanation
Indices: 132661--132710 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
132651 ACAGCACAAC
132661 AAAAACAAAACGAAAC-
1 AAAAACAAAA--AAACG
132677 AAAAAC-AAAAAACAG
1 AAAAACAAAAAAAC-G
132692 AAAAACAAAAAAACG
1 AAAAACAAAAAAACG
132707 AAAA
1 AAAA
132711 CGATGCCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
13 4 0.13
15 14 0.45
16 13 0.42
ACGTcount: A:0.80, C:0.14, G:0.06, T:0.00
Consensus pattern (15 bp):
AAAAACAAAAAAACG
Found at i:135211 original size:25 final size:26
Alignment explanation
Indices: 135161--135213 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
135151 ACTTGGTGTC
*
135161 AACTGTCATGAAACCAAAAAAAAAAA
1 AACTATCATGAAACCAAAAAAAAAAA
*
135187 AACTATCATGAAACGAAAAAAAAAAA
1 AACTATCATGAAACCAAAAAAAAAAA
135213 A
1 A
135214 GAGGTTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.68, C:0.13, G:0.08, T:0.11
Consensus pattern (26 bp):
AACTATCATGAAACCAAAAAAAAAAA
Found at i:140328 original size:41 final size:41
Alignment explanation
Indices: 140227--140316 Score: 126
Period size: 41 Copynumber: 2.2 Consensus size: 41
140217 TATAATCTTA
* * *
140227 AATCAGGGACAAAATTGAATCAATAAATAAATATCAACCTC
1 AATCAGGGACGAAATTGAACCAATAAAGAAATATCAACCTC
* * *
140268 AATCAGGGACGAAATTGAACCAATTAAGAAATGTTAACCTC
1 AATCAGGGACGAAATTGAACCAATAAAGAAATATCAACCTC
140309 AATCAGGG
1 AATCAGGG
140317 GGCAAATTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.47, C:0.17, G:0.16, T:0.21
Consensus pattern (41 bp):
AATCAGGGACGAAATTGAACCAATAAAGAAATATCAACCTC
Found at i:142758 original size:10 final size:10
Alignment explanation
Indices: 142745--142770 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
142735 ATTTTTTTAA
142745 TGTATTTTTC
1 TGTATTTTTC
142755 TGTATTTTTC
1 TGTATTTTTC
142765 TGTATT
1 TGTATT
142771 ATTATTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.12, C:0.08, G:0.12, T:0.69
Consensus pattern (10 bp):
TGTATTTTTC
Found at i:143102 original size:29 final size:28
Alignment explanation
Indices: 143068--143144 Score: 109
Period size: 29 Copynumber: 2.7 Consensus size: 28
143058 ATGTGAACTT
*
143068 AAAATGACCAAAATACCCCTGAATGTGCA
1 AAAATGACCAAAATGCCCCTGAAT-TGCA
* *
143097 AAAATGACCAAAATGCCCCTGAATTTCG
1 AAAATGACCAAAATGCCCCTGAATTGCA
*
143125 AAAATGACCGAAATGCCCCT
1 AAAATGACCAAAATGCCCCT
143145 AGATGACCCT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
28 21 0.48
29 23 0.52
ACGTcount: A:0.42, C:0.26, G:0.14, T:0.18
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCTGAATTGCA
Found at i:143591 original size:32 final size:32
Alignment explanation
Indices: 143555--143618 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
143545 GAGTTTTGAT
*
143555 TAATCGAGCATCGAGTTACTCGAGCTCGGCTC
1 TAATCGAGCATCGAGCTACTCGAGCTCGGCTC
* *
143587 TAATCGAGTATCGAGCTACTCGAGTTCGGCTC
1 TAATCGAGCATCGAGCTACTCGAGCTCGGCTC
143619 GACAAGTTCG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.27
Consensus pattern (32 bp):
TAATCGAGCATCGAGCTACTCGAGCTCGGCTC
Found at i:147393 original size:62 final size:61
Alignment explanation
Indices: 147297--147423 Score: 236
Period size: 62 Copynumber: 2.1 Consensus size: 61
147287 TATTATCAAT
*
147297 ATTGAAATGCATTCGTACCTAATTTCCCTAATGCCTACTGATTTCCACTTAGATCATCCAA
1 ATTGAAATGCACTCGTACCTAATTTCCCTAATGCCTACTGATTTCCACTTAGATCATCCAA
147358 ATTGAAATGGCACTCGTACCTAATTTCCCTAATGCCTACTGATTTCCACTTAGATCATCCAA
1 ATTGAAAT-GCACTCGTACCTAATTTCCCTAATGCCTACTGATTTCCACTTAGATCATCCAA
147420 ATTG
1 ATTG
147424 GTGACAATCT
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
61 8 0.12
62 56 0.88
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (61 bp):
ATTGAAATGCACTCGTACCTAATTTCCCTAATGCCTACTGATTTCCACTTAGATCATCCAA
Found at i:150202 original size:19 final size:19
Alignment explanation
Indices: 150162--150198 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
150152 AATTTTTAAG
150162 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
150181 TAAAAATATAATAT-TAAA
1 TAAAAATATAATATATAAA
150199 ATAATTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:150613 original size:18 final size:18
Alignment explanation
Indices: 150592--150650 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
150582 ACTTAATTTC
150592 CTTGAAATTAAGTCTTTG
1 CTTGAAATTAAGTCTTTG
* ** * *
150610 CTTG-ATTTACTTAATTTC
1 CTTGAAATTAAGT-CTTTG
150628 CTTGAAATTAAGTCTTTG
1 CTTGAAATTAAGTCTTTG
150646 CTTGA
1 CTTGA
150651 TTTTACCTAA
Statistics
Matches: 29, Mismatches: 10, Indels: 4
0.67 0.23 0.09
Matches are distributed among these distances:
17 5 0.17
18 19 0.66
19 5 0.17
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.47
Consensus pattern (18 bp):
CTTGAAATTAAGTCTTTG
Found at i:150873 original size:108 final size:108
Alignment explanation
Indices: 150457--151166 Score: 853
Period size: 108 Copynumber: 6.6 Consensus size: 108
150447 AATTGCCCTG
* * *
150457 AATTAAGTTCTTT-ATTGACTTTACTTAATTA-CCTCGAATTAAGT-T-T-ATTGACTCTACTTA
1 AATTAAG-TCTTTGCTTGA-TTTACTTAATTACCCT-GAATTAAGTCTGTGCTTGA-TTTACTTA
* * * * *
150517 ACTACCCTGAATTAAGTCCTTG-AC-TGCT-TTTACTTAATTACCCTG-
62 ATTACCCTGAATTAAGT-CTTGTGCTTG-TATTTACCTAATTTCCTTGA
* * * *
150562 AATTAAGTCTTAG-TTGATTTACTTAATTTCCTTGAAATTAAGTCTTTGCTTGATTTACTTAATT
1 AATTAAGTCTTTGCTTGATTTACTTAATTACCCTG-AATTAAGTCTGTGCTTGATTTACTTAATT
* * *
150626 TCCTTGAAATTAAGTCTT-TGCTTG-ATTTTACCTAATTTCCTTAA
65 ACCCTG-AATTAAGTCTTGTGCTTGTA-TTTACCTAATTTCCTTGA
* * * * * *
150670 AATTAAGTCTCTGCTTGATTTTACCTAATTTCCTTAAAATTAAGTCTTTGCTTGATTTACTTAAT
1 AATTAAGTCTTTGCTTGA-TTTACTTAATTACCCT-GAATTAAGTCTGTGCTTGATTTACTTAAT
150735 TACCCTGAATTAAGTC-TGTGCTTG-ATTTTACCTAATTTCCTTGA
64 TACCCTGAATTAAGTCTTGTGCTTGTA-TTTACCTAATTTCCTTGA
*
150779 AATTAAGTCTTTGCTTGATTTACTTAATTACCCTGAATTAAGTATGTGCTTGTATTTACTTAATT
1 AATTAAGTCTTTGCTTGATTTACTTAATTACCCTGAATTAAGTCTGTGCTTG-ATTTACTTAATT
*
150844 ACCCTGAATTAAGT-TTGTGCTTGTATTTACTTAATTTCCTTGA
65 ACCCTGAATTAAGTCTTGTGCTTGTATTTACCTAATTTCCTTGA
*
150887 AATTAAGTCTTTGCTTGATTTACTTAATTACCCTGAATTAAGTGTGTGCTTGTATTTACTTAATT
1 AATTAAGTCTTTGCTTGATTTACTTAATTACCCTGAATTAAGTCTGTGCTTG-ATTTACTTAATT
*
150952 ACCCTGAATTAAGT-TTGTGCTTGTATTTACTTAATTTCCTTGA
65 ACCCTGAATTAAGTCTTGTGCTTGTATTTACCTAATTTCCTTGA
* *
150995 AATTAAGTCTTTGTTTGATTTACTTAATTACCCTGAATTAAGTTTGTGCTTGATTTTACTTAATT
1 AATTAAGTCTTTGCTTGATTTACTTAATTACCCTGAATTAAGTCTGTGCTTGA-TTTACTTAATT
* *
151060 ACCCTAAATTAAGTCTT-TGCTTGT-TCTTACCCAATTTCCTTGA
65 ACCCTGAATTAAGTCTTGTGCTTGTAT-TTACCTAATTTCCTTGA
* * *
151103 AATTAAGTCTTTGCTTGATTTACTTAATTACCCTGAATTGAGTCTTTGCTTGTGTTTACTTAAT
1 AATTAAGTCTTTGCTTGATTTACTTAATTACCCTGAATTAAGTCTGTGCTTG-ATTTACTTAAT
151167 CCATTGATGC
Statistics
Matches: 543, Mismatches: 39, Indels: 43
0.87 0.06 0.07
Matches are distributed among these distances:
103 12 0.02
104 18 0.03
105 8 0.01
106 18 0.03
107 44 0.08
108 337 0.62
109 58 0.11
110 48 0.09
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.47
Consensus pattern (108 bp):
AATTAAGTCTTTGCTTGATTTACTTAATTACCCTGAATTAAGTCTGTGCTTGATTTACTTAATTA
CCCTGAATTAAGTCTTGTGCTTGTATTTACCTAATTTCCTTGA
Found at i:151081 original size:36 final size:36
Alignment explanation
Indices: 150443--151166 Score: 729
Period size: 36 Copynumber: 20.2 Consensus size: 36
150433 TATTGACCCC
* * *
150443 ACTTAATTGCCCTGAATTAAGTTCTTT-ATTGACTTT
1 ACTTAATTACCCTGAATTAAG-TCTTTGCTTGATTTT
* * *
150479 ACTTAATTA-CCTCGAATTAAG--TTT-ATTGACTCT
1 ACTTAATTACCCT-GAATTAAGTCTTTGCTTGATTTT
* * *
150512 ACTTAACTACCCTGAATTAAGTCCTTGAC-TGCTTTT
1 ACTTAATTACCCTGAATTAAGTCTTTG-CTTGATTTT
*
150548 ACTTAATTACCCTGAATTAAGTCTTAG-TTGA-TTT
1 ACTTAATTACCCTGAATTAAGTCTTTGCTTGATTTT
* *
150582 ACTTAATTTCCTTGAAATTAAGTCTTTGCTTGA-TTT
1 ACTTAATTACCCTG-AATTAAGTCTTTGCTTGATTTT
* *
150618 ACTTAATTTCCTTGAAATTAAGTCTTTGCTTGATTTT
1 ACTTAATTACCCTG-AATTAAGTCTTTGCTTGATTTT
* * * * *
150655 ACCTAATTTCCTTAAAATTAAGTCTCTGCTTGATTTT
1 ACTTAATTACCCT-GAATTAAGTCTTTGCTTGATTTT
* * * *
150692 ACCTAATTTCCTTAAAATTAAGTCTTTGCTTGA-TTT
1 ACTTAATTACCCT-GAATTAAGTCTTTGCTTGATTTT
*
150728 ACTTAATTACCCTGAATTAAGTCTGTGCTTGATTTT
1 ACTTAATTACCCTGAATTAAGTCTTTGCTTGATTTT
* * *
150764 ACCTAATTTCCTTGAAATTAAGTCTTTGCTTGA-TTT
1 ACTTAATTACCCTG-AATTAAGTCTTTGCTTGATTTT
* *
150800 ACTTAATTACCCTGAATTAAGTATGTGCTTG-TATTT
1 ACTTAATTACCCTGAATTAAGTCTTTGCTTGAT-TTT
150836 ACTTAATTACCCTGAATTAAGT-TTGTGCTTG-TATTT
1 ACTTAATTACCCTGAATTAAGTCTT-TGCTTGAT-TTT
* *
150872 ACTTAATTTCCTTGAAATTAAGTCTTTGCTTGA-TTT
1 ACTTAATTACCCTG-AATTAAGTCTTTGCTTGATTTT
* *
150908 ACTTAATTACCCTGAATTAAGTGTGTGCTTG-TATTT
1 ACTTAATTACCCTGAATTAAGTCTTTGCTTGAT-TTT
150944 ACTTAATTACCCTGAATTAAGT-TTGTGCTTG-TATTT
1 ACTTAATTACCCTGAATTAAGTCTT-TGCTTGAT-TTT
* * *
150980 ACTTAATTTCCTTGAAATTAAGTCTTTGTTTGA-TTT
1 ACTTAATTACCCTG-AATTAAGTCTTTGCTTGATTTT
151016 ACTTAATTACCCTGAATTAAGT-TTGTGCTTGATTTT
1 ACTTAATTACCCTGAATTAAGTCTT-TGCTTGATTTT
*
151052 ACTTAATTACCCTAAATTAAGTCTTTGCTTG-TTCTT
1 ACTTAATTACCCTGAATTAAGTCTTTGCTTGATT-TT
** * *
151088 ACCCAATTTCCTTGAAATTAAGTCTTTGCTTGA-TTT
1 ACTTAATTACCCTG-AATTAAGTCTTTGCTTGATTTT
*
151124 ACTTAATTACCCTGAATTGAGTCTTTGCTTG-TGTTT
1 ACTTAATTACCCTGAATTAAGTCTTTGCTTGAT-TTT
151160 ACTTAAT
1 ACTTAAT
151167 CCATTGATGC
Statistics
Matches: 597, Mismatches: 58, Indels: 66
0.83 0.08 0.09
Matches are distributed among these distances:
33 27 0.05
34 20 0.03
35 100 0.17
36 314 0.53
37 132 0.22
38 4 0.01
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.47
Consensus pattern (36 bp):
ACTTAATTACCCTGAATTAAGTCTTTGCTTGATTTT
Found at i:153284 original size:17 final size:17
Alignment explanation
Indices: 153262--153297 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
153252 CTTTTGTTTT
*
153262 TATGCCTACTTGATGCA
1 TATGCCTACCTGATGCA
153279 TATGCCTACCTGATGCA
1 TATGCCTACCTGATGCA
153296 TA
1 TA
153298 CTGTGTTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (17 bp):
TATGCCTACCTGATGCA
Found at i:156537 original size:79 final size:79
Alignment explanation
Indices: 156406--156564 Score: 273
Period size: 79 Copynumber: 2.0 Consensus size: 79
156396 TATAATAATA
* *
156406 TATATTGGTTTTCTCCCAACCAATCACCTTTGGACAAATATCAGCATGATAAGAGTCAAATACTG
1 TATATTGGTTTTCTCCCAACCAATCACCTTGGGACAAATATCAGCATGATAAGAGCCAAATACTG
156471 AGCATAAAACAGTT
66 AGCATAAAACAGTT
* *
156485 TATATTGGTTTTCTCCCAACCAATCACCTTGGGGCAAATGTCAGCATGATAAGAGCCAAATACTG
1 TATATTGGTTTTCTCCCAACCAATCACCTTGGGACAAATATCAGCATGATAAGAGCCAAATACTG
*
156550 AGCATACAACAGTT
66 AGCATAAAACAGTT
156564 T
1 T
156565 GGGGATAACT
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 75 1.00
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (79 bp):
TATATTGGTTTTCTCCCAACCAATCACCTTGGGACAAATATCAGCATGATAAGAGCCAAATACTG
AGCATAAAACAGTT
Found at i:161139 original size:29 final size:29
Alignment explanation
Indices: 161097--161158 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
161087 TGTGTATCTA
*
161097 ATTTGTTAATCAGGCTTCCATCGGTATGG
1 ATTTGTTAATCAGGCTTCCATCGGTATCG
161126 ATTTGTTAATCAGGCTTCCATCGGTATCG
1 ATTTGTTAATCAGGCTTCCATCGGTATCG
161155 ATTT
1 ATTT
161159 CTTCCCTTCC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.40
Consensus pattern (29 bp):
ATTTGTTAATCAGGCTTCCATCGGTATCG
Found at i:168326 original size:16 final size:16
Alignment explanation
Indices: 168301--168333 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
168291 TGGGCCATGT
*
168301 TATTATTATATATTAA
1 TATTAATATATATTAA
168317 TATTAATATATATTAA
1 TATTAATATATATTAA
168333 T
1 T
168334 TTGACGTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTAATATATATTAA
Found at i:175887 original size:10 final size:11
Alignment explanation
Indices: 175868--175897 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
175858 AATTTCGCCG
175868 AAATTATTAAT
1 AAATTATTAAT
175879 AAA-TATTAAT
1 AAATTATTAAT
175889 AAATTATTA
1 AAATTATTA
175898 TTATTATTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
AAATTATTAAT
Found at i:183874 original size:59 final size:59
Alignment explanation
Indices: 183782--183900 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
183772 CTAAGTATGC
183782 TGCTTTTATAAGGGTGTTATCATCACAAATATTTTAACGGCAATTGATATTAAGCAGTT
1 TGCTTTTATAAGGGTGTTATCATCACAAATATTTTAACGGCAATTGATATTAAGCAGTT
183841 TGCTTTTATAAGGGTGTTATCATCACAAATATTTTAACGGCAATTGATATTAAGCAGTT
1 TGCTTTTATAAGGGTGTTATCATCACAAATATTTTAACGGCAATTGATATTAAGCAGTT
183900 T
1 T
183901 TGGGTAAGAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (59 bp):
TGCTTTTATAAGGGTGTTATCATCACAAATATTTTAACGGCAATTGATATTAAGCAGTT
Found at i:186728 original size:6 final size:6
Alignment explanation
Indices: 186719--186769 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
186709 TCGGGTTAAG
* *
186719 TCGGGT TC-GGT CTCGGG- TAGGGT TCGGGC TCGGGT TCGGG- TCGGGT
1 TCGGGT TCGGGT -TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT
186765 TCGGG
1 TCGGG
186770 CTCGAGTTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
5 12 0.32
6 23 0.62
7 2 0.05
ACGTcount: A:0.02, C:0.20, G:0.51, T:0.27
Consensus pattern (6 bp):
TCGGGT
Found at i:186751 original size:23 final size:22
Alignment explanation
Indices: 186719--186773 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 22
186709 TCGGGTTAAG
*
186719 TCGGGTTCGGTCTCGGGTAGGGT
1 TCGGGCTCGGT-TCGGGTAGGGT
*
186742 TCGGGCTCGGGTTCGGGTCGGGT
1 TCGGGCTC-GGTTCGGGTAGGGT
186765 TCGGGCTCG
1 TCGGGCTCG
186774 AGTTTGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 1 0.03
23 25 0.86
24 3 0.10
ACGTcount: A:0.02, C:0.22, G:0.49, T:0.27
Consensus pattern (22 bp):
TCGGGCTCGGTTCGGGTAGGGT
Found at i:186753 original size:12 final size:12
Alignment explanation
Indices: 186738--186773 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
186728 GTCTCGGGTA
186738 GGGTTCGGGCTC
1 GGGTTCGGGCTC
186750 GGGTTCGGG-TC
1 GGGTTCGGGCTC
186761 GGGTTCGGGCTC
1 GGGTTCGGGCTC
186773 G
1 G
186774 AGTTTGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.48
12 12 0.52
ACGTcount: A:0.00, C:0.22, G:0.53, T:0.25
Consensus pattern (12 bp):
GGGTTCGGGCTC
Found at i:186762 original size:11 final size:11
Alignment explanation
Indices: 186731--186769 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
186721 GGGTTCGGTC
*
186731 TCGGGTAGGGT
1 TCGGGTCGGGT
186742 TCGGGCTCGGGT
1 TCGGG-TCGGGT
186754 TCGGGTCGGGT
1 TCGGGTCGGGT
186765 TCGGG
1 TCGGG
186770 CTCGAGTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 16 0.62
12 10 0.38
ACGTcount: A:0.03, C:0.18, G:0.54, T:0.26
Consensus pattern (11 bp):
TCGGGTCGGGT
Found at i:186762 original size:17 final size:17
Alignment explanation
Indices: 186718--186769 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
186708 CTCGGGTTAA
*
186718 GTCGGGTTCGGTCTCGG
1 GTCGGGTTCGGGCTCGG
*
186735 GTAGGGTTCGGGCTCGG
1 GTCGGGTTCGGGCTCGG
*
186752 GTTCGGG-TCGGGTTCGG
1 G-TCGGGTTCGGGCTCGG
186769 G
1 G
186770 CTCGAGTTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 26 0.87
18 4 0.13
ACGTcount: A:0.02, C:0.19, G:0.52, T:0.27
Consensus pattern (17 bp):
GTCGGGTTCGGGCTCGG
Found at i:186931 original size:13 final size:12
Alignment explanation
Indices: 186908--186954 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
186898 AAGTTTATTG
186908 ATAATATATAAT
1 ATAATATATAAT
186920 ATAATAATATAAT
1 ATAAT-ATATAAT
* *
186933 ATAACAT-TATT
1 ATAATATATAAT
186944 ATCAATATATA
1 AT-AATATATA
186955 TTAAGATTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 13 0.45
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAATATATAAT
Found at i:187306 original size:22 final size:21
Alignment explanation
Indices: 187281--187328 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
187271 TCTCAACCTT
187281 AATCAATCAAAACAACATCAAA
1 AATCAA-CAAAACAACATCAAA
** *
187303 AATCAACCCAACAACATCTAA
1 AATCAACAAAACAACATCAAA
187324 AATCA
1 AATCA
187329 TGGAGGGGCG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.58, C:0.27, G:0.00, T:0.15
Consensus pattern (21 bp):
AATCAACAAAACAACATCAAA
Found at i:187541 original size:17 final size:17
Alignment explanation
Indices: 187521--187553 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
187511 AATTAAATTA
187521 ATTATTTATTA-GTTATT
1 ATTATTT-TTAGGTTATT
187538 ATTATTTTTAGGTTAT
1 ATTATTTTTAGGTTAT
187554 CTAATTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (17 bp):
ATTATTTTTAGGTTATT
Found at i:187729 original size:20 final size:22
Alignment explanation
Indices: 187704--187752 Score: 75
Period size: 20 Copynumber: 2.3 Consensus size: 22
187694 AGAATTAGGA
187704 TTATTAAGTATTAA-TATG-TT
1 TTATTAAGTATTAATTATGATT
*
187724 TTATTAATTATTAATTATGATT
1 TTATTAAGTATTAATTATGATT
187746 TTATTAA
1 TTATTAA
187753 AATATGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 13 0.50
21 4 0.15
22 9 0.35
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (22 bp):
TTATTAAGTATTAATTATGATT
Found at i:196410 original size:26 final size:23
Alignment explanation
Indices: 196380--196426 Score: 67
Period size: 26 Copynumber: 1.9 Consensus size: 23
196370 CTTGAAAAAT
196380 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAAC-TTGAT-GAT-AGATGGA
196406 TGAAAAACTTGATGATAGATG
1 TGAAAAACTTGATGATAGATG
196427 AATAGAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (23 bp):
TGAAAAACTTGATGATAGATGGA
Found at i:199004 original size:20 final size:20
Alignment explanation
Indices: 198981--199026 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
198971 TAATAAATAT
198981 TAAAATTAATTTAATTAAAA
1 TAAAATTAATTTAATTAAAA
* **
199001 TAAAATAAATTTTTTTAAAA
1 TAAAATTAATTTAATTAAAA
199021 -AAAATT
1 TAAAATT
199027 GGACCGGTCG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAAATTAATTTAATTAAAA
Found at i:199140 original size:22 final size:21
Alignment explanation
Indices: 199099--199140 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
199089 CTGCCCAAGC
*
199099 CTAATCGCGACCGGCCCGTGG
1 CTAATCGCGACCGGACCGTGG
*
199120 CTAAGTCGCGACCGGATCGTG
1 CTAA-TCGCGACCGGACCGTG
199141 ACTTGCCCGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.17, C:0.33, G:0.33, T:0.17
Consensus pattern (21 bp):
CTAATCGCGACCGGACCGTGG
Found at i:199154 original size:33 final size:32
Alignment explanation
Indices: 199102--199206 Score: 113
Period size: 33 Copynumber: 3.2 Consensus size: 32
199092 CCCAAGCCTA
**
199102 ATCGCGACCGGCCCGTGGCTAAGTCGCGACCGG
1 ATCGCGACATGCCCGTGGCT-AGTCGCGACCGG
* * * *
199135 ATCGTGACTTGCCCGTGGCTAGTCGTGACTGG
1 ATCGCGACATGCCCGTGGCTAGTCGCGACCGG
*
199167 ATCGCGACATGCCCGTCGGTTA-TCGCGATCCGG
1 ATCGCGACATGCCCGT-GGCTAGTCGCGA-CCGG
199200 ATCGCGA
1 ATCGCGA
199207 TTAGCCCATG
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
32 29 0.48
33 31 0.52
ACGTcount: A:0.15, C:0.31, G:0.33, T:0.20
Consensus pattern (32 bp):
ATCGCGACATGCCCGTGGCTAGTCGCGACCGG
Found at i:199169 original size:32 final size:33
Alignment explanation
Indices: 199102--199206 Score: 108
Period size: 32 Copynumber: 3.2 Consensus size: 33
199092 CCCAAGCCTA
**
199102 ATCGCGACCGGCCCGTGGCTAAGTCGCGACCGG
1 ATCGCGACATGCCCGTGGCTAAGTCGCGACCGG
* * * *
199135 ATCGTGACTTGCCCGTGGCT-AGTCGTGACTGG
1 ATCGCGACATGCCCGTGGCTAAGTCGCGACCGG
*
199167 ATCGCGACATGCCCGTCGG-TTA-TCGCGATCCGG
1 ATCGCGACATGCCCGT-GGCTAAGTCGCGA-CCGG
199200 ATCGCGA
1 ATCGCGA
199207 TTAGCCCATG
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
32 30 0.50
33 30 0.50
ACGTcount: A:0.15, C:0.31, G:0.33, T:0.20
Consensus pattern (33 bp):
ATCGCGACATGCCCGTGGCTAAGTCGCGACCGG
Found at i:199873 original size:2 final size:2
Alignment explanation
Indices: 199868--199900 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
199858 ATATAAGTTT
199868 TA TA TA TA TA TA TA TA TA TA TA -A T- TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
199901 TTAGTAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:213575 original size:26 final size:25
Alignment explanation
Indices: 213546--213596 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
213536 TGCTCGAGCT
*
213546 TGAGCCAAGTTTTGAGCTCCAAACCC
1 TGAGCCAAG-CTTGAGCTCCAAACCC
* *
213572 TGAGTCAAGCTTGAGTTCCAAACCC
1 TGAGCCAAGCTTGAGCTCCAAACCC
213597 CAATCGAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (25 bp):
TGAGCCAAGCTTGAGCTCCAAACCC
Found at i:213637 original size:11 final size:11
Alignment explanation
Indices: 213621--213647 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
213611 CTCAGGTATC
213621 CTACTATTTTA
1 CTACTATTTTA
213632 CTACTATTTTA
1 CTACTATTTTA
213643 CTACT
1 CTACT
213648 TAGCTCGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.22, G:0.00, T:0.52
Consensus pattern (11 bp):
CTACTATTTTA
Done.