Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015103.1 Kokia drynarioides strain JFW-HI SEQ_130147, 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: 203165
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:3325 original size:57 final size:57
Alignment explanation
Indices: 3237--3364 Score: 256
Period size: 57 Copynumber: 2.2 Consensus size: 57
3227 ACTAATGTAG
3237 AAGGTGTGGCTGATTGGTTGCCGACTAATGTTTTTCCAAGTCCAAAACAATTAGAAA
1 AAGGTGTGGCTGATTGGTTGCCGACTAATGTTTTTCCAAGTCCAAAACAATTAGAAA
3294 AAGGTGTGGCTGATTGGTTGCCGACTAATGTTTTTCCAAGTCCAAAACAATTAGAAA
1 AAGGTGTGGCTGATTGGTTGCCGACTAATGTTTTTCCAAGTCCAAAACAATTAGAAA
3351 AAGGTGTGGCTGAT
1 AAGGTGTGGCTGAT
3365 ATTGAACAAG
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 71 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (57 bp):
AAGGTGTGGCTGATTGGTTGCCGACTAATGTTTTTCCAAGTCCAAAACAATTAGAAA
Found at i:6984 original size:18 final size:18
Alignment explanation
Indices: 6961--6997 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
6951 TTTAATTTTA
* *
6961 AAAAATTATTAAAAGTAT
1 AAAAATTATAAAAAATAT
6979 AAAAATTATAAAAAATAT
1 AAAAATTATAAAAAATAT
6997 A
1 A
6998 TATTTTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (18 bp):
AAAAATTATAAAAAATAT
Found at i:15451 original size:24 final size:23
Alignment explanation
Indices: 15415--15460 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
15405 TATATTATTT
*
15415 TCATAAAAAATGGATAATTAATA
1 TCATAAAAAATGGATAACTAATA
*
15438 TCATAAAAAAATGGTTAACTAAT
1 TCAT-AAAAAATGGATAACTAAT
15461 TGTTGTTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.54, C:0.07, G:0.09, T:0.30
Consensus pattern (23 bp):
TCATAAAAAATGGATAACTAATA
Found at i:30927 original size:22 final size:19
Alignment explanation
Indices: 30893--30936 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 19
30883 ATATAGATTA
30893 TAAATAGGATTAATTAAGGC
1 TAAATAGGATTAATTAA-GC
30913 TAAATAAGTGATTAATTAAGC
1 TAAAT-AG-GATTAATTAAGC
30934 TAA
1 TAA
30937 TCATGAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.23
21 7 0.32
22 10 0.45
ACGTcount: A:0.48, C:0.05, G:0.16, T:0.32
Consensus pattern (19 bp):
TAAATAGGATTAATTAAGC
Found at i:33388 original size:28 final size:28
Alignment explanation
Indices: 33315--33381 Score: 111
Period size: 26 Copynumber: 2.5 Consensus size: 28
33305 CTCTCAACCG
33315 TTAATCGAATCAATTTTTCTTTAAAAAA
1 TTAATCGAATCAATTTTTCTTTAAAAAA
*
33343 TTAACCGAATCAATTTTT-TTT-AAAAA
1 TTAATCGAATCAATTTTTCTTTAAAAAA
33369 TTAATCGAATCAA
1 TTAATCGAATCAA
33382 ACTTTTTCGA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
26 17 0.46
27 3 0.08
28 17 0.46
ACGTcount: A:0.43, C:0.12, G:0.04, T:0.40
Consensus pattern (28 bp):
TTAATCGAATCAATTTTTCTTTAAAAAA
Found at i:40903 original size:6 final size:6
Alignment explanation
Indices: 40892--40916 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
40882 AATCATTCAC
40892 AAATAT AAATAT AAATAT AAATAT A
1 AAATAT AAATAT AAATAT AAATAT A
40917 TAATTTTAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATAT
Found at i:42161 original size:20 final size:20
Alignment explanation
Indices: 42138--42180 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
42128 AACGGTCAAA
42138 GTCAATAGTCAA-AGTCAACG
1 GTCAA-AGTCAATAGTCAACG
* *
42158 GTCAACGTCAATGGTCAACG
1 GTCAAAGTCAATAGTCAACG
42178 GTC
1 GTC
42181 GATCAACAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.21
Consensus pattern (20 bp):
GTCAAAGTCAATAGTCAACG
Found at i:42161 original size:26 final size:26
Alignment explanation
Indices: 42125--42175 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
42115 CAGAAAGAAT
42125 GTCAACGGTCAAAGTCAATAGTCAAA
1 GTCAACGGTCAAAGTCAATAGTCAAA
* *
42151 GTCAACGGTCAACGTCAATGGTCAA
1 GTCAACGGTCAAAGTCAATAGTCAA
42176 CGGTCGATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.20
Consensus pattern (26 bp):
GTCAACGGTCAAAGTCAATAGTCAAA
Found at i:42177 original size:13 final size:13
Alignment explanation
Indices: 42125--42175 Score: 66
Period size: 13 Copynumber: 3.9 Consensus size: 13
42115 CAGAAAGAAT
42125 GTCAACGGTCAAA
1 GTCAACGGTCAAA
**
42138 GTCAATAGTCAAA
1 GTCAACGGTCAAA
*
42151 GTCAACGGTCAAC
1 GTCAACGGTCAAA
*
42164 GTCAATGGTCAA
1 GTCAACGGTCAA
42176 CGGTCGATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.20
Consensus pattern (13 bp):
GTCAACGGTCAAA
Found at i:42347 original size:22 final size:22
Alignment explanation
Indices: 42282--42341 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
42272 TTTGGTTCAA
*
42282 AAAAAGTTTGGGTTTCTTTATTT
1 AAAAGGTTTGGGTTTC-TTATTT
42305 AAAAGGTTTGGGTTTCTTATTT
1 AAAAGGTTTGGGTTTCTTATTT
42327 AAAAGGTTTGGGTTT
1 AAAAGGTTTGGGTTT
42342 GCTATTGGGT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
22 21 0.58
23 15 0.42
ACGTcount: A:0.25, C:0.03, G:0.23, T:0.48
Consensus pattern (22 bp):
AAAAGGTTTGGGTTTCTTATTT
Found at i:49098 original size:30 final size:30
Alignment explanation
Indices: 49045--49342 Score: 257
Period size: 30 Copynumber: 10.3 Consensus size: 30
49035 AAAAATCAAA
49045 TTTTACCC-CTGAACTTC-CAAAAATTATAT
1 TTTTACCCTC-GAACTTCTCAAAAATTATAT
* * *
49074 TTTTACCCTCGAACCTCTCAAAAATCACAT
1 TTTTACCCTCGAACTTCTCAAAAATTATAT
49104 TTTTACCCTCGAACTTCTCAAAAATT-TCA-
1 TTTTACCCTCGAACTTCTCAAAAATTAT-AT
* * *
49133 TTTTACCCCCAAACTTC-CAAAAATCACT-T
1 TTTTACCCTCGAACTTCTCAAAAATTA-TAT
* **
49162 TTTTACCATTAAACTTCTCAAAAATTATA-
1 TTTTACCCTCGAACTTCTCAAAAATTATAT
* *
49191 TTTTACCC-CTACACTTC-CAAAAATTACAT
1 TTTTACCCTCGA-ACTTCTCAAAAATTATAT
* *
49220 TTTTATCCTCGAACTTCTCAAAAATCATAT
1 TTTTACCCTCGAACTTCTCAAAAATTATAT
* * *
49250 TTTTACCCTCGAACTTATCAAAAATCACA-
1 TTTTACCCTCGAACTTCTCAAAAATTATAT
* *
49279 TTTT-CCCTCGAATTTC-CAAAAATTACAT
1 TTTTACCCTCGAACTTCTCAAAAATTATAT
* * * *
49307 TTTCA-CC-CGAACTTTTCCAAAATTACA-
1 TTTTACCCTCGAACTTCTCAAAAATTATAT
49334 TTTTACCCT
1 TTTTACCCT
49343 TAAACTCTCT
Statistics
Matches: 220, Mismatches: 32, Indels: 34
0.77 0.11 0.12
Matches are distributed among these distances:
27 20 0.09
28 45 0.20
29 72 0.33
30 83 0.38
ACGTcount: A:0.34, C:0.28, G:0.02, T:0.36
Consensus pattern (30 bp):
TTTTACCCTCGAACTTCTCAAAAATTATAT
Found at i:49154 original size:58 final size:57
Alignment explanation
Indices: 49031--49302 Score: 268
Period size: 58 Copynumber: 4.7 Consensus size: 57
49021 TTCCTGAACA
* * *
49031 TTCCAAAAATCA-AATTTTACCC-CTGAACTTC-CAAAAATTATATTTTTACCCTCGAAC
1 TTCCAAAAATCACATTTTTACCCTC-GAACTTCTCAAAAATT-TA-TTTTACCCCCAAAC
*
49088 CTCTCAAAAATCACATTTTTACCCTCGAACTTCTCAAAAATTTCATTTTACCCCCAAAC
1 TTC-CAAAAATCACATTTTTACCCTCGAACTTCTCAAAAATTT-ATTTTACCCCCAAAC
* * ** * *
49147 TTCCAAAAATCACTTTTTTACCATTAAACTTCTCAAAAATTATATTTTACCCCTACAC
1 TTCCAAAAATCACATTTTTACCCTCGAACTTCTCAAAAATT-TATTTTACCCCCAAAC
* * * * *
49205 TTCCAAAAATTACATTTTTATCCTCGAACTTCTCAAAAATCATATTTTTACCCTCGAAC
1 TTCCAAAAATCACATTTTTACCCTCGAACTTCTCAAAAAT-TTA-TTTTACCCCCAAAC
* *
49264 TTATCAAAAATCACA-TTTT-CCCTCGAATTTC-CAAAAATT
1 TT-CCAAAAATCACATTTTTACCCTCGAACTTCTCAAAAATT
49303 ACATTTTCAC
Statistics
Matches: 179, Mismatches: 27, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
57 9 0.05
58 102 0.57
59 48 0.27
60 20 0.11
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.35
Consensus pattern (57 bp):
TTCCAAAAATCACATTTTTACCCTCGAACTTCTCAAAAATTTATTTTACCCCCAAAC
Found at i:49400 original size:29 final size:29
Alignment explanation
Indices: 49325--49394 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
49315 GAACTTTTCC
* *
49325 AAAATTACATTTT-ACCCTTAAACTCTCTA
1 AAAACTACATTTTAACCC-CAAACTCTCTA
*
49354 AAAACTACGTTTTAACCCCAAACTCTCT-
1 AAAACTACATTTTAACCCCAAACTCTCTA
*
49382 AAAACTTCATTTT
1 AAAACTACATTTT
49395 CGACCCTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 11 0.31
29 20 0.57
30 4 0.11
ACGTcount: A:0.37, C:0.26, G:0.01, T:0.36
Consensus pattern (29 bp):
AAAACTACATTTTAACCCCAAACTCTCTA
Found at i:54163 original size:15 final size:15
Alignment explanation
Indices: 54143--54172 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
54133 AGCAAGGACA
54143 CCATCGAACTAACTT
1 CCATCGAACTAACTT
54158 CCATCGAACTAACTT
1 CCATCGAACTAACTT
54173 TACACCTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.33, G:0.07, T:0.27
Consensus pattern (15 bp):
CCATCGAACTAACTT
Found at i:54772 original size:10 final size:9
Alignment explanation
Indices: 54755--54879 Score: 107
Period size: 9 Copynumber: 13.8 Consensus size: 9
54745 AGGAAAATGG
54755 AAGAAAAATA
1 AAGAAAAA-A
*
54765 AA-AGAAAA
1 AAGAAAAAA
54773 AAGAAGAAAA
1 AAGAA-AAAA
54783 AAGAAAAATA
1 AAGAAAAA-A
*
54793 AA-AGAAAA
1 AAGAAAAAA
54801 AAGAAGAAAA
1 AAGAA-AAAA
*
54811 AAG-GAAAA
1 AAGAAAAAA
54819 AAGAAAAAGA
1 AAGAAAAA-A
54829 AAG--AAAA
1 AAGAAAAAA
*
54836 AAGAAGAAA
1 AAGAAAAAA
54845 AAGAAAAAA
1 AAGAAAAAA
54854 AAGAGAAAAA
1 AAGA-AAAAA
**
54864 AAGAGGAAA
1 AAGAAAAAA
54873 AAGAAAA
1 AAGAAAA
54880 GAAGAGGTCG
Statistics
Matches: 93, Mismatches: 12, Indels: 21
0.74 0.10 0.17
Matches are distributed among these distances:
7 4 0.04
8 16 0.17
9 39 0.42
10 34 0.37
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.02
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:54793 original size:28 final size:27
Alignment explanation
Indices: 54755--54882 Score: 136
Period size: 28 Copynumber: 4.6 Consensus size: 27
54745 AGGAAAATGG
*
54755 AAGAAAAATAAAAGAAAAAAGAAGAAAA
1 AAGAAAAAGAAAAGAAAAAAGAA-AAAA
*
54783 AAGAAAAATAAAAGAAAAAAGAAGAAAA
1 AAGAAAAAGAAAAGAAAAAAGAA-AAAA
*
54811 AAGGAAAAA-AGAAA-AAGAAAGAAAAAA
1 AA-GAAAAAGA-AAAGAAAAAAGAAAAAA
*
54838 GAAGAAAAAGAAAA-AAAAGAGAAAAAA
1 -AAGAAAAAGAAAAGAAAAAAGAAAAAA
54865 AGAGGAAAAAGAAAAGAA
1 A-A-GAAAAAGAAAAGAA
54883 GAGGTCGAGG
Statistics
Matches: 90, Mismatches: 3, Indels: 13
0.85 0.03 0.12
Matches are distributed among these distances:
26 1 0.01
27 25 0.28
28 53 0.59
29 11 0.12
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (27 bp):
AAGAAAAAGAAAAGAAAAAAGAAAAAA
Found at i:54819 original size:35 final size:34
Alignment explanation
Indices: 54764--54877 Score: 140
Period size: 35 Copynumber: 3.2 Consensus size: 34
54754 GAAGAAAAAT
54764 AAAAGAA-AAAAGAAGAAAAAAGAAAAATAAAAGAA
1 AAAAGAAGAAAA-AAGAAAAAAGAAAAA-AAAAGAA
*
54799 AAAAGAAGAAAAAAGGAAAAAAGAAAAAGAAAGAA
1 AAAAGAAGAAAAAA-GAAAAAAGAAAAAAAAAGAA
* *
54834 AAAAGAAGAAAAAGAAAAAAAAGAGAAAAAAAGAGGA
1 AAAAGAAGAAAAA-AGAAAAAAGA-AAAAAAA-AGAA
54871 AAAAGAA
1 AAAAGAA
54878 AAGAAGAGGT
Statistics
Matches: 70, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
35 36 0.51
36 24 0.34
37 10 0.14
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (34 bp):
AAAAGAAGAAAAAAGAAAAAAGAAAAAAAAAGAA
Found at i:56227 original size:39 final size:39
Alignment explanation
Indices: 56180--56779 Score: 375
Period size: 39 Copynumber: 15.4 Consensus size: 39
56170 CTTTTACCTT
56180 GAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCC
1 GAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCC
* **
56219 AAGCTTGGGGCAGAT-TGCAGTCAGCCAATCTCTTACCCC
1 GAGCTTGGGGCAGATCACCA-TCAGCCAATCTCTTACCCC
* * * * * *
56258 GAGCTTGGGGTAGATTA-CAGTCATCTAATCTTTTACCAC
1 GAGCTTGGGGCAGATCACCA-TCAGCCAATCTCTTACCCC
*
56297 GAGCTTGGGGCAGATCACCATCAGCNAATCTCTTACCCC
1 GAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCC
* * * * **
56336 GAGCTTGGGGCAGATTA-TAGTTAGTCAATCTCTTACCTT
1 GAGCTTGGGGCAGATCACCA-TCAGCCAATCTCTTACCCC
* * * * * * * * *
56375 GAGCCTGAGGCAAATTA-TAGCCATCCAATCTTTTATCCC
1 GAGCTTGGGGCAGATCACCA-TCAGCCAATCTCTTACCCC
* * * *
56414 GAGCTTGGGGTAGATCACCATCAACTAATCTCTTACCTC
1 GAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCC
* ** ** *
56453 GAGCCTAAGGCAGAT-TGCAGTCAACCAATCTCTTACCCC
1 GAGCTTGGGGCAGATCACCA-TCAGCCAATCTCTTACCCC
* * * * * * *
56492 GAGCCTGGGGTAGATTA-CAGCCATCCGATCTTTTACCCC
1 GAGCTTGGGGCAGATCACCA-TCAGCCAATCTCTTACCCC
* * * * * * *
56531 TAGCCTAGGGTAGATCACCATC-GTTCGATCTCTTACCCT
1 GAGCTTGGGGCAGATCACCATCAG-CCAATCTCTTACCCC
* *
56570 GAGCTTGGGGCAGATCACCATCAGCCAATCTCTTGCCAC
1 GAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCC
* * * **
56609 GAGCTTGGGGCAAATTGCAGTCATTAG---ATCTCTTACCTT
1 GAGCTTGGGGCAGA-T-CA-CCATCAGCCAATCTCTTACCCC
* * * *
56648 GAGAC-TGAGGCAAATCACCATAAGTCAATCTCTTACCCC
1 GAG-CTTGGGGCAGATCACCATCAGCCAATCTCTTACCCC
* *
56687 GAG-TCTGGGGCAGATTGCACCCATTAG---ATCTTTTACCCC
1 GAGCT-TGGGGCAGA-T-CA-CCATCAGCCAATCTCTTACCCC
* * *
56726 GGGCTTGAGGCAGATCACCATCAGCCAATCTATTACCCC
1 GAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCC
56765 GAGCTTGGGGCAGAT
1 GAGCTTGGGGCAGAT
56780 TGCAACCATT
Statistics
Matches: 435, Mismatches: 100, Indels: 52
0.74 0.17 0.09
Matches are distributed among these distances:
36 11 0.03
37 4 0.01
38 7 0.02
39 388 0.89
40 10 0.02
41 4 0.01
42 11 0.03
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (39 bp):
GAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCC
Found at i:56236 original size:78 final size:78
Alignment explanation
Indices: 56129--56801 Score: 482
Period size: 78 Copynumber: 8.6 Consensus size: 78
56119 GAAGATTCCG
* * * * * * **
56129 ATCTCTTACCCGGAGCCTGGAGCATATTGCAGTCATCCGATCTTTTACCTTGAGCTTGGGGCAGA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGTCATCCAATCTCTTACCCCGAGCTTGGGGCAGA
56194 TCACCATCAGCCA
66 TCACCATCAGCCA
* * *
56207 ATCTCTTACCCCAAGCTTGGGGCAGATTGCAGTCAGCCAATCTCTTACCCCGAGCTTGGGGTAGA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGTCATCCAATCTCTTACCCCGAGCTTGGGGCAGA
* * *
56272 TTA-CAGTCATCTA
66 TCACCA-TCAGCCA
* * ** * *
56285 ATCTTTTACCACGAGCTTGGGGCAGATCACCA-TCAGCNAATCTCTTACCCCGAGCTTGGGGCAG
1 ATCTCTTACCCCGAGCTTGGGGCAGAT-TGCAGTCATCCAATCTCTTACCCCGAGCTTGGGGCAG
* * * *
56349 ATTA-TAGTTAGTCA
65 ATCACCA-TCAGCCA
** * * * ** * * * *
56363 ATCTCTTACCTTGAGCCTGAGGCAAATTATAGCCATCCAATCTTTTATCCCGAGCTTGGGGTAGA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGTCATCCAATCTCTTACCCCGAGCTTGGGGCAGA
* *
56428 TCACCATCAACTA
66 TCACCATCAGCCA
* * ** * * *
56441 ATCTCTTACCTCGAGCCTAAGGCAGATTGCAGTCAACCAATCTCTTACCCCGAGCCTGGGGTAGA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGTCATCCAATCTCTTACCCCGAGCTTGGGGCAGA
* * * *
56506 TTA-CAGCCATCCG
66 TCACCA-TCAGCCA
* * * * * ** * * * *
56519 ATCTTTTACCCCTAGCCTAGGGTAGATCACCA-TCGTTCGATCTCTTACCCTGAGCTTGGGGCAG
1 ATCTCTTACCCCGAGCTTGGGGCAGAT-TGCAGTCATCCAATCTCTTACCCCGAGCTTGGGGCAG
56583 ATCACCATCAGCCA
65 ATCACCATCAGCCA
* * * * ** *
56597 ATCTCTTGCCACGAGCTTGGGGCAAATTGCAGTCAT-TAGATCTCTTACCTTGAGAC-TGAGGCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGTCATCCA-ATCTCTTACCCCGAG-CTTGGGGCA
* * *
56660 AATCACCATAAGTCA
64 GATCACCATCAGCCA
** * * * *
56675 ATCTCTTACCCCGAG-TCTGGGGCAGATTGCACCCAT-TAGATCTTTTACCCCGGGCTTGAGGCA
1 ATCTCTTACCCCGAGCT-TGGGGCAGATTGCAGTCATCCA-ATCTCTTACCCCGAGCTTGGGGCA
56738 GATCACCATCAGCCA
64 GATCACCATCAGCCA
* ** * *
56753 ATCTATTACCCCGAGCTTGGGGCAGATTGCAACCATTCAATATCTTACC
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGTCATCCAATCTCTTACC
56802 TAAAAAAAAT
Statistics
Matches: 466, Mismatches: 115, Indels: 28
0.77 0.19 0.05
Matches are distributed among these distances:
77 9 0.02
78 447 0.96
79 10 0.02
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (78 bp):
ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGTCATCCAATCTCTTACCCCGAGCTTGGGGCAGA
TCACCATCAGCCA
Found at i:56335 original size:117 final size:116
Alignment explanation
Indices: 56129--56705 Score: 554
Period size: 117 Copynumber: 4.9 Consensus size: 116
56119 GAAGATTCCG
* * * * * *
56129 ATCTCTTACCCGGAGCCTGGAGCATATTGCAGTCATCCGATCTTTTACCTTGAGCTTGGGGCAGA
1 ATCTCTTACCCCGAGCCTGGGGCAAATTACAGTCATCCAATCTTTTACCTCGAGCTTGGGGCAGA
*
56194 TCACCATCAGCCAATCTCTTACCCCAAGCTTGGGGCAGATTGCAGTCAGCCA
66 TCACCATCAG-CAATCTCTTACCCCGAGCTTGGGGCAGATTGCAGTCAGCCA
* * * * *
56246 ATCTCTTACCCCGAGCTTGGGGTAGATTACAGTCATCTAATCTTTTACCACGAGCTTGGGGCAGA
1 ATCTCTTACCCCGAGCCTGGGGCAAATTACAGTCATCCAATCTTTTACCTCGAGCTTGGGGCAGA
** * *
56311 TCACCATCAGCNAATCTCTTACCCCGAGCTTGGGGCAGATTATAGTTAGTCA
66 TCACCATCAGC-AATCTCTTACCCCGAGCTTGGGGCAGATTGCAGTCAGCCA
** * * * *
56363 ATCTCTTACCTTGAGCCTGAGGCAAATTATAGCCATCCAATCTTTTATCC-CGAGCTTGGGGTAG
1 ATCTCTTACCCCGAGCCTGGGGCAAATTACAGTCATCCAATCTTTTA-CCTCGAGCTTGGGGCAG
* * * ** *
56427 ATCACCATCAACTAATCTCTTACCTCGAGCCTAAGGCAGATTGCAGTCAACCA
65 ATCACCATCAGC-AATCTCTTACCCCGAGCTTGGGGCAGATTGCAGTCAGCCA
* * * * * * * * *
56480 ATCTCTTACCCCGAGCCTGGGGTAGATTACAGCCATCCGATCTTTTACCCCTAGCCTAGGGTAGA
1 ATCTCTTACCCCGAGCCTGGGGCAAATTACAGTCATCCAATCTTTTACCTCGAGCTTGGGGCAGA
* * **
56545 TCACCATC-GTTCGATCTCTTACCCTGAGCTTGGGGCAGATCACCA-TCAGCCA
66 TCACCATCAG--CAATCTCTTACCCCGAGCTTGGGGCAGAT-TGCAGTCAGCCA
* * * * * * * *
56597 ATCTCTTGCCACGAGCTTGGGGCAAATTGCAGTCAT-TAGATCTCTTACCTTGAGAC-TGAGGCA
1 ATCTCTTACCCCGAGCCTGGGGCAAATTACAGTCATCCA-ATCTTTTACCTCGAG-CTTGGGGCA
* *
56660 AATCACCATAAGTCAATCTCTTACCCCGAG-TCTGGGGCAGATTGCA
64 GATCACCATCAG-CAATCTCTTACCCCGAGCT-TGGGGCAGATTGCA
56706 CCCATTAGAT
Statistics
Matches: 372, Mismatches: 78, Indels: 21
0.79 0.17 0.04
Matches are distributed among these distances:
116 6 0.02
117 359 0.97
118 7 0.02
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (116 bp):
ATCTCTTACCCCGAGCCTGGGGCAAATTACAGTCATCCAATCTTTTACCTCGAGCTTGGGGCAGA
TCACCATCAGCAATCTCTTACCCCGAGCTTGGGGCAGATTGCAGTCAGCCA
Found at i:57625 original size:24 final size:24
Alignment explanation
Indices: 57598--57643 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
57588 TATTTTAAAA
*
57598 ATTATTAATG-CATTTACTTATTAC
1 ATTACTAATGTCATTTA-TTATTAC
57622 ATTACTAATGTCATTTATTATT
1 ATTACTAATGTCATTTATTATT
57644 TTCAAGCATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.33, C:0.11, G:0.04, T:0.52
Consensus pattern (24 bp):
ATTACTAATGTCATTTATTATTAC
Found at i:58953 original size:30 final size:30
Alignment explanation
Indices: 58860--59250 Score: 326
Period size: 29 Copynumber: 13.3 Consensus size: 30
58850 AAAAATCATA
* *
58860 TTTTACCCCCGAACTTC-CAAAAATTATAT
1 TTTTACCCTCGAACTTCTCAAAAATTACAT
* * * *
58889 TTTTGCCCCCGAACTT-TTAAAAATCACAT
1 TTTTACCCTCGAACTTCTCAAAAATTACAT
* *
58918 GTTTACCCTCAAACTTCTCAAAAATTACAT
1 TTTTACCCTCGAACTTCTCAAAAATTACAT
**
58948 TTTTACCCCTTTAACTTCTCAAAAATTACAT
1 TTTTA-CCCTCGAACTTCTCAAAAATTACAT
* *
58979 TTTTACTCCT-GAACTTC-CAAAAATCACGT
1 TTTTAC-CCTCGAACTTCTCAAAAATTACAT
** * *
59008 TTTTACCCTTAAACTTTTCAAAAATTACAC
1 TTTTACCCTCGAACTTCTCAAAAATTACAT
* * * * *
59038 TTTTGCCCCCAAACTTCT-AAAAACTATAT
1 TTTTACCCTCGAACTTCTCAAAAATTACAT
*
59067 TTTTACCCTCGAACTTCTCAAAAATCACATT
1 TTTTACCCTCGAACTTCTCAAAAATTACA-T
* *
59098 TTTTACCCTCGAACTTATCAAAAATCACA-
1 TTTTACCCTCGAACTTCTCAAAAATTACAT
*
59127 TTTTACCCCCGAACTTC-CAAAAATTACAT
1 TTTTACCCTCGAACTTCTCAAAAATTACAT
*
59156 TTTCACCCT-GAACTTTCTC--AAATTACAT
1 TTTTACCCTCGAAC-TTCTCAAAAATTACAT
* * *
59184 TTTTA-TCTCTAAAC-TCTCCAAAAACTACAT
1 TTTTACCCTC-GAACTTCT-CAAAAATTACAT
* *
59214 TTTAACCC-CGAAC-TCTTCAAAACTT-CAT
1 TTTTACCCTCGAACTTC-TCAAAAATTACAT
59242 TTTTGACCC
1 TTTT-ACCC
59251 CTTTTTTTTT
Statistics
Matches: 293, Mismatches: 50, Indels: 38
0.77 0.13 0.10
Matches are distributed among these distances:
27 5 0.02
28 37 0.13
29 123 0.42
30 67 0.23
31 61 0.21
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.36
Consensus pattern (30 bp):
TTTTACCCTCGAACTTCTCAAAAATTACAT
Found at i:58981 original size:90 final size:87
Alignment explanation
Indices: 58841--59251 Score: 364
Period size: 90 Copynumber: 4.7 Consensus size: 87
58831 GAAAGTTCTT
* * * * *
58841 AAACTT-TCCAAAAATCATATTTTACCCCCGAACTTCCAAAAATTATATTTTTGCCCCCGAACTT
1 AAACTTAT-CAAAAATTACATTTTACCCCCAAACTTCCAAAAATTACATTTTTACCCCCGAACTT
* *
58905 TTAAAAATCACATGTTTACCCTC
65 TCAAAAATCACATTTTTACCCTC
* ** * *
58928 AAACTTCTCAAAAATTACATTTTTACCCCTTTAACTTCTCAAAAATTACATTTTTACTCCTGAAC
1 AAACTTATCAAAAATTACA-TTTTACCCC-CAAACTTC-CAAAAATTACATTTTTACCCCCGAAC
* * *
58993 TTCCAAAAATCACGTTTTTACCCTT
63 TTTCAAAAATCACATTTTTACCCTC
* * * * * *
59018 AAACTTTTCAAAAATTACACTTTTGCCCCCAAACTTCTAAAAACTATATTTTTACCCTCGAACTT
1 AAACTTATCAAAAATTACA-TTTTACCCCCAAACTTCCAAAAATTACATTTTTACCCCCGAACTT
59083 CTCAAAAATCACATTTTTTACCCTC
65 -TCAAAAATCACA-TTTTTACCCTC
* * * * *
59108 GAACTTATCAAAAATCACATTTTACCCCCGAACTTCCAAAAATTACATTTTCA-CCCTGAACTTT
1 AAACTTATCAAAAATTACATTTTACCCCCAAACTTCCAAAAATTACATTTTTACCCCCGAACTTT
** * *
59172 CTCAAATTACATTTTTA-TCTC
66 CAAAAATCACATTTTTACCCTC
* * * * * *
59193 TAAACTCT-CCAAAAACTACATTTTAACCCCGAACTCTTCAAAACTT-CATTTTTGACCCC
1 -AAACT-TATCAAAAATTACATTTTACCCCCAAACT-TCCAAAAATTACATTTTT-ACCCC
59252 TTTTTTTTTT
Statistics
Matches: 263, Mismatches: 50, Indels: 21
0.79 0.15 0.06
Matches are distributed among these distances:
85 3 0.01
86 39 0.15
87 34 0.13
88 43 0.16
89 50 0.19
90 94 0.36
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.35
Consensus pattern (87 bp):
AAACTTATCAAAAATTACATTTTACCCCCAAACTTCCAAAAATTACATTTTTACCCCCGAACTTT
CAAAAATCACATTTTTACCCTC
Found at i:59031 original size:59 final size:58
Alignment explanation
Indices: 58842--59188 Score: 265
Period size: 59 Copynumber: 5.9 Consensus size: 58
58832 AAAGTTCTTA
* * * * * *
58842 AACTTTCCAAAAA-T-CATATTTTACCCCCGAACTTCCAAAAATTATATTTTTGCCCCCG
1 AACTTTTCAAAAATTACAT-TTTTA-CCCTGAACTTCCAAAAATCACATTTTTACCCTCG
* * * * **
58900 AACTTTT-AAAAATCACATGTTTACCCTCAAACTTCTCAAAAATTACATTTTTACCCCTTT
1 AACTTTTCAAAAATTACATTTTTACCCT-GAACTTC-CAAAAATCACATTTTTA-CCCTCG
* * **
58960 AACTTCTCAAAAATTACATTTTTACTCCTGAACTTCCAAAAATCACGTTTTTACCCTTA
1 AACTTTTCAAAAATTACATTTTTAC-CCTGAACTTCCAAAAATCACATTTTTACCCTCG
** ** * *
59019 AACTTTTCAAAAATTACACTTTTGCCCCCAAACTTCTAAAAA-CTATATTTTTACCCTCG
1 AACTTTTCAAAAATTACA-TTTTTACCCTGAACTTCCAAAAATC-ACATTTTTACCCTCG
* * * *
59078 AACTTCTCAAAAATCACATTTTTTACCCTCGAACTTATCAAAAATCACA-TTTTACCCCCG
1 AACTTTTCAAAAATTACA-TTTTTACCCT-GAACTT-CCAAAAATCACATTTTTACCCTCG
* * * ** *
59138 AAC-TTCCAAAAATTACATTTTCACCCTGAACTTTCTCAAATTACATTTTTA
1 AACTTTTCAAAAATTACATTTTTACCCTGAACTTCCAAAAATCACATTTTTA
59189 TCTCTAAACT
Statistics
Matches: 231, Mismatches: 45, Indels: 27
0.76 0.15 0.09
Matches are distributed among these distances:
56 9 0.04
57 19 0.08
58 26 0.11
59 98 0.42
60 47 0.20
61 28 0.12
62 4 0.02
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36
Consensus pattern (58 bp):
AACTTTTCAAAAATTACATTTTTACCCTGAACTTCCAAAAATCACATTTTTACCCTCG
Found at i:63368 original size:13 final size:15
Alignment explanation
Indices: 63340--63369 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
63330 TTTTTATAAG
63340 TTTTTTTAGAATTTT
1 TTTTTTTAGAATTTT
63355 TTTTTTTA-AATTTT
1 TTTTTTTAGAATTTT
63369 T
1 T
63370 ATATATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTTTTTAGAATTTT
Found at i:63400 original size:21 final size:21
Alignment explanation
Indices: 63374--63422 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
63364 ATTTTTATAT
*
63374 ATTTTTTAAATATATATTTTGA
1 ATTTTTGAAA-ATATATTTTGA
* *
63396 ATTTTTGAAAATTTTTTTTGA
1 ATTTTTGAAAATATATTTTGA
63417 ATTTTT
1 ATTTTT
63423 TTTTTTATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (21 bp):
ATTTTTGAAAATATATTTTGA
Found at i:65783 original size:20 final size:20
Alignment explanation
Indices: 65758--65811 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
65748 CTCCAGTGAG
* *
65758 ACTTCTACCGGTAGAACTCA
1 ACTTCTACCGATACAACTCA
* *
65778 ACTTCTACTGATACAACTCC
1 ACTTCTACCGATACAACTCA
65798 ACTTCTACCGATAC
1 ACTTCTACCGATAC
65812 CTTGAAGACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.30, C:0.33, G:0.09, T:0.28
Consensus pattern (20 bp):
ACTTCTACCGATACAACTCA
Found at i:66050 original size:20 final size:20
Alignment explanation
Indices: 65997--66075 Score: 70
Period size: 20 Copynumber: 4.0 Consensus size: 20
65987 CTACCTTAGG
* *
65997 ACTTCTACCGATAAAACTCC
1 ACTTCTACCGATACAACTAC
* *
66017 TCTTCTACTGATACAACTAC
1 ACTTCTACCGATACAACTAC
* * *
66037 AGTTCTACCGATACAAGTAT
1 ACTTCTACCGATACAACTAC
*
66057 GCTTCTACCGGA-ACAACTA
1 ACTTCTACC-GATACAACTA
66076 AGTTGCAAAC
Statistics
Matches: 46, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 44 0.96
21 2 0.04
ACGTcount: A:0.33, C:0.29, G:0.10, T:0.28
Consensus pattern (20 bp):
ACTTCTACCGATACAACTAC
Found at i:68933 original size:20 final size:20
Alignment explanation
Indices: 68908--68957 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
68898 CTACCGGTAG
68908 ACTTCTACCGGAAGAACTCC
1 ACTTCTACCGGAAGAACTCC
* *
68928 ACTTCTACCGGTAGAATTCC
1 ACTTCTACCGGAAGAACTCC
*
68948 CCTTCTACCG
1 ACTTCTACCG
68958 ATACAACTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.36, G:0.14, T:0.26
Consensus pattern (20 bp):
ACTTCTACCGGAAGAACTCC
Found at i:73803 original size:20 final size:21
Alignment explanation
Indices: 73780--73823 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
73770 TTATTATTTA
73780 ATTAAA-TT-TATTTTATATCT
1 ATTAAATTTATATTTTATAT-T
73800 ATTAAATTTATATTTTATATT
1 ATTAAATTTATATTTTATATT
73821 ATT
1 ATT
73824 TTTACATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.27
21 6 0.27
22 10 0.45
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTAAATTTATATTTTATATT
Found at i:74458 original size:33 final size:33
Alignment explanation
Indices: 74416--74493 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 33
74406 AGTCACACAA
*
74416 GCTGCATTTACAA-GAGCTGCAGTCGCATAAACT
1 GCTGCATTTACAAGGA-CTGCAGTCACATAAACT
*
74449 GCTGCATTTACATGGACTGCAGTCACATAAACT
1 GCTGCATTTACAAGGACTGCAGTCACATAAACT
* *
74482 GTTTCATTTACA
1 GCTGCATTTACA
74494 GAAACTACAG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
33 38 0.95
34 2 0.05
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.29
Consensus pattern (33 bp):
GCTGCATTTACAAGGACTGCAGTCACATAAACT
Found at i:74505 original size:33 final size:33
Alignment explanation
Indices: 74416--74505 Score: 92
Period size: 33 Copynumber: 2.7 Consensus size: 33
74406 AGTCACACAA
* * * *
74416 GCTGCATTTACAAGAGCTGCAGTCGCATAAACT
1 GCTGCATTTACATGAACTACAGTCACATAAACT
* *
74449 GCTGCATTTACATGGACTGCAGTCACATAAACT
1 GCTGCATTTACATGAACTACAGTCACATAAACT
* *
74482 GTTTCATTTACA-GAAACTACAGTC
1 GCTGCATTTACATG-AACTACAGTC
74506 GCATGAGCTG
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
32 1 0.02
33 47 0.98
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (33 bp):
GCTGCATTTACATGAACTACAGTCACATAAACT
Found at i:75332 original size:12 final size:12
Alignment explanation
Indices: 75315--75339 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
75305 TATCAGATCA
75315 TCGGTAACCATG
1 TCGGTAACCATG
75327 TCGGTAACCATG
1 TCGGTAACCATG
75339 T
1 T
75340 ATGTTTAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (12 bp):
TCGGTAACCATG
Found at i:76086 original size:17 final size:17
Alignment explanation
Indices: 76061--76094 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
76051 TTTTCTCGTG
*
76061 TTTGTAAAATAATTTAC
1 TTTGAAAAATAATTTAC
*
76078 TTTGAAAAATCATTTAC
1 TTTGAAAAATAATTTAC
76095 AACCAAACAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (17 bp):
TTTGAAAAATAATTTAC
Found at i:78604 original size:22 final size:21
Alignment explanation
Indices: 78571--78621 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
78561 ACTATTAAAA
78571 ATATTTTTTATA-TAAATATTT
1 ATATTTTTTATACTAAA-ATTT
*
78592 ATATTTTTCTATACTTAAATTT
1 ATATTTTT-TATACTAAAATTT
78614 A-ATTTTTT
1 ATATTTTTT
78622 TTATTTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 1 0.04
21 14 0.52
22 9 0.33
23 3 0.11
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (21 bp):
ATATTTTTTATACTAAAATTT
Found at i:78629 original size:20 final size:21
Alignment explanation
Indices: 78574--78631 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 21
78564 ATTAAAAATA
*
78574 TTTTTTATATAAATATTTATATT
1 TTTTTTAT-TTAA-ATTTATATT
* *
78597 TTTCTATACTTAAATTTA-ATT
1 TTT-TTTATTTAAATTTATATT
78618 TTTTTTATTTAAAT
1 TTTTTTATTTAAAT
78632 CGAATTTTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
20 9 0.31
21 6 0.21
22 5 0.17
23 6 0.21
24 3 0.10
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTTTATTTAAATTTATATT
Found at i:84492 original size:16 final size:17
Alignment explanation
Indices: 84468--84521 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
84458 CCTTCACCTT
84468 TTTATTCCTTGTCTTAG
1 TTTATTCCTTGTCTTAG
**
84485 TTTA-TCCTTCACCTT--
1 TTTATTCCTT-GTCTTAG
84500 TTTATTCCTTGTCTTAG
1 TTTATTCCTTGTCTTAG
84517 TTTAT
1 TTTAT
84522 CTTTGCTAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
15 7 0.24
16 10 0.34
17 12 0.41
ACGTcount: A:0.13, C:0.20, G:0.07, T:0.59
Consensus pattern (17 bp):
TTTATTCCTTGTCTTAG
Found at i:84495 original size:32 final size:32
Alignment explanation
Indices: 84458--84522 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
84448 TTCACTTCCC
84458 CCTTCACCTTTTTATTCCTTGTCTTAGTTTAT
1 CCTTCACCTTTTTATTCCTTGTCTTAGTTTAT
84490 CCTTCACCTTTTTATTCCTTGTCTTAGTTTAT
1 CCTTCACCTTTTTATTCCTTGTCTTAGTTTAT
84522 C
1 C
84523 TTTGCTAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.12, C:0.26, G:0.06, T:0.55
Consensus pattern (32 bp):
CCTTCACCTTTTTATTCCTTGTCTTAGTTTAT
Found at i:92285 original size:48 final size:48
Alignment explanation
Indices: 92224--92317 Score: 136
Period size: 48 Copynumber: 2.0 Consensus size: 48
92214 ATCCATCAGG
*
92224 TTTAATGTAAAATATACTT-ACCTCTATCATTTAAAAATACTCACTTGA
1 TTTAATGTAAAATATACTTAATCT-TATCATTTAAAAATACTCACTTGA
* * *
92272 TTTAATGTGAAATATACTTAATCTTATCATTTAAAAGTATTCACTT
1 TTTAATGTAAAATATACTTAATCTTATCATTTAAAAATACTCACTT
92318 ACCCCTTAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 38 0.93
49 3 0.07
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.43
Consensus pattern (48 bp):
TTTAATGTAAAATATACTTAATCTTATCATTTAAAAATACTCACTTGA
Found at i:93455 original size:18 final size:19
Alignment explanation
Indices: 93432--93470 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
93422 TTAGTAATAA
*
93432 TTTTATCTCAAAAATG-TT
1 TTTTATCCCAAAAATGCTT
93450 TTTTATCCCAAAAATGCTT
1 TTTTATCCCAAAAATGCTT
93469 TT
1 TT
93471 AAGAAACAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.31, C:0.15, G:0.05, T:0.49
Consensus pattern (19 bp):
TTTTATCCCAAAAATGCTT
Found at i:96880 original size:14 final size:14
Alignment explanation
Indices: 96854--96889 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
96844 TTTTCAAAAA
*
96854 AAAAAACATTTTTT
1 AAAAAATATTTTTT
*
96868 AATAAATATTTTTT
1 AAAAAATATTTTTT
96882 AAAAAATA
1 AAAAAATA
96890 AATTTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (14 bp):
AAAAAATATTTTTT
Found at i:103924 original size:24 final size:22
Alignment explanation
Indices: 103887--103939 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 22
103877 TAATTTTAAA
103887 AATTTTATACGATTTAAATAATAT
1 AATTTTATACGATTT--ATAATAT
* *
103911 AATTTTTTAGGATTTATAATAT
1 AATTTTATACGATTTATAATAT
*
103933 AACTTTA
1 AATTTTA
103940 GAAATTTTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 12 0.48
24 13 0.52
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.49
Consensus pattern (22 bp):
AATTTTATACGATTTATAATAT
Found at i:104679 original size:35 final size:33
Alignment explanation
Indices: 104619--104686 Score: 91
Period size: 35 Copynumber: 2.0 Consensus size: 33
104609 TATTGATTAA
* *
104619 GATTTTTTTCTTAAAAATTATAATATTTAAAAT
1 GATTTTTTTCTTAAAAATAAGAATATTTAAAAT
*
104652 GATTATTTTTGCTTATAAATAAGAATATTTAAAAT
1 GATT-TTTTT-CTTAAAAATAAGAATATTTAAAAT
104687 AATATATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 4 0.13
34 5 0.17
35 21 0.70
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (33 bp):
GATTTTTTTCTTAAAAATAAGAATATTTAAAAT
Found at i:106077 original size:31 final size:31
Alignment explanation
Indices: 106028--106110 Score: 103
Period size: 31 Copynumber: 2.7 Consensus size: 31
106018 CTAAATATTA
* * *
106028 TTTTGGTCCAAATAGGTACTTGAACTTGGTT
1 TTTTAGTCCAAATTGGTACTTGAACTTGGCT
* * *
106059 TTTTAGTTCAAATTGGTACCTGAATTTGGCT
1 TTTTAGTCCAAATTGGTACTTGAACTTGGCT
*
106090 TTTTAGTCCAAATTAGTACTT
1 TTTTAGTCCAAATTGGTACTT
106111 AGTTATTTGA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.24, C:0.13, G:0.18, T:0.45
Consensus pattern (31 bp):
TTTTAGTCCAAATTGGTACTTGAACTTGGCT
Found at i:115058 original size:17 final size:17
Alignment explanation
Indices: 115036--115115 Score: 115
Period size: 17 Copynumber: 4.7 Consensus size: 17
115026 TAAATAAATT
*
115036 TAAATTTAAATTTATAA
1 TAAATTTAAATTTAAAA
*
115053 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTAAAA
115070 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
115087 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
*
115104 TAAATTCAAATT
1 TAAATTTAAATT
115116 CTGTTGGGCC
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 55 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:115058 original size:23 final size:23
Alignment explanation
Indices: 115023--115070 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
115013 AATTGGAGTT
115023 ATTTAAATAAATTTAAATTT-AA
1 ATTTAAATAAATTTAAATTTCAA
115045 ATTTATAATAAATTTAAATTTCAA
1 ATTTA-AATAAATTTAAATTTCAA
115069 AT
1 AT
115071 AAATTTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 5 0.21
23 15 0.62
24 4 0.17
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTAAATAAATTTAAATTTCAA
Found at i:115073 original size:11 final size:10
Alignment explanation
Indices: 115023--115080 Score: 59
Period size: 10 Copynumber: 5.8 Consensus size: 10
115013 AATTGGAGTT
115023 ATTTAAATAA
1 ATTTAAATAA
115033 ATTTAAATTTAA
1 ATTTAAA--TAA
115045 ATTTATAATAA
1 ATTTA-AATAA
115056 ATTTAAAT--
1 ATTTAAATAA
*
115064 -TTCAAATAA
1 ATTTAAATAA
115073 ATTTAAAT
1 ATTTAAAT
115081 TTAAAATAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
7 6 0.15
10 16 0.40
11 8 0.20
12 8 0.20
13 2 0.05
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (10 bp):
ATTTAAATAA
Found at i:115079 original size:23 final size:23
Alignment explanation
Indices: 115028--115085 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
115018 GAGTTATTTA
**
115028 AATAAATTTAAATTTAAATTTAT
1 AATAAATTTAAATTTAAATAAAT
115051 AATAAATTTAAATTTCAAATAAAT
1 AATAAATTTAAATTT-AAATAAAT
*
115075 -TTAAATTTAAA
1 AATAAATTTAAA
115086 ATAAACTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 25 0.81
24 6 0.19
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
AATAAATTTAAATTTAAATAAAT
Found at i:115087 original size:7 final size:6
Alignment explanation
Indices: 115030--115115 Score: 67
Period size: 6 Copynumber: 15.0 Consensus size: 6
115020 GTTATTTAAA
115030 TAAATT TAAATT TAAATT TATAA-- TAAATT TAAATT TCAAA-- TAAATT
1 TAAATT TAAATT TAAATT TA-AATT TAAATT TAAATT T-AAATT TAAATT
* * * * *
115076 TAAATT TAAA-A TAAACT TAATTT TAAA-A TAAATT CAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
115116 CTGTTGGGCC
Statistics
Matches: 64, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
4 5 0.08
5 11 0.17
6 43 0.67
7 5 0.08
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (6 bp):
TAAATT
Found at i:116052 original size:115 final size:114
Alignment explanation
Indices: 115733--116064 Score: 380
Period size: 116 Copynumber: 2.9 Consensus size: 114
115723 AATTTGGTCC
* * * * * *
115733 ACTTCTCAGTATCTCATTAGGAAACTAACCTTTTGTTGCTTCGCCCTGCTTCTCAGTATCTCATC
1 ACTTCTCTGTATCTCATCAGGAAGCTAACCTTTTATTGTTTCGACCTGCTTCTCAGTATCTCATC
** * *
115798 AGGAAGCTGGGGTTCGAAGATTTGCTCGTATCGAGTCCTGAGTTGGTAT
66 AGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCCCTGAGTTAGTAT
* * * * * * ** *
115847 TCTTCTTTGTATCTCATCAGTAAGATGA-CTGCCTTACTTGTTTTAATCC-GCTTCTCTGTATCT
1 ACTTCTCTGTATCTCATCAGGAAGCTAACCT--TTTA-TTGTTTCGA-CCTGCTTCTCAGTATCT
* * *
115910 CATCAGGAAGCTGGGATTCGAAAATTTGATCACATCGAGCCCTGAGTTAGTAT
62 CATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCCCTGAGTTAGTAT
* *
115963 ACTTCTCTGTACCTCATCAGGAAGCTAACCATTTTATTATTTCGACCTGCTTCTCAGTATCTCAT
1 ACTTCTCTGTATCTCATCAGGAAGCTAACC-TTTTATTGTTTCGACCTGCTTCTCAGTATCTCAT
*
116028 CAGGAAGCTGGGGTTCGCAGATTTGCTCACATCGAGC
65 CAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGC
116065 GTGGGTTTGA
Statistics
Matches: 174, Mismatches: 37, Indels: 13
0.78 0.17 0.06
Matches are distributed among these distances:
113 2 0.01
114 22 0.13
115 57 0.33
116 89 0.51
117 3 0.02
118 1 0.01
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (114 bp):
ACTTCTCTGTATCTCATCAGGAAGCTAACCTTTTATTGTTTCGACCTGCTTCTCAGTATCTCATC
AGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCCCTGAGTTAGTAT
Found at i:116316 original size:205 final size:205
Alignment explanation
Indices: 115963--116649 Score: 1059
Period size: 205 Copynumber: 3.3 Consensus size: 205
115953 GAGTTAGTAT
* * *
115963 ACTTCTCTGTACCTCATCAGGAAGCTAACCATTTTATTATTTCGACCTGCTTCTCAGTATCTCAT
1 ACTTCTCAGTATCTCATCAGGAAGCTAACC-TTTTATTACTTCGACCTGCTTCTCAGTATCTCAT
* * * *
116028 CAGGAAGCTGGGGTTCGCAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAAC
65 CAGGAAGTTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTAGTCTTCTTCTCAAT
* *
116093 ATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATTCGCTTCTCTGTATCTCATTAGGAAGAC
130 ATCTCATCAGGAAGATGACTGCGTCGTTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAGAC
116158 GAATTTGGTCC
195 GAATTTGGTCC
* * *
116169 ACTTCTCAATATCTCATCAGGAAGCTAACCTTTTATTACTTCGACCTGCTTCTTAGTATCTTATC
1 ACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTACTTCGACCTGCTTCTCAGTATCTCATC
* * * * *
116234 AGGAAGTTGGGGCTCGAAGATTTGCTCACATTGAGCATGAGTTTGATTTAGTCTTCTTCTCAGTA
66 AGGAAGTTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTAGTCTTCTTCTCAATA
* **
116299 TCTTATCAGGAAGATGACTGCGTCGTTTGTTTCAATTTACTTCTCTGTATCTCATCAGGAAGACG
131 TCTCATCAGGAAGATGACTGCGTCGTTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAGACG
116364 AATTTGGTCC
196 AATTTGGTCC
* ** ** *
116374 ACTTCTCAGTATCTTATCAGGAAGCTAACCTTTTATTGTTTCTCCCTGCTTCTTAGTATCTCATC
1 ACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTACTTCGACCTGCTTCTCAGTATCTCATC
* *
116439 AGGAAGTTGGGATTCGAAGATTTACTCACATCGAGCGTGGGTTTGATTTAGTCTTCTTCTCAATA
66 AGGAAGTTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTAGTCTTCTTCTCAATA
* * *
116504 TCTCATCAAGAAGCTAACTGCGTCGTTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAGACG
131 TCTCATCAGGAAGATGACTGCGTCGTTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAGACG
116569 AATTTGGTCC
196 AATTTGGTCC
* * *
116579 ACTTCTCAGTATCTCATTAGGAAGCTAACCTTTTATTGCTTCGCCCTGCTTCTCAGTATCTCATC
1 ACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTACTTCGACCTGCTTCTCAGTATCTCATC
116644 AGGAAG
66 AGGAAG
116650 CTGAGATTCA
Statistics
Matches: 436, Mismatches: 45, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
205 409 0.94
206 27 0.06
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.37
Consensus pattern (205 bp):
ACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTACTTCGACCTGCTTCTCAGTATCTCATC
AGGAAGTTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTAGTCTTCTTCTCAATA
TCTCATCAGGAAGATGACTGCGTCGTTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAGACG
AATTTGGTCC
Found at i:128147 original size:13 final size:13
Alignment explanation
Indices: 128129--128154 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
128119 TGGGCTTTGA
128129 TTTGTAATTGGAC
1 TTTGTAATTGGAC
128142 TTTGTAATTGGAC
1 TTTGTAATTGGAC
128155 ATTATTTAAA
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:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (13 bp):
TTTGTAATTGGAC
Found at i:128176 original size:6 final size:6
Alignment explanation
Indices: 128165--128218 Score: 69
Period size: 6 Copynumber: 9.3 Consensus size: 6
128155 ATTATTTAAA
*
128165 TAAATT TAAATT TAAATT TATAA-- TAAATT TAAATT TAAA-A TAAATT
1 TAAATT TAAATT TAAATT TA-AATT TAAATT TAAATT TAAATT TAAATT
128211 TAAATT TA
1 TAAATT TA
128219 TAATAAACTT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
4 2 0.05
5 6 0.14
6 32 0.76
7 2 0.05
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
TAAATT
Found at i:128193 original size:17 final size:17
Alignment explanation
Indices: 128171--128250 Score: 115
Period size: 17 Copynumber: 4.7 Consensus size: 17
128161 TAAATAAATT
*
128171 TAAATTTAAATTTATAA
1 TAAATTTAAATTTAAAA
128188 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
128205 TAAATTTAAATTTATAA
1 TAAATTTAAATTTAAAA
* *
128222 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
*
128239 TAAATTCAAATT
1 TAAATTTAAATT
128251 ATGTTGGGCC
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 55 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:128212 original size:34 final size:34
Alignment explanation
Indices: 128171--128250 Score: 133
Period size: 34 Copynumber: 2.4 Consensus size: 34
128161 TAAATAAATT
*
128171 TAAATTTAAATTTATAATAAATTTAAATTTAAAA
1 TAAATTTAAATTTATAATAAACTTAAATTTAAAA
*
128205 TAAATTTAAATTTATAATAAACTTAATTTTAAAA
1 TAAATTTAAATTTATAATAAACTTAAATTTAAAA
*
128239 TAAATTCAAATT
1 TAAATTTAAATT
128251 ATGTTGGGCC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (34 bp):
TAAATTTAAATTTATAATAAACTTAAATTTAAAA
Found at i:128216 original size:23 final size:22
Alignment explanation
Indices: 128158--128203 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 22
128148 ATTGGACATT
128158 ATTTAAATAAATTTAAATTTAA
1 ATTTAAATAAATTTAAATTTAA
128180 ATTTATAATAAATTTAAATTTAA
1 ATTTA-AATAAATTTAAATTTAA
128203 A
1 A
128204 ATAAATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATTTAAATAAATTTAAATTTAA
Found at i:130780 original size:18 final size:18
Alignment explanation
Indices: 130753--130787 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
130743 TATTTACTAA
130753 GAAAAGTTTAAATAAAAT
1 GAAAAGTTTAAATAAAAT
* *
130771 GAAAATTTTAAGTAAAA
1 GAAAAGTTTAAATAAAA
130788 CTAAATTAGG
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:0.60, C:0.00, G:0.11, T:0.29
Consensus pattern (18 bp):
GAAAAGTTTAAATAAAAT
Found at i:132214 original size:13 final size:13
Alignment explanation
Indices: 132196--132221 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
132186 AATAAAAGAC
132196 GGTTAGAGCTGTA
1 GGTTAGAGCTGTA
132209 GGTTAGAGCTGTA
1 GGTTAGAGCTGTA
132222 ATAATCATCC
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:0.23, C:0.08, G:0.38, T:0.31
Consensus pattern (13 bp):
GGTTAGAGCTGTA
Found at i:136475 original size:133 final size:133
Alignment explanation
Indices: 136237--136484 Score: 469
Period size: 133 Copynumber: 1.9 Consensus size: 133
136227 ACTTGCGTAG
* *
136237 AAGTTTCATAAAAACTGACACTTCTTCATAAAGCTGGTAGAACAGGTTCCAGCCTAGAAGCTCGT
1 AAGTTTCATAAAAACTGACACTTCTTCATAAAGCCGGTAGAACAGATTCCAGCCTAGAAGCTCGT
136302 CCATGTTGATTGGAGCTCTTAACGGTCTAAGTTCAAGAAAACTCAAGTTTTGCACAAGTTAAAAG
66 CCATGTTGATTGGAGCTCTTAACGGTCTAAGTTCAAGAAAACTCAAGTTTTGCACAAGTTAAAAG
136367 TAA
131 TAA
*
136370 AAGTTTCATAAAAACTGACACTTCTTCATAAAGCCGGTAGAACAGATTCTAGCCTAGAAGCTCGT
1 AAGTTTCATAAAAACTGACACTTCTTCATAAAGCCGGTAGAACAGATTCCAGCCTAGAAGCTCGT
136435 CCATGTTGATTGGAGCTCTTAACGGTCTAAGTTCAAGAAAACTCAAGTTT
66 CCATGTTGATTGGAGCTCTTAACGGTCTAAGTTCAAGAAAACTCAAGTTT
136485 ATAATAGATT
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
133 112 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (133 bp):
AAGTTTCATAAAAACTGACACTTCTTCATAAAGCCGGTAGAACAGATTCCAGCCTAGAAGCTCGT
CCATGTTGATTGGAGCTCTTAACGGTCTAAGTTCAAGAAAACTCAAGTTTTGCACAAGTTAAAAG
TAA
Found at i:137152 original size:20 final size:18
Alignment explanation
Indices: 137129--137171 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 18
137119 TGATTTTTTA
137129 TATTTTTTATTTAATATAAT
1 TATTTTTTATTT--TATAAT
*
137149 TA-TTCTTATTTTATAAT
1 TATTTTTTATTTTATAAT
137166 TATTTT
1 TATTTT
137172 AATTTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
17 8 0.40
18 2 0.10
19 8 0.40
20 2 0.10
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
TATTTTTTATTTTATAAT
Found at i:137666 original size:19 final size:20
Alignment explanation
Indices: 137631--137670 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
137621 ATTAAGGATT
*
137631 AATTAATTAAAGTTTAATTA
1 AATTAATTAAAGGTTAATTA
137651 AATTAATT-AAGGTTAATTA
1 AATTAATTAAAGGTTAATTA
137670 A
1 A
137671 CTCATAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.42
Consensus pattern (20 bp):
AATTAATTAAAGGTTAATTA
Found at i:137688 original size:11 final size:10
Alignment explanation
Indices: 137633--137670 Score: 51
Period size: 11 Copynumber: 3.8 Consensus size: 10
137623 TAAGGATTAA
137633 TTAATTAAAG
1 TTAATTAAAG
137643 TTTAATTAAA-
1 -TTAATTAAAG
*
137653 TTAATTAAGG
1 TTAATTAAAG
137663 TTAATTAA
1 TTAATTAA
137671 CTCATAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
9 8 0.32
10 8 0.32
11 9 0.36
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (10 bp):
TTAATTAAAG
Found at i:138794 original size:30 final size:30
Alignment explanation
Indices: 138756--138931 Score: 192
Period size: 30 Copynumber: 5.9 Consensus size: 30
138746 AGTAACCATG
* *
138756 ATTATAATGTTAGCTTGTGTGAACAATTCA
1 ATTATAATGTCAGCTTGTGTGAGCAATTCA
* * * * * *
138786 ATTTTAATGTTAGCTTCTATGAACAATTCG
1 ATTATAATGTCAGCTTGTGTGAGCAATTCA
*
138816 ATTATAATGTCAGTTTGTGTGAGCAATTCA
1 ATTATAATGTCAGCTTGTGTGAGCAATTCA
* * **
138846 ATTATAATATCAGCTTGTGCGAGCAATTTG
1 ATTATAATGTCAGCTTGTGTGAGCAATTCA
*
138876 ATTATAATGTTAGCTTGTGTGAGCAA-TCTA
1 ATTATAATGTCAGCTTGTGTGAGCAATTC-A
* *
138906 ATTATAATGTCAGCTTATGTAAGCAA
1 ATTATAATGTCAGCTTGTGTGAGCAA
138932 CCATAAAAAT
Statistics
Matches: 121, Mismatches: 24, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
29 1 0.01
30 120 0.99
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (30 bp):
ATTATAATGTCAGCTTGTGTGAGCAATTCA
Found at i:138834 original size:60 final size:60
Alignment explanation
Indices: 138755--138921 Score: 219
Period size: 60 Copynumber: 2.8 Consensus size: 60
138745 AAGTAACCAT
* * * *
138755 GATTATAATGTTAGCTTGTGTGAACAATTCAATTTTAATGTTAGCTTCTATGAACAATTC
1 GATTATAATGTTAGCTTGTGTGAGCAATTCAATTATAATGTCAGCTTCTACGAACAATTC
* * * * * * *
138815 GATTATAATGTCAGTTTGTGTGAGCAATTCAATTATAATATCAGCTTGTGCGAGCAATTT
1 GATTATAATGTTAGCTTGTGTGAGCAATTCAATTATAATGTCAGCTTCTACGAACAATTC
138875 GATTATAATGTTAGCTTGTGTGAGCAA-TCTAATTATAATGTCAGCTT
1 GATTATAATGTTAGCTTGTGTGAGCAATTC-AATTATAATGTCAGCTT
138922 ATGTAAGCAA
Statistics
Matches: 92, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
59 2 0.02
60 90 0.98
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (60 bp):
GATTATAATGTTAGCTTGTGTGAGCAATTCAATTATAATGTCAGCTTCTACGAACAATTC
Found at i:139321 original size:36 final size:34
Alignment explanation
Indices: 139266--139339 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 34
139256 CTACTTTTTA
*
139266 AAATTTATTTTAAGATTAAATTTA-TCTCAAATTT
1 AAATTTATTTTAAGATTAAAATTATTCT-AAATTT
139300 AAATTTAATTTTTAA-ATTTAAAATTATTCTAAATTT
1 AAATTT-A-TTTTAAGA-TTAAAATTATTCTAAATTT
139336 AAAT
1 AAAT
139340 AAATAAAGTC
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
34 6 0.17
35 2 0.06
36 24 0.69
37 3 0.09
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.50
Consensus pattern (34 bp):
AAATTTATTTTAAGATTAAAATTATTCTAAATTT
Found at i:139561 original size:6 final size:6
Alignment explanation
Indices: 139550--139639 Score: 73
Period size: 6 Copynumber: 15.7 Consensus size: 6
139540 GGCCCAACAG
* * * *
139550 AATTTA AATTT- ATTTTA AAATTA AATTT- ATTTTA AGTTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
* * *
139595 ACTTAA AATTTA AATTT- -ATTATA AATTTA AGTTTA AATTTA AATT
1 AATTTA AATTTA AATTTA AATT-TA AATTTA AATTTA AATTTA AATT
139640 AATGTCCAAA
Statistics
Matches: 65, Mismatches: 13, Indels: 12
0.72 0.14 0.13
Matches are distributed among these distances:
4 3 0.05
5 12 0.18
6 47 0.72
7 3 0.05
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (6 bp):
AATTTA
Found at i:139641 original size:17 final size:17
Alignment explanation
Indices: 139550--139639 Score: 108
Period size: 17 Copynumber: 5.2 Consensus size: 17
139540 GGCCCAACAG
139550 AATTTAAATTTATTTTA
1 AATTTAAATTTATTTTA
*
139567 AAATTAAATTTATTTTA
1 AATTTAAATTTATTTTA
* * *
139584 AGTTTAAATTTACTTAA
1 AATTTAAATTTATTTTA
*
139601 AATTTAAATTTATTATA
1 AATTTAAATTTATTTTA
* *
139618 AATTTAAGTTTAAATTTA
1 AATTTAAATTT-ATTTTA
139636 AATT
1 AATT
139640 AATGTCCAAA
Statistics
Matches: 60, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
17 52 0.87
18 8 0.13
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (17 bp):
AATTTAAATTTATTTTA
Found at i:140322 original size:3 final size:3
Alignment explanation
Indices: 140314--140398 Score: 73
Period size: 3 Copynumber: 28.0 Consensus size: 3
140304 TAAATGACAT
* **
140314 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA -ATA TTG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
* * * * *
140359 TAA TAA TGA TAA TAT TAA TTAA TAT TAA TAT TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA
140399 AAAAGAGCCA
Statistics
Matches: 64, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
2 1 0.02
3 60 0.94
4 3 0.05
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:141497 original size:30 final size:29
Alignment explanation
Indices: 141454--141615 Score: 137
Period size: 29 Copynumber: 5.5 Consensus size: 29
141444 GAAGGTCCTT
* *
141454 AAACTATCCAAAATTCCATTTTTAACCCCA
1 AAACTTTCAAAAATTCCATTTTT-ACCCCA
* *
141484 AAAC-TTCTAAAAATTACATTTTTACCCCC
1 AAACTTTC-AAAAATTCCATTTTTACCCCA
* * * ***
141513 GAACTTTCAAAAATTCCATTTTAAGCTTG
1 AAACTTTCAAAAATTCCATTTTTACCCCA
** * * **
141542 AAACTTTTGAAAATTACAATTTTACCCTT
1 AAACTTTCAAAAATTCCATTTTTACCCCA
*
141571 AAACTTTCAAAAATCCCATTTTTGACCCCA
1 AAACTTTCAAAAATTCCATTTTT-ACCCCA
141601 AAACTTTCAAAAATT
1 AAACTTTCAAAAATT
141616 ATCATTTTAC
Statistics
Matches: 101, Mismatches: 28, Indels: 6
0.75 0.21 0.04
Matches are distributed among these distances:
29 63 0.62
30 38 0.38
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.35
Consensus pattern (29 bp):
AAACTTTCAAAAATTCCATTTTTACCCCA
Found at i:141640 original size:29 final size:29
Alignment explanation
Indices: 141608--141703 Score: 97
Period size: 29 Copynumber: 3.3 Consensus size: 29
141598 CCAAAACTTT
* *
141608 CAAAAATTATCATTTTACCCTCGGATGTC
1 CAAAAATTACCATTTTACCCTCGAATGTC
* **
141637 CAAAAACT-CCATTTTTGA-CCTCGAAACTC
1 CAAAAATTACCA-TTTT-ACCCTCGAATGTC
*
141666 TTAAAAATTACCATTTTACCCTCGAATGTC
1 -CAAAAATTACCATTTTACCCTCGAATGTC
141696 CAAAAATT
1 CAAAAATT
141704 TTGTTTTCTA
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
28 2 0.04
29 27 0.52
30 20 0.38
31 3 0.06
ACGTcount: A:0.35, C:0.25, G:0.07, T:0.32
Consensus pattern (29 bp):
CAAAAATTACCATTTTACCCTCGAATGTC
Found at i:141689 original size:30 final size:29
Alignment explanation
Indices: 141463--141691 Score: 118
Period size: 30 Copynumber: 7.8 Consensus size: 29
141453 TAAACTATCC
*
141463 AAAATT-CCATTTTTAACCC-CAAAACTTCTA
1 AAAATTACCA-TTTT-ACCCTCGAAACTT-TA
*
141493 AAAATTA-CATTTTTACCCCCG-AACTTTCA
1 AAAATTACCA-TTTTACCCTCGAAACTTT-A
** * *
141522 AAAATT-CCATTTTAAGCTTGAAACTTTTG
1 AAAATTACCATTTTACCCTCGAAAC-TTTA
* *
141551 AAAATTACAATTTTACCCT-TAAACTTTCA
1 AAAATTACCATTTTACCCTCGAAACTTT-A
* *
141580 AAAA-TCCCATTTTTGACCC-CAAAACTTTCA
1 AAAATTACCA-TTTT-ACCCTCGAAACTTT-A
* * ** **
141610 AAAATTATCATTTTACCCTCGGATGTCCA
1 AAAATTACCATTTTACCCTCGAAACTTTA
*
141639 AAAACT-CCATTTTTGA-CCTCGAAACTCTTA
1 AAAATTACCA-TTTT-ACCCTCGAAACT-TTA
141669 AAAATTACCATTTTACCCTCGAA
1 AAAATTACCATTTTACCCTCGAA
141692 TGTCCAAAAA
Statistics
Matches: 151, Mismatches: 30, Indels: 36
0.70 0.14 0.17
Matches are distributed among these distances:
28 16 0.11
29 61 0.40
30 68 0.45
31 6 0.04
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.34
Consensus pattern (29 bp):
AAAATTACCATTTTACCCTCGAAACTTTA
Found at i:141689 original size:59 final size:59
Alignment explanation
Indices: 141463--141702 Score: 197
Period size: 59 Copynumber: 4.1 Consensus size: 59
141453 TAAACTATCC
* * * *
141463 AAAATTCCATTTTTAACCCCAAAAC-TTCTAAAAATTA-CATTTTTACCCCCGAACT-TTCA
1 AAAATCCCATTTTTGACCCCAAAACTTTC-AAAAATTACCA-TTTTACCCTCGAA-TGTCCA
* * * *** ** * ** *
141522 AAAATTCCA-TTTTAAGCTTGAAACTTTTGAAAATTACAATTTTACCCTTAAACT-TTCA
1 AAAATCCCATTTTTGACCCCAAAACTTTCAAAAATTACCATTTTACCCTCGAA-TGTCCA
* *
141580 AAAATCCCATTTTTGACCCCAAAACTTTCAAAAATTATCATTTTACCCTCGGATGTCCA
1 AAAATCCCATTTTTGACCCCAAAACTTTCAAAAATTACCATTTTACCCTCGAATGTCCA
* *
141639 AAAA-CTCCATTTTTGACCTCGAAACTCTT-AAAAATTACCATTTTACCCTCGAATGTCCA
1 AAAATC-CCATTTTTGACCCCAAAACT-TTCAAAAATTACCATTTTACCCTCGAATGTCCA
141698 AAAAT
1 AAAAT
141703 TTTGTTTTCT
Statistics
Matches: 146, Mismatches: 28, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
58 44 0.30
59 100 0.68
60 2 0.01
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (59 bp):
AAAATCCCATTTTTGACCCCAAAACTTTCAAAAATTACCATTTTACCCTCGAATGTCCA
Found at i:144002 original size:28 final size:29
Alignment explanation
Indices: 143864--144154 Score: 184
Period size: 30 Copynumber: 9.9 Consensus size: 29
143854 GAAGGTCCTT
* *
143864 GAACTATCCAAAAATCATATTTTGACCCT-
1 GAACT-TCCAAAAATCACATTTTTACCCTC
* *
143893 TACACTTTTCC-AAAATCACATTTTGACACC-C
1 GA-AC--TTCCAAAAATCACATTTTTAC-CCTC
* * *
143924 GAACTTCCCAAAAATTATATTTTGAACCC-C
1 GAACTT-CCAAAAATCACATTTT-TACCCTC
* * ** *
143954 AAAATTTCCAAAAATTTCATTTTT-CCCTT
1 -GAACTTCCAAAAATCACATTTTTACCCTC
**
143983 GAACTTCTTAAAATCACATTTTTACCC-C
1 GAACTTCCAAAAATCACATTTTTACCCTC
** * **
144011 GAACTTTAAAAAAATTACATTTTGCCCCT-
1 GAAC-TTCCAAAAATCACATTTTTACCCTC
*
144040 GAACTTCCAAAAATCATATTTTTACCCTC
1 GAACTTCCAAAAATCACATTTTTACCCTC
* * *
144069 GAACCTCCAAAAAATCCCATTTTTACCATC
1 GAACTTCC-AAAAATCACATTTTTACCCTC
144099 GAACTTCCAAAAATCACATTTTTA-CCTC
1 GAACTTCCAAAAATCACATTTTTACCCTC
* * **
144127 GAATTTTCCTAAAATGGCATTTTTACCC
1 GAA-CTTCCAAAAATCACATTTTTACCC
144155 CTAAAACTTT
Statistics
Matches: 203, Mismatches: 42, Indels: 33
0.73 0.15 0.12
Matches are distributed among these distances:
28 50 0.25
29 66 0.33
30 74 0.36
31 12 0.06
32 1 0.00
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.34
Consensus pattern (29 bp):
GAACTTCCAAAAATCACATTTTTACCCTC
Found at i:144135 original size:29 final size:28
Alignment explanation
Indices: 143899--144155 Score: 151
Period size: 29 Copynumber: 8.9 Consensus size: 28
143889 CCCTTACACT
*
143899 TTTCC-AAAATCACATTTTGACACCCGAA
1 TTTCCAAAAATCACATTTTTAC-CCCGAA
* * * * *
143927 CTTCCCAAAAATTATATTTTGAACCCCAAAA
1 -TTTCCAAAAATCACATTTT-TACCCC-GAA
** *
143958 TTTCCAAAAATTTCATTTTT-CCCTTGAA
1 TTTCCAAAAATCACATTTTTACCC-CGAA
* **
143986 CTTCTTAAAATCACATTTTTACCCCGAA
1 TTTCCAAAAATCACATTTTTACCCCGAA
** * *
144014 CTTTAAAAAAATTACA-TTTTGCCCCTGAA
1 -TTTCCAAAAATCACATTTTTACCCC-GAA
* *
144043 CTTCCAAAAATCATATTTTTACCCTCGAA
1 TTTCCAAAAATCACATTTTTACCC-CGAA
** * *
144072 CCTCCAAAAAATCCCATTTTTACCATCGAA
1 TTTCC-AAAAATCACATTTTTACC-CCGAA
* *
144102 CTTCCAAAAATCACATTTTTACCTCGAA
1 TTTCCAAAAATCACATTTTTACCCCGAA
* **
144130 TTTTCCTAAAATGGCATTTTTACCCC
1 -TTTCCAAAAATCACATTTTTACCCC
144156 TAAAACTTTT
Statistics
Matches: 176, Mismatches: 40, Indels: 24
0.73 0.17 0.10
Matches are distributed among these distances:
28 46 0.26
29 71 0.40
30 55 0.31
31 4 0.02
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.34
Consensus pattern (28 bp):
TTTCCAAAAATCACATTTTTACCCCGAA
Found at i:144163 original size:59 final size:57
Alignment explanation
Indices: 143899--144156 Score: 184
Period size: 58 Copynumber: 4.5 Consensus size: 57
143889 CCCTTACACT
* * * * * *
143899 TTTCC-AAAATCACATTTTGACACCC-GAACTTCCCAAAAATTATATTTTGAACCCCAAAA
1 TTTCCAAAAATCACATTTTTAC-CCCTGAACTT-CCAAAAATCACATTTT-TACCTC-GAA
** * ** *
143958 TTTCCAAAAATTTCATTTTT-CCCTTGAACTTCTTAAAATCACATTTTTACCCCGAA
1 TTTCCAAAAATCACATTTTTACCCCTGAACTTCCAAAAATCACATTTTTACCTCGAA
** * * *
144014 CTTTAAAAAAATTACA-TTTTGCCCCTGAACTTCCAAAAATCATATTTTTACCCTCGAA
1 -TTTCCAAAAATCACATTTTTACCCCTGAACTTCCAAAAATCACATTTTTA-CCTCGAA
** * *
144072 CCTCCAAAAAATCCCATTTTTA-CCATCGAACTTCCAAAAATCACATTTTTACCTCGAA
1 TTTCC-AAAAATCACATTTTTACCCCT-GAACTTCCAAAAATCACATTTTTACCTCGAA
* **
144130 TTTTCCTAAAATGGCATTTTTACCCCT
1 -TTTCCAAAAATCACATTTTTACCCCT
144157 AAAACTTTTT
Statistics
Matches: 156, Mismatches: 33, Indels: 20
0.75 0.16 0.10
Matches are distributed among these distances:
56 6 0.04
57 43 0.28
58 51 0.33
59 45 0.29
60 11 0.07
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.34
Consensus pattern (57 bp):
TTTCCAAAAATCACATTTTTACCCCTGAACTTCCAAAAATCACATTTTTACCTCGAA
Found at i:155248 original size:209 final size:209
Alignment explanation
Indices: 154957--155508 Score: 863
Period size: 209 Copynumber: 2.6 Consensus size: 209
154947 AGTAAAGCCT
* * *
154957 AAAGTGAGAAAATCTTCGAA-CCTCAACTTCTTGATGAGATACTGAGAAGCGGGTTGAAGCAATA
1 AAAGTGAGAAAATCTTCGAACCCT-AACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATA
* * * * *
155021 AAACGGTTACCTTCCTGATAAGATACAGAGAAGTGAACCAAATTCGTCTTCCTGATGAGACACAG
65 AAGCGGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATAAGACACAG
155086 AGAAGTGGATCAAAACAAGTGATGCGGTCATCTTCCTAATGAGATACTGAGAAGTAGACCAAATC
130 AGAAGTGGATCAAAACAAGTGATGCGGTCATCTTCCTAATGAGATACTGAGAAGTAGACCAAATC
155151 CATGAAACCAGGCTC
195 CATGAAACCAGGCTC
155166 AAAGTGAGAAAATCTTCGAACCCTAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAA
1 AAAGTGAGAAAATCTTCGAACCCTAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAA
* * * * *
155231 AGCGGTTACCTTCCTGATGAGATACAAAGAAGTGAACCAGATCCATCTTCCTAATTAGACACAAA
66 AGCGGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATAAGACACAGA
* *
155296 GAAGTGGATCAAAATAAGTGATGCGTTCATCTTCCTAATGAGATACTGAGAAGTAGACCAAATCC
131 GAAGTGGATCAAAACAAGTGATGCGGTCATCTTCCTAATGAGATACTGAGAAGTAGACCAAATCC
155361 ATGAAACCAGGCTC
196 ATGAAACCAGGCTC
* * * *
155375 AAAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAGGTCGAAGCAATAA
1 AAAGTGAGAAAATCTTCGAACCCTAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAA
* * * * * *
155440 AGTGGTTACCTTCTTAATGAGATATAGAGAAGTGAACCAGATCCGTCTTCCTGATAAGATACTGA
66 AGCGGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATAAGACACAGA
155505 GAAG
131 GAAG
155509 CAGGTCGAAG
Statistics
Matches: 313, Mismatches: 29, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
209 310 0.99
210 3 0.01
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.22
Consensus pattern (209 bp):
AAAGTGAGAAAATCTTCGAACCCTAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAA
AGCGGTTACCTTCCTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATAAGACACAGA
GAAGTGGATCAAAACAAGTGATGCGGTCATCTTCCTAATGAGATACTGAGAAGTAGACCAAATCC
ATGAAACCAGGCTC
Found at i:155545 original size:85 final size:85
Alignment explanation
Indices: 155401--155586 Score: 264
Period size: 85 Copynumber: 2.2 Consensus size: 85
155391 CGAACCCCAG
*** ** *
155401 CTTCCTGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAGTGGTTACCTTCTTAATGAGATATA
1 CTTCCTGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAGCAATTACCTTCCGAATGAGATACA
*
155466 GAGAAGTGAACCAGATCCGT
66 GAGAAGTGAACCAAATCCGT
* * *
155486 CTTCCTGATAAGATACTGAGAAGCAGGTCGAAGCAATAAAGCAATTACCTTCCGGATGAGATACA
1 CTTCCTGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAGCAATTACCTTCCGAATGAGATACA
* *
155551 GAGAAGTGGACCAAATTCGT
66 GAGAAGTGAACCAAATCCGT
155571 CTTCCTGATGAGATAC
1 CTTCCTGATGAGATAC
155587 AGGGAAAATG
Statistics
Matches: 88, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
85 88 1.00
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (85 bp):
CTTCCTGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAGCAATTACCTTCCGAATGAGATACA
GAGAAGTGAACCAAATCCGT
Found at i:156106 original size:30 final size:29
Alignment explanation
Indices: 156074--156154 Score: 90
Period size: 30 Copynumber: 2.8 Consensus size: 29
156064 TGGACCTCCA
*
156074 AAAATCACGTTTTTACCCCAAAATTTTCC
1 AAAATCACGTTTTTACCCCAAAACTTTCC
* * *
156103 AAAATGACATTTTTACCCCTAAAACTTTCT
1 AAAATCACGTTTTTACCCC-AAAACTTTCC
* * *
156133 AAAATTATGTTTTAACCCCAAA
1 AAAATCACGTTTTTACCCCAAA
156155 CTCTCTGAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 20 0.47
30 23 0.53
ACGTcount: A:0.38, C:0.23, G:0.04, T:0.35
Consensus pattern (29 bp):
AAAATCACGTTTTTACCCCAAAACTTTCC
Found at i:156115 original size:29 final size:30
Alignment explanation
Indices: 156074--156137 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
156064 TGGACCTCCA
* *
156074 AAAATCACGTTTTTACCCC-AAAATTTTCC
1 AAAATCACATTTTTACCCCTAAAACTTTCC
* *
156103 AAAATGACATTTTTACCCCTAAAACTTTCT
1 AAAATCACATTTTTACCCCTAAAACTTTCC
156133 AAAAT
1 AAAAT
156138 TATGTTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 17 0.57
30 13 0.43
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.34
Consensus pattern (30 bp):
AAAATCACATTTTTACCCCTAAAACTTTCC
Found at i:157842 original size:20 final size:20
Alignment explanation
Indices: 157804--157842 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
157794 GGTAGGCATG
157804 TGAACCCTTTTAGTACATGTA
1 TGAACCCTTTTA-TACATGTA
157825 TGAACCCTGTTT-TACATG
1 TGAACCCT-TTTATACATG
157843 GTGCAAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 8 0.47
22 3 0.18
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (20 bp):
TGAACCCTTTTATACATGTA
Found at i:161562 original size:28 final size:30
Alignment explanation
Indices: 161499--161589 Score: 107
Period size: 31 Copynumber: 3.1 Consensus size: 30
161489 ATAATTTACA
*
161499 AAAATTA-AGTCAAATCAAAATTTTATATAT
1 AAAATTACAATCAAATCAAAA-TTTATATAT
161529 AAAATTAC-A-CAAATCAAAATTTATATAT
1 AAAATTACAATCAAATCAAAATTTATATAT
* * *
161557 ACAATTACAAATTAAATCATAATTTATATAT
1 AAAATTAC-AATCAAATCAAAATTTATATAT
161588 AA
1 AA
161590 TTTTAATATT
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
28 16 0.31
29 10 0.19
30 8 0.15
31 18 0.35
ACGTcount: A:0.55, C:0.09, G:0.01, T:0.35
Consensus pattern (30 bp):
AAAATTACAATCAAATCAAAATTTATATAT
Found at i:162334 original size:22 final size:23
Alignment explanation
Indices: 162308--162352 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
162298 TATTATTCTA
*
162308 AATTTAATATATTTA-AAAAATT
1 AATTTAACATATTTATAAAAATT
* *
162330 AATTTCACATTTTTATAAAAATT
1 AATTTAACATATTTATAAAAATT
162353 TAAAATGCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (23 bp):
AATTTAACATATTTATAAAAATT
Found at i:163206 original size:24 final size:24
Alignment explanation
Indices: 163144--163207 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 24
163134 TAATATATGT
163144 ATATAAATATATTTACAAATATTAA
1 ATATAAA-ATATTTACAAATATTAA
*
163169 AT-TAATAATAATTTATAAA-ATTAAA
1 ATATAA-AAT-ATTTACAAATATT-AA
163194 ATATAAAATATTTA
1 ATATAAAATATTTA
163208 GAGAGTGATA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
24 13 0.38
25 18 0.53
26 3 0.09
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (24 bp):
ATATAAAATATTTACAAATATTAA
Found at i:164092 original size:21 final size:23
Alignment explanation
Indices: 164049--164093 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
164039 CCCTTTTTAT
*
164049 TATTATTTGGCATCCATTTTAAAA
1 TATTATTTGGCAT-CATTGTAAAA
164073 TATTATTTGG-AT-ATTGTAAAA
1 TATTATTTGGCATCATTGTAAAA
164094 ATTTTGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
23 2 0.10
24 10 0.50
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.47
Consensus pattern (23 bp):
TATTATTTGGCATCATTGTAAAA
Found at i:164215 original size:41 final size:43
Alignment explanation
Indices: 164157--164244 Score: 135
Period size: 41 Copynumber: 2.1 Consensus size: 43
164147 AAAGGATGCT
*
164157 TATTGTATTTTCAATTTGTTTGTTGTTTTACGAATTGTTTTAA
1 TATTGTATTTTCAATTTGTTTGTTGTTTTAAGAATTGTTTTAA
* *
164200 TATTGT-TTTT-AATTTGTTTGTTGTTTTAATATTTGTTTTAA
1 TATTGTATTTTCAATTTGTTTGTTGTTTTAAGAATTGTTTTAA
164241 TATT
1 TATT
164245 TTTAAGTGTA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
41 32 0.76
42 4 0.10
43 6 0.14
ACGTcount: A:0.20, C:0.02, G:0.12, T:0.65
Consensus pattern (43 bp):
TATTGTATTTTCAATTTGTTTGTTGTTTTAAGAATTGTTTTAA
Found at i:164235 original size:19 final size:18
Alignment explanation
Indices: 164164--164237 Score: 58
Period size: 18 Copynumber: 3.8 Consensus size: 18
164154 GCTTATTGTA
*
164164 TTTTCAATTTGTTTGTTG
1 TTTTAAATTTGTTTGTTG
* *
164182 TTTTACGAATTGTTTTAATATTG
1 TTTTA--AATT-TGTT--TGTTG
*
164205 TTTTTAATTTGTTTGTTG
1 TTTTAAATTTGTTTGTTG
164223 TTTTAATATTTGTTT
1 TTTTAA-ATTTGTTT
164238 TAATATTTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 11
0.70 0.11 0.18
Matches are distributed among these distances:
18 13 0.30
19 8 0.19
20 7 0.16
21 7 0.16
23 8 0.19
ACGTcount: A:0.18, C:0.03, G:0.14, T:0.66
Consensus pattern (18 bp):
TTTTAAATTTGTTTGTTG
Found at i:164237 original size:12 final size:12
Alignment explanation
Indices: 164220--164245 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
164210 AATTTGTTTG
164220 TTGTTTTAATAT
1 TTGTTTTAATAT
164232 TTGTTTTAATAT
1 TTGTTTTAATAT
164244 TT
1 TT
164246 TTAAGTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (12 bp):
TTGTTTTAATAT
Found at i:193044 original size:86 final size:87
Alignment explanation
Indices: 192864--193050 Score: 254
Period size: 86 Copynumber: 2.2 Consensus size: 87
192854 AACATATCAT
* * *
192864 ATCATACAC-AGGCATAAATATATTAAAATATGGCAAAATAAAGACATACATATATTAAAAACAA
1 ATCATACACAAGGCATAAATACATTAAAAAATGACAAAATAAAGACATACATATATTAAAAACAA
* * * *
192928 CATGTGATCAGTCCTACCAGCA
66 AATGTGATCAGCCCCACCAGAA
192950 ATCATACACAAGGCATAAATACATTAAAAAATGACAAAATAAAGACATACATATATT-AAAACAA
1 ATCATACACAAGGCATAAATACATTAAAAAATGACAAAATAAAGACATACATATATTAAAAACAA
* **
193014 AATGTG-GCTAGCCCCATTAGAA
66 AATGTGATC-AGCCCCACCAGAA
193036 ATCATACACAAGGCA
1 ATCATACACAAGGCA
193051 GAATAAAGGC
Statistics
Matches: 89, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
85 1 0.01
86 44 0.49
87 44 0.49
ACGTcount: A:0.50, C:0.18, G:0.11, T:0.21
Consensus pattern (87 bp):
ATCATACACAAGGCATAAATACATTAAAAAATGACAAAATAAAGACATACATATATTAAAAACAA
AATGTGATCAGCCCCACCAGAA
Found at i:201298 original size:29 final size:28
Alignment explanation
Indices: 201248--201308 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
201238 AAAATGCGAT
***
201248 TTTTGGATGCCCGGGGGTAAAACGGTAA
1 TTTTGGATGCCCGGGAACAAAACGGTAA
*
201276 TTTTGGATGCTCCGGGAACAAAATGGTAA
1 TTTTGGATGC-CCGGGAACAAAACGGTAA
201305 TTTT
1 TTTT
201309 TGAAAGGTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 10 0.36
29 18 0.64
ACGTcount: A:0.26, C:0.13, G:0.30, T:0.31
Consensus pattern (28 bp):
TTTTGGATGCCCGGGAACAAAACGGTAA
Found at i:201366 original size:29 final size:28
Alignment explanation
Indices: 201333--201427 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 28
201323 TTAAAAATGA
* *
201333 AATTTTTAGATATTTGAGGGTAGAATGGT
1 AATTTTTAGACATTT-AGGGTAAAATGGT
* * * *
201362 AATTTTTGGAAGATTCAAGGTTAAAAATGG-
1 AATTTTTAG-ACATT-TAGGGT-AAAATGGT
201392 AATTTTTAGACATTTAGGGGTAAAATGGT
1 AATTTTTAGACATTTA-GGGTAAAATGGT
201421 AATTTTT
1 AATTTTT
201428 GGAAGGTTTG
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
28 8 0.15
29 22 0.42
30 16 0.31
31 6 0.12
ACGTcount: A:0.35, C:0.02, G:0.23, T:0.40
Consensus pattern (28 bp):
AATTTTTAGACATTTAGGGTAAAATGGT
Found at i:201447 original size:59 final size:59
Alignment explanation
Indices: 201295--201435 Score: 212
Period size: 59 Copynumber: 2.4 Consensus size: 59
201285 CTCCGGGAAC
* * *
201295 AAAATGGTAATTTTTGAAAGGTTCAGGGTTAAAAATGAAATTTTTAGATATTTGAGGGT
1 AAAATGGTAATTTTTGGAAGGTTCAGGGTTAAAAATGGAATTTTTAGACATTTGAGGGT
* * *
201354 AGAATGGTAATTTTTGGAAGATTCAAGGTTAAAAATGGAATTTTTAGACATTT-AGGGGT
1 AAAATGGTAATTTTTGGAAGGTTCAGGGTTAAAAATGGAATTTTTAGACATTTGA-GGGT
201413 AAAATGGTAATTTTTGGAAGGTT
1 AAAATGGTAATTTTTGGAAGGTT
201436 TGGGGATAAA
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
58 1 0.01
59 72 0.99
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.37
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGAAGGTTCAGGGTTAAAAATGGAATTTTTAGACATTTGAGGGT
Found at i:201454 original size:59 final size:58
Alignment explanation
Indices: 201295--201456 Score: 209
Period size: 59 Copynumber: 2.7 Consensus size: 58
201285 CTCCGGGAAC
* *
201295 AAAATGGTAATTTTTGAAAGGTTCAGGGTTAAAAATGAAATTTTTAGATATTTGAGGGT
1 AAAATGGTAATTTTTGGAAGGTTCAGGGTTAAAAATG-AATTTTTAGACATTTGAGGGT
* * *
201354 AGAATGGTAATTTTTGGAAGATTCAAGGTTAAAAATGGAATTTTTAGACATTT-AGGGGT
1 AAAATGGTAATTTTTGGAAGGTTCAGGGTTAAAAAT-GAATTTTTAGACATTTGA-GGGT
** *
201413 AAAATGGTAATTTTTGGAAGGTTTGGGGATAAAAAATGAATTTT
1 AAAATGGTAATTTTTGGAAGGTTCAGGG-TTAAAAATGAATTTT
201457 GGAAAGCTCG
Statistics
Matches: 89, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
58 1 0.01
59 80 0.90
60 8 0.09
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.36
Consensus pattern (58 bp):
AAAATGGTAATTTTTGGAAGGTTCAGGGTTAAAAATGAATTTTTAGACATTTGAGGGT
Found at i:201604 original size:90 final size:89
Alignment explanation
Indices: 201442--201605 Score: 197
Period size: 90 Copynumber: 1.8 Consensus size: 89
201432 GGTTTGGGGA
* *
201442 TAAAAAATGAATTTTGGAAAGCTCGGTGGTAAAAATGCAATTTTTGGAAAGTTCGAGGGTAAAAA
1 TAAAAAATGAATTTTAGAAAGCTAGGTGGTAAAAATGCAATTTTTGGAAAGTTCGAGGGTAAAAA
**
201507 TTTAATTTTCATAAAGTTCGAGGT
66 TGGAATTTTCATAAAGTTCGAGGT
* * * * * *
201531 TAAAAAATGGAATTTTAGAAAGTTTAGG-GGTAAAATTGTAATTTTTGGATAGTT-TAGGGTCAT
1 TAAAAAAT-GAATTTTAGAAAG-CTAGGTGGTAAAAATGCAATTTTTGGAAAGTTCGAGGGT-AA
201594 AAATGGAATTTT
63 AAATGGAATTTT
201606 TGAAAGTTTG
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
89 13 0.21
90 46 0.74
91 3 0.05
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.35
Consensus pattern (89 bp):
TAAAAAATGAATTTTAGAAAGCTAGGTGGTAAAAATGCAATTTTTGGAAAGTTCGAGGGTAAAAA
TGGAATTTTCATAAAGTTCGAGGT
Found at i:201604 original size:149 final size:147
Alignment explanation
Indices: 201379--201648 Score: 357
Period size: 149 Copynumber: 1.8 Consensus size: 147
201369 GGAAGATTCA
* *
201379 AGGTTAAAAATGGAATTTTTAGACATTTAGGGGTAAAATGGTAATTTTTGGAAGGTTTGGGGATA
1 AGGTTAAAAATGGAATTTTTAGAAATTTAGGGGTAAAATGGTAATTTTTGGAAGGTTTAGGGATA
* * *
201444 AAAAATGAATTTTGGAAAGCTCGGTGGTAAAAATGCAATTTTTGGAAAGTTCGAGGGTAAAAATT
66 AAAAATGAATTTTGGAAAGCTCGGCGGTAAAAATACAATTTTTAGAAAGTTC-AGGGTAAAAATT
201509 TAATTTTCATAAAGTTCG
130 TAATTTTCATAAAGTTCG
*
201527 AGGTTAAAAAATGGAA-TTTTAGAAAGTTTAGGGGTAAAATTGTAATTTTTGGATA-GTTTAGGG
1 AGGTT-AAAAATGGAATTTTTAGAAA-TTTAGGGGTAAAATGGTAATTTTTGGA-AGGTTTAGGG
* * * * * * *
201590 -TCATAAATGGAATTTTTGAAAGTTTGGCGGTAAAAATATAATTTTTAGACAGTTCAGGG
63 ATAAAAAAT-GAATTTTGGAAAGCTCGGCGGTAAAAATACAATTTTTAGAAAGTTCAGGG
201649 ACCTTCTGGG
Statistics
Matches: 105, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
148 23 0.22
149 81 0.77
150 1 0.01
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.35
Consensus pattern (147 bp):
AGGTTAAAAATGGAATTTTTAGAAATTTAGGGGTAAAATGGTAATTTTTGGAAGGTTTAGGGATA
AAAAATGAATTTTGGAAAGCTCGGCGGTAAAAATACAATTTTTAGAAAGTTCAGGGTAAAAATTT
AATTTTCATAAAGTTCG
Found at i:201626 original size:29 final size:29
Alignment explanation
Indices: 201295--201635 Score: 171
Period size: 30 Copynumber: 11.5 Consensus size: 29
201285 CTCCGGGAAC
* *
201295 AAAATGGTAATTTTT-GAAAGGTTCAGGGTTA
1 AAAATGG-AATTTTTGGAAA-GTT-TGGGGTA
* * *
201326 AAAATGAAATTTTTAGATA-TTTGAGGGT-
1 AAAATGGAATTTTTGGAAAGTTTG-GGGTA
* ** *
201354 AGAATGGTAATTTTTGG-AAGATTCAAGGTTA
1 AAAATGG-AATTTTTGGAAAG-TT-TGGGGTA
* *
201385 AAAATGGAATTTTTAGACA-TTTAGGGGT-
1 AAAATGGAATTTTTGGAAAGTTT-GGGGTA
*
201413 AAAATGGTAATTTTTGGAAGGTTTGGGGATAA
1 AAAATGG-AATTTTTGGAAAGTTTGGGG-T-A
* *
201445 AAAAT-GAA-TTTTGGAAAGCTCGGTGGTA
1 AAAATGGAATTTTTGGAAAGTTTGG-GGTA
* *
201473 AAAATGCAATTTTTGGAAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAAGTTTG-GGGTA
** *** * *
201503 AAAATTTAATTTTCATAAAGTTCGAGGTTAA
1 AAAATGGAATTTTTGGAAAGTTTG-GGGT-A
*
201534 AAAATGGAA-TTTTAGAAAGTTTAGGGGTA
1 AAAATGGAATTTTTGGAAAGTTT-GGGGTA
* * * *
201563 AAATTGTAATTTTTGGATAGTTTAGGGTCA
1 AAAATGGAATTTTTGGAAAGTTTGGGGT-A
*
201593 TAAATGGAATTTTT-GAAAGTTTGGCGGTA
1 AAAATGGAATTTTTGGAAAGTTTGG-GGTA
**
201622 AAAATATAATTTTT
1 AAAATGGAATTTTT
201636 AGACAGTTCA
Statistics
Matches: 237, Mismatches: 50, Indels: 48
0.71 0.15 0.14
Matches are distributed among these distances:
28 20 0.08
29 78 0.33
30 107 0.45
31 27 0.11
32 5 0.02
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAAGTTTGGGGTA
Done.