Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1269
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: 53968
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:1958 original size:18 final size:18
Alignment explanation
Indices: 1935--1975 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
1925 GTAGTTAGGA
1935 CGTGTAACAAACTGAGGT
1 CGTGTAACAAACTGAGGT
1953 CGTGTAACAAACTGAGGT
1 CGTGTAACAAACTGAGGT
1971 CGTGT
1 CGTGT
1976 GGATCAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.24
Consensus pattern (18 bp):
CGTGTAACAAACTGAGGT
Found at i:3756 original size:17 final size:17
Alignment explanation
Indices: 3734--3768 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3724 TCTTTATGTT
*
3734 ATATAAATATTATAATA
1 ATATAAATATAATAATA
*
3751 ATATAATTATAATAATA
1 ATATAAATATAATAATA
3768 A
1 A
3769 CATTATTTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATAAATATAATAATA
Found at i:5410 original size:28 final size:28
Alignment explanation
Indices: 5351--5476 Score: 164
Period size: 28 Copynumber: 4.5 Consensus size: 28
5341 ACGGAGTCCA
* * *
5351 CCACAAAGGC-TAATCTTTCATAGCTCA
1 CCACAAAGGCTTATTCTTTCATAGTTCG
* * *
5378 TCACAAAGGTTTATTCCTTCATAGTTCG
1 CCACAAAGGCTTATTCTTTCATAGTTCG
*
5406 CCACAAAGGCTTATTCTTTCATAGTTTG
1 CCACAAAGGCTTATTCTTTCATAGTTCG
* *
5434 CCACAAAGGTTTATTCTTTCATTGTTCG
1 CCACAAAGGCTTATTCTTTCATAGTTCG
5462 CCACAAAGGCTTATT
1 CCACAAAGGCTTATT
5477 ATTTATTGAT
Statistics
Matches: 84, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
27 8 0.10
28 76 0.90
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (28 bp):
CCACAAAGGCTTATTCTTTCATAGTTCG
Found at i:5439 original size:56 final size:56
Alignment explanation
Indices: 5351--5476 Score: 182
Period size: 56 Copynumber: 2.3 Consensus size: 56
5341 ACGGAGTCCA
* *
5351 CCACAAAGGC-TAATCTTTCATAGCTCATCACAAAGGTTTATTCCTTCATAGTTCG
1 CCACAAAGGCTTATTCTTTCATAGCTCACCACAAAGGTTTATTCCTTCATAGTTCG
* ** * *
5406 CCACAAAGGCTTATTCTTTCATAGTTTGCCACAAAGGTTTATTCTTTCATTGTTCG
1 CCACAAAGGCTTATTCTTTCATAGCTCACCACAAAGGTTTATTCCTTCATAGTTCG
5462 CCACAAAGGCTTATT
1 CCACAAAGGCTTATT
5477 ATTTATTGAT
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
55 10 0.16
56 53 0.84
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (56 bp):
CCACAAAGGCTTATTCTTTCATAGCTCACCACAAAGGTTTATTCCTTCATAGTTCG
Found at i:7496 original size:20 final size:20
Alignment explanation
Indices: 7471--7513 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
7461 ATTTTAGTTA
7471 TTTTAAAAGAAAATTTAAAT
1 TTTTAAAAGAAAATTTAAAT
* * *
7491 TTTTAAAATAAAGTTTTAAT
1 TTTTAAAAGAAAATTTAAAT
7511 TTT
1 TTT
7514 GTTTTCAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
TTTTAAAAGAAAATTTAAAT
Found at i:7645 original size:154 final size:152
Alignment explanation
Indices: 7462--7834 Score: 493
Period size: 152 Copynumber: 2.4 Consensus size: 152
7452 TTTTATTTTA
* *
7462 TTTTAGTTATTTTAAAAGAAAATTTAAATTTTTAAAATAAAGTTTTAATTTTGTTTTCAACTATT
1 TTTTAGTCATTTT-AAAGAAAATTTAAATTTTTAAAACAAAGTTTTAATTTT-TTTT-AACTATT
* * * * * * *
7527 TCAAAGTAAAAGCTTTAATCTTTAAGAAAAATAGTGTTTTTTTTT-AAATAAAA-GAGAAAGTTT
63 TAAAAATAAAAACTTCAAACTTTAAGAAAAATAGTATTTTTTTTTAAAAAAAAAGGAGAAAGTTT
7590 AGATTTTGAAAAATAAAAATATAG-T
128 AGATTTTGAAAAATAAAAATAT-GTT
* * * *
7615 TTTTAGTCATTTTAAAGGAAATTGTAAAATTTCAAAACAAAGTTTT-ATTTTTTTTGAAACTATG
1 TTTTAGTCATTTTAAAGAAAATT-TAAATTTTTAAAACAAAGTTTTAATTTTTTTT--AACTATT
* *
7679 TAAAAATAAAAACTTCAAACTTTAATAAAATTAGTATTTTTTTTTAAAAAAAAAGGAGAAAGTTT
63 TAAAAATAAAAACTTCAAACTTTAAGAAAAATAGTATTTTTTTTTAAAAAAAAAGGAGAAAGTTT
7744 AGATTTTGAAAAATAAAAATATGTTT
128 AGATTTTGAAAAATAAAAATATG-TT
7770 TTTTAAGTCATTTTAAAGAAAAGTTTAAATTTTTAAAACAAAGTTTTAATTTTTTTTAACTATTT
1 TTTT-AGTCATTTTAAAGAAAA-TTTAAATTTTTAAAACAAAGTTTTAATTTTTTTTAACTATTT
7835 TGAAATAAGC
Statistics
Matches: 191, Mismatches: 20, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
151 4 0.02
152 57 0.30
153 39 0.20
154 32 0.17
155 12 0.06
156 36 0.19
157 11 0.06
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.43
Consensus pattern (152 bp):
TTTTAGTCATTTTAAAGAAAATTTAAATTTTTAAAACAAAGTTTTAATTTTTTTTAACTATTTAA
AAATAAAAACTTCAAACTTTAAGAAAAATAGTATTTTTTTTTAAAAAAAAAGGAGAAAGTTTAGA
TTTTGAAAAATAAAAATATGTT
Found at i:7824 original size:21 final size:20
Alignment explanation
Indices: 7780--7823 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
7770 TTTTAAGTCA
7780 TTTTAAAGAAAAGTTTAAAT
1 TTTTAAAGAAAAGTTTAAAT
*
7800 TTTTAAA-ACAAAGTTTTAAT
1 TTTTAAAGA-AAAGTTTAAAT
7820 TTTT
1 TTTT
7824 TTTAACTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (20 bp):
TTTTAAAGAAAAGTTTAAAT
Found at i:7857 original size:154 final size:151
Alignment explanation
Indices: 7410--7885 Score: 468
Period size: 154 Copynumber: 3.1 Consensus size: 151
7400 AAAGTTGTAA
* * * ** *
7410 TTTTTTTTAAAAAAAACAG--AGTTTAGATTTTTATAAATAATATTTTAT-TTTATTTTAGTTAT
1 TTTTTTTTAAAAAAAAGAGAAAGTTTAGATTTTGAAAAATAA-A-AATATGTTT-TTTTAGTCAT
* * * *
7472 TTTAAAAGAAAATTTAAATTTTTAAAATAAAGTTTTAATTTTGTTTTCAACTATTTCAAAGTAAA
63 TTT-AAAGAAAATTTAAATTTTTAAAACAAAGTTTTAATTTT-TTTTAAACTATTTTAAAAT-AA
* * *
7537 AGC-TTTAATCTTTAAGAAAAATAGTGT
125 AGCTTTTACT-TTTAACAAAAATAGTAT
*
7564 TTTTTTTTAAATAAAAGAGAAAGTTTAGATTTTGAAAAATAAAAATATAG--TTTTTAGTCATTT
1 TTTTTTTTAAAAAAAAGAGAAAGTTTAGATTTTGAAAAATAAAAATAT-GTTTTTTTAGTCATTT
* * * * * *
7627 TAAAGGAAATTGTAAAATTTCAAAACAAAGTTTT-ATTTTTTTTGAAACTATGTAAAAATAAAAA
65 TAAAGAAAATT-TAAATTTTTAAAACAAAGTTTTAATTTTTTTT-AAACTATTTTAAAAT-AAAG
** * *
7691 CTTCAAAC-TTTAATAAAATTAGTAT
127 CTT-TTACTTTTAACAAAAATAGTAT
7716 TTTTTTTTAAAAAAAAAGGAGAAAGTTTAGATTTTGAAAAATAAAAATATGTTTTTTTAAGTCAT
1 TTTTTTTT-AAAAAAAA-GAGAAAGTTTAGATTTTGAAAAATAAAAATATGTTTTTTT-AGTCAT
*
7781 TTTAAAGAAAAGTTTAAATTTTTAAAACAAAGTTTTAATTTTTTTT-AACTATTTTGAAAT-AAG
63 TTTAAAGAAAA-TTTAAATTTTTAAAACAAAGTTTTAATTTTTTTTAAACTATTTTAAAATAAAG
* *
7844 CTTTTGACTTTTAACAAAACTAATAT
127 CTTTT-ACTTTTAACAAAAATAGTAT
* *
7870 TTTTTTCTAAATAAAA
1 TTTTTTTTAAAAAAAA
7886 CTTTGATTTT
Statistics
Matches: 268, Mismatches: 37, Indels: 35
0.79 0.11 0.10
Matches are distributed among these distances:
151 4 0.01
152 52 0.19
153 54 0.20
154 75 0.28
155 17 0.06
156 55 0.21
157 11 0.04
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.44
Consensus pattern (151 bp):
TTTTTTTTAAAAAAAAGAGAAAGTTTAGATTTTGAAAAATAAAAATATGTTTTTTTAGTCATTTT
AAAGAAAATTTAAATTTTTAAAACAAAGTTTTAATTTTTTTTAAACTATTTTAAAATAAAGCTTT
TACTTTTAACAAAAATAGTAT
Found at i:8412 original size:21 final size:21
Alignment explanation
Indices: 8388--8429 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
8378 TTTATTCACA
8388 CTTGTATAATTTTTATTTATT
1 CTTGTATAATTTTTATTTATT
* *
8409 CTTGTTTCATTTTTATTTATT
1 CTTGTATAATTTTTATTTATT
8430 TTCATGTCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.07, G:0.05, T:0.69
Consensus pattern (21 bp):
CTTGTATAATTTTTATTTATT
Found at i:8442 original size:22 final size:23
Alignment explanation
Indices: 8396--8453 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 23
8386 CACTTGTATA
* *
8396 ATTTTTATTTA--TTCTTGTTTC
1 ATTTTTATTTATTTTCATGTCTC
8417 ATTTTTATTTATTTTCATGTCT-
1 ATTTTTATTTATTTTCATGTCTC
* *
8439 ATTTATATTTTTTTT
1 ATTTTTATTTATTTT
8454 ACACATTCCC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 11 0.35
22 13 0.42
23 7 0.23
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.72
Consensus pattern (23 bp):
ATTTTTATTTATTTTCATGTCTC
Found at i:8828 original size:27 final size:27
Alignment explanation
Indices: 8787--8839 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
8777 TTTACATTTG
8787 GATTTAGGTTAGTCCTTAAGATCTTAA
1 GATTTAGGTTAGTCCTTAAGATCTTAA
*
8814 GATTTAGGTTCGTCCTTAAGATCTTA
1 GATTTAGGTTAGTCCTTAAGATCTTA
8840 CCTACCATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (27 bp):
GATTTAGGTTAGTCCTTAAGATCTTAA
Found at i:10636 original size:358 final size:357
Alignment explanation
Indices: 9980--10693 Score: 1410
Period size: 358 Copynumber: 2.0 Consensus size: 357
9970 ATTTGTTCAT
9980 TTCATTTACTTATCCTTTTTTAATATGAATTCCAATGTGTTTGTTTATTCTTTTATCGATAAAAT
1 TTCATTTACTTATCCTTTTTTAATATGAATTCCAATGTGTTTGTTTATTCTTTTATCGATAAAAT
10045 TGATTAATGTGTATGTCGGTTGTACCGTCGTGGGCGGCTATAATTATAATTCATGTTGCATTTTG
66 TGATTAATGTGTATGTCGGTTGTACCGTCGTGGGCGGCTATAATTATAATTCATGTTGCATTTTG
10110 CTTTCGATCCTACACCCGAGCCTATCCCGTTTAGGAGGAGTAGCCTTAGGCTTTCATGTGACAAT
131 CTTTCGATCCTACACCCGAGCCTATCCCGTTTAGGAGGAGTAGCCTTAGGCTTTCATGTGACAAT
10175 ATGTCACCACATAAGTTTAAGGACTACTCCATGGTTAAGATGGACATAGATGTTCATGTAGCAAA
196 ATGTCACCACATAAGTTTAAGGACTACTCCATGGTTAAGATGGACATAGATGTTCATGTAGCAAA
10240 TGCTACCATGTACACTATGAAAGTCTCACCACTCAAGGGCCAACCCTTTTTAAAAGGGGAACGCA
261 TGCTACCATGTACACTATGAAAGTCTCACCACTCAAGGGCCAACCCTTTTTAAAAGGGGAACGCA
*
10305 TCCCTATGGGTGTCATATTTAAGTCTTGGGTG
326 TCCCTATAGGTGTCATATTTAAGTCTTGGGTG
10337 TTCATTTACTTATCCTTTTTTAATATGAATTCCAATGTGTTTGTTTATTCTTTTATCGATAAAAT
1 TTCATTTACTTATCCTTTTTTAATATGAATTCCAATGTGTTTGTTTATTCTTTTATCGATAAAAT
10402 TGATTAATGTGTATGTCGGTTGTACCGTCGTGGGGCGGCTATAATTATAATTCATGTTGCATTTT
66 TGATTAATGTGTATGTCGGTTGTACCGTCGT-GGGCGGCTATAATTATAATTCATGTTGCATTTT
10467 GCTTTCGATCCTACACCCGAGCCTATCCCGTTTAGGAGGAGTAGCCTTAGGCTTTCATGTGACAA
130 GCTTTCGATCCTACACCCGAGCCTATCCCGTTTAGGAGGAGTAGCCTTAGGCTTTCATGTGACAA
10532 TATGTCACCACATAAGTTTAAGGACTACTCCATGGTTAAGATGGACATAGATGTTCATGTAGCAA
195 TATGTCACCACATAAGTTTAAGGACTACTCCATGGTTAAGATGGACATAGATGTTCATGTAGCAA
10597 ATGCTACCATGTACACTATGAAAGTCTCACCACTCAAGGGCCAACCCTTTTTAAAAGGGGAACGC
260 ATGCTACCATGTACACTATGAAAGTCTCACCACTCAAGGGCCAACCCTTTTTAAAAGGGGAACGC
10662 ATCCCTATAGGTGTCATATTTAAGTCTTGGGT
325 ATCCCTATAGGTGTCATATTTAAGTCTTGGGT
10694 TCCCCGTGCA
Statistics
Matches: 355, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
357 96 0.27
358 259 0.73
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (357 bp):
TTCATTTACTTATCCTTTTTTAATATGAATTCCAATGTGTTTGTTTATTCTTTTATCGATAAAAT
TGATTAATGTGTATGTCGGTTGTACCGTCGTGGGCGGCTATAATTATAATTCATGTTGCATTTTG
CTTTCGATCCTACACCCGAGCCTATCCCGTTTAGGAGGAGTAGCCTTAGGCTTTCATGTGACAAT
ATGTCACCACATAAGTTTAAGGACTACTCCATGGTTAAGATGGACATAGATGTTCATGTAGCAAA
TGCTACCATGTACACTATGAAAGTCTCACCACTCAAGGGCCAACCCTTTTTAAAAGGGGAACGCA
TCCCTATAGGTGTCATATTTAAGTCTTGGGTG
Found at i:22388 original size:42 final size:42
Alignment explanation
Indices: 22323--22730 Score: 525
Period size: 42 Copynumber: 9.8 Consensus size: 42
22313 AAGGAAAACA
* * *
22323 TTCATTGCATCTAGAGACACAGGTATGGAGGTCCATTCACTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTCACTT
* *** * *
22365 TTCATTGCATTTAAAGACCCAGGTGTTTTGATCCGTTCACTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTCACTT
*
22407 TTCATTGCATTTAGAAACCCAGGTGTGGAGGTCCATTCACTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTCACTT
*
22449 TTCATTGCATTTAGAGACCCAGGTGTGGGGGTCCATTCACTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTCACTT
*** * *
22491 TTCATTGCATTTAGAGACCCAGGTGTTTTGATCCGTTCACTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTCACTT
*
22533 TTCATTGCATTTAGAAACCCAGGTGTGGAGGTCCATTCACTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTCACTT
* * * *
22575 TTCATTGCATTTAGAGACCCAGGTCTGGAGGTTCGTTCATTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTCACTT
* *
22617 TTAATTGCATTTAGAGACCCAGGTGTGGAGGTTCATTCACTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTCACTT
* * * *
22659 TTCATTGCATTTAGAGACCCAAGTGTGGAGGTACGTTTACTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTCACTT
* * *
22701 TTC-TAG--TTTAGAGGCCCAGGTGTAGAGGTC
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTC
22731 TATTTACGTT
Statistics
Matches: 318, Mismatches: 48, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
39 20 0.06
41 2 0.01
42 296 0.93
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (42 bp):
TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTCACTT
Found at i:22548 original size:126 final size:126
Alignment explanation
Indices: 22323--22730 Score: 579
Period size: 126 Copynumber: 3.3 Consensus size: 126
22313 AAGGAAAACA
* * * *
22323 TTCATTGCATCTAGAGACACAGGTATGGAGGTCCATTCACTTTTCATTGCATTTAAAGACCCAGG
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTCACTTTTCATTGCATTTAGAGACCCAGG
22388 TGTTTTGATCCGTTCACTTTTCATTGCATTTAGAAACCCAGGTGTGGAGGTCCATTCACTT
66 TGTTTTGATCCGTTCACTTTTCATTGCATTTAGAAACCCAGGTGTGGAGGTCCATTCACTT
*
22449 TTCATTGCATTTAGAGACCCAGGTGTGGGGGTCCATTCACTTTTCATTGCATTTAGAGACCCAGG
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTCACTTTTCATTGCATTTAGAGACCCAGG
22514 TGTTTTGATCCGTTCACTTTTCATTGCATTTAGAAACCCAGGTGTGGAGGTCCATTCACTT
66 TGTTTTGATCCGTTCACTTTTCATTGCATTTAGAAACCCAGGTGTGGAGGTCCATTCACTT
* * * * *
22575 TTCATTGCATTTAGAGACCCAGGTCTGGAGGTTCGTTCATTTTTAATTGCATTTAGAGACCCAGG
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTCACTTTTCATTGCATTTAGAGACCCAGG
*** * * * * * * * *
22640 TGTGGAGGTTCATTCACTTTTCATTGCATTTAGAGACCCAAGTGTGGAGGTACGTTTACTT
66 TGTTTTGATCCGTTCACTTTTCATTGCATTTAGAAACCCAGGTGTGGAGGTCCATTCACTT
* * *
22701 TTC-TAG--TTTAGAGGCCCAGGTGTAGAGGTC
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTC
22731 TATTTACGTT
Statistics
Matches: 255, Mismatches: 27, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
123 20 0.08
125 2 0.01
126 233 0.91
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (126 bp):
TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTCACTTTTCATTGCATTTAGAGACCCAGG
TGTTTTGATCCGTTCACTTTTCATTGCATTTAGAAACCCAGGTGTGGAGGTCCATTCACTT
Found at i:22729 original size:39 final size:38
Alignment explanation
Indices: 22626--22749 Score: 131
Period size: 39 Copynumber: 3.1 Consensus size: 38
22616 TTTAATTGCA
* *
22626 TTTAGAGACCCAGGTGTGGAGGTTCATTCACTTTTCATTG
1 TTTAGAGACCCAGGTGTGGAGG-TCATTTACTTTTC-TAG
* *
22666 CATTTAGAGACCCAAGTGTGGAGGTACGTTTACTTTTCTAG
1 --TTTAGAGACCCAGGTGTGGAGGT-CATTTACTTTTCTAG
* * *
22707 TTTAGAGGCCCAGGTGTAGAGGTCTATTTACGTTTCTAG
1 TTTAGAGACCCAGGTGTGGAGGTC-ATTTACTTTTCTAG
22746 TTTA
1 TTTA
22750 CTTTTCATTT
Statistics
Matches: 71, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
38 1 0.01
39 36 0.51
41 3 0.04
42 31 0.44
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.37
Consensus pattern (38 bp):
TTTAGAGACCCAGGTGTGGAGGTCATTTACTTTTCTAG
Found at i:23752 original size:159 final size:155
Alignment explanation
Indices: 23499--23922 Score: 615
Period size: 159 Copynumber: 2.7 Consensus size: 155
23489 AAAAGTTTTG
* * *
23499 ATTTTTTTTTTAAAAAAA-GAGAAAGTTTAGATTTTCACAAAT---AATTTTTTTTTTAGTTATT
1 ATTTTTTTTTTAAAAAAAGGAGAAAGTTTAGATTTTGAAAAATAAAAATTTTTTTTTTAGTCATT
* *
23560 TTAAAGGAAA-TGTTAAATTTTTAAAACAAAGTTTTGATTTTTTTTTTCAACTACTTCAAAGTAA
66 TTAAAGGAAAGT-TTAAAATTTTAAAACAAAGTTTTGATTTTTTTTTTCAACTACTTCAAAATAA
* *
23624 AAGCTTTAATCTTTAAGAAAAATAAT
130 AAGCTTCAATCTTTAAGAAAAACAAT
23650 ATTTTTTTATTTAAAAAAAAGGAGAAAGTTTAGATTTTGAAAAATAAAAATCTATTTTTTTTAGT
1 ATTTTTTT-TTT-AAAAAAAGGAGAAAGTTTAGATTTTGAAAAATAAAAAT-T-TTTTTTTTAGT
* *
23715 CATTTTAAAGGAAAGTTTAAAATTTTAAAATAAAGTTTTGATTTTTTTTTTCAACTATTTCAAAA
62 CATTTTAAAGGAAAGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTTTTCAACTACTTCAAAA
*
23780 TAAAAGCTTCAATCTTTAAGAAAAACAGTGT
127 TAAAAGCTTCAATCTTTAAGAAAAACA--AT
* * *
23811 GTTTTTTTTTTTAAATAAGGAGAAAGTTTAGATTTTGAAAAATAAAAATTTGTTTTTTTAAGTCA
1 ATTTTTTTTTTAAAAAAAGGAGAAAGTTTAGATTTTGAAAAATAAAAATTT-TTTTTTT-AGTCA
23876 TTTTAAAGGAAAGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTT
64 TTTTAAAGGAAAGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTT
23923 AACTATTTAG
Statistics
Matches: 246, Mismatches: 14, Indels: 18
0.88 0.05 0.06
Matches are distributed among these distances:
151 8 0.03
152 3 0.01
153 7 0.03
154 22 0.09
157 4 0.02
158 9 0.04
159 181 0.74
160 4 0.02
161 8 0.03
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (155 bp):
ATTTTTTTTTTAAAAAAAGGAGAAAGTTTAGATTTTGAAAAATAAAAATTTTTTTTTTAGTCATT
TTAAAGGAAAGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTTTTCAACTACTTCAAAATAAA
AGCTTCAATCTTTAAGAAAAACAAT
Found at i:24490 original size:25 final size:24
Alignment explanation
Indices: 24462--24508 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
24452 TCACTTGCAT
24462 TTATACA-TTATATATTTAATGTTAA
1 TTATACACTT-TAT-TTTAATGTTAA
*
24487 TTATGCACTTTATTTTAATGTT
1 TTATACACTTTATTTTAATGTT
24509 TTATATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 9 0.45
25 9 0.45
26 2 0.10
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.55
Consensus pattern (24 bp):
TTATACACTTTATTTTAATGTTAA
Found at i:24539 original size:21 final size:21
Alignment explanation
Indices: 24514--24561 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
24504 ATGTTTTATA
24514 TTTATTCACACTTATATAATT
1 TTTATTCACACTTATATAATT
* **
24535 TTTATTTATTCTTATATAATT
1 TTTATTCACACTTATATAATT
24556 TTTATT
1 TTTATT
24562 TATTTTCATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTATTCACACTTATATAATT
Found at i:24562 original size:21 final size:21
Alignment explanation
Indices: 24524--24565 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
24514 TTTATTCACA
24524 CTTATATAATTTTTATTTATT
1 CTTATATAATTTTTATTTATT
24545 CTTATATAATTTTTATTTATT
1 CTTATATAATTTTTATTTATT
24566 TTCATGTCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (21 bp):
CTTATATAATTTTTATTTATT
Found at i:36184 original size:26 final size:29
Alignment explanation
Indices: 36155--36210 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
36145 TAATAACTGT
36155 AAGATGA-AAAAGT-TTTTA-ATAAAATA
1 AAGATGATAAAAGTATTTTATATAAAATA
*
36181 AAGATGATTAAAATTATTTTATATAAAATA
1 AAGATGA-TAAAAGTATTTTATATAAAATA
36211 CTATTTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 7 0.28
28 5 0.20
29 5 0.20
30 8 0.32
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (29 bp):
AAGATGATAAAAGTATTTTATATAAAATA
Found at i:36616 original size:20 final size:20
Alignment explanation
Indices: 36555--36617 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
36545 AAATTTCATA
*
36555 AAATAAAAATATATGATGATAGT
1 AAATAAAAATA-AT-AT-ATATT
* * * *
36578 ACATAAAATTATTAAATATT
1 AAATAAAAATAATATATATT
36598 AAATAAAAATAATATATATT
1 AAATAAAAATAATATATATT
36618 TTAAACAATT
Statistics
Matches: 31, Mismatches: 9, Indels: 3
0.72 0.21 0.07
Matches are distributed among these distances:
20 20 0.65
21 1 0.03
22 1 0.03
23 9 0.29
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.35
Consensus pattern (20 bp):
AAATAAAAATAATATATATT
Found at i:40455 original size:43 final size:42
Alignment explanation
Indices: 40395--40602 Score: 211
Period size: 43 Copynumber: 4.8 Consensus size: 42
40385 TTTGGGATTG
* *
40395 CGCCACTAAAGACCATGACCTTTAGCGGCACTTGTTCGACAAA
1 CGCCGCTAAAGACCATGACCTTTAGCGGCACTT-TTCCACAAA
* * *
40438 CGCCGCTAAA-AGTCATGACCTTTAGCGGCGCTTTTCCTACAAT
1 CGCCGCTAAAGA-CCATGACCTTTAGCGGCACTTTTCC-ACAAA
* * *
40481 CGCCGCTAAAGACCCTGACCTTTAGCGGAACTCTTTCCACAAG
1 CGCCGCTAAAGACCATGACCTTTAGCGGCACT-TTTCCACAAA
* * *
40524 CGCCGCTAAAGACCTTGACCTTTAGCGGTGATTTTTTCCACAAA
1 CGCCGCTAAAGACCATGACCTTTAGCGG-CA-CTTTTCCACAAA
* * * * *
40568 CGCCGCTAATGACAACGACCTTTAACGGCGCTTTT
1 CGCCGCTAAAGACCATGACCTTTAGCGGCACTTTT
40603 TTAAAAAACG
Statistics
Matches: 137, Mismatches: 22, Indels: 13
0.80 0.13 0.08
Matches are distributed among these distances:
42 8 0.06
43 89 0.65
44 39 0.28
45 1 0.01
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (42 bp):
CGCCGCTAAAGACCATGACCTTTAGCGGCACTTTTCCACAAA
Found at i:40826 original size:19 final size:19
Alignment explanation
Indices: 40802--40838 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
40792 ACAAAAATGA
*
40802 TAAAAGTTAAAATGATAAT
1 TAAAAGTCAAAATGATAAT
40821 TAAAAGTCAAAATGATAA
1 TAAAAGTCAAAATGATAA
40839 AAATATTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.03, G:0.11, T:0.27
Consensus pattern (19 bp):
TAAAAGTCAAAATGATAAT
Found at i:46382 original size:25 final size:23
Alignment explanation
Indices: 46353--46512 Score: 127
Period size: 25 Copynumber: 6.8 Consensus size: 23
46343 ATAATTAAGC
46353 TATGTAAGTTATGTAAGTTATGTAT
1 TATGTAAGTTATGT-A-TTATGTAT
*
46378 TATGTAAGTTATTTATTATGAATAT
1 TATGTAAGTTATGTATTATG--TAT
*
46403 TATGTAAGTTATGTATTATGAAAAT
1 TATGTAAGTTATGTATTATG--TAT
*
46428 TATGTAAGTTGTGTATTATGTAAGT
1 TATGTAAGTTATGTATTATGT-A-T
46453 TATGT-A-TTATGTA--A-G--T
1 TATGTAAGTTATGTATTATGTAT
* *
46469 TATGTAAGTTATTTATTATGAAAAT
1 TATGTAAGTTATGTATTATG--TAT
*
46494 TAAGTAAGTTATGTATTAT
1 TATGTAAGTTATGTATTAT
46513 ATTAAAAATA
Statistics
Matches: 113, Mismatches: 9, Indels: 26
0.76 0.06 0.18
Matches are distributed among these distances:
16 6 0.05
17 1 0.01
18 6 0.05
20 2 0.02
21 2 0.02
23 11 0.10
24 3 0.03
25 82 0.73
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (23 bp):
TATGTAAGTTATGTATTATGTAT
Found at i:46406 original size:41 final size:41
Alignment explanation
Indices: 46361--46488 Score: 179
Period size: 41 Copynumber: 3.1 Consensus size: 41
46351 GCTATGTAAG
*
46361 TTATGTAAGTTATGTATTATGTAAGTTAT-TTA-TTATGAATA
1 TTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTATG--TA
* * *
46402 TTATGTAAGTTATGTATTATGAAAATTATGTAAGTTGTGTA
1 TTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTATGTA
*
46443 TTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTATTTA
1 TTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTATGTA
46484 TTATG
1 TTATG
46489 AAAATTAAGT
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
41 71 0.92
42 2 0.03
43 4 0.05
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (41 bp):
TTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTATGTA
Found at i:46444 original size:66 final size:66
Alignment explanation
Indices: 46361--46512 Score: 243
Period size: 66 Copynumber: 2.3 Consensus size: 66
46351 GCTATGTAAG
*
46361 TTATGTAAGTTATGTATTATGTAAGTTATTTATTATG-AATATTATGTAAGTTATGTATTATGAA
1 TTATGTAAGTTATGTATTATGTAAGTTATGTATTATGTAA-ATTATGTAAGTTATGTATTATGAA
46425 AA
65 AA
* * *
46427 TTATGTAAGTTGTGTATTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTATTTATTATGAAA
1 TTATGTAAGTTATGTATTATGTAAGTTATGTATTATGTAAATTATGTAAGTTATGTATTATGAAA
46492 A
66 A
*
46493 TTAAGTAAGTTATGTATTAT
1 TTATGTAAGTTATGTATTAT
46513 ATTAAAAATA
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
66 77 0.97
67 2 0.03
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (66 bp):
TTATGTAAGTTATGTATTATGTAAGTTATGTATTATGTAAATTATGTAAGTTATGTATTATGAAA
A
Found at i:46488 original size:16 final size:16
Alignment explanation
Indices: 46361--46474 Score: 126
Period size: 16 Copynumber: 7.0 Consensus size: 16
46351 GCTATGTAAG
46361 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
*
46377 TTATGTAAGTTATTTA
1 TTATGTAAGTTATGTA
*
46393 TTATG-AATATTATGTAA
1 TTATGTAA-GTTATGT-A
*
46410 GTTATGT-A-TTATGAAAA
1 -TTATGTAAGTTATG--TA
*
46427 TTATGTAAGTTGTGTA
1 TTATGTAAGTTATGTA
46443 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
46459 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
46475 AGTTATTTAT
Statistics
Matches: 83, Mismatches: 7, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
15 2 0.02
16 68 0.82
17 3 0.04
18 10 0.12
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.49
Consensus pattern (16 bp):
TTATGTAAGTTATGTA
Found at i:46549 original size:20 final size:20
Alignment explanation
Indices: 46516--46553 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
46506 GTATTATATT
*
46516 AAAAATATAAATTAAATTTC
1 AAAAAAATAAATTAAATTTC
*
46536 AAAAAAATATATTAAATT
1 AAAAAAATAAATTAAATT
46554 AAATTTTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAAAAATAAATTAAATTTC
Found at i:46556 original size:25 final size:24
Alignment explanation
Indices: 46516--46566 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
46506 GTATTATATT
46516 AAAAATATAAATTAAA-TTTCAAA
1 AAAAATATAAATTAAATTTTCAAA
46539 AAAATATATTAAATTAAATTTTCAAA
1 AAAA-ATA-TAAATTAAATTTTCAAA
46565 AA
1 AA
46567 TGGGATTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 4 0.16
24 3 0.12
25 9 0.36
26 9 0.36
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (24 bp):
AAAAATATAAATTAAATTTTCAAA
Found at i:46834 original size:22 final size:22
Alignment explanation
Indices: 46809--46850 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
46799 TAATTAAGTT
46809 ATGTAAGTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
*
46831 ATGTAAGTTATGTATTATAT
1 ATGTAAGTTATGTATAATAT
46851 AATAACAGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (22 bp):
ATGTAAGTTATGTATAATATTA
Found at i:47767 original size:12 final size:12
Alignment explanation
Indices: 47747--47786 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
47737 CAAACAGTTT
*
47747 CAAACTTATGAA
1 CAAAATTATGAA
*
47759 CAAAATTATTAA
1 CAAAATTATGAA
*
47771 CAAAATTATGAG
1 CAAAATTATGAA
47783 CAAA
1 CAAA
47787 CAGTATTACA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.55, C:0.12, G:0.07, T:0.25
Consensus pattern (12 bp):
CAAAATTATGAA
Found at i:47797 original size:24 final size:24
Alignment explanation
Indices: 47736--47797 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
47726 ATCCTGTAAT
*
47736 ACAAACAGT-TT-CAAACTTATGA
1 ACAAACAGTATTACAAAATTATGA
*
47758 ACAAA-ATTATTAACAAAATTATGA
1 ACAAACAGTATT-ACAAAATTATGA
*
47782 GCAAACAGTATTACAA
1 ACAAACAGTATTACAA
47798 GCCTGCAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
21 2 0.06
22 7 0.22
24 18 0.56
25 5 0.16
ACGTcount: A:0.52, C:0.15, G:0.08, T:0.26
Consensus pattern (24 bp):
ACAAACAGTATTACAAAATTATGA
Found at i:48276 original size:24 final size:24
Alignment explanation
Indices: 48251--48296 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
48241 TCAAGAATTG
48251 GGGGA-AAATTCGAGGGGAATTTT
1 GGGGAGAAATTCGAGGGGAATTTT
* *
48274 GGGGAGAAATTTGGGGGGAATTT
1 GGGGAGAAATTCGAGGGGAATTT
48297 CGGCTAAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.28, C:0.02, G:0.43, T:0.26
Consensus pattern (24 bp):
GGGGAGAAATTCGAGGGGAATTTT
Found at i:48661 original size:16 final size:16
Alignment explanation
Indices: 48612--48667 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
48602 TAAATCTCAC
*
48612 ATCTTTTATTTATT-T
1 ATCTTTTATTAATTGT
* * *
48627 ATTTATTTCTTAATAGT
1 ATCT-TTTATTAATTGT
48644 ATCTTTTATTAATTGT
1 ATCTTTTATTAATTGT
48660 ATCTTTTA
1 ATCTTTTA
48668 ATTACTAAGT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
15 3 0.09
16 25 0.78
17 4 0.12
ACGTcount: A:0.25, C:0.07, G:0.04, T:0.64
Consensus pattern (16 bp):
ATCTTTTATTAATTGT
Found at i:49366 original size:22 final size:22
Alignment explanation
Indices: 49340--49447 Score: 78
Period size: 22 Copynumber: 5.0 Consensus size: 22
49330 ACCCAAAACA
*
49340 CTAAATCCCTAACTCCTAACCC
1 CTAAATCCCTAACCCCTAACCC
* *
49362 TTAAATCCCAAACCCCTAACCC
1 CTAAATCCCTAACCCCTAACCC
** *
49384 CT-AATCCCTAAACCAATAAACC
1 CTAAATCCCT-AACCCCTAACCC
* ** *
49406 TTAAA-CTCCTAACTTCTAACCT
1 CTAAATC-CCTAACCCCTAACCC
*
49428 CT-AACCCCTAACCCCTAACC
1 CTAAATCCCTAACCCCTAACC
49448 AATAAACCTT
Statistics
Matches: 65, Mismatches: 17, Indels: 9
0.71 0.19 0.10
Matches are distributed among these distances:
21 20 0.31
22 40 0.62
23 5 0.08
ACGTcount: A:0.35, C:0.43, G:0.00, T:0.22
Consensus pattern (22 bp):
CTAAATCCCTAACCCCTAACCC
Found at i:49384 original size:7 final size:7
Alignment explanation
Indices: 49346--49447 Score: 60
Period size: 7 Copynumber: 14.1 Consensus size: 7
49336 AACACTAAAT
49346 CCCTAAC
1 CCCTAAC
*
49353 TCCTAAC
1 CCCTAAC
* *
49360 CCTTAAAT
1 CCCT-AAC
*
49368 CCCAAAC
1 CCCTAAC
49375 CCCTAAC
1 CCCTAAC
*
49382 CCCTAAT
1 CCCTAAC
49389 CCCTAAAC
1 CCCT-AAC
** *
49397 CAATAAA
1 CCCTAAC
*
49404 CCTTAAAC
1 CCCT-AAC
*
49412 TCCTAAC
1 CCCTAAC
**
49419 TTCTAAC
1 CCCTAAC
*
49426 CTCTAAC
1 CCCTAAC
49433 CCCTAAC
1 CCCTAAC
49440 CCCTAAC
1 CCCTAAC
49447 C
1 C
49448 AATAAACCTT
Statistics
Matches: 71, Mismatches: 21, Indels: 6
0.72 0.21 0.06
Matches are distributed among these distances:
7 59 0.83
8 12 0.17
ACGTcount: A:0.34, C:0.44, G:0.00, T:0.22
Consensus pattern (7 bp):
CCCTAAC
Found at i:49496 original size:14 final size:15
Alignment explanation
Indices: 49479--49511 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
49469 CTTAAATCAG
49479 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
49493 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
49508 AATC
1 AATC
49512 TATAAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:49947 original size:41 final size:41
Alignment explanation
Indices: 49890--50239 Score: 423
Period size: 41 Copynumber: 8.5 Consensus size: 41
49880 AAATGTTTTT
* * *
49890 GCGGCGCTTCTACAAAAACGTCGCTAAAGGCCCGAGCACTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTA
* *
49931 GCGGCGCTTCCTCAAAAACGCCGCTAAAGGCCCGACCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTA
* * *
49972 GCGGCGCTTCTTCAAAAACACCGCTAAGGGCCCGAGTATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTA
50013 GCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTA
* * * * *
50054 GCGGTGCTGCTTCAAAAACGCCGCTAAAGACCCCAGCAGTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTA
* * * *
50095 GCGGCG-TTTTTGAAGAAACGTCGCTAAAGGCCAGAGCATTA
1 GCGGCGCTTCTTCAA-AAACGCCGCTAAAGGCCCGAGCATTA
* * * * * * **
50136 GCGACACTGCTTAAAAAATGTCGCTAAAGGCTAGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTA
* * *
50177 GCGGCGCTTCTTCAAAAACGTCGCTGACGGCCCGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTA
*
50218 GCGGCGCTTCTTAAAAAACGCC
1 GCGGCGCTTCTTCAAAAACGCC
50240 ACTATATGCC
Statistics
Matches: 262, Mismatches: 45, Indels: 4
0.84 0.14 0.01
Matches are distributed among these distances:
40 5 0.02
41 252 0.96
42 5 0.02
ACGTcount: A:0.28, C:0.29, G:0.25, T:0.18
Consensus pattern (41 bp):
GCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTA
Found at i:53387 original size:21 final size:21
Alignment explanation
Indices: 53348--53387 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
53338 AACTTTTGAT
***
53348 ATCAAGTTACAAGCTAACTTG
1 ATCAAGTTACAAAAGAACTTG
53369 ATCAAGTTACAAAAGAACT
1 ATCAAGTTACAAAAGAACT
53388 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.25
Consensus pattern (21 bp):
ATCAAGTTACAAAAGAACTTG
Done.