Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold529
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: 90491
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.33
Warning! 5725 characters in sequence are not A, C, G, or T
Found at i:599 original size:3 final size:3
Alignment explanation
Indices: 593--681 Score: 67
Period size: 3 Copynumber: 29.7 Consensus size: 3
583 TTTAGCATTT
* * * * *
593 TTA TTA TT- TTC TTCA TTA TTT TTA ATA -TA TTA TCA TCTT TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
* *
638 TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA CTTA TCA -TA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TT
682 GGTTTAAATA
Statistics
Matches: 68, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
2 5 0.07
3 57 0.84
4 6 0.09
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1128 original size:487 final size:486
Alignment explanation
Indices: 195--1159 Score: 1704
Period size: 487 Copynumber: 2.0 Consensus size: 486
185 AAAAAAATGG
* *
195 GGTTTAAATACCCTGAATGAAACGGCGCCGTTTTGCACTCAAGGGTCAGGTGCCAAAACGACGTC
1 GGTTTAAATACCCTGAACGAAACGACGCCGTTTTGCACTCAAGGGTCAGGTGCCAAAACGACGTC
* * *
260 GTTTTTGCCCTGACCCGCGTGGTGACGCGACCCAAGGGGAGGATCCGCGTGTTTTCCAAAAGGGG
66 GTTTTGGCCCTGACCCGCGTGGTGACCCGACCCAAGGGGAGGATCCGCGTGTTTTCCAAAAGGGA
*
325 GATATTTGCGTGCGTAGTCCCCTCTATTTGCGCCGCGTTACAATTTGCCCCTTTTTCATTATTTT
131 GATATTTGCGTGCGTAGTCCCCTCTATTTGCGACGCGTTACAATTTGCCCCTTTTTCATTATTTT
390 CTTTTATTTTTAATTTAGCCCCGTAATTTTGTTTTTGCTTCAATTTGGTCCATTTCAACCCTGCG
196 CTTTTATTTTTAATTTAGCCCCGTAATTTTGTTTTTGCTTCAATTTGGTCCATTTCAACCCTGCG
*
455 TTTTGGTGCTGTGGATTATTTGCAGTTTTGGTCCCCTCTCTCTCAGCGCATCACAATTTAGTCCC
261 TTTTGGTGCTATGGATTATTTGCAGTTTTGGTCCCCTCTCTCTCAGCGCATCACAATTTAGTCCC
*
520 TTTTATTTTTTTTATTTCGATTTCGCCCGTATATCTTGCTTTTACTTCGATTTAACCCCTTTTTT
326 TTTTATTTTTTTTATTTCGATTTCGCCCGTATATCGTGCTTTTACTTCGATTTAACCCCTTTTTT
585 TAGCATTTTTATTATTTTCTTCATTATTTTTAATATATTATCATCTTTTATTATTATTATTATTA
391 TAGCATTTTTATTATTTTCTTCATTATTTTTAATATATTATCATC-TTTATTATTATTATTATTA
650 TTATTATTA-TCATTATTACTTATCATATTATT
455 TTATTATTAGTCATTATTA-TTATCATATTATT
*
682 GGTTTAAATACCCTGAACGAAACGACGCCGTTTTGTACTCAAGGGTCAGGTGCCAAAACGACGTC
1 GGTTTAAATACCCTGAACGAAACGACGCCGTTTTGCACTCAAGGGTCAGGTGCCAAAACGACGTC
*
747 GTTTTGGCCCTGACCCGCGTGGTGACCCGACCCAAGGGGAGGATCCGCGTGTTTTCTAAAAGGGA
66 GTTTTGGCCCTGACCCGCGTGGTGACCCGACCCAAGGGGAGGATCCGCGTGTTTTCCAAAAGGGA
*
812 GATATTTGCGTGCTTAGTCCCCTCTATTTGCGACGCGTTACAATTTGCCCCTTTTTCATTATTTT
131 GATATTTGCGTGCGTAGTCCCCTCTATTTGCGACGCGTTACAATTTGCCCCTTTTTCATTATTTT
*
877 CTTTTATTTTTAATTTTGCCCCGTAATTTTGTTTTTGCTTCAATTTGGTCCATTTCAACCCTGCG
196 CTTTTATTTTTAATTTAGCCCCGTAATTTTGTTTTTGCTTCAATTTGGTCCATTTCAACCCTGCG
942 TTTTGGTGCTATGGATTATTTGCAGTTTTGGTCCCCTCTCTCTCAGCGCATCACAATTTAGTCCC
261 TTTTGGTGCTATGGATTATTTGCAGTTTTGGTCCCCTCTCTCTCAGCGCATCACAATTTAGTCCC
1007 TTTTATCTTTTTTTTTATTTCGATTTCGCCCCGTATATCGTGCTTTTACTTCGATTTAACCCC-T
326 TTTTA---TTTTTTTTATTTCGATTTCG-CCCGTATATCGTGCTTTTACTTCGATTTAACCCCTT
* *
1071 TTTTTAGCATTTTTATTATTTTCTTCATTATTTTTAATATATTATCATC-TT-TTATTATTGTTG
387 TTTTTAGCATTTTTATTATTTTCTTCATTATTTTTAATATATTATCATCTTTATTATTATTATTA
* *
1134 TTGTTATTATTAGTTATTATTATTAT
452 TTATTATTATTAGTCATTATTATTAT
1160 TTCCTCATCT
Statistics
Matches: 457, Mismatches: 16, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
487 344 0.75
488 10 0.02
490 70 0.15
491 33 0.07
ACGTcount: A:0.19, C:0.21, G:0.16, T:0.44
Consensus pattern (486 bp):
GGTTTAAATACCCTGAACGAAACGACGCCGTTTTGCACTCAAGGGTCAGGTGCCAAAACGACGTC
GTTTTGGCCCTGACCCGCGTGGTGACCCGACCCAAGGGGAGGATCCGCGTGTTTTCCAAAAGGGA
GATATTTGCGTGCGTAGTCCCCTCTATTTGCGACGCGTTACAATTTGCCCCTTTTTCATTATTTT
CTTTTATTTTTAATTTAGCCCCGTAATTTTGTTTTTGCTTCAATTTGGTCCATTTCAACCCTGCG
TTTTGGTGCTATGGATTATTTGCAGTTTTGGTCCCCTCTCTCTCAGCGCATCACAATTTAGTCCC
TTTTATTTTTTTTATTTCGATTTCGCCCGTATATCGTGCTTTTACTTCGATTTAACCCCTTTTTT
TAGCATTTTTATTATTTTCTTCATTATTTTTAATATATTATCATCTTTATTATTATTATTATTAT
TATTATTAGTCATTATTATTATCATATTATT
Found at i:1268 original size:2 final size:2
Alignment explanation
Indices: 1263--1324 Score: 54
Period size: 2 Copynumber: 30.5 Consensus size: 2
1253 ATTTTTACAA
* * * * *
1263 AT AT AT AT AC AT ACT A- AT AT AT TT AT AT AGT TT AT AT GT AC AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
1306 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
1325 CATGCGCATG
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
1 1 0.02
2 43 0.91
3 3 0.06
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1299 original size:31 final size:31
Alignment explanation
Indices: 1264--1322 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
1254 TTTTTACAAA
*
1264 TATATATACATACTA-ATATATTTATATAGTT
1 TATATATACATA-TATATATATATATATAGTT
*
1295 TATATGTACATATATATATATATATATA
1 TATATATACATATATATATATATATATA
1323 TACATGCGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 2 0.08
31 23 0.92
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.47
Consensus pattern (31 bp):
TATATATACATATATATATATATATATAGTT
Found at i:2119 original size:21 final size:21
Alignment explanation
Indices: 2081--2121 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2071 TGTCAACAGT
*
2081 ATGATTTACCAAACTAAAACA
1 ATGATTTACAAAACTAAAACA
* *
2102 ATGATTTTCAAAATTAAAAC
1 ATGATTTACAAAACTAAAAC
2122 TTTAGAAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.15, G:0.05, T:0.29
Consensus pattern (21 bp):
ATGATTTACAAAACTAAAACA
Found at i:4596 original size:129 final size:127
Alignment explanation
Indices: 4320--4605 Score: 342
Period size: 128 Copynumber: 2.2 Consensus size: 127
4310 AAAAATGCCA
* * * * *
4320 CTAAAGAGCATGATCTTTAGTGGCGTTTTACCTAAAAATGCAGCTAAAGAACATGACATTTAGCG
1 CTAAAGAACATGATATTTAGCGGCG-TTTACCCAAAAACGCAGCTAAAGAACATGACATTTAGCG
* * * * *
4385 GTGCTTTGCCACAAATGCTGCTAAAGAACATGACCATTAGCGGCGCTTTACCCACAAACGCCG
65 GCGCTTTCCCACAAACGCCGCTAAAGAACATGACCATTAGCGGCGCTTTACCCACAAACACCG
* * *
4448 CTAAAGAACATGATCTTTAGCGGCGCTTTACCCACAAACGCCGCTAAAGAACATGATC-TTTAGC
1 CTAAAGAACATGATATTTAGCGGCG-TTTACCCAAAAACGCAGCTAAAGAACATGA-CATTTAGC
* * *
4512 GGCGCTTTACCCACAAACGCCGCTAAAGAACATGACCTTTAGCGGTGGTTTACCCACAAACACCG
64 GGCGCTTT-CCCACAAACGCCGCTAAAGAACATGACCATTAGCGGCGCTTTACCCACAAACACCG
** *
4577 CTAAA-AGTATGGTTATTTAGCGGCGTTTA
1 CTAAAGAACAT-GATATTTAGCGGCGTTTA
4606 TGAAAAAACG
Statistics
Matches: 136, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
128 69 0.51
129 67 0.49
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (127 bp):
CTAAAGAACATGATATTTAGCGGCGTTTACCCAAAAACGCAGCTAAAGAACATGACATTTAGCGG
CGCTTTCCCACAAACGCCGCTAAAGAACATGACCATTAGCGGCGCTTTACCCACAAACACCG
Found at i:4599 original size:43 final size:43
Alignment explanation
Indices: 4320--4581 Score: 348
Period size: 43 Copynumber: 6.1 Consensus size: 43
4310 AAAAATGCCA
* * * * * * *
4320 CTAAAGAGCATGATCTTTAGTGGCGTTTTACCTAAAAATGCAG
1 CTAAAGAACATGATCTTTAGCGGCGCTTTACCCACAAACGCCG
* * * *
4363 CTAAAGAACATGA-CATTTAGCGGTGCTTT-GCCACAAATGCTG
1 CTAAAGAACATGATC-TTTAGCGGCGCTTTACCCACAAACGCCG
* *
4405 CTAAAGAACATGACCATTAGCGGCGCTTTACCCACAAACGCCG
1 CTAAAGAACATGATCTTTAGCGGCGCTTTACCCACAAACGCCG
4448 CTAAAGAACATGATCTTTAGCGGCGCTTTACCCACAAACGCCG
1 CTAAAGAACATGATCTTTAGCGGCGCTTTACCCACAAACGCCG
4491 CTAAAGAACATGATCTTTAGCGGCGCTTTACCCACAAACGCCG
1 CTAAAGAACATGATCTTTAGCGGCGCTTTACCCACAAACGCCG
* * * *
4534 CTAAAGAACATGACCTTTAGCGGTGGTTTACCCACAAACACCG
1 CTAAAGAACATGATCTTTAGCGGCGCTTTACCCACAAACGCCG
4577 CTAAA
1 CTAAA
4582 AGTATGGTTA
Statistics
Matches: 197, Mismatches: 19, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
42 35 0.18
43 162 0.82
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (43 bp):
CTAAAGAACATGATCTTTAGCGGCGCTTTACCCACAAACGCCG
Found at i:5175 original size:28 final size:29
Alignment explanation
Indices: 5106--5175 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
5096 TAGAGATATG
* * * *
5106 ATCAAATAAGTCCCTCTACTATTAAATGG
1 ATCAAATAAGTCCCTATACTATAAAAAGA
* * *
5135 ATCAATTCAGTCCCTATCCTATAAAAAGA
1 ATCAAATAAGTCCCTATACTATAAAAAGA
5164 ATCAAAT-AGTCC
1 ATCAAATAAGTCC
5176 ATTTTCCAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
28 5 0.15
29 28 0.85
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.29
Consensus pattern (29 bp):
ATCAAATAAGTCCCTATACTATAAAAAGA
Found at i:5829 original size:86 final size:84
Alignment explanation
Indices: 5702--6033 Score: 353
Period size: 86 Copynumber: 3.9 Consensus size: 84
5692 GTTTATGTGA
* * * ** * *
5702 AACAAATTAGCCAAAATCAACT-ATTCATAGTTCATATATTTACCGGCAATAGGGCTAAATCTTC
1 AACAAATTAGCAAAAATCAA-TGGTTCA-AGTTCATGTATTTACCAACAATA-GACTAAATTTTC
* * *
5766 AATTTCTATAACGATTTATATGT
63 AATTT-TATAACAACTTATATGC
* * *
5789 AACAAGTTAGCAAAAATCAATGGTTCAAGTTCATGTATTTACCAAAAATCAGACTAATTTTTCAA
1 AACAAATTAGCAAAAATCAATGGTTCAAGTTCATGTATTTACCAACAAT-AGACTAAATTTTCAA
5854 TATTTATAACAACTTATATGC
65 T-TTTATAACAACTTATATGC
* * *
5875 AACAAATTAGCAAAAATAAATGGTTCAAGTTCATGCATTTACCAACAACCAGACTAAATTTTCAA
1 AACAAATTAGCAAAAATCAATGGTTCAAGTTCATGTATTTACCAACAA-TAGACTAAATTTTCAA
*
5940 TTTTTATAACAACTTATGTGC
65 -TTTTATAACAACTTATATGC
** * * * *
5961 AACAAATTAG-AAAAATCAACAGTTCAAGTTCATGCATTGACCAACAACCAGACCAAATTTTCAA
1 AACAAATTAGCAAAAATCAATGGTTCAAGTTCATGTATTTACCAACAA-TAGACTAAATTTTCAA
6025 CTTTTATAA
65 -TTTTATAA
6034 AGTAGAAAGA
Statistics
Matches: 214, Mismatches: 26, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
85 57 0.27
86 131 0.61
87 26 0.12
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.32
Consensus pattern (84 bp):
AACAAATTAGCAAAAATCAATGGTTCAAGTTCATGTATTTACCAACAATAGACTAAATTTTCAAT
TTTATAACAACTTATATGC
Found at i:6019 original size:85 final size:86
Alignment explanation
Indices: 5756--6033 Score: 387
Period size: 86 Copynumber: 3.2 Consensus size: 86
5746 GGCAATAGGG
* * * * * *
5756 CTAAATCTTCAATTTCTATAACGATTTATATGTAACAAGTTAGCAAAAATCAATGGTTCAAGTTC
1 CTAAATTTTCAATTTTTATAACAACTTATATGCAACAAATTAGCAAAAATCAATGGTTCAAGTTC
* * *
5821 ATGTATTTACCAAAAATCAGA
66 ATGCATTTACCAACAACCAGA
* * *
5842 CTAATTTTTCAATATTTATAACAACTTATATGCAACAAATTAGCAAAAATAAATGGTTCAAGTTC
1 CTAAATTTTCAATTTTTATAACAACTTATATGCAACAAATTAGCAAAAATCAATGGTTCAAGTTC
5907 ATGCATTTACCAACAACCAGA
66 ATGCATTTACCAACAACCAGA
* **
5928 CTAAATTTTCAATTTTTATAACAACTTATGTGCAACAAATTAG-AAAAATCAACAGTTCAAGTTC
1 CTAAATTTTCAATTTTTATAACAACTTATATGCAACAAATTAGCAAAAATCAATGGTTCAAGTTC
*
5992 ATGCATTGACCAACAACCAGA
66 ATGCATTTACCAACAACCAGA
* *
6013 CCAAATTTTCAACTTTTATAA
1 CTAAATTTTCAATTTTTATAA
6034 AGTAGAAAGA
Statistics
Matches: 171, Mismatches: 21, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
85 57 0.33
86 114 0.67
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.32
Consensus pattern (86 bp):
CTAAATTTTCAATTTTTATAACAACTTATATGCAACAAATTAGCAAAAATCAATGGTTCAAGTTC
ATGCATTTACCAACAACCAGA
Found at i:6559 original size:168 final size:168
Alignment explanation
Indices: 6337--6770 Score: 753
Period size: 168 Copynumber: 2.6 Consensus size: 168
6327 CAGACTTAAA
** * *
6337 CAAA-TAAGATGATGGAAGTCTAACAAATTAAAGTTTCCAATTAAATTCAGACTTACACCATTAA
1 CAAATTAAGATGATCAAATTCTAACAAATTAAAGTTTCCAATGAAATTCAGACTTACACCATTAA
*
6401 ATAAATAAGAGTTTTAAACTATCGGAGATCAAAACAAATTAGCAAAAACCAACTGTTCAAGTGCA
66 GTAAATAAGAGTTTTAAACTATCGGAGATCAAAACAAATTAGCAAAAACCAACTGTTCAAGTGCA
6466 TGTATGCACCAAAAACAGGACCAAATTTCCAATTTTTG
131 TGTATGCACCAAAAACAGGACCAAATTTCCAATTTTTG
*
6504 CAAATTAAGATGATCAAATTCTAACAAATTAAAGTTTCCAATGAAATTTAGACTTACACCATTAA
1 CAAATTAAGATGATCAAATTCTAACAAATTAAAGTTTCCAATGAAATTCAGACTTACACCATTAA
6569 GTAAATAAGAGTTTTAAACTATCGGAGATCAAAACAAATTAGCAAAAACCAACTGTTCAAGTGCA
66 GTAAATAAGAGTTTTAAACTATCGGAGATCAAAACAAATTAGCAAAAACCAACTGTTCAAGTGCA
6634 TGTATGCACCAAAAACAGGACCAAATTTCCAATTTTTG
131 TGTATGCACCAAAAACAGGACCAAATTTCCAATTTTTG
* * *
6672 CAAATTAAGATGATCAAATTCTAACAAATTAAAGTTTCCAATGAAATTCAAAATTACATCATTAA
1 CAAATTAAGATGATCAAATTCTAACAAATTAAAGTTTCCAATGAAATTCAGACTTACACCATTAA
* * *
6737 GTAAATAAGAGTTTTAAATTACCTGAGATCAAAA
66 GTAAATAAGAGTTTTAAACTATCGGAGATCAAAA
6771 ACCCATTTTG
Statistics
Matches: 253, Mismatches: 13, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
167 4 0.02
168 249 0.98
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.28
Consensus pattern (168 bp):
CAAATTAAGATGATCAAATTCTAACAAATTAAAGTTTCCAATGAAATTCAGACTTACACCATTAA
GTAAATAAGAGTTTTAAACTATCGGAGATCAAAACAAATTAGCAAAAACCAACTGTTCAAGTGCA
TGTATGCACCAAAAACAGGACCAAATTTCCAATTTTTG
Found at i:9740 original size:10 final size:11
Alignment explanation
Indices: 9715--9757 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
9705 TATTTTTTAA
**
9715 ATTTTAAAAAA
1 ATTTTAAAATC
9726 ATTTTAAAATC
1 ATTTTAAAATC
9737 -TTTTAAAATTC
1 ATTTTAAAA-TC
9748 ATTTTAAAAT
1 ATTTTAAAAT
9758 TTTAAATCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 8 0.29
11 12 0.43
12 8 0.29
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (11 bp):
ATTTTAAAATC
Found at i:9754 original size:12 final size:12
Alignment explanation
Indices: 9726--9758 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
9716 TTTTAAAAAA
9726 ATTTTAAAA-TC
1 ATTTTAAAATTC
9737 -TTTTAAAATTC
1 ATTTTAAAATTC
9748 ATTTTAAAATT
1 ATTTTAAAATT
9759 TTAAATCATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 8 0.40
11 2 0.10
12 10 0.50
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (12 bp):
ATTTTAAAATTC
Found at i:10234 original size:14 final size:14
Alignment explanation
Indices: 10214--10420 Score: 84
Period size: 14 Copynumber: 14.4 Consensus size: 14
10204 ACTAGTTAAT
*
10214 CTAAACCCTAAACC
1 CTAAACCATAAACC
*
10228 ATAAACCATAAACC
1 CTAAACCATAAACC
*
10242 TTAAAACTC-TAAAACC
1 CT-AAAC-CAT-AAACC
* *
10258 ATAAACGATAAACC
1 CTAAACCATAAACC
*
10272 CTTAACACAT-AACC
1 CTAAAC-CATAAACC
*
10286 TCTAAACCTTAAACC
1 -CTAAACCATAAACC
* *
10301 C-CAACCTTTAAACC
1 CTAAACC-ATAAACC
* *
10315 ATAAATCATAAA-C
1 CTAAACCATAAACC
* *
10328 CAAAACCTCTAAACC
1 CTAAACC-ATAAACC
* *
10343 CATAATCCATGAACC
1 C-TAAACCATAAACC
* *
10358 TTAAA--ATGGTAACAC
1 CTAAACCAT--AAAC-C
* *
10373 CTAAACCTTAAACT
1 CTAAACCATAAACC
*
10387 CTAAACCATATACC
1 CTAAACCATAAACC
*
10401 CTAAACCAAAAACC
1 CTAAACCATAAACC
10415 CTAAAC
1 CTAAAC
10421 TATAGTGATA
Statistics
Matches: 141, Mismatches: 35, Indels: 34
0.67 0.17 0.16
Matches are distributed among these distances:
12 2 0.01
13 9 0.06
14 79 0.56
15 39 0.28
16 11 0.08
17 1 0.01
ACGTcount: A:0.47, C:0.31, G:0.02, T:0.20
Consensus pattern (14 bp):
CTAAACCATAAACC
Found at i:10239 original size:21 final size:21
Alignment explanation
Indices: 10215--10328 Score: 63
Period size: 21 Copynumber: 5.3 Consensus size: 21
10205 CTAGTTAATC
10215 TAAACCCTAAACCATAAACCA
1 TAAACCCTAAACCATAAACCA
*
10236 TAAACCTTAAAACTC-TAAAACCA
1 TAAACCCT-AAAC-CAT-AAACCA
** * *
10259 TAAACGATAAACCCTTAACACA
1 TAAACCCTAAACCATAAAC-CA
*
10281 T-AACCTCTAAACCTTAAACC-
1 TAAACC-CTAAACCATAAACCA
** * *
10301 CCAACCTTTAAACCATAAATCA
1 TAAACC-CTAAACCATAAACCA
10323 TAAACC
1 TAAACC
10329 AAAACCTCTA
Statistics
Matches: 71, Mismatches: 14, Indels: 15
0.71 0.14 0.15
Matches are distributed among these distances:
21 31 0.44
22 27 0.38
23 13 0.18
ACGTcount: A:0.48, C:0.31, G:0.01, T:0.20
Consensus pattern (21 bp):
TAAACCCTAAACCATAAACCA
Found at i:10756 original size:163 final size:163
Alignment explanation
Indices: 10486--10779 Score: 471
Period size: 163 Copynumber: 1.8 Consensus size: 163
10476 NNNNNNNNNN
* * *
10486 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTCTAAAATGCCAATAAAGCACTGAGC
1 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGACGCTTTCTCAAAAACGCCAATAAAGCACTGAGC
* *
10551 ATTAGCGGCGCTTTCTCAAAACCACCGCTAAAGCACTGAGCATTAGCGGCGCTTTCTCAGAAACG
66 ATTAGCGGCGCTTTCTCAAAAACACCGCTAAAGCACTGAGCATTAGCGGCGCTTTCTCAAAAACG
10616 CCACTAAAGACTGAGCATTAGCGGCTCTTTTTT
131 CCACTAAAGACTGAGCATTAGCGGCTCTTTTTT
** *
10649 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGACGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGC
1 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGACGCTTTCTCAAAAACGCCAATAAAGCACTGAGC
* * * * *
10714 ATTAGCGGCGCTTTCTTAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGTGCTTTTTCAAAAACG
66 ATTAGCGGCGCTTTCTCAAAAACACCGCTAAAGCACTGAGCATTAGCGGCGCTTTCTCAAAAACG
10779 C
131 C
10780 TGTTAAAGCC
Statistics
Matches: 118, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
163 118 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (163 bp):
AAAAACGCCGCTAAAGCCCTGAGCATTAGCGACGCTTTCTCAAAAACGCCAATAAAGCACTGAGC
ATTAGCGGCGCTTTCTCAAAAACACCGCTAAAGCACTGAGCATTAGCGGCGCTTTCTCAAAAACG
CCACTAAAGACTGAGCATTAGCGGCTCTTTTTT
Found at i:10834 original size:41 final size:41
Alignment explanation
Indices: 10487--10831 Score: 430
Period size: 41 Copynumber: 8.4 Consensus size: 41
10477 NNNNNNNNNA
10487 AAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTCT
1 AAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTCT
* ** *
10528 AAAATGCCAATAAAGCACTGAGCATTAGCGGCGCTTTCTC-
1 AAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTCT
* *
10568 AAAACCACCGCTAAAGCACTGAGCATTAGCGGCGCTTTCTC-
1 AAAA-CGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTCT
* * * *
10609 AGAAACGCCACTAAAG-ACTGAGCATTAGCGGCTCTTT-TTT
1 A-AAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTCT
* *
10649 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGACGCTTTCTCA
1 -AAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTCT
10691 AAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCT-T
1 AAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTCT
* * *
10731 AAAAACGCCGCTAAAGCCCTGAGCATTAGCGGTGCTTTTTCA
1 -AAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTCT
* * * *
10773 AAAACGCTGTTAAAGCCCCGAGCATTAGCGGTGCTTTCTCT
1 AAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTCT
* *
10814 AAAATGTCGCTAAAGCCC
1 AAAACGCCGCTAAAGCCC
10832 CGAAAGCTCG
Statistics
Matches: 264, Mismatches: 32, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
39 1 0.00
40 37 0.14
41 222 0.84
42 4 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.23
Consensus pattern (41 bp):
AAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTCT
Found at i:10915 original size:39 final size:40
Alignment explanation
Indices: 10866--10952 Score: 97
Period size: 39 Copynumber: 2.2 Consensus size: 40
10856 TGGGCTTAGG
* **
10866 TTTTTTGCGGCGCTTTCTGGAAAA-CACCGCTAATGCTT-A
1 TTTTTAGCGGCGCTTTC-CAAAAAGCACCGCTAATGCTTGA
* *
10905 TTTTTAGCGGCGTTTTCCAAAAAGCGCCGCTAATGCTTGA
1 TTTTTAGCGGCGCTTTCCAAAAAGCACCGCTAATGCTTGA
*
10945 TCTTTAGC
1 TTTTTAGC
10953 TGCGTTTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
38 4 0.10
39 28 0.70
40 8 0.20
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.36
Consensus pattern (40 bp):
TTTTTAGCGGCGCTTTCCAAAAAGCACCGCTAATGCTTGA
Found at i:12869 original size:14 final size:15
Alignment explanation
Indices: 12850--12883 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
12840 TGTAATTTGC
12850 TTTTGGGTTTTC-TT
1 TTTTGGGTTTTCGTT
*
12864 TTTTGGTTTTTCGTT
1 TTTTGGGTTTTCGTT
12879 TTTTG
1 TTTTG
12884 CTGGATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.00, C:0.06, G:0.21, T:0.74
Consensus pattern (15 bp):
TTTTGGGTTTTCGTT
Found at i:13026 original size:13 final size:13
Alignment explanation
Indices: 13008--13072 Score: 71
Period size: 13 Copynumber: 5.0 Consensus size: 13
12998 GTTTGGCAAA
13008 GCTTTTGAAAAGT
1 GCTTTTGAAAAGT
13021 GCTTTTGAAAAGT
1 GCTTTTGAAAAGT
*
13034 GAC--GTGAAAAAGT
1 G-CTTTTG-AAAAGT
* *
13047 ACTTTTGAGAAGT
1 GCTTTTGAAAAGT
13060 GCTTTTGAAAAGT
1 GCTTTTGAAAAGT
13073 TTGGTTTAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
12 3 0.07
13 36 0.86
14 3 0.07
ACGTcount: A:0.34, C:0.08, G:0.25, T:0.34
Consensus pattern (13 bp):
GCTTTTGAAAAGT
Found at i:14785 original size:19 final size:19
Alignment explanation
Indices: 14730--14810 Score: 108
Period size: 19 Copynumber: 4.1 Consensus size: 19
14720 ATTGGGTGGA
14730 TCAGCTCTTACGAGCTTCTGT
1 TCAGCT-TT-CGAGCTTCTGT
*
14751 TCAGCTCTTACGAGCTTCTAT
1 TCAGCT-TT-CGAGCTTCTGT
*
14772 TCAACTTTCGAGCTTCTGT
1 TCAGCTTTCGAGCTTCTGT
14791 TCAGCTTTCGAGCTTCTGT
1 TCAGCTTTCGAGCTTCTGT
14810 T
1 T
14811 GGCGTGTTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
19 29 0.52
20 2 0.04
21 25 0.45
ACGTcount: A:0.15, C:0.27, G:0.17, T:0.41
Consensus pattern (19 bp):
TCAGCTTTCGAGCTTCTGT
Found at i:20164 original size:25 final size:24
Alignment explanation
Indices: 20063--20181 Score: 96
Period size: 25 Copynumber: 4.8 Consensus size: 24
20053 TAGCTCTTCG
* * *
20063 GAGCTTCCCGATATTGGCTCACTT
1 GAGCTTCCCGTTAATGGCTCACAT
* * * **
20087 GAATCTTCCCGATATTGGCTCGTAT
1 G-AGCTTCCCGTTAATGGCTCACAT
*
20112 GAGCTTCCCGTTAATGGCTCTC-T
1 GAGCTTCCCGTTAATGGCTCACAT
* *
20135 AGAGCCTCCCGTTACGTGGCTCACAT
1 -GAGCTTCCCGTTA-ATGGCTCACAT
20161 GAGCTTCCCGTTATATGGCTC
1 GAGCTTCCCGTTA-ATGGCTC
20182 GAGAGAAAGA
Statistics
Matches: 76, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
23 1 0.01
24 29 0.38
25 45 0.59
26 1 0.01
ACGTcount: A:0.17, C:0.29, G:0.22, T:0.32
Consensus pattern (24 bp):
GAGCTTCCCGTTAATGGCTCACAT
Found at i:20493 original size:18 final size:17
Alignment explanation
Indices: 20466--20507 Score: 75
Period size: 18 Copynumber: 2.4 Consensus size: 17
20456 ATGTTTCTTG
20466 ATGTTTATATGAAATAC
1 ATGTTTATATGAAATAC
20483 ATGTCTTATATGAAATAC
1 ATGT-TTATATGAAATAC
20501 ATGTTTA
1 ATGTTTA
20508 ACATTGTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 7 0.29
18 17 0.71
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.43
Consensus pattern (17 bp):
ATGTTTATATGAAATAC
Found at i:39151 original size:134 final size:135
Alignment explanation
Indices: 38989--39260 Score: 537
Period size: 134 Copynumber: 2.0 Consensus size: 135
38979 GTGATTACTT
38989 ATGCTCCCATGACATTAATATATATATATATATATAAATTAATTTTTTTATGGTAAAACGATATA
1 ATGCTCCCATGACATTAATATATATATATATATATAAATTAATTTTTTTATGGTAAAACGATATA
39054 GCACATAAGGAGCAAAACGCCCTTTTGTTTTCTTTTGGTCGACCTCGTTAATATGGCAGATGTTC
66 GCACATAAGGAGCAAAACGCCCTTTTGTTTTCTTTTGGTCGACCTCGTTAATATGGCAGATGTTC
39119 CTTCC
131 CTTCC
39124 ATGCTCCCATG-CATTAATATATATATATATATATAAATTAATTTTTTTATGGTAAAACGATATA
1 ATGCTCCCATGACATTAATATATATATATATATATAAATTAATTTTTTTATGGTAAAACGATATA
39188 GCACATAAGGAGCAAAACGCCCTTTTGTTTTCTTTTGGTCGACCTCGTTAATATGGCAGATGTTC
66 GCACATAAGGAGCAAAACGCCCTTTTGTTTTCTTTTGGTCGACCTCGTTAATATGGCAGATGTTC
39253 CTTCC
131 CTTCC
39258 ATG
1 ATG
39261 GTGAAAAATC
Statistics
Matches: 137, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
134 126 0.92
135 11 0.08
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (135 bp):
ATGCTCCCATGACATTAATATATATATATATATATAAATTAATTTTTTTATGGTAAAACGATATA
GCACATAAGGAGCAAAACGCCCTTTTGTTTTCTTTTGGTCGACCTCGTTAATATGGCAGATGTTC
CTTCC
Found at i:39750 original size:113 final size:113
Alignment explanation
Indices: 39421--39767 Score: 341
Period size: 113 Copynumber: 3.1 Consensus size: 113
39411 GATTCACAAA
* * * *
39421 AAGCGCCGCAAAAAA-ATAAGGCCAACGACGCCGTTTACTAAGTTTTTGGGCCATTAGCGGCGTT
1 AAGCGCCGCAAAAAACCTAAGGGCAACGACGCCGTTTTCTAAGTTTTTGGGCCTTTAGCGGCGTT
* * ** * * *
39485 TTTATAAAAACGCTGCTAATGCTCGGGGGA-CTTT-GCGGCGATTTCTAAA
66 TTT-TAAAAGCGCCGCTAATGCTC--ATGATCTTTAGCGGCGTTTTCTGAG
* * * ** ** *
39534 AAGTGCCGCAAAAAACCTAA-TGCAAACGACGTCG-TTTCCGAGTTTTTGTCCCTTTTGCGGCGC
1 AAGCGCCGCAAAAAACCTAAGGGC-AACGACGCCGTTTTCTAAGTTTTTGGGCCTTTAGCGGCG-
*
39597 TTTTTTAAAAGCGCCGGTAATGCTCAT-ATCTTTAGCGGCGTTTTCTGAG
64 TTTTTTAAAAGCGCCGCTAATGCTCATGATCTTTAGCGGCGTTTTCTGAG
**
39646 AAGCGCCGCAAAAAACCTAAGGGCAACGACGCCGTTTTCTTTGTTTTTGGGCCTTTAGCGGCGTT
1 AAGCGCCGCAAAAAACCTAAGGGCAACGACGCCGTTTTCTAAGTTTTTGGGCCTTTAGCGGCGTT
* * * *
39711 TTCTTAAAAGCGCCGCTAATGAT-TTGTTCTTTAGCGGCGTTTTTTTG-G
66 TT-TTAAAAGCGCCGCTAATGCTCATGATCTTTAGCGGCG-TTTTCTGAG
39759 AAGCGCCGC
1 AAGCGCCGC
39768 TAATAGTAAT
Statistics
Matches: 190, Mismatches: 34, Indels: 20
0.78 0.14 0.08
Matches are distributed among these distances:
110 1 0.01
111 4 0.02
112 45 0.24
113 117 0.62
114 23 0.12
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.30
Consensus pattern (113 bp):
AAGCGCCGCAAAAAACCTAAGGGCAACGACGCCGTTTTCTAAGTTTTTGGGCCTTTAGCGGCGTT
TTTTAAAAGCGCCGCTAATGCTCATGATCTTTAGCGGCGTTTTCTGAG
Found at i:40150 original size:18 final size:21
Alignment explanation
Indices: 40104--40152 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 21
40094 TAGTTCGACT
40104 AAATTAATATATAAATCAAAC
1 AAATTAATATATAAATCAAAC
* *
40125 AAAGTAATATA-AAA-C-ACC
1 AAATTAATATATAAATCAAAC
40143 AAATTAATAT
1 AAATTAATAT
40153 CGTGATTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 11 0.44
19 1 0.04
20 3 0.12
21 10 0.40
ACGTcount: A:0.61, C:0.10, G:0.02, T:0.27
Consensus pattern (21 bp):
AAATTAATATATAAATCAAAC
Found at i:40739 original size:14 final size:14
Alignment explanation
Indices: 40700--40785 Score: 61
Period size: 14 Copynumber: 6.2 Consensus size: 14
40690 TGGTTTTTGA
40700 GTTTGGGGTTTA-G
1 GTTTGGGGTTTAGG
*
40713 TTTTCGGGG-TTAGG
1 GTTT-GGGGTTTAGG
40727 GTTTGGGGTTTAGG
1 GTTTGGGGTTTAGG
* * * *
40741 ATTTGGGTTTTTGA
1 GTTTGGGGTTTAGG
*
40755 GTTTAGGGTTT-GG
1 GTTTGGGGTTTAGG
* *
40768 TGTTTGAGGTTAAGG
1 -GTTTGGGGTTTAGG
40783 GTT
1 GTT
40786 NNNNNNNNNN
Statistics
Matches: 55, Mismatches: 13, Indels: 9
0.71 0.17 0.12
Matches are distributed among these distances:
13 11 0.20
14 42 0.76
15 2 0.04
ACGTcount: A:0.10, C:0.01, G:0.42, T:0.47
Consensus pattern (14 bp):
GTTTGGGGTTTAGG
Found at i:40783 original size:21 final size:21
Alignment explanation
Indices: 40719--40785 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
40709 TTAGTTTTCG
* *
40719 GGGTTAGG-GTTTGGGGTTTA
1 GGGTTTGGTGTTTGAGGTTTA
* *
40739 GGATTTGGGTTTTTGA-GTTTA
1 GGGTTT-GGTGTTTGAGGTTTA
*
40760 GGGTTTGGTGTTTGAGGTTAA
1 GGGTTTGGTGTTTGAGGTTTA
40781 GGGTT
1 GGGTT
40786 NNNNNNNNNN
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
20 12 0.32
21 21 0.57
22 4 0.11
ACGTcount: A:0.12, C:0.00, G:0.43, T:0.45
Consensus pattern (21 bp):
GGGTTTGGTGTTTGAGGTTTA
Found at i:42055 original size:231 final size:230
Alignment explanation
Indices: 41370--42039 Score: 1063
Period size: 231 Copynumber: 2.9 Consensus size: 230
41360 NNNNNNNNNN
41370 AAAACGCCGCAAGTATGTTTTCTTTGTTACGGAAACGGCGTCGTTTTCCATTGTTATTAGTGGCG
1 AAAACGCCGCAAGTATGTTTTCTTTGTTAC-GAAACGGCGTCGTTTTCCATTGTTATTAGTGGCG
*
41435 TTACACCCAAAACGCCGCAAATATATTTTAAAGATTACACGAGTTTGCATTAAACGACTGCGTTT
65 TTACACCCAAAACGCCGCAAATATATTTTAAAGATTACAGGAGTTTGCATTAAACGACTGCGTTT
* *
41500 GACCTTATATTTAGTGTCACTTATATATAAACGCCGCAAAATCGAAATGGTGTTACGAAAAACGG
130 GACCTTATATTTAGTGGCGCTTATATATAAACGCCGCAAAATCGAAATGGTGTTACGAAAAACGG
* *
41565 CGCCCTTTTTTTATTACATTTAGTGGCGTTTTAGAG
195 CGCCGTTTTCTTATTACATTTAGTGGCGTTTTAGAG
*
41601 AAAACGCCGCAAGTATGTTTTCTTTGTTACGTAAACGGCGTCGTTTTCCTTTGTTATTAGTGGCG
1 AAAACGCCGCAAGTATGTTTTCTTTGTTACG-AAACGGCGTCGTTTTCCATTGTTATTAGTGGCG
* * * * *
41666 TTATACCCGAAATGCCGCAAATAAATTTTAAAGATTACAGGAGTTTGCGTTAAACGACTGCGTTT
65 TTACACCCAAAACGCCGCAAATATATTTTAAAGATTACAGGAGTTTGCATTAAACGACTGCGTTT
*
41731 GACCTTATATTTAGTGGCGCTTATATATAAACGCCGCAAACTCGAAAATGGTGTTACGAAAAACG
130 GACCTTATATTTAGTGGCGCTTATATATAAACGCCGCAAAATCG-AAATGGTGTTACGAAAAACG
* *
41796 GCACCGTTTTCTTATTACATTTAGTGGCGTTTTAGAT
194 GCGCCGTTTTCTTATTACATTTAGTGGCGTTTTAGAG
* ** * *
41833 AAAACGCCGCAAGTATATTTTCTTTGTTACAGAAACGGCGTCGTTTT-CAAGGATATTTGTGGCG
1 AAAACGCCGCAAGTATGTTTTCTTTGTTAC-GAAACGGCGTCGTTTTCCATTGTTATTAGTGGCG
* * *
41897 TTACACCCAAAACGCCGTAAATATATTTTAAAGATTACAGGAGTTTGCTTTAAACGATTGCGTTT
65 TTACACCCAAAACGCCGCAAATATATTTTAAAGATTACAGGAGTTTGCATTAAACGACTGCGTTT
* *
41962 GACCTTATATTTGGTGGCGCTTATATATAAACGCCGCAAAATCGAAATGGTGTTACGGAAAACGG
130 GACCTTATATTTAGTGGCGCTTATATATAAACGCCGCAAAATCGAAATGGTGTTACGAAAAACGG
* *
42027 TGCCGTTTCCTTA
195 CGCCGTTTTCTTA
42040 GTTGGTTTTA
Statistics
Matches: 403, Mismatches: 33, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
230 31 0.08
231 274 0.68
232 97 0.24
233 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (230 bp):
AAAACGCCGCAAGTATGTTTTCTTTGTTACGAAACGGCGTCGTTTTCCATTGTTATTAGTGGCGT
TACACCCAAAACGCCGCAAATATATTTTAAAGATTACAGGAGTTTGCATTAAACGACTGCGTTTG
ACCTTATATTTAGTGGCGCTTATATATAAACGCCGCAAAATCGAAATGGTGTTACGAAAAACGGC
GCCGTTTTCTTATTACATTTAGTGGCGTTTTAGAG
Found at i:42143 original size:231 final size:230
Alignment explanation
Indices: 41370--42126 Score: 1043
Period size: 231 Copynumber: 3.3 Consensus size: 230
41360 NNNNNNNNNN
*
41370 AAAACGCCGCAAGTATGTTTTCTTTGTTACGGAAACGGCGTCGTTTTCCATTGTTATTAGTGGCG
1 AAAACGCCGCAAGTATGTTTTCTTTGTTAAGGAAACGGCGTCGTTTTCCATTGTTATTAGTGGCG
*
41435 TTACACCCAAAACGCCGCAAATATATTTTAAAGATTACACGAGTTTGCATTAAACGACTGCGTTT
66 TTACACCCAAAACGCCGCAAATATATTTTAAAGATTACAGGAGTTTGCATTAAACGACTGCGTTT
* *
41500 GACCTTATATTTAGTGTCACTTATATATAAACGCCGCAAAATCGAAATGGTGTTACGAAAAACGG
131 GACCTTATATTTAGTGGCGCTTATATATAAACGCCGCAAAATCGAAATGGTGTTACGAAAAACGG
* * *
41565 CGCCCTTTTTTTATTACATTTAGTGGCGTTTTAGAG
196 CGCCGTTTTCTTATTACATTTAGTGGCGTTTTA-AT
* * *
41601 AAAACGCCGCAAGTATGTTTTCTTTGTTACGTAAACGGCGTCGTTTTCCTTTGTTATTAGTGGCG
1 AAAACGCCGCAAGTATGTTTTCTTTGTTAAGGAAACGGCGTCGTTTTCCATTGTTATTAGTGGCG
* * * * *
41666 TTATACCCGAAATGCCGCAAATAAATTTTAAAGATTACAGGAGTTTGCGTTAAACGACTGCGTTT
66 TTACACCCAAAACGCCGCAAATATATTTTAAAGATTACAGGAGTTTGCATTAAACGACTGCGTTT
*
41731 GACCTTATATTTAGTGGCGCTTATATATAAACGCCGCAAACTCGAAAATGGTGTTACGAAAAACG
131 GACCTTATATTTAGTGGCGCTTATATATAAACGCCGCAAAATCG-AAATGGTGTTACGAAAAACG
*
41796 GCACCGTTTTCTTATTACATTTAGTGGCGTTTTAGAT
195 GCGCCGTTTTCTTATTACATTTAGTGGCGTTTTA-AT
* ** * *
41833 AAAACGCCGCAAGTATATTTTCTTTGTTACA-GAAACGGCGTCGTTTT-CAAGGATATTTGTGGC
1 AAAACGCCGCAAGTATGTTTTCTTTGTTA-AGGAAACGGCGTCGTTTTCCATTGTTATTAGTGGC
* * *
41896 GTTACACCCAAAACGCCGTAAATATATTTTAAAGATTACAGGAGTTTGCTTTAAACGATTGCGTT
65 GTTACACCCAAAACGCCGCAAATATATTTTAAAGATTACAGGAGTTTGCATTAAACGACTGCGTT
* *
41961 TGACCTTATATTTGGTGGCGCTTATATATAAACGCCGCAAAATCGAAATGGTGTTACGGAAAACG
130 TGACCTTATATTTAGTGGCGCTTATATATAAACGCCGCAAAATCGAAATGGTGTTACGAAAAACG
* * ***
42026 GTGCCGTTTCCTTAGTTGGTTTTAGTGGCGCTTTT-AT
195 GCGCCGTTTTCTTA-TTACATTTAGTGGCG-TTTTAAT
* * * * ** * *** * *
42063 TAAACACCGCAAATTTGCATTATAACTTAAGGAAACTGCGTCGTTTTCCATTGTTAGTAGTGGC
1 AAAACGCCGCAAGTATGTTTTCTTTGTTAAGGAAACGGCGTCGTTTTCCATTGTTATTAGTGGC
42127 ACTTTGCTTA
Statistics
Matches: 464, Mismatches: 56, Indels: 12
0.87 0.11 0.02
Matches are distributed among these distances:
229 1 0.00
230 65 0.14
231 298 0.64
232 100 0.22
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (230 bp):
AAAACGCCGCAAGTATGTTTTCTTTGTTAAGGAAACGGCGTCGTTTTCCATTGTTATTAGTGGCG
TTACACCCAAAACGCCGCAAATATATTTTAAAGATTACAGGAGTTTGCATTAAACGACTGCGTTT
GACCTTATATTTAGTGGCGCTTATATATAAACGCCGCAAAATCGAAATGGTGTTACGAAAAACGG
CGCCGTTTTCTTATTACATTTAGTGGCGTTTTAAT
Found at i:42424 original size:19 final size:19
Alignment explanation
Indices: 42402--42445 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
42392 CAGACATCTC
*
42402 CCCCAAATCCCTAAAATTT
1 CCCCAAATCCCTAAAAGTT
* * *
42421 CCCCTAATTCCTAACAGTT
1 CCCCAAATCCCTAAAAGTT
42440 CCCCAA
1 CCCCAA
42446 CGTAGTCCAG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.32, C:0.41, G:0.02, T:0.25
Consensus pattern (19 bp):
CCCCAAATCCCTAAAAGTT
Found at i:43365 original size:136 final size:137
Alignment explanation
Indices: 43199--43471 Score: 530
Period size: 136 Copynumber: 2.0 Consensus size: 137
43189 TTTTTTTTAA
43199 GCTATTTGTAAAAAAATATTAATATATGGCAGAATTAAAATGCATTGTCACTTTTCATGTGGTTA
1 GCTATTTGTAAAAAAATATTAATATATGGCAGAATTAAAATGCATTGTCACTTTTCATGTGGTTA
*
43264 CTTAATCAATTAATAGAATGTAGTACTAAATTAGGTCAAGCAGAAATTTAGGAGTAAAGTGAGAA
66 CTTAATCAATTAATAGAATGTAGTACCAAATTAGGTCAAGCAGAAATTTAGGAGTAAAGTGAGAA
43329 AAATGAT
131 AAATGAT
43336 GCTATTTGT-AAAAAATATTAATATATGGCAGAATTAAAATGCATTGTCACTTTTCATGTGGTTA
1 GCTATTTGTAAAAAAATATTAATATATGGCAGAATTAAAATGCATTGTCACTTTTCATGTGGTTA
43400 CTTAATCAATTAATAGAATGTAGTACCAAATTAGGTCAAGCAGAAATTTAGGAGTAAAGTGAGAA
66 CTTAATCAATTAATAGAATGTAGTACCAAATTAGGTCAAGCAGAAATTTAGGAGTAAAGTGAGAA
43465 AAATGAT
131 AAATGAT
43472 ATTTTTAAGA
Statistics
Matches: 135, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
136 126 0.93
137 9 0.07
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (137 bp):
GCTATTTGTAAAAAAATATTAATATATGGCAGAATTAAAATGCATTGTCACTTTTCATGTGGTTA
CTTAATCAATTAATAGAATGTAGTACCAAATTAGGTCAAGCAGAAATTTAGGAGTAAAGTGAGAA
AAATGAT
Found at i:43739 original size:18 final size:18
Alignment explanation
Indices: 43679--43743 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
43669 TACTCAAAAA
43679 ATAAATAAATTAGTCTTT
1 ATAAATAAATTAGTCTTT
* ** **
43697 ATAAAAAAATTTTA-AATAA
1 ATAAATAAA--TTAGTCTTT
43716 ATAAATAAATTAGTCTTT
1 ATAAATAAATTAGTCTTT
43734 ATAAATAAAT
1 ATAAATAAAT
43744 AGATAAAATT
Statistics
Matches: 34, Mismatches: 10, Indels: 6
0.68 0.20 0.12
Matches are distributed among these distances:
17 3 0.09
18 19 0.56
19 9 0.26
20 3 0.09
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (18 bp):
ATAAATAAATTAGTCTTT
Found at i:48206 original size:21 final size:21
Alignment explanation
Indices: 48180--48250 Score: 88
Period size: 21 Copynumber: 3.4 Consensus size: 21
48170 CTACAACTTA
* *
48180 AAGCAGAGGCGGAAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
*
48201 AAGCAGCGGCTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* *
48222 AAGCGGAGGCTGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGGG
*
48243 AAGTAGAG
1 AAGCAGAG
48251 CAGAGCAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.31, C:0.17, G:0.48, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:48493 original size:14 final size:14
Alignment explanation
Indices: 48474--48507 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
48464 ATTGCTATTG
48474 GTTGCTTTTGAATT
1 GTTGCTTTTGAATT
48488 GTTGCTTTTGAATT
1 GTTGCTTTTGAATT
*
48502 TTTGCT
1 GTTGCT
48508 ACAGGAGGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.12, C:0.09, G:0.21, T:0.59
Consensus pattern (14 bp):
GTTGCTTTTGAATT
Found at i:48627 original size:42 final size:41
Alignment explanation
Indices: 48575--48780 Score: 182
Period size: 42 Copynumber: 4.9 Consensus size: 41
48565 GTTTTTGTAT
* *
48575 AAAAGCGCCACTAAAGAACATGTTCTTTAGCAGCGTTTGTAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCAGCGTTTG-AA
* * * *
48617 AAAAATGCCACTAAAGAACATGTTCTTTAGCGGCGCTTGTAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCAGCGTTTG-AA
* * **
48659 AAAAACGCCGCTAAAGAACACGTTCTTTAG-AGGCGCTTAGGG
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCA-GCG-TTTGAA
* * * * * *
48701 AAAAATGGCGCTAAAGAACACGTTCTTTAG-AGGCAATTAGGA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCA-GC-GTTTGAA
* *
48743 AAAAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTT
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCAGCGTTT
48781 TTCCTTTCTT
Statistics
Matches: 137, Mismatches: 23, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
41 2 0.01
42 133 0.97
43 2 0.01
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (41 bp):
AAAAACGCCGCTAAAGAACATGTTCTTTAGCAGCGTTTGAA
Found at i:48715 original size:84 final size:84
Alignment explanation
Indices: 48569--48779 Score: 230
Period size: 84 Copynumber: 2.5 Consensus size: 84
48559 AGTGGCGTTT
* * * *
48569 TTGTATAAAAGCGCCACTAAAGAACATGTTCTTTAGCA-GCGTTTGTAAAAAAATGCCACTAAAG
1 TTGTAAAAAAACGCCGCTAAAGAACATGTTCTTTAG-AGGCGTTAGTAAAAAAATGCCACTAAAG
* * **
48633 AACATGTTCTTTAGCGGCGC
65 AACACGTTCTTTAGAGGCAA
* ** * *
48653 TTGTAAAAAAACGCCGCTAAAGAACACGTTCTTTAGAGGCGCTTAG-GGAAAAATGGCGCTAAAG
1 TTGTAAAAAAACGCCGCTAAAGAACATGTTCTTTAGAGGCG-TTAGTAAAAAAATGCCACTAAAG
48717 AACACGTTCTTTAGAGGCAA
65 AACACGTTCTTTAGAGGCAA
* * *
48737 TTAG-GAAAAAACGCCGCTAAAGAACATGATCTTTAGCGGCGTT
1 TT-GTAAAAAAACGCCGCTAAAGAACATGTTCTTTAGAGGCGTT
48780 TTTCCTTTCT
Statistics
Matches: 107, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
83 3 0.03
84 100 0.93
85 4 0.04
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (84 bp):
TTGTAAAAAAACGCCGCTAAAGAACATGTTCTTTAGAGGCGTTAGTAAAAAAATGCCACTAAAGA
ACACGTTCTTTAGAGGCAA
Found at i:50298 original size:40 final size:40
Alignment explanation
Indices: 50236--50314 Score: 95
Period size: 40 Copynumber: 2.0 Consensus size: 40
50226 GGACAAAAAA
* *
50236 CGCCAGTAAAAATAGAGCATTAGTGGTGCTTTATGGAAAT
1 CGCCACTAAAAATAGAGCATTAGCGGTGCTTTATGGAAAT
* * * * *
50276 CGCCACTAAAGATTGAGGATTAGCGGTGTTTTTTGGAAA
1 CGCCACTAAAAATAGAGCATTAGCGGTGCTTTATGGAAA
50315 AGCGCTGCAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.29
Consensus pattern (40 bp):
CGCCACTAAAAATAGAGCATTAGCGGTGCTTTATGGAAAT
Found at i:50422 original size:41 final size:41
Alignment explanation
Indices: 50360--51380 Score: 1920
Period size: 41 Copynumber: 24.9 Consensus size: 41
50350 TTCTGACCTT
* * * *
50360 TCGGGGCTTTAGCGGCGTTTTTAAAAAAGCGCCGCTAATAC
1 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
* * *
50401 TCGGGGCTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGC
1 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
* *
50442 TCGGG--TATTAGCGGCGTTTTTGAAAAGGCGCCGCTAATGC
1 TCGGGCCT-TTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
*
50482 TCGGGGCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
1 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
50523 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
1 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
50564 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
1 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
50605 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
1 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
50646 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
1 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
50687 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
1 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
50728 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
1 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
50769 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
1 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
50810 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
1 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
50851 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
1 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
50892 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
1 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
50933 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
1 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
50974 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
1 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
51015 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
1 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
51056 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
1 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
51097 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
1 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
51138 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
1 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
51179 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
1 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
51220 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
1 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
51261 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
1 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
51302 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
1 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
*
51343 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAA
1 TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAA
51381 AAACATTTTA
Statistics
Matches: 968, Mismatches: 9, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
39 1 0.00
40 36 0.04
41 930 0.96
42 1 0.00
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (41 bp):
TCGGGCCTTTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGC
Found at i:51746 original size:7 final size:7
Alignment explanation
Indices: 51734--51814 Score: 65
Period size: 7 Copynumber: 11.6 Consensus size: 7
51724 GAGTATAGAT
51734 TTAGGGA
1 TTAGGGA
51741 TTAGGGA
1 TTAGGGA
51748 TTAGGGA
1 TTAGGGA
51755 TTAGGGA
1 TTAGGGA
* *
51762 TTATGGT
1 TTAGGGA
*
51769 TTAAGGA
1 TTAGGGA
*
51776 TT-GTGA
1 TTAGGGA
* *
51782 TTTAAGGT
1 -TTAGGGA
*
51790 TTAGGGG
1 TTAGGGA
*
51797 TTAGGGT
1 TTAGGGA
*
51804 TTAGGGG
1 TTAGGGA
51811 TTAG
1 TTAG
51815 ACATTATGGG
Statistics
Matches: 59, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
6 2 0.03
7 56 0.95
8 1 0.02
ACGTcount: A:0.23, C:0.00, G:0.40, T:0.37
Consensus pattern (7 bp):
TTAGGGA
Found at i:51760 original size:21 final size:21
Alignment explanation
Indices: 51734--51814 Score: 74
Period size: 21 Copynumber: 3.9 Consensus size: 21
51724 GAGTATAGAT
*
51734 TTAGGGATTAGGGATTAGGGA
1 TTAGGGATTAGGGTTTAGGGA
* *
51755 TTAGGGATTATGGTTTAAGGA
1 TTAGGGATTAGGGTTTAGGGA
* * *
51776 TT-GTGATTTAAGGTTTAGGGG
1 TTAGGGA-TTAGGGTTTAGGGA
* *
51797 TTAGGGTTTAGGGGTTAG
1 TTAGGGATTAGGGTTTAG
51815 ACATTATGGG
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
20 3 0.06
21 42 0.89
22 2 0.04
ACGTcount: A:0.23, C:0.00, G:0.40, T:0.37
Consensus pattern (21 bp):
TTAGGGATTAGGGTTTAGGGA
Found at i:52057 original size:15 final size:14
Alignment explanation
Indices: 52038--52080 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
52028 ACTATTTTAA
52038 GGTTTATGGATTAT
1 GGTTTATGGATTAT
* *
52052 GAGTTTAGGGATTAC
1 G-GTTTATGGATTAT
*
52067 GGTTTATGGTTTAT
1 GGTTTATGGATTAT
52081 TATTTAAGGG
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.21, C:0.02, G:0.30, T:0.47
Consensus pattern (14 bp):
GGTTTATGGATTAT
Found at i:52058 original size:22 final size:22
Alignment explanation
Indices: 52010--52058 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
52000 ATGGTGTAGG
*
52010 GTTTAAGGTTTAAGGGTTACTA
1 GTTTAAGGTTTAAGGATTACTA
* *
52032 TTTTAAGGTTTATGGATTA-TGA
1 GTTTAAGGTTTAAGGATTACT-A
52054 GTTTA
1 GTTTA
52059 GGGATTACGG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.27, C:0.02, G:0.24, T:0.47
Consensus pattern (22 bp):
GTTTAAGGTTTAAGGATTACTA
Found at i:52121 original size:22 final size:22
Alignment explanation
Indices: 52083--52133 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
52073 TGGTTTATTA
*
52083 TTTAAGGGTTGGGATTTAAG-G
1 TTTAGGGGTTGGGATTTAAGAG
*
52104 TTTAGGGGTTAGGGATTTAAGAT
1 TTTAGGGGTT-GGGATTTAAGAG
52127 TTTAGGG
1 TTTAGGG
52134 TTTAAGGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 9 0.35
22 10 0.38
23 7 0.27
ACGTcount: A:0.24, C:0.00, G:0.37, T:0.39
Consensus pattern (22 bp):
TTTAGGGGTTGGGATTTAAGAG
Found at i:54736 original size:24 final size:24
Alignment explanation
Indices: 54689--54736 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
54679 TAGGCCATTT
**
54689 TAATTAACACCATCATTTTTCTTC
1 TAATTAACACCATCATTTAGCTTC
54713 TAATTAACACCAT-AGTTTAGCTTC
1 TAATTAACACCATCA-TTTAGCTTC
54737 GCATTTTGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.31, C:0.23, G:0.04, T:0.42
Consensus pattern (24 bp):
TAATTAACACCATCATTTAGCTTC
Found at i:62064 original size:25 final size:26
Alignment explanation
Indices: 62030--62082 Score: 99
Period size: 25 Copynumber: 2.1 Consensus size: 26
62020 CCTTGTTGTC
62030 ATATGTGCTTTAGGTGATGTAT-CTT
1 ATATGTGCTTTAGGTGATGTATACTT
62055 ATATGTGCTTTAGGTGATGTATACTT
1 ATATGTGCTTTAGGTGATGTATACTT
62081 AT
1 AT
62083 TGTATAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 22 0.81
26 5 0.19
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.47
Consensus pattern (26 bp):
ATATGTGCTTTAGGTGATGTATACTT
Found at i:64217 original size:15 final size:15
Alignment explanation
Indices: 64197--64225 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
64187 AATACTGTTG
64197 CTGTGTAGGAGAAGA
1 CTGTGTAGGAGAAGA
64212 CTGTGTAGGAGAAG
1 CTGTGTAGGAGAAG
64226 GTTATGTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.07, G:0.41, T:0.21
Consensus pattern (15 bp):
CTGTGTAGGAGAAGA
Found at i:65631 original size:33 final size:34
Alignment explanation
Indices: 65573--65642 Score: 124
Period size: 33 Copynumber: 2.1 Consensus size: 34
65563 ATATGTTTTG
65573 CAAAAATTCAGACTCTTTTTAACAAGTAACTATA
1 CAAAAATTCAGACTCTTTTTAACAAGTAACTATA
*
65607 CAAAAATTCGGACTC-TTTTAACAAGTAACTATA
1 CAAAAATTCAGACTCTTTTTAACAAGTAACTATA
65640 CAA
1 CAA
65643 GGTTTTTATC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 21 0.60
34 14 0.40
ACGTcount: A:0.44, C:0.19, G:0.07, T:0.30
Consensus pattern (34 bp):
CAAAAATTCAGACTCTTTTTAACAAGTAACTATA
Found at i:73078 original size:16 final size:18
Alignment explanation
Indices: 73052--73084 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
73042 TTAATTTACA
73052 TAAATTAA-TTTCTCAAT
1 TAAATTAATTTTCTCAAT
73069 TAAA-TAATTTTCTCAA
1 TAAATTAATTTTCTCAA
73085 CCTAATTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:75475 original size:23 final size:23
Alignment explanation
Indices: 75448--75496 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
75438 TAATTAAGGC
* * *
75448 TTAATTAACTTAGTTAATCATGT
1 TTAATTAACTTAATAAAACATGT
*
75471 TTAATTAATTTAATAAAACATGT
1 TTAATTAACTTAATAAAACATGT
75494 TTA
1 TTA
75497 TCCATTTAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (23 bp):
TTAATTAACTTAATAAAACATGT
Found at i:81885 original size:43 final size:42
Alignment explanation
Indices: 81824--82067 Score: 265
Period size: 43 Copynumber: 5.7 Consensus size: 42
81814 ACTTTGATTC
* *
81824 ATCCGATGATGCATTGTGTGTGCCAATATATTTGCTTCGGTAT
1 ATCCGATGATGCACTGTGTGTGCCAGTATATTT-CTTCGGTAT
* * * *
81867 ATCCGATGATGCATTGTGTGTGCCAGTATATTTTTTCAGTTT
1 ATCCGATGATGCACTGTGTGTGCCAGTATATTTCTTCGGTAT
* * ** *
81909 ATTCGATGATGCACTATGTGTGTTAGTATATTT-TTTGGTAT
1 ATCCGATGATGCACTGTGTGTGCCAGTATATTTCTTCGGTAT
* * *
81950 ATCTGATGATACACTGTGTGTGACAGTATATTTGCTTCGGTAT
1 ATCCGATGATGCACTGTGTGTGCCAGTATATTT-CTTCGGTAT
* * *
81993 ATCCGATGATGCACTATGTGTGCCAGTATATTTTTCTTTGGTTTT
1 ATCCGATGATGCACTGTGTGTGCCAGTATA--TTTCTTCGG-TAT
* *
82038 ATCTGATGATGCACTGTGTGTGCTAGTATA
1 ATCCGATGATGCACTGTGTGTGCCAGTATA
82068 GTAGCTTCGA
Statistics
Matches: 168, Mismatches: 28, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
41 32 0.19
42 34 0.20
43 65 0.39
44 5 0.03
45 32 0.19
ACGTcount: A:0.21, C:0.14, G:0.23, T:0.43
Consensus pattern (42 bp):
ATCCGATGATGCACTGTGTGTGCCAGTATATTTCTTCGGTAT
Found at i:81980 original size:126 final size:129
Alignment explanation
Indices: 81828--82067 Score: 353
Period size: 126 Copynumber: 1.9 Consensus size: 129
81818 TGATTCATCC
* * * * *
81828 GATGATGCATTGTGTGTGCCAATATATTTGCTTCGGTATATCCGATGATGCATTGTGTGTGCCAG
1 GATGATACACTGTGTGTGACAATATATTTGCTTCGGTATATCCGATGATGCACTATGTGTGCCAG
*
81893 TATA-TTTT-TTCAG-TTTAT-TCGATGATGCACTATGTGTGTTAGTATATTTTTTGGTATATCT
66 TATATTTTTCTTCAGTTTTATCT-GATGATGCACTATGTGTGCTAGTATATTTTTTGGTATATCT
*
81954 GATGATACACTGTGTGTGACAGTATATTTGCTTCGGTATATCCGATGATGCACTATGTGTGCCAG
1 GATGATACACTGTGTGTGACAATATATTTGCTTCGGTATATCCGATGATGCACTATGTGTGCCAG
** *
82019 TATATTTTTCTTTGGTTTTATCTGATGATGCACTGTGTGTGCTAGTATA
66 TATATTTTTCTTCAGTTTTATCTGATGATGCACTATGTGTGCTAGTATA
82068 GTAGCTTCGA
Statistics
Matches: 100, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
126 63 0.63
127 4 0.04
128 3 0.03
129 29 0.29
130 1 0.01
ACGTcount: A:0.21, C:0.13, G:0.23, T:0.43
Consensus pattern (129 bp):
GATGATACACTGTGTGTGACAATATATTTGCTTCGGTATATCCGATGATGCACTATGTGTGCCAG
TATATTTTTCTTCAGTTTTATCTGATGATGCACTATGTGTGCTAGTATATTTTTTGGTATATCT
Found at i:82110 original size:88 final size:88
Alignment explanation
Indices: 81912--82103 Score: 191
Period size: 88 Copynumber: 2.2 Consensus size: 88
81902 TCAGTTTATT
** ** *
81912 CGATGATGCACTATGTGTGTTAGTATA--TTT-TTTGG-TATATCTGATGATACACTGTGTGTGA
1 CGATGATGCACTATACGTGCCAGTATATTTTTCTTTGGTTTTATCTGATGATACACTGTGTGTGA
* * *
81973 CAGTATATTTGCTTCGGTATATC
66 CAGTATAGTAGCTTCGCTATATC
** *
81996 CGATGATGCACTATGTGTGCCAGTATATTTTTCTTTGGTTTTATCTGATGATGCACTGTGTGTG-
1 CGATGATGCACTATACGTGCCAGTATATTTTTCTTTGGTTTTATCTGATGATACACTGTGTGTGA
82060 CTAGTATAGTAGCTTCGACT-TCATC
66 C-AGTATAGTAGCTTCG-CTAT-ATC
* *
82085 TGGTGATGCACT-TACGTGC
1 CGATGATGCACTATACGTGC
82104 TGGTATAATT
Statistics
Matches: 90, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
84 25 0.28
86 3 0.03
87 6 0.07
88 42 0.47
89 14 0.16
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.41
Consensus pattern (88 bp):
CGATGATGCACTATACGTGCCAGTATATTTTTCTTTGGTTTTATCTGATGATACACTGTGTGTGA
CAGTATAGTAGCTTCGCTATATC
Found at i:88013 original size:2 final size:2
Alignment explanation
Indices: 88006--88045 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
87996 CAAATGTACA
*
88006 AT AT AT AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
88046 TACTACACCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:90346 original size:21 final size:22
Alignment explanation
Indices: 90322--90363 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
90312 ACAGCAGAAC
*
90322 AGGT-TTTAGCGGCGTTTTTTT
1 AGGTCTTTAGCGGCGCTTTTTT
90343 AGGTCTTTAGCGGCGCTTTTT
1 AGGTCTTTAGCGGCGCTTTTT
90364 AACGCCACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.10, C:0.14, G:0.29, T:0.48
Consensus pattern (22 bp):
AGGTCTTTAGCGGCGCTTTTTT
Found at i:90364 original size:21 final size:21
Alignment explanation
Indices: 90322--90364 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
90312 ACAGCAGAAC
*
90322 AGGTTTTAGCGGCGTTTTTTT
1 AGGTTTTAGCGGCGTCTTTTT
90343 AGGTCTTTAGCGGCG-CTTTTT
1 AGGT-TTTAGCGGCGTCTTTTT
90364 A
1 A
90365 ACGCCACTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.12, C:0.14, G:0.28, T:0.47
Consensus pattern (21 bp):
AGGTTTTAGCGGCGTCTTTTT
Done.