Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008826.1 Hibiscus syriacus cultivar Beakdansim tig00112000_pilon, 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: 3884024
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 18
Found at i:3059580 original size:29 final size:31
Alignment explanation
Indices: 3059548--3059622 Score: 111
Period size: 29 Copynumber: 2.5 Consensus size: 31
3059538 ACCGATTCAG
3059548 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
3059577 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
* *
3059607 ACCAGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
3059623 TCCAGCAGCC
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.59
30 14 0.34
31 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:3059600 original size:19 final size:18
Alignment explanation
Indices: 3059523--3059601 Score: 79
Period size: 19 Copynumber: 4.2 Consensus size: 18
3059513 GGTCGGGTCG
3059523 GGTCAGACCGGTCAAACC
1 GGTCAGACCGGTCAAACC
*
3059541 GATTCAGACCGGTCAAACC
1 G-GTCAGACCGGTCAAACC
*
3059560 GGTTC-GAACCGGTTGAAACC
1 GG-TCAG-ACCGG-TCAAACC
*
3059580 GGTCAAACCGGTCAGAACC
1 GGTCAGACCGGTCA-AACC
3059599 GGT
1 GGT
3059602 TGAAAACCAG
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
18 4 0.08
19 38 0.76
20 8 0.16
ACGTcount: A:0.28, C:0.29, G:0.28, T:0.15
Consensus pattern (18 bp):
GGTCAGACCGGTCAAACC
Found at i:3065801 original size:21 final size:21
Alignment explanation
Indices: 3065745--3065802 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 21
3065735 TCGATACCTA
*
3065745 CCCTTGAAGAGGAACCGATTCC
1 CCCTTGAAG-GGAACCAATTCC
3065767 CCCTTTGAATGGGAACCAATTCC
1 CCC-TTGAA-GGGAACCAATTCC
3065790 CTCCTT-AAGGGAA
1 C-CCTTGAAGGGAA
3065803 TCGATACCCC
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
21 5 0.16
22 5 0.16
23 19 0.59
24 3 0.09
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (21 bp):
CCCTTGAAGGGAACCAATTCC
Found at i:3069297 original size:117 final size:115
Alignment explanation
Indices: 3069131--3069366 Score: 337
Period size: 117 Copynumber: 2.0 Consensus size: 115
3069121 TGGGATGTCA
* * * * * *
3069131 ATCCACTTCCTTGTGTGATGGAATCACCAGGGTTGAGCAAATTCTTCTCATTATGAAGTTCTTCT
1 ATCCACCTCCTTCTGTGATGGAAACACCAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCT
* * *
3069196 CCCTTGTCGGATGAGTTCTTCTTATTATGAACTCTTCACCGAAAATGTTG
66 CCCTCGTCGGATGAGTTCTTCTCATTATGAACTCTCCACCGAAAATGTTG
* *
3069246 ATCCACCTCCTTCTGTGATGGAAACAAGCTAAGGTTGAACAAATTCTTCTCATTATTAACTTCTT
1 ATCCACCTCCTTCTGTGATGGAAAC-A-CCAAGGTTGAACAAATTCTTCTCATTATGAACTTCTT
* *
3069311 CTCCCTCGTCGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTG
64 CTCCCTCGTCGGATGAGTTCTTCTCATTATGAACTCTCCACCGAAAATGTTG
3069363 ATCC
1 ATCC
3069367 TAGGTTGAAC
Statistics
Matches: 106, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
115 22 0.21
116 1 0.01
117 83 0.78
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.36
Consensus pattern (115 bp):
ATCCACCTCCTTCTGTGATGGAAACACCAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCT
CCCTCGTCGGATGAGTTCTTCTCATTATGAACTCTCCACCGAAAATGTTG
Found at i:3069387 original size:91 final size:90
Alignment explanation
Indices: 3069279--3069620 Score: 492
Period size: 91 Copynumber: 3.8 Consensus size: 90
3069269 ACAAGCTAAG
* * *
3069279 GTTGAACAAATTCTTCTCATTATTAACTTCTTCTCCCTCGTCGGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCCTCTCCCTCGTCGGATGAGTTCTTCTCATTATGAA
*
3069344 CTCTCCACTGGAAATGTTGATCCTAG
66 CTCTCCACTGGAAATGTTGATCC-AA
* *
3069370 GTTGAACAAGTTATTCTCATTATGAAC-T--TCTCCCTCGTCGGATGAGTTCTTCTCATTCTGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCCTCTCCCTCGTCGGATGAGTTCTTCTCATTATGAA
*
3069432 CTCTCCACTGGAAATATTGATCCAA
66 CTCTCCACTGGAAATGTTGATCCAA
* *
3069457 GTTCGAACAAGTTCTTCTCATTATGAACTTCCTCTCCCTCGTTGGATGAGTTATTCTCATTATGA
1 GTT-GAACAAGTTCTTCTCATTATGAACTTCCTCTCCCTCGTCGGATGAGTTCTTCTCATTATGA
* * *
3069522 ACTCTACACTGGAAATGTTAAGCCAAA
65 ACTCTCCACTGGAAATGTTGATCC-AA
* * * *
3069549 GTAGAACAAGTTCCTCTCATTATGAACTTCCTCTCCCTCGTTGGATGAGTTCTTCTCATTACGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCCTCTCCCTCGTCGGATGAGTTCTTCTCATTATGAA
3069614 CTCTCCA
66 CTCTCCA
3069621 TCAGAAATGT
Statistics
Matches: 227, Mismatches: 19, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
87 4 0.02
88 78 0.34
89 1 0.00
90 1 0.00
91 139 0.61
92 4 0.02
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.36
Consensus pattern (90 bp):
GTTGAACAAGTTCTTCTCATTATGAACTTCCTCTCCCTCGTCGGATGAGTTCTTCTCATTATGAA
CTCTCCACTGGAAATGTTGATCCAA
Found at i:3072777 original size:181 final size:181
Alignment explanation
Indices: 3072473--3072839 Score: 689
Period size: 181 Copynumber: 2.0 Consensus size: 181
3072463 TTAGAAAACT
* *
3072473 AATTTTACAAATAAAATTAACCCTGAGGGGTGGAATAAAATCTGAAGATAGTCTTTCCACTTAGA
1 AATTTTACAAATAAAATTAACCCTGAGGGGCGAAATAAAATCTGAAGATAGTCTTTCCACTTAGA
3072538 AACCCATATATGATTAGAAAGGATTTTTCAGGCATGTAATGTAGGTCGGAGCTCACGGTTATGAA
66 AACCCATATATGATTAGAAAGGATTTTTCAGGCATGTAATGTAGGTCGGAGCTCACGGTTATGAA
3072603 ATAAAGAGATAAATAGGTCTAAATAAGTGTTTAAGGATTGAACCAAGGATC
131 ATAAAGAGATAAATAGGTCTAAATAAGTGTTTAAGGATTGAACCAAGGATC
*
3072654 AATTTTACAAATAAAATTAACCCTGAGGGGCGAAATGAAATCTGAAGATAGTCTTTCCACTTAGA
1 AATTTTACAAATAAAATTAACCCTGAGGGGCGAAATAAAATCTGAAGATAGTCTTTCCACTTAGA
*
3072719 AACCCATATATGATTAGAAAGGATTTTTCAGGCATGTAATGTAGGTTGGAGCTCACGGTTATGAA
66 AACCCATATATGATTAGAAAGGATTTTTCAGGCATGTAATGTAGGTCGGAGCTCACGGTTATGAA
*
3072784 ATAAAGAGATAAATAGGTCTAAATATGTGTTTAAGGATTGAACCAAGGATC
131 ATAAAGAGATAAATAGGTCTAAATAAGTGTTTAAGGATTGAACCAAGGATC
3072835 AATTT
1 AATTT
3072840 GCCCTACTGT
Statistics
Matches: 181, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
181 181 1.00
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (181 bp):
AATTTTACAAATAAAATTAACCCTGAGGGGCGAAATAAAATCTGAAGATAGTCTTTCCACTTAGA
AACCCATATATGATTAGAAAGGATTTTTCAGGCATGTAATGTAGGTCGGAGCTCACGGTTATGAA
ATAAAGAGATAAATAGGTCTAAATAAGTGTTTAAGGATTGAACCAAGGATC
Found at i:3073011 original size:19 final size:18
Alignment explanation
Indices: 3072973--3073020 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
3072963 ATTTGATCGA
*
3072973 TTTTCTTTCTTATTTCTTC
1 TTTTTTTTC-TATTTCTTC
*
3072992 TCTTTTTTTCTATTTTTTC
1 T-TTTTTTTCTATTTCTTC
3073011 TTTTTTTTCT
1 TTTTTTTTCT
3073021 CTTCTCCTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 9 0.35
19 10 0.38
20 7 0.27
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTTTTTCTATTTCTTC
Found at i:3073012 original size:33 final size:32
Alignment explanation
Indices: 3072973--3073082 Score: 91
Period size: 33 Copynumber: 3.4 Consensus size: 32
3072963 ATTTGATCGA
3072973 TTTTCTTTCTTATTTCTTCTCTTTTTTTCTATT
1 TTTTCTTTCTT-TTTCTTCTCTTTTTTTCTATT
* * * *
3073006 TTTTCTTTTTTTTCTCTTCTCCTCTTCTCT-TT
1 TTTTCTTTCTTTT-TCTTCTCTTTTTTTCTATT
* * *
3073038 TTTGCTATCTTTTTATGTCT-TTTTTTTCTATAT
1 TTTTCTTTCTTTTTCT-TCTCTTTTTTTCTAT-T
3073071 ATTTTC-TTCTTT
1 -TTTTCTTTCTTT
3073083 CTCTCTGTGT
Statistics
Matches: 59, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
31 8 0.14
32 18 0.31
33 29 0.49
34 4 0.07
ACGTcount: A:0.06, C:0.19, G:0.02, T:0.73
Consensus pattern (32 bp):
TTTTCTTTCTTTTTCTTCTCTTTTTTTCTATT
Found at i:3073081 original size:23 final size:22
Alignment explanation
Indices: 3072985--3073082 Score: 62
Period size: 23 Copynumber: 4.5 Consensus size: 22
3072975 TTCTTTCTTA
3072985 TTTCTTCTCTTTTTTTC---TAT
1 TTTCTTCT-TTTTTTTCTATTAT
* *
3073005 TTT-TTCTTTTTTTTCTCTTCT
1 TTTCTTCTTTTTTTTCTATTAT
** *
3073026 CCTCTTCTCTTTTTTGCTATCT-T
1 TTTCTTCT-TTTTTTTCTAT-TAT
*
3073049 TTTATGTCTTTTTTTTCTATATAT
1 TTTCT-TCTTTTTTTTCTAT-TAT
3073073 TTTCTTCTTT
1 TTTCTTCTTT
3073083 CTCTCTGTGT
Statistics
Matches: 59, Mismatches: 11, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
18 8 0.14
19 4 0.07
20 3 0.05
21 3 0.05
22 4 0.07
23 28 0.47
24 9 0.15
ACGTcount: A:0.06, C:0.19, G:0.02, T:0.72
Consensus pattern (22 bp):
TTTCTTCTTTTTTTTCTATTAT
Found at i:3073324 original size:2 final size:2
Alignment explanation
Indices: 3073317--3073512 Score: 257
Period size: 2 Copynumber: 98.0 Consensus size: 2
3073307 AGACACAAGG
3073317 AT AT AT AT AT AT AT 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 AT
3073359 AT AT AT AT AT AT AT 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 AT
* *
3073401 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * * * * *
3073443 AT GT AT GT AT AT AT AT AT AT GT GT GT GT GT GT GT 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 AT
* * * *
3073485 AT AT AC AT AC AT AT AC AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3073513 TTGAAAAGAT
Statistics
Matches: 176, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 176 1.00
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3078023 original size:2 final size:2
Alignment explanation
Indices: 3078018--3078043 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3078008 ACATGCACAA
3078018 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
3078044 TATGTTTGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3078563 original size:3 final size:3
Alignment explanation
Indices: 3078555--3078597 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
3078545 TTTGGGTTTG
* *
3078555 TAA TAA TAA TAA TAA TAT TAA TAA T-A TAA TAA TAT TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3078598 TGGATGTTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:3078598 original size:9 final size:9
Alignment explanation
Indices: 3078555--3078598 Score: 72
Period size: 9 Copynumber: 5.0 Consensus size: 9
3078545 TTTGGGTTTG
*
3078555 TAATAATAA
1 TAATAATAT
3078564 TAATAATAT
1 TAATAATAT
3078573 TAATAATA-
1 TAATAATAT
3078581 TAATAATAT
1 TAATAATAT
3078590 TAATAATAT
1 TAATAATAT
3078599 GGATGTTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
8 8 0.24
9 25 0.76
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
TAATAATAT
Found at i:3082301 original size:633 final size:639
Alignment explanation
Indices: 3081106--3082344 Score: 1877
Period size: 633 Copynumber: 1.9 Consensus size: 639
3081096 TTTGGTTGGG
* * *
3081106 GGAATGTGAGATTCTCACGGGAATGGAATCCACATTCCCCCGTTTGGTTGGCCGGGAATGTCATT
1 GGAATGTGAGATTCCCACGGGAATGGAATCCACATTCCCACGTTTGGTTGGCCGGGAATCTCATT
* * * * *
3081171 CCCGGTAATCTTACATTATCAATAGTGGATTTTTTGGGATATATTACCGGGAATGTCATTACTTC
66 CCCGGTAATCTTACATCACCAACAGTAGATTTTTTGGGATATATTACCGGGAATGTCATTACCTC
* *
3081236 CCTTTCCTTAGGTATTATTGGATTACCGACGTTTTGGACTAAAATACCCTTAAAAAAAATTTTCT
131 ACTTTCCTTAGATATTATTGGATTACCGACGTTTTGGACTAAAATACCCTT-----AAATTTTCT
3081301 TTTAAAAAATATCATTAATCTGTCATTGAATAATAAAAATTCTATAAAGGTTAAATTACAAATTT
191 TTTAAAAAATATCATTAATCTGTCATTGAATAATAAAAATTCTATAAAGGTTAAATTACAAATTT
* * *
3081366 ATCCTTAAACTATTTTAGATTTACAAAAAAAAGTTTATAATTAAAATTTTATATGAAGTTCAGGG
256 ATCCCTAAACTATTTTAGATTTACAAAAAAAAGTATATAATTAAAATTTTATATAAAGTTCAGGG
3081431 GTTAAAATAAAATTTTACCCTTTCATTAAACCTTTTTATATTTTCAATTTCGTAAAAAAAATTAT
321 GTTAAAATAAAATTTTACCCTTTCATTAAACCTTTTTATATTTTCAATTTCGTAAAAAAAATTAT
* *
3081496 ATAAATTTTATGAATTTAATTTTTTTAAAGAAAATATATAAATATTTTCCAACTTGTTAAAAAAA
386 ATAAATATTATGAATTTAAATTTTTTAAAGAAAATATATAAATATTTTCCAACTTGTTAAAAAAA
3081561 CAAATATATAATAAGGACAATTTGGTCAAATATACACTCCAATAATCTTTTATTCTCTTAACCAA
451 CAAATATATAATAAGGACAATTTGGTCAAATATACACTCCAATAATCTTTTATTCTCTTAACCAA
3081626 ACACAGTAATATTACATTCCTGCTAAACCAACCAAACACAAAATACAACATTCACAGTAATCATA
516 ACACAGTAATATTACATTCCTGCTAAACCAACCAAACACAAAATACAACATTCACAGTAATCATA
3081691 TTCCCTGGTAATCTTACATTCCGTGAACCAAACGCACCCTTAGGGGGTGTTTGGATCAA
581 TTCCCTGGTAATCTTACATTCCGTGAACCAAACGCACCCTTAGGGGGTGTTTGGATCAA
* * * *
3081750 GGAATGTGGGATTCCCATGGGAATGGAATCCATATTCCCATGTTTGGTTGGCCGGGAATCTCATT
1 GGAATGTGAGATTCCCACGGGAATGGAATCCACATTCCCACGTTTGGTTGGCCGGGAATCTCATT
* ** * *
3081815 CCCGGTAATGTTTTATCACCAACAGTAGATTTTTTGGGGGTCTATTACCGGGAATGTCATTACCT
66 CCCGGTAATCTTACATCACCAACAGTAGATTTTTT-GGGATATATTACCGGGAATGTCATTACCT
* *
3081880 CACTTTCCTTAGATATTGTTGGATTATCGACGTTTTGGACTAAAATGA-CCTT-AATTTT-TTTT
130 CACTTTCCTTAGATATTATTGGATTACCGACGTTTTGGACTAAAAT-ACCCTTAAATTTTCTTTT
* * * ** ** *
3081942 CAAATATATTATTCTTCTGTCATTGAATAATAAAAATTCTA-CGATGTTAAATTACAAATTTATC
194 AAAAAATATCATTAATCTGTCATTGAATAATAAAAATTCTATAAAGGTTAAATTACAAATTTATC
**
3082006 CCTAAACTATTTTTTATTTAC-AAAAAAAGTATATAATTAAAATTTTATATAAAGTTC-GAGGGT
259 CCTAAACTATTTTAGATTTACAAAAAAAAGTATATAATTAAAATTTTATATAAAGTTCAG-GGGT
* * * *
3082069 TAAAATAAAATTTTACCCTTTCATTAAACCTTTTTATATTTTTAATTTTGT-AAATATA-TATAT
323 TAAAATAAAATTTTACCCTTTCATTAAACCTTTTTATATTTTCAATTTCGTAAAAAAAATTATAT
* * *
3082132 ATATATTATGAATTTAAATTTTTTAAAGAAAATATATAAATATTTTTCAACTTGTT-AAAAAATA
388 AAATATTATGAATTTAAATTTTTTAAAGAAAATATATAAATATTTTCCAACTTGTTAAAAAAACA
* *
3082196 AATATATAATAAGGACAATTTGGTCAAATATACATTCTAATAATCTTTTATTC-CTTTAACCAAA
453 AATATATAATAAGGACAATTTGGTCAAATATACACTCCAATAATCTTTTATTCTC-TTAACCAAA
* * * * *
3082260 CACGGTAATCTTACATTCCTGCTAAACCAACCAAACACAAAATACAATATTCCCAGTAATCCTAT
517 CACAGTAATATTACATTCCTGCTAAACCAACCAAACACAAAATACAACATTCACAGTAATCATAT
3082325 TCCCTGGTAATCTTACATTC
582 TCCCTGGTAATCTTACATTC
3082345 ACACTGGTAA
Statistics
Matches: 541, Mismatches: 50, Indels: 19
0.89 0.08 0.03
Matches are distributed among these distances:
632 1 0.00
633 147 0.27
634 57 0.11
635 6 0.01
636 87 0.16
637 38 0.07
638 40 0.07
639 6 0.01
644 86 0.16
645 72 0.13
646 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.37
Consensus pattern (639 bp):
GGAATGTGAGATTCCCACGGGAATGGAATCCACATTCCCACGTTTGGTTGGCCGGGAATCTCATT
CCCGGTAATCTTACATCACCAACAGTAGATTTTTTGGGATATATTACCGGGAATGTCATTACCTC
ACTTTCCTTAGATATTATTGGATTACCGACGTTTTGGACTAAAATACCCTTAAATTTTCTTTTAA
AAAATATCATTAATCTGTCATTGAATAATAAAAATTCTATAAAGGTTAAATTACAAATTTATCCC
TAAACTATTTTAGATTTACAAAAAAAAGTATATAATTAAAATTTTATATAAAGTTCAGGGGTTAA
AATAAAATTTTACCCTTTCATTAAACCTTTTTATATTTTCAATTTCGTAAAAAAAATTATATAAA
TATTATGAATTTAAATTTTTTAAAGAAAATATATAAATATTTTCCAACTTGTTAAAAAAACAAAT
ATATAATAAGGACAATTTGGTCAAATATACACTCCAATAATCTTTTATTCTCTTAACCAAACACA
GTAATATTACATTCCTGCTAAACCAACCAAACACAAAATACAACATTCACAGTAATCATATTCCC
TGGTAATCTTACATTCCGTGAACCAAACGCACCCTTAGGGGGTGTTTGGATCAA
Found at i:3087389 original size:27 final size:26
Alignment explanation
Indices: 3087332--3087394 Score: 81
Period size: 27 Copynumber: 2.4 Consensus size: 26
3087322 ATAGATTTAT
*
3087332 TTCTTTTATTAAAAGAGATTTATTAC
1 TTCTTTTATTAAAAGAGATTTAATAC
* * *
3087358 CTCTTTTGTTTAAAAGAGATTTAATAG
1 TTCTTTT-ATTAAAAGAGATTTAATAC
3087385 TTCTTTTATT
1 TTCTTTTATT
3087395 GGAATTAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
26 8 0.27
27 22 0.73
ACGTcount: A:0.30, C:0.08, G:0.10, T:0.52
Consensus pattern (26 bp):
TTCTTTTATTAAAAGAGATTTAATAC
Found at i:3094915 original size:2 final size:2
Alignment explanation
Indices: 3094910--3094944 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3094900 AGAAAAAAAA
3094910 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3094945 ATTTGAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3095157 original size:111 final size:112
Alignment explanation
Indices: 3094961--3095183 Score: 421
Period size: 111 Copynumber: 2.0 Consensus size: 112
3094951 AATTTTGTTA
*
3094961 GAGACAATTGTTTACACACGTCCCTTCCATCAATCATTGATGTTATAGAAAACTGCGATGAGATA
1 GAGACAATTGTTTACACACGTCCCTTCCATCAATCATTGATGTTATAGAAAACTGCGATGACATA
3095026 ATCCAACTGAATGCTAGATCAAAATAGACCCAGTAGGTTTGTATCGG
66 ATCCAACTGAATGCTAGATCAAAATAGACCCAGTAGGTTTGTATCGG
*
3095073 GAGACAATTGTTTCCACACGTCCCTTCCATCAATCATTGATG-TATAGAAAACTGCGATGACATA
1 GAGACAATTGTTTACACACGTCCCTTCCATCAATCATTGATGTTATAGAAAACTGCGATGACATA
3095137 ATCCAACTGAATGCTAGATCAAAATAGACCCAGTAGGTTTGTATCGG
66 ATCCAACTGAATGCTAGATCAAAATAGACCCAGTAGGTTTGTATCGG
3095184 ATCAAGGAAA
Statistics
Matches: 109, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
111 68 0.62
112 41 0.38
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (112 bp):
GAGACAATTGTTTACACACGTCCCTTCCATCAATCATTGATGTTATAGAAAACTGCGATGACATA
ATCCAACTGAATGCTAGATCAAAATAGACCCAGTAGGTTTGTATCGG
Found at i:3095960 original size:2 final size:2
Alignment explanation
Indices: 3095913--3095942 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3095903 ATCTCAAAAC
3095913 AT 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
3095943 TTTAAAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3096122 original size:30 final size:30
Alignment explanation
Indices: 3096087--3096146 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
3096077 TGGTAGTTTC
*
3096087 ACGGTGTTTCAAGCTGATATATGGGACATA
1 ACGGTGTTTCAAGCTGAGATATGGGACATA
3096117 ACGGTGTTTCAAGCTGAGATATGGGACATA
1 ACGGTGTTTCAAGCTGAGATATGGGACATA
3096147 TCTTATGGCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.28
Consensus pattern (30 bp):
ACGGTGTTTCAAGCTGAGATATGGGACATA
Found at i:3097284 original size:35 final size:35
Alignment explanation
Indices: 3097245--3097316 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
3097235 TTGATGTTAT
*
3097245 TTATAATAAGTCATGTCATTTGGTAAAT-AGACTTA
1 TTATAATAAGTCATGTCACTTGGTAAATGA-ACTTA
*
3097280 TTATAATAAGTCATGTCACTTGGTGAATGAACTTA
1 TTATAATAAGTCATGTCACTTGGTAAATGAACTTA
3097315 TT
1 TT
3097317 TTTTTGGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 33 0.97
36 1 0.03
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (35 bp):
TTATAATAAGTCATGTCACTTGGTAAATGAACTTA
Found at i:3098089 original size:20 final size:21
Alignment explanation
Indices: 3098064--3098115 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3098054 TTTTCCCAAT
*
3098064 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
3098084 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
3098105 TCGCAATGCGA
1 TCGCAATGCGA
3098116 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:3098129 original size:20 final size:20
Alignment explanation
Indices: 3098104--3098218 Score: 99
Period size: 20 Copynumber: 5.7 Consensus size: 20
3098094 AATTGGGAAA
3098104 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
3098124 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
3098145 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
3098165 TTCGCAATGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
3098185 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
3098205 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
3098219 TTTCAAAGCG
Statistics
Matches: 75, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
19 4 0.05
20 45 0.60
21 24 0.32
22 2 0.03
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:3098414 original size:22 final size:22
Alignment explanation
Indices: 3098386--3098429 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
3098376 CACTCTCTCA
3098386 CCCATCTCC-GACGAAATCCGTC
1 CCCATCTCCAG-CGAAATCCGTC
3098408 CCCATCTCCAGCGAAATCCGTC
1 CCCATCTCCAGCGAAATCCGTC
3098430 TATCTCCATC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCAGCGAAATCCGTC
Found at i:3098436 original size:20 final size:21
Alignment explanation
Indices: 3098386--3098437 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
3098376 CACTCTCTCA
3098386 CCCATCTCC-GACGAAATCCGT
1 CCCATCTCCAG-CGAAATCCGT
3098407 CCCCATCTCCAGCGAAATCCGT
1 -CCCATCTCCAGCGAAATCCGT
*
3098429 -CTATCTCCA
1 CCCATCTCCA
3098438 TCTCTCAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 8 0.29
22 19 0.68
23 1 0.04
ACGTcount: A:0.23, C:0.44, G:0.12, T:0.21
Consensus pattern (21 bp):
CCCATCTCCAGCGAAATCCGT
Found at i:3098724 original size:20 final size:20
Alignment explanation
Indices: 3098671--3098734 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 20
3098661 GCGATTTTAG
*
3098671 TTTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTCAT
* * *
3098691 ATTCGCATTACGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
3098711 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
3098731 TTTC
1 TTTC
3098735 AGAAACTATT
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:3100066 original size:18 final size:18
Alignment explanation
Indices: 3100045--3100089 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
3100035 TCCACTTCGG
*
3100045 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
3100063 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
3100081 GAGCCATCA
1 GAGCCATCA
3100090 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:3100625 original size:19 final size:20
Alignment explanation
Indices: 3100571--3100637 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
3100561 TAGTTTACTT
* *
3100571 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
3100591 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
3100611 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
3100630 TCGCAACG
1 TCGCAACG
3100638 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:3100664 original size:18 final size:18
Alignment explanation
Indices: 3100610--3100672 Score: 71
Period size: 18 Copynumber: 3.7 Consensus size: 18
3100600 GGAAATGGCT
3100610 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
*
3100629 ATCGCAA--CGACA--AA
1 ATCGCAATGCGAAATGAA
3100643 ATCGCAATGCGAAATGAA
1 ATCGCAATGCGAAATGAA
*
3100661 ATCGCATTGCGA
1 ATCGCAATGCGA
3100673 TTTTGTCGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 9 0.24
16 4 0.11
17 4 0.11
18 13 0.35
19 7 0.19
ACGTcount: A:0.43, C:0.21, G:0.21, T:0.16
Consensus pattern (18 bp):
ATCGCAATGCGAAATGAA
Found at i:3100725 original size:20 final size:19
Alignment explanation
Indices: 3100691--3100746 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
3100681 TTGCGATTTT
*
3100691 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
3100710 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
3100730 CATTTTCGTGTTGCGAT
1 CA-TTTCGCGTTGCGAT
3100747 TTTAAGTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 24 0.75
21 3 0.09
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:3101172 original size:21 final size:20
Alignment explanation
Indices: 3101112--3101172 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
3101102 GACTCACCGG
3101112 TCATCCCTCAAGAGTCCCCT
1 TCATCCCTCAAGAGTCCCCT
* ** *
3101132 CCAATCGTTCAAGAGGCCCCT
1 TC-ATCCCTCAAGAGTCCCCT
*
3101153 ATCATCCCTCAAGATTCCCC
1 -TCATCCCTCAAGAGTCCCC
3101173 CCACCGTTCA
Statistics
Matches: 30, Mismatches: 9, Indels: 3
0.71 0.21 0.07
Matches are distributed among these distances:
20 1 0.03
21 28 0.93
22 1 0.03
ACGTcount: A:0.23, C:0.43, G:0.11, T:0.23
Consensus pattern (20 bp):
TCATCCCTCAAGAGTCCCCT
Found at i:3101198 original size:40 final size:42
Alignment explanation
Indices: 3101111--3101198 Score: 126
Period size: 40 Copynumber: 2.1 Consensus size: 42
3101101 CGACTCACCG
* *
3101111 GTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCT
1 GTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACT
* *
3101153 ATCATCCCTCAAGATTCCCC-CC-ACCGTTCAAGAGGCCACT
1 GTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACT
3101193 GTCATC
1 GTCATC
3101199 GTTGAAGAGG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
40 21 0.51
41 2 0.05
42 18 0.44
ACGTcount: A:0.23, C:0.41, G:0.15, T:0.22
Consensus pattern (42 bp):
GTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCACT
Found at i:3102632 original size:14 final size:14
Alignment explanation
Indices: 3102613--3102649 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3102603 GATTGTTTAA
3102613 ATGATTTGTAAAAG
1 ATGATTTGTAAAAG
*
3102627 ATGATTTGTAAATG
1 ATGATTTGTAAAAG
*
3102641 TTGATTTGT
1 ATGATTTGT
3102650 TTAATTGATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (14 bp):
ATGATTTGTAAAAG
Found at i:3102757 original size:20 final size:20
Alignment explanation
Indices: 3102732--3102770 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3102722 ATGTTGAAGG
3102732 CAAAACAGACTATCGCAACA
1 CAAAACAGACTATCGCAACA
*
3102752 CAAAACTGACTATCGCAAC
1 CAAAACAGACTATCGCAAC
3102771 GAGAGAATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.31, G:0.10, T:0.13
Consensus pattern (20 bp):
CAAAACAGACTATCGCAACA
Found at i:3102800 original size:19 final size:19
Alignment explanation
Indices: 3102776--3102840 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
3102766 GCAACGAGAG
3102776 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3102795 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3102814 AATCGCAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
3102828 AATCGCAATGCGA
1 AATCGCAATGCGA
3102841 TTTTCATTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
14 11 0.26
15 1 0.02
16 2 0.05
17 2 0.05
19 27 0.63
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:3102908 original size:20 final size:20
Alignment explanation
Indices: 3102866--3103014 Score: 266
Period size: 20 Copynumber: 7.5 Consensus size: 20
3102856 GCGATTTTGT
3102866 CGTTGCGATAGCCA-TTTCG
1 CGTTGCGATAGCCATTTTCG
*
3102885 CGTTGCGATAGCCATTTTCA
1 CGTTGCGATAGCCATTTTCG
3102905 CGTTGCGATAGCCA-TTTCG
1 CGTTGCGATAGCCATTTTCG
*
3102924 CGTTGCGATAGCCATTTTCA
1 CGTTGCGATAGCCATTTTCG
3102944 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
3102964 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
3102984 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
3103004 CGTTGCGATAG
1 CGTTGCGATAG
3103015 TCAAATGAAT
Statistics
Matches: 124, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
19 32 0.26
20 92 0.74
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCG
Found at i:3104054 original size:24 final size:24
Alignment explanation
Indices: 3103996--3104042 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
3103986 AGTCAGTATT
* *
3103996 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATATTGGTCAATACC
3104020 CGAACTTTGATATTGGTCAATAC
1 CGAACTTTGATATTGGTCAATAC
3104043 TCGGATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATATTGGTCAATACC
Found at i:3104246 original size:12 final size:12
Alignment explanation
Indices: 3104229--3104253 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3104219 ATATAATCCT
3104229 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3104241 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3104253 G
1 G
3104254 TCATCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:3106591 original size:33 final size:33
Alignment explanation
Indices: 3106545--3106671 Score: 175
Period size: 33 Copynumber: 3.8 Consensus size: 33
3106535 GGAAATTACT
3106545 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* **
3106578 ATCACAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
3106610 TTTCGCAATGCGAAATGAAAATCACAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
3106644 ATTGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
3106672 CGAATTTAAT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
32 1 0.01
33 78 0.98
34 1 0.01
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:3106628 original size:66 final size:66
Alignment explanation
Indices: 3106546--3106678 Score: 221
Period size: 66 Copynumber: 2.0 Consensus size: 66
3106536 GAAATTACTA
* *
3106546 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCACAACGAGAGAATCACAATGCGAAATGAAAATCGCAACGCGAAT
3106611 T
66 T
* **
3106612 TCGCAATGCGAAATGAAAATCACAACGAGGGAATTGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCACAACGAGAGAATCACAATGCGAAATGAAAATCGCAACGCGAAT
3106677 T
66 T
3106678 T
1 T
3106679 AATTTCGCGT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCACAACGAGAGAATCACAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:3106703 original size:14 final size:14
Alignment explanation
Indices: 3106686--3106742 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3106676 TTTAATTTCG
3106686 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
3106700 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
3106719 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3106733 CGTTGCGATT
1 CGTTGCGATT
3106743 TTAATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3106722 original size:33 final size:33
Alignment explanation
Indices: 3106671--3106757 Score: 147
Period size: 33 Copynumber: 2.6 Consensus size: 33
3106661 AAATCGCAAC
*
3106671 GCGAATTTAATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTAATTTCGCGTTGCGATTCTCTCGTT
*
3106704 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTAATTTCGCGTTGCGATTCTCTCGTT
*
3106737 GCGATTTTAATTTCGCATTGC
1 GCGATTTTAATTTCGCGTTGC
3106758 AATAGTACTT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.44
Consensus pattern (33 bp):
GCGATTTTAATTTCGCGTTGCGATTCTCTCGTT
Found at i:3106886 original size:14 final size:14
Alignment explanation
Indices: 3106867--3106903 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3106857 CATCAATTAA
3106867 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3106881 ACAAATCACCTTTT
1 ACAAATCAACTTTT
3106895 ACAAATCAA
1 ACAAATCAA
3106904 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3108319 original size:42 final size:41
Alignment explanation
Indices: 3108260--3108465 Score: 155
Period size: 42 Copynumber: 4.9 Consensus size: 41
3108250 GTGAATCGGG
* *
3108260 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGA-CTCTTCAAGGATGACAGTGGC
* * *
3108302 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * * *
3108344 CTCTTCAATGATAGGAGTGGACTCTTGAGGGATGACAGTGGC
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAGTGGC
* * *
3108386 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * * *
3108428 CTCTTCAATGATAGGAGTGGACTCTTGAGGGATGACAG
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAG
3108466 GCGAGTCGGG
Statistics
Matches: 125, Mismatches: 31, Indels: 16
0.73 0.18 0.09
Matches are distributed among these distances:
41 9 0.07
42 105 0.84
43 11 0.09
ACGTcount: A:0.23, C:0.17, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGACTCTTCAAGGATGACAGTGGC
Found at i:3108326 original size:21 final size:21
Alignment explanation
Indices: 3108260--3108326 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
3108250 GTGAATCGGG
*
3108260 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
3108280 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
3108302 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
3108323 CTCT
1 CTCT
3108327 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:3108401 original size:84 final size:84
Alignment explanation
Indices: 3108290--3108465 Score: 352
Period size: 84 Copynumber: 2.1 Consensus size: 84
3108280 CCTCTTCAAC
3108290 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAATGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAATGA
3108355 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
3108374 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAATGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAATGA
3108439 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
3108458 GATGACAG
1 GATGACAG
3108466 GCGAGTCGGG
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 92 1.00
ACGTcount: A:0.23, C:0.16, G:0.38, T:0.22
Consensus pattern (84 bp):
GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAATGA
TAGGAGTGGACTCTTGAGG
Found at i:3108860 original size:91 final size:90
Alignment explanation
Indices: 3108682--3108868 Score: 286
Period size: 91 Copynumber: 2.0 Consensus size: 90
3108672 ATATTTCAAA
*
3108682 ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTAACAGTGTTAAAGAATACACAGTTTA
1 ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTAACAGTGTT--A-AATAAACAGTTTA
3108747 GCAGAATTGGCAGCAACCGAATAAATTT
63 GCAGAATTGGCAGCAACCGAATAAATTT
*
3108775 ACTTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAG
1 ACTTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTAACAGTGTTAAATAAACAGTTTAG
* *
3108839 CGGTATTGGCAGCAACCGAATAAATTT
64 CAGAATTGGCAGCAACCGAATAAATTT
3108866 ACT
1 ACT
3108869 AAGCAATCTA
Statistics
Matches: 88, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
91 41 0.47
93 21 0.24
95 26 0.30
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.21
Consensus pattern (90 bp):
ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTAACAGTGTTAAATAAACAGTTTAGCA
GAATTGGCAGCAACCGAATAAATTT
Found at i:3109104 original size:63 final size:63
Alignment explanation
Indices: 3109037--3109161 Score: 241
Period size: 63 Copynumber: 2.0 Consensus size: 63
3109027 AAGTAGACAC
3109037 CTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTGAG
1 CTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTGAG
*
3109100 CTCCACACGCTATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTGA
1 CTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTGA
3109162 CCTCATCACG
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.24, C:0.34, G:0.20, T:0.22
Consensus pattern (63 bp):
CTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTGAG
Found at i:3110669 original size:19 final size:19
Alignment explanation
Indices: 3110618--3110781 Score: 177
Period size: 19 Copynumber: 9.1 Consensus size: 19
3110608 TCTTTTGGTT
*
3110618 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
3110637 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
** *
3110657 GAAATGACTATCGTAA--C
1 GAAATGAAAATCGCAACGC
*
3110674 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
3110690 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
3110709 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
3110728 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
3110745 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
3110761 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
3110780 GA
1 GA
3110782 TTTTGGTTTC
Statistics
Matches: 122, Mismatches: 12, Indels: 22
0.78 0.08 0.14
Matches are distributed among these distances:
14 18 0.15
15 2 0.02
16 4 0.03
17 4 0.03
18 2 0.02
19 75 0.61
20 17 0.14
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:3110685 original size:33 final size:33
Alignment explanation
Indices: 3110643--3110776 Score: 187
Period size: 33 Copynumber: 3.9 Consensus size: 33
3110633 ACGAGATAAT
** *
3110643 GAGAATCGCAACGCGAAATGACTATCGTAACGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
3110676 GAGAATCGCAACGCGAAATGAAAATCGCAACGCGAAA
1 GAGAATCGCAACGCGAAATGAAAATCGCAA--CG--A
*
3110713 TGAAAATCGCAACGCGAAATGAAAATCGCAACGA
1 -GAGAATCGCAACGCGAAATGAAAATCGCAACGA
3110747 GAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGAAAATCGCAA
3110777 TGCGATTTTG
Statistics
Matches: 91, Mismatches: 5, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
33 56 0.62
34 1 0.01
35 2 0.02
36 2 0.02
37 1 0.01
38 29 0.32
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGAAAATCGCAACGA
Found at i:3110746 original size:71 final size:72
Alignment explanation
Indices: 3110618--3110782 Score: 269
Period size: 71 Copynumber: 2.3 Consensus size: 72
3110608 TCTTTTGGTT
* * ** *
3110618 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGCGAAATGACTATCGTAACGAGAGAATC
1 GAAATGAAAATCGCAACGCGATAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATC
3110683 GCAACGC
66 GCAACGC
3110690 GAAATGAAAATCGCAACGCGA-AATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATC
1 GAAATGAAAATCGCAACGCGATAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATC
3110754 GCAACGC
66 GCAACGC
*
3110761 GAAATGAAAATCGCAATGCGAT
1 GAAATGAAAATCGCAACGCGAT
3110783 TTTGGTTTCG
Statistics
Matches: 86, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
71 66 0.77
72 20 0.23
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (72 bp):
GAAATGAAAATCGCAACGCGATAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATC
GCAACGC
Found at i:3110799 original size:19 final size:19
Alignment explanation
Indices: 3110777--3110821 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
3110767 AAAATCGCAA
*
3110777 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
* *
3110796 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
3110815 TGCGATT
1 TGCGATT
3110822 CTCTCGTTGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.07, C:0.16, G:0.27, T:0.51
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:3111400 original size:20 final size:20
Alignment explanation
Indices: 3111375--3111427 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
3111365 GCGCTATGTA
3111375 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
3111395 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
3111415 TATCTCGTTGCGA
1 AATCGCGTTGCGA
3111428 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:3111461 original size:20 final size:20
Alignment explanation
Indices: 3111436--3111486 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
3111426 GATTTTGTAT
3111436 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
3111456 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
3111476 TATCGCATTGC
1 TATCGCATTGC
3111487 AATTTTCCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:3111492 original size:61 final size:61
Alignment explanation
Indices: 3111376--3111492 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
3111366 CGCTATGTAA
* * * * * *
3111376 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCAATTTTGTATT
* * *
3111437 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCAATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCAATTTT
3111493 CCCAATTCGC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCAATTTTGTATT
Found at i:3111508 original size:61 final size:61
Alignment explanation
Indices: 3111376--3111510 Score: 146
Period size: 61 Copynumber: 2.2 Consensus size: 61
3111366 CGCTATGTAA
* * * * * * ** *
3111376 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCAATTTTCCAAT
* * *
3111437 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCAATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCAATTTT-CCAAT
3111499 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
3111511 TTACTTATTC
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
61 58 0.97
62 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCAATTTTCCAAT
Found at i:3111600 original size:21 final size:21
Alignment explanation
Indices: 3111560--3111600 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3111550 ACTGTAGACC
**
3111560 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
3111581 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
3111601 GCGAATTTGC
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:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:3112159 original size:2 final size:2
Alignment explanation
Indices: 3112152--3112184 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3112142 ATTTGAATTC
3112152 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3112185 TTTGGGTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3113649 original size:23 final size:23
Alignment explanation
Indices: 3113623--3113712 Score: 85
Period size: 23 Copynumber: 3.9 Consensus size: 23
3113613 CTATTTCCAG
* *
3113623 TTATGTTCCTTTATGTTCATTTA
1 TTATGTTCATTTATGTTCGTTTA
*
3113646 TTATGTTCATTTACGTTCGTTTA
1 TTATGTTCATTTATGTTCGTTTA
* *
3113669 TTGTGTT-GTTTATGTTCGTTTA
1 TTATGTTCATTTATGTTCGTTTA
* *
3113691 -CACCCGTTCATTTATGTTCGTT
1 TTA--TGTTCATTTATGTTCGTT
3113713 CATTTGTGTT
Statistics
Matches: 54, Mismatches: 10, Indels: 5
0.78 0.14 0.07
Matches are distributed among these distances:
22 13 0.24
23 29 0.54
24 12 0.22
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.57
Consensus pattern (23 bp):
TTATGTTCATTTATGTTCGTTTA
Found at i:3113651 original size:13 final size:13
Alignment explanation
Indices: 3113633--3113658 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3113623 TTATGTTCCT
3113633 TTATGTTCATTTA
1 TTATGTTCATTTA
3113646 TTATGTTCATTTA
1 TTATGTTCATTTA
3113659 CGTTCGTTTA
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:0.08, T:0.62
Consensus pattern (13 bp):
TTATGTTCATTTA
Found at i:3113712 original size:14 final size:14
Alignment explanation
Indices: 3113695--3113726 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3113685 CGTTTACACC
3113695 CGTTCATTTATGTT
1 CGTTCATTTATGTT
*
3113709 CGTTCATTTGTGTT
1 CGTTCATTTATGTT
3113723 CGTT
1 CGTT
3113727 TATCATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.16, G:0.19, T:0.56
Consensus pattern (14 bp):
CGTTCATTTATGTT
Found at i:3114820 original size:13 final size:13
Alignment explanation
Indices: 3114802--3114832 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
3114792 ATTATTGTCA
3114802 GTGAGATATTTGT
1 GTGAGATATTTGT
3114815 GTGAGATATTTGT
1 GTGAGATATTTGT
3114828 GTGAG
1 GTGAG
3114833 GTATGTCATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.35, T:0.42
Consensus pattern (13 bp):
GTGAGATATTTGT
Found at i:3115085 original size:35 final size:35
Alignment explanation
Indices: 3115045--3115116 Score: 108
Period size: 35 Copynumber: 2.1 Consensus size: 35
3115035 TTGATGCTAT
*
3115045 TTATAATAAGTCATGCCACTTGGTAAATAGACTTA
1 TTATAATAAGTCATGCCACTTGATAAATAGACTTA
* * *
3115080 TTATAATAAGTCATGTCACTTGATGAATTGACTTA
1 TTATAATAAGTCATGCCACTTGATAAATAGACTTA
3115115 TT
1 TT
3115117 TTTTAGTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (35 bp):
TTATAATAAGTCATGCCACTTGATAAATAGACTTA
Found at i:3115286 original size:13 final size:13
Alignment explanation
Indices: 3115268--3115297 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3115258 AATCTTAGAC
3115268 ACAACTTTGAGAA
1 ACAACTTTGAGAA
*
3115281 ACAACTTTGAGAC
1 ACAACTTTGAGAA
3115294 ACAA
1 ACAA
3115298 TTCACAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.20, G:0.13, T:0.20
Consensus pattern (13 bp):
ACAACTTTGAGAA
Found at i:3120253 original size:13 final size:13
Alignment explanation
Indices: 3120235--3120261 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3120225 ATAGTTGAAA
3120235 CAGTCTTCATATG
1 CAGTCTTCATATG
3120248 CAGTCTTCATATG
1 CAGTCTTCATATG
3120261 C
1 C
3120262 GCGTCTGTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:3124053 original size:44 final size:42
Alignment explanation
Indices: 3123991--3124100 Score: 121
Period size: 44 Copynumber: 2.5 Consensus size: 42
3123981 GGAGGTTCAA
* * * *
3123991 TTTTTAAATATTTTTTATTATGAGCATACTCTTAAAATTTTCTT
1 TTTTTAAACATTTATTATTATGAGC-TACCCTTAAAA-TTTATT
* *
3124035 TTTTTTAACATTTGTTATTATGAAGCTACCCTTAAAATTTATT
1 TTTTTAAACATTTATTATTATG-AGCTACCCTTAAAATTTATT
* *
3124078 TTTTTCAACACTTATTATTATGA
1 TTTTTAAACATTTATTATTATGA
3124101 ACAATTATTT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
42 1 0.02
43 24 0.42
44 29 0.51
45 3 0.05
ACGTcount: A:0.30, C:0.11, G:0.05, T:0.54
Consensus pattern (42 bp):
TTTTTAAACATTTATTATTATGAGCTACCCTTAAAATTTATT
Found at i:3124096 original size:43 final size:45
Alignment explanation
Indices: 3124005--3124101 Score: 128
Period size: 43 Copynumber: 2.2 Consensus size: 45
3123995 TAAATATTTT
* * * * *
3124005 TTATTATG-AGCATACTCTTAAAATTTTCTTTTTTTTAACATTTG
1 TTATTATGAAGCATACCCTTAAAATTTTATTTTTTTCAACACTTA
3124049 TTATTATGAAGC-TACCCTTAAAA-TTTATTTTTTTCAACACTTA
1 TTATTATGAAGCATACCCTTAAAATTTTATTTTTTTCAACACTTA
3124092 TTATTATGAA
1 TTATTATGAA
3124102 CAATTATTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
43 26 0.55
44 18 0.38
45 3 0.06
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.51
Consensus pattern (45 bp):
TTATTATGAAGCATACCCTTAAAATTTTATTTTTTTCAACACTTA
Found at i:3127239 original size:18 final size:18
Alignment explanation
Indices: 3127216--3127262 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
3127206 TGACCGTCAC
3127216 AACCCGACCCGACCCATT
1 AACCCGACCCGACCCATT
*
3127234 AACCCGA-CCGACCCGTT
1 AACCCGACCCGACCCATT
*
3127251 TACACCGACCCG
1 AAC-CCGACCCG
3127263 TTGACCCGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 11 0.44
18 11 0.44
19 3 0.12
ACGTcount: A:0.26, C:0.49, G:0.15, T:0.11
Consensus pattern (18 bp):
AACCCGACCCGACCCATT
Found at i:3127276 original size:18 final size:17
Alignment explanation
Indices: 3127217--3127286 Score: 74
Period size: 18 Copynumber: 4.2 Consensus size: 17
3127207 GACCGTCACA
* *
3127217 ACCCGACCCGACCCATTA
1 ACCCGA-CCGACCCGTTG
*
3127235 ACCCGACCGACCCGTTT
1 ACCCGACCGACCCGTTG
3127252 A--C-ACCGACCCGTTG
1 ACCCGACCGACCCGTTG
3127266 ACCCGACCCGACCCGTTG
1 ACCCGA-CCGACCCGTTG
3127284 ACC
1 ACC
3127287 GTTGACCGAG
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
14 12 0.27
15 1 0.02
16 1 0.02
17 11 0.24
18 20 0.44
ACGTcount: A:0.21, C:0.49, G:0.17, T:0.13
Consensus pattern (17 bp):
ACCCGACCGACCCGTTG
Found at i:3127286 original size:13 final size:14
Alignment explanation
Indices: 3127240--3127275 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3127230 CATTAACCCG
*
3127240 ACCGACCCGTTTAC
1 ACCGACCCGTTGAC
3127254 ACCGACCCGTTGAC
1 ACCGACCCGTTGAC
3127268 -CCGACCCG
1 ACCGACCCG
3127276 ACCCGTTGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.19, C:0.47, G:0.19, T:0.14
Consensus pattern (14 bp):
ACCGACCCGTTGAC
Found at i:3128612 original size:18 final size:18
Alignment explanation
Indices: 3128586--3128621 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3128576 TCGAAAGGAC
*
3128586 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
3128604 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
3128622 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:3129797 original size:12 final size:12
Alignment explanation
Indices: 3129782--3129839 Score: 71
Period size: 12 Copynumber: 4.8 Consensus size: 12
3129772 GATAAATGAC
3129782 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
3129794 CTGATTTCTGAT
1 CTGAATTCTGTT
*
3129806 CTGGATTCTGTT
1 CTGAATTCTGTT
3129818 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
3129830 TTGATTTCTG
1 CTGAATTCTG
3129840 ATATCTTCAT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.14, C:0.16, G:0.19, T:0.52
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:3129814 original size:24 final size:23
Alignment explanation
Indices: 3129745--3129827 Score: 94
Period size: 24 Copynumber: 3.5 Consensus size: 23
3129735 AAATATTTTA
3129745 TCTGATTTCTGACTTGAATTCTGT
1 TCTGATTTCTGAC-TGAATTCTGT
***
3129769 TCTGATAAATGACCTGAATTCTGT
1 TCTGATTTCTGA-CTGAATTCTGT
*
3129793 TCTGATTTCTGATCTGGATTCTGT
1 TCTGATTTCTGA-CTGAATTCTGT
*
3129817 TCTGAATTCTG
1 TCTGATTTCTG
3129828 TTTTGATTTC
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
24 48 0.98
25 1 0.02
ACGTcount: A:0.19, C:0.17, G:0.18, T:0.46
Consensus pattern (23 bp):
TCTGATTTCTGACTGAATTCTGT
Found at i:3131635 original size:21 final size:21
Alignment explanation
Indices: 3131606--3131658 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
3131596 ATTCTGACTA
3131606 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
3131627 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
3131648 TCGCAATGCGA
1 TCGCATTGCGA
3131659 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:3131793 original size:20 final size:20
Alignment explanation
Indices: 3131605--3131934 Score: 319
Period size: 20 Copynumber: 16.3 Consensus size: 20
3131595 GATTCTGACT
* **
3131605 ATCGCATTGCGATTTCCCAA
1 ATCGCATTGCGATTTACGTA
* * *
3131625 ATTCGCGTTGCGATTTTCCTA
1 A-TCGCATTGCGATTTACGTA
* *
3131646 ATTCGCAATGCGA-ATACGTAA
1 A-TCGCATTGCGATTTACGT-A
* * *
3131667 ATCACAATGGGA-TTACGTAA
1 ATCGCATTGCGATTTACGT-A
* * * *
3131687 ATCGCAATGCGAATTAGGAAA
1 ATCGCATTGCGATTTACG-TA
*
3131708 ATCGCAATGCGA-TTACGTAA
1 ATCGCATTGCGATTTACGT-A
* * *
3131728 ATCGCAATGTGA-ATACGTA
1 ATCGCATTGCGATTTACGTA
3131747 ATCGCATTGCGATTTACGTA
1 ATCGCATTGCGATTTACGTA
3131767 ATCGCATTGCGATTTACGTA
1 ATCGCATTGCGATTTACGTA
* *
3131787 ATCGCATTGCGATTTTCCTA
1 ATCGCATTGCGATTTACGTA
3131807 ATTCGCATTGCGATTTACGTA
1 A-TCGCATTGCGATTTACGTA
* *
3131828 ATCGCATTGCGATTTTCCTA
1 ATCGCATTGCGATTTACGTA
3131848 ATTCGCATTGCGATTTACGTA
1 A-TCGCATTGCGATTTACGTA
* *
3131869 ATCGTATTGTGATTTACGTA
1 ATCGCATTGCGATTTACGTA
3131889 ATCGCATTGCGATTTACGTA
1 ATCGCATTGCGATTTACGTA
3131909 ATCGCATTGCGATTTA-GTAA
1 ATCGCATTGCGATTTACGT-A
3131929 ATCGCA
1 ATCGCA
3131935 ACGAGATTCT
Statistics
Matches: 267, Mismatches: 34, Indels: 18
0.84 0.11 0.06
Matches are distributed among these distances:
19 13 0.05
20 172 0.64
21 82 0.31
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATTTACGTA
Found at i:3131825 original size:41 final size:41
Alignment explanation
Indices: 3131606--3131934 Score: 330
Period size: 41 Copynumber: 8.1 Consensus size: 41
3131596 ATTCTGACTA
* ** * * *
3131606 TCGCATTGCGATTTCCCAAATTCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGTAA-TCGCATTGCGATTTACGTAAT
* * * * * *
3131648 TCGCAATGCGA-ATACGTAAATCACAATGGGA-TTACGTAAA
1 TCGCATTGCGATTTACGT-AATCGCATTGCGATTTACGTAAT
* * * * * *
3131688 TCGCAATGCGAATTAGGAAAATCGCAATGCGA-TTACGTAAA
1 TCGCATTGCGATTTACG-TAATCGCATTGCGATTTACGTAAT
* * *
3131729 TCGCAATGTGA-ATACGTAATCGCATTGCGATTTACGTAA-
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTAAT
* *
3131768 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTAAT
* *
3131809 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTAAT
* *
3131850 TCGCATTGCGATTTACGTAATCGTATTGTGATTTACGTAA-
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTAAT
*
3131890 TCGCATTGCGATTTACGTAATCGCATTGCGATTTA-GTAAA
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTAAT
3131930 TCGCA
1 TCGCA
3131935 ACGAGATTCT
Statistics
Matches: 247, Mismatches: 33, Indels: 16
0.83 0.11 0.05
Matches are distributed among these distances:
39 25 0.10
40 91 0.37
41 119 0.48
42 12 0.05
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (41 bp):
TCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTAAT
Found at i:3131829 original size:61 final size:60
Alignment explanation
Indices: 3131605--3131934 Score: 319
Period size: 61 Copynumber: 5.4 Consensus size: 60
3131595 GATTCTGACT
* ** * * * * *
3131605 ATCGCATTGCGATTTCCCAAATTCGCGTTGCGATTTTCCTAATTCGCAATGCGA-ATACGTAA
1 ATCGCATTGCGATTTACGTAA-TCGCATTGCGATTTACGTAA-TCGCATTGCGATTTACGT-A
* * * * * * * *
3131667 ATCACAATGGGA-TTACGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGA-TTACGTAA
1 ATCGCATTGCGATTTACGT-AATCGCATTGCGATTTACG-TAATCGCATTGCGATTTACGT-A
* * *
3131728 ATCGCAATGTGA-ATACGTAATCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTA
1 ATCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTA
* * * *
3131787 ATCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTA
1 ATCGCATTGCGATTTACGTAA-TCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTA
* *
3131848 ATTCGCATTGCGATTTACGTAATCGTATTGTGATTTACGTAATCGCATTGCGATTTACGTA
1 A-TCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTA
3131909 ATCGCATTGCGATTTA-GTAAATCGCA
1 ATCGCATTGCGATTTACGT-AATCGCA
3131935 ACGAGATTCT
Statistics
Matches: 225, Mismatches: 36, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
59 25 0.11
60 48 0.21
61 121 0.54
62 31 0.14
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (60 bp):
ATCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTA
Found at i:3135363 original size:19 final size:20
Alignment explanation
Indices: 3135321--3135364 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
3135311 CAATCATCTT
*
3135321 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAACGCGGA
*
3135341 AATGACTATCGCAATGC-GA
1 AATGACTATCGCAACGCGGA
3135360 AATGA
1 AATGA
3135365 AAATCACAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.20
Consensus pattern (20 bp):
AATGACTATCGCAACGCGGA
Found at i:3135390 original size:33 final size:33
Alignment explanation
Indices: 3135348--3135483 Score: 245
Period size: 33 Copynumber: 4.1 Consensus size: 33
3135338 GGAAATGACT
*
3135348 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
3135381 ATCGCAATGCGAAATGAAAATCGCAATGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
3135414 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
3135447 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
3135480 ATCG
1 ATCG
3135484 TTGTGATTTT
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 98 1.00
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:3135404 original size:19 final size:19
Alignment explanation
Indices: 3135328--3135472 Score: 104
Period size: 19 Copynumber: 8.4 Consensus size: 19
3135318 CTTAATGTCT
* **
3135328 ATCGCAACGCGGAAATGACT
1 ATCGCAATGC-GAAATGAAA
3135348 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
3135367 ATCACAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
3135381 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3135400 ATCGCAAT--G--A-GAGA
1 ATCGCAATGCGAAATGAAA
3135414 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
3135433 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
3135447 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3135466 ATCGCAA
1 ATCGCAA
3135473 CGAGAGAATC
Statistics
Matches: 97, Mismatches: 13, Indels: 31
0.69 0.09 0.22
Matches are distributed among these distances:
14 29 0.30
15 3 0.03
16 5 0.05
17 5 0.05
18 3 0.03
19 43 0.44
20 9 0.09
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3135510 original size:19 final size:19
Alignment explanation
Indices: 3135482--3135558 Score: 76
Period size: 19 Copynumber: 4.3 Consensus size: 19
3135472 ACGAGAGAAT
*
3135482 CGTTGTGATTTT-AGTTTCG
1 CGTTGCGATTTTCA-TTTCG
3135501 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
3135520 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
3135534 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
3135553 CATTGC
1 CGTTGC
3135559 AATAGACATT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
14 10 0.21
16 3 0.06
17 3 0.06
19 31 0.65
20 1 0.02
ACGTcount: A:0.10, C:0.21, G:0.22, T:0.47
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:3135687 original size:14 final size:14
Alignment explanation
Indices: 3135668--3135704 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3135658 CATCAATTAA
3135668 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3135682 ACAAATCATCTTTT
1 ACAAATCAACTTTT
3135696 ACAAATCAA
1 ACAAATCAA
3135705 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3137120 original size:21 final size:21
Alignment explanation
Indices: 3137054--3137120 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
3137044 GTGAATCGGG
*
3137054 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
3137074 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
3137096 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
3137117 CTCT
1 CTCT
3137121 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:3137139 original size:42 final size:41
Alignment explanation
Indices: 3137054--3137176 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
3137044 GTGAATCGGG
* * * *
3137054 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
3137096 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
3137138 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
3137177 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:3137632 original size:20 final size:19
Alignment explanation
Indices: 3137595--3137664 Score: 95
Period size: 19 Copynumber: 3.6 Consensus size: 19
3137585 AAAAATGACT
*
3137595 ATCGCAACGTGAAATGAAA
1 ATCGCAACGAGAAATGAAA
3137614 ATCGCAACGAGAGAATGAAA
1 ATCGCAACGAGA-AATGAAA
* **
3137634 ATCGCAACGCGAAAAAAAA
1 ATCGCAACGAGAAATGAAA
3137653 ATCGCAACGAGA
1 ATCGCAACGAGA
3137665 GAATCGCAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
19 27 0.60
20 18 0.40
ACGTcount: A:0.50, C:0.19, G:0.21, T:0.10
Consensus pattern (19 bp):
ATCGCAACGAGAAATGAAA
Found at i:3137732 original size:20 final size:20
Alignment explanation
Indices: 3137703--3137779 Score: 129
Period size: 20 Copynumber: 3.9 Consensus size: 20
3137693 CGCGATTATA
*
3137703 GTTTCACGTTGCGATTTTTG
1 GTTTCGCGTTGCGATTTTTG
3137723 GTTTCGCGTTGCGATTTTTG
1 GTTTCGCGTTGCGATTTTTG
*
3137743 GTTTCGCGTTGCGA-TTTTC
1 GTTTCGCGTTGCGATTTTTG
3137762 GTTTCGCGTTGCGATTTT
1 GTTTCGCGTTGCGATTTT
3137780 CATTCTCTCA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
19 18 0.33
20 36 0.67
ACGTcount: A:0.06, C:0.17, G:0.27, T:0.49
Consensus pattern (20 bp):
GTTTCGCGTTGCGATTTTTG
Found at i:3137737 original size:39 final size:38
Alignment explanation
Indices: 3137694--3137777 Score: 114
Period size: 39 Copynumber: 2.2 Consensus size: 38
3137684 AAATCGCAAC
*
3137694 GCGATTATAGTTTCACGTTGCGATTTTTGGTTTCGCGTT
1 GCGATTATAGTTTCACGTTGCGA-TTTTCGTTTCGCGTT
* * *
3137733 GCGATTTTTGGTTTCGCGTTGCGATTTTCGTTTCGCGTT
1 GCGA-TTATAGTTTCACGTTGCGATTTTCGTTTCGCGTT
3137772 GCGATT
1 GCGATT
3137778 TTCATTCTCT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
38 2 0.05
39 22 0.55
40 16 0.40
ACGTcount: A:0.10, C:0.17, G:0.27, T:0.46
Consensus pattern (38 bp):
GCGATTATAGTTTCACGTTGCGATTTTCGTTTCGCGTT
Found at i:3137778 original size:39 final size:40
Alignment explanation
Indices: 3137703--3137779 Score: 129
Period size: 39 Copynumber: 1.9 Consensus size: 40
3137693 CGCGATTATA
*
3137703 GTTTCACGTTGCGATTTTTGGTTTCGCGTTGCGATTTTTG
1 GTTTCACGTTGCGATTTTTCGTTTCGCGTTGCGATTTTTG
*
3137743 GTTTCGCGTTGCGA-TTTTCGTTTCGCGTTGCGATTTT
1 GTTTCACGTTGCGATTTTTCGTTTCGCGTTGCGATTTT
3137780 CATTCTCTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 22 0.63
40 13 0.37
ACGTcount: A:0.06, C:0.17, G:0.27, T:0.49
Consensus pattern (40 bp):
GTTTCACGTTGCGATTTTTCGTTTCGCGTTGCGATTTTTG
Found at i:3137794 original size:39 final size:39
Alignment explanation
Indices: 3137711--3137805 Score: 111
Period size: 39 Copynumber: 2.4 Consensus size: 39
3137701 TAGTTTCACG
* ** *
3137711 TTGCGATTTTTGGTTTCGCGTTGCGATTTTTGGTTTCGCG
1 TTGCGA-TTTTCGTTTCGCGTTGCGATTTTTCATTTCGCA
*
3137751 TTGCGATTTTCGTTTCGCGTTGCGA-TTTTCATTCTCTCA
1 TTGCGATTTTCGTTTCGCGTTGCGATTTTTCATT-TCGCA
*
3137790 TTGCGATTTTCATTTC
1 TTGCGATTTTCGTTTC
3137806 AACCAAAAGA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
38 6 0.12
39 36 0.75
40 6 0.12
ACGTcount: A:0.08, C:0.19, G:0.22, T:0.51
Consensus pattern (39 bp):
TTGCGATTTTCGTTTCGCGTTGCGATTTTTCATTTCGCA
Found at i:3137795 original size:20 final size:19
Alignment explanation
Indices: 3137724--3137805 Score: 83
Period size: 20 Copynumber: 4.2 Consensus size: 19
3137714 CGATTTTTGG
* **
3137724 TTTCGCGTTGCGATTTTTGG
1 TTTCGCATTGCGA-TTTTCA
* *
3137744 TTTCGCGTTGCGATTTTCG
1 TTTCGCATTGCGATTTTCA
*
3137763 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
*
3137782 TTCTCTCATTGCGATTTTCA
1 TT-TCGCATTGCGATTTTCA
3137802 TTTC
1 TTTC
3137806 AACCAAAAGA
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
19 27 0.47
20 30 0.53
ACGTcount: A:0.09, C:0.21, G:0.21, T:0.50
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:3137995 original size:94 final size:94
Alignment explanation
Indices: 3137893--3138268 Score: 586
Period size: 94 Copynumber: 4.1 Consensus size: 94
3137883 ATGGATTGCA
* *
3137893 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
3137957 TTAGCAGAATTGGCAGCAAACGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAATAAAT
*
3137986 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACATAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* * *
3138051 TTAGCAGAATTGACAGTAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAATAAAT
*
3138080 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAAT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
3138145 TTAGCAAAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAATAAAT
*
3138174 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCATAGTGTTAATA-AAT----A
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAA-AGAATACACA
*
3138233 GTTTAGCAGTATTGGCAGCAACCGAATAAAT
64 GTTTAGCAGAATTGGCAGCAACCGAATAAAT
3138264 TTACT
1 TTACT
3138269 AAGCAATCTA
Statistics
Matches: 262, Mismatches: 17, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
90 33 0.13
93 23 0.09
94 205 0.78
95 1 0.00
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.23
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAATAAAT
Found at i:3140057 original size:19 final size:19
Alignment explanation
Indices: 3139959--3140049 Score: 128
Period size: 19 Copynumber: 4.7 Consensus size: 19
3139949 TCTTTTGGTT
*
3139959 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
3139978 GAGAATGAAAATCACAACGC
1 GA-AATGAAAATCGCAACGC
**
3139998 AGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
3140018 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
3140037 GAAATGAAAATCG
1 GAAATGAAAATCG
3140050 TAATGCGATT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
19 32 0.51
20 29 0.46
21 2 0.03
ACGTcount: A:0.48, C:0.19, G:0.21, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:3140124 original size:40 final size:40
Alignment explanation
Indices: 3140080--3140174 Score: 122
Period size: 40 Copynumber: 2.4 Consensus size: 40
3140070 GTTGCGATTA
3140080 TCTCGTTGCGATTTTCA-TTTCGCGTTGCGATTTTCATTT
1 TCTCGTTGCGATTTTCATTTTCGCGTTGCGATTTTCATTT
** * *
3140119 CTCTCGTTGCGATAGTCATTTTTGTGTTGCGATTTTCATTT
1 -TCTCGTTGCGATTTTCATTTTCGCGTTGCGATTTTCATTT
3140160 TCAT-GTTGCGATTTT
1 TC-TCGTTGCGATTTT
3140175 AAGTTTAGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
40 26 0.55
41 21 0.45
ACGTcount: A:0.12, C:0.18, G:0.19, T:0.52
Consensus pattern (40 bp):
TCTCGTTGCGATTTTCATTTTCGCGTTGCGATTTTCATTT
Found at i:3140172 original size:20 final size:20
Alignment explanation
Indices: 3140084--3140174 Score: 105
Period size: 20 Copynumber: 4.5 Consensus size: 20
3140074 CGATTATCTC
*
3140084 GTTGCGATTTTCA-TTTCGC
1 GTTGCGATTTTCATTTTCGT
3140103 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCGT
** *
3140123 CGTTGCGATAGTCATTTTTGT
1 -GTTGCGATTTTCATTTTCGT
*
3140144 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCGT
3140164 GTTGCGATTTT
1 GTTGCGATTTT
3140175 AAGTTTAGAA
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
19 13 0.22
20 30 0.50
21 17 0.28
ACGTcount: A:0.12, C:0.16, G:0.20, T:0.52
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:3140740 original size:20 final size:20
Alignment explanation
Indices: 3140717--3140806 Score: 135
Period size: 20 Copynumber: 4.5 Consensus size: 20
3140707 CGATAGTCAG
3140717 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
3140737 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
3140757 AATTCGCATTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGT
* *
3140778 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
3140798 ATTCGCATT
1 ATTCGCATT
3140807 ACGAATTAGG
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
20 43 0.70
21 18 0.30
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:3140769 original size:41 final size:40
Alignment explanation
Indices: 3140717--3140824 Score: 135
Period size: 41 Copynumber: 2.7 Consensus size: 40
3140707 CGATAGTCAG
* *
3140717 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
* *
3140757 AATTCGCATTGCGATTTACGTAATCGCGTTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
* * * *
3140798 ATTCGCATTACGAATTAGGAAATCGCA
1 ATTCGCATTGCGATTTACGTAATCGCA
3140825 ACGCGAATTT
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
40 22 0.38
41 36 0.62
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.36
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
Found at i:3140831 original size:20 final size:21
Alignment explanation
Indices: 3140808--3140851 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3140798 ATTCGCATTA
3140808 CGAA-TTAGGAAATCGCAACG
1 CGAATTTAGGAAATCGCAACG
* *
3140828 CGAATTTGGGAAATCGCAATG
1 CGAATTTAGGAAATCGCAACG
3140849 CGA
1 CGA
3140852 TAATCAGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.18
Consensus pattern (21 bp):
CGAATTTAGGAAATCGCAACG
Found at i:3141043 original size:3 final size:3
Alignment explanation
Indices: 3141037--3141129 Score: 168
Period size: 3 Copynumber: 31.0 Consensus size: 3
3141027 TATTAAAATA
3141037 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
3141085 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3141130 GTGTTTGACT
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 86 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:3161849 original size:53 final size:53
Alignment explanation
Indices: 3161788--3161891 Score: 183
Period size: 53 Copynumber: 2.0 Consensus size: 53
3161778 TACTTAGGAC
*
3161788 ACTATGTGTG-TATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCGGT
1 ACTATGTGTGCT-CCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCGGT
3161841 ACTATGTGTGCTCCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCG
1 ACTATGTGTGCTCCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCG
3161892 TTACCTTAGT
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
53 48 0.98
54 1 0.02
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.40
Consensus pattern (53 bp):
ACTATGTGTGCTCCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCGGT
Found at i:3164677 original size:20 final size:20
Alignment explanation
Indices: 3164652--3164697 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
3164642 GAAGTCTTTT
3164652 CAGGTACAACTTTGATCAAG
1 CAGGTACAACTTTGATCAAG
*
3164672 CAGGTACAATTTTGATCAAG
1 CAGGTACAACTTTGATCAAG
*
3164692 CTGGTA
1 CAGGTA
3164698 AATCCTTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (20 bp):
CAGGTACAACTTTGATCAAG
Found at i:3168548 original size:29 final size:29
Alignment explanation
Indices: 3168512--3168635 Score: 124
Period size: 29 Copynumber: 4.3 Consensus size: 29
3168502 CATTTTACAC
*
3168512 AAATAGCACCCTTTTTAAAATAATTACCA
1 AAATAGCACCCTTTTCAAAATAATTACCA
* *
3168541 AAATAGCACCCTTTTCAAATTAATTCCCA
1 AAATAGCACCCTTTTCAAAATAATTACCA
** * * *
3168570 AAATAGCACCAATTTCGAATTAATTCCCA
1 AAATAGCACCCTTTTCAAAATAATTACCA
* * * * *
3168599 GAATATCA-CTTTTTCAAAAAAAATACCA
1 AAATAGCACCCTTTTCAAAATAATTACCA
3168627 AAATAGCAC
1 AAATAGCAC
3168636 TAATTTCGAA
Statistics
Matches: 77, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
28 19 0.25
29 58 0.75
ACGTcount: A:0.44, C:0.23, G:0.05, T:0.28
Consensus pattern (29 bp):
AAATAGCACCCTTTTCAAAATAATTACCA
Found at i:3168630 original size:86 final size:85
Alignment explanation
Indices: 3168522--3168689 Score: 221
Period size: 86 Copynumber: 2.0 Consensus size: 85
3168512 AAATAGCACC
* * ** ***
3168522 CTTTTTAAAATAATTACCAAAATAGCACCCTTTTCAAATTAATTCCCAA-AATAGCACCAATTTC
1 CTTTTTAAAAAAAATACCAAAATAGCACCAATTTCAAATTAATT-CCAAGAATAGCACCAAAACC
*
3168586 GAATTAATTCCCAGAATATCA
65 GAATTAATTCCCAAAATATCA
* *
3168607 CTTTTTCAAAAAAAATACCAAAATAGCACTAATTTCGAATTAATTCCAAGAATAGCACCAAAACC
1 CTTTTT-AAAAAAAATACCAAAATAGCACCAATTTCAAATTAATTCCAAGAATAGCACCAAAACC
3168672 GAATTAATTCCCAAAATA
65 GAATTAATTCCCAAAATA
3168690 GTACCGGTCA
Statistics
Matches: 71, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
85 10 0.14
86 61 0.86
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (85 bp):
CTTTTTAAAAAAAATACCAAAATAGCACCAATTTCAAATTAATTCCAAGAATAGCACCAAAACCG
AATTAATTCCCAAAATATCA
Found at i:3168660 original size:29 final size:28
Alignment explanation
Indices: 3168532--3168690 Score: 122
Period size: 29 Copynumber: 5.5 Consensus size: 28
3168522 CTTTTTAAAA
** *
3168532 TAATTACCAAAATAGCACCCTTTTCAAAT
1 TAATT-CCAAAATAGCACCAATTTCGAAT
3168561 TAATTCCCAAAATAGCACCAATTTCGAAT
1 TAATT-CCAAAATAGCACCAATTTCGAAT
* * ** * *
3168590 TAATTCCCAGAATATCA-CTTTTTCAAAAA
1 TAATT-CCAAAATAGCACCAATTTC-GAAT
* * *
3168619 AAATACCAAAATAGCACTAATTTCGAAT
1 TAATTCCAAAATAGCACCAATTTCGAAT
***
3168647 TAATTCCAAGAATAGCACCAAAACCGAAT
1 TAATTCCAA-AATAGCACCAATTTCGAAT
3168676 TAATTCCCAAAATAG
1 TAATT-CCAAAATAG
3168691 TACCGGTCAA
Statistics
Matches: 101, Mismatches: 25, Indels: 8
0.75 0.19 0.06
Matches are distributed among these distances:
28 23 0.23
29 74 0.73
30 4 0.04
ACGTcount: A:0.45, C:0.22, G:0.06, T:0.27
Consensus pattern (28 bp):
TAATTCCAAAATAGCACCAATTTCGAAT
Found at i:3175846 original size:29 final size:28
Alignment explanation
Indices: 3175810--3175961 Score: 108
Period size: 29 Copynumber: 5.2 Consensus size: 28
3175800 CATTTTACAC
*
3175810 AAATAGCATCCTTTTTAAAATAATTACCA
1 AAATAGCA-CCTTTTTAAAATAATTCCCA
*
3175839 AAATAGCACC-CTTTAAGAATTAATTCCCA
1 AAATAGCACCTTTTTAA-AA-TAATTCCCA
** * *
3175868 AAATAGCATCAATTTCAAATTAATTCCCA
1 AAATAGCA-CCTTTTTAAAATAATTCCCA
* * * *
3175897 GAATATCACCTTTTTCGAAACAAAATTACCA
1 AAATAGCACCTTTTT--AAA-ATAATTCCCA
* *
3175928 AAATAGCACCTATTTCAAATTAATTCCCA
1 AAATAGCACCT-TTTTAAAATAATTCCCA
*
3175957 GAATA
1 AAATA
3175962 ACATAAAAAC
Statistics
Matches: 94, Mismatches: 21, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
27 5 0.05
28 8 0.09
29 50 0.53
30 8 0.09
31 20 0.21
32 3 0.03
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.30
Consensus pattern (28 bp):
AAATAGCACCTTTTTAAAATAATTCCCA
Found at i:3177502 original size:17 final size:17
Alignment explanation
Indices: 3177470--3177501 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
3177460 GGAAAATGAT
3177470 ATTATTATAAAAATATA
1 ATTATTATAAAAATATA
3177487 ATTATT-T-AAAATATA
1 ATTATTATAAAAATATA
3177502 TCTAAGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.53
16 1 0.07
17 6 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTATTATAAAAATATA
Found at i:3178212 original size:22 final size:22
Alignment explanation
Indices: 3178184--3178225 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
3178174 AGTGCCCAAC
3178184 AATAACAAAACCGGTAGAAAAA
1 AATAACAAAACCGGTAGAAAAA
*
3178206 AATAACAAAATCGGTAGAAA
1 AATAACAAAACCGGTAGAAA
3178226 TAATAATATT
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:0.62, C:0.12, G:0.14, T:0.12
Consensus pattern (22 bp):
AATAACAAAACCGGTAGAAAAA
Found at i:3179376 original size:36 final size:38
Alignment explanation
Indices: 3179327--3179401 Score: 102
Period size: 36 Copynumber: 2.0 Consensus size: 38
3179317 AAAATAGAAA
*
3179327 TTTTAGAATATTTTAAAAATATATGAAAATAAATT-ATT
1 TTTTAGAATATTTTAAAAATAT-TGAAAAAAAATTCATT
*
3179365 TTTTA-AA-ATTTTAAAAATATTTAAAAAAAATTCATT
1 TTTTAGAATATTTTAAAAATATTGAAAAAAAATTCATT
3179401 T
1 T
3179402 ATCAAAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 10 0.29
36 17 0.50
37 2 0.06
38 5 0.15
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (38 bp):
TTTTAGAATATTTTAAAAATATTGAAAAAAAATTCATT
Found at i:3179893 original size:15 final size:15
Alignment explanation
Indices: 3179873--3179909 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
3179863 TTATGTAACT
3179873 TTTAAAAATTAAATA
1 TTTAAAAATTAAATA
3179888 TTTAAAAATTAAATA
1 TTTAAAAATTAAATA
3179903 -TTAAAAA
1 TTTAAAAA
3179910 AGATAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 7 0.32
15 15 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TTTAAAAATTAAATA
Found at i:3180646 original size:2 final size:2
Alignment explanation
Indices: 3180639--3180664 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3180629 GTAAGTTTTA
3180639 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
3180665 GATTGAGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3183848 original size:44 final size:44
Alignment explanation
Indices: 3183785--3183950 Score: 260
Period size: 44 Copynumber: 3.7 Consensus size: 44
3183775 TTGGAGAATT
3183785 GGACGGCAACCAATATATATATAGAGAGAGAGAGGGGCAAAAGG
1 GGACGGCAACCAATATATATATAGAGAGAGAGAGGGGCAAAAGG
*
3183829 GGACGGCAACCAATATATATAAAGAGAGAGAGAGGGGCAAAAGG
1 GGACGGCAACCAATATATATATAGAGAGAGAGAGGGGCAAAAGG
*
3183873 GGACGGCAACCTATATATATATATATATAGAGAGAGAGGGGCAAAAGG
1 GGACGGCAACC---A-ATATATATATAGAGAGAGAGAGGGGCAAAAGG
* *
3183921 GGATGACAACCAATATATATATAGAGAGAG
1 GGACGGCAACCAATATATATATAGAGAGAG
3183951 GGATAGAAGG
Statistics
Matches: 112, Mismatches: 6, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
44 71 0.63
45 1 0.01
47 1 0.01
48 39 0.35
ACGTcount: A:0.44, C:0.11, G:0.31, T:0.14
Consensus pattern (44 bp):
GGACGGCAACCAATATATATATAGAGAGAGAGAGGGGCAAAAGG
Found at i:3184285 original size:2 final size:2
Alignment explanation
Indices: 3184278--3184341 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
3184268 TTAAGTCGTG
3184278 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3184320 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
3184342 AGTTTAAGAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3198795 original size:23 final size:24
Alignment explanation
Indices: 3198769--3198813 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
3198759 ACTCATACCC
*
3198769 TAACTCTATTTTAATT-ATATTTG
1 TAACTCTATTTCAATTCATATTTG
*
3198792 TAACTTTATTTCAATTCATATT
1 TAACTCTATTTCAATTCATATT
3198814 AATCCCTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.31, C:0.11, G:0.02, T:0.56
Consensus pattern (24 bp):
TAACTCTATTTCAATTCATATTTG
Found at i:3215717 original size:2 final size:2
Alignment explanation
Indices: 3215710--3215738 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3215700 ACATTTGAAT
3215710 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3215739 TCACCATTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3216218 original size:21 final size:21
Alignment explanation
Indices: 3216194--3216234 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3216184 TTCTGCTACT
*
3216194 TTATCACTTACTCTTTTATTA
1 TTATCACTTACACTTTTATTA
* *
3216215 TTATTACTTTCACTTTTATT
1 TTATCACTTACACTTTTATT
3216235 CCGCGAACTT
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:0.22, C:0.17, G:0.00, T:0.61
Consensus pattern (21 bp):
TTATCACTTACACTTTTATTA
Found at i:3216921 original size:6 final size:6
Alignment explanation
Indices: 3216910--3216935 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3216900 AGGTAAGGTC
3216910 GGATTG GGATTG GGATTG GGATTG GG
1 GGATTG GGATTG GGATTG GGATTG GG
3216936 TTCGGGTTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.54, T:0.31
Consensus pattern (6 bp):
GGATTG
Found at i:3217159 original size:35 final size:35
Alignment explanation
Indices: 3217102--3217194 Score: 114
Period size: 35 Copynumber: 2.6 Consensus size: 35
3217092 AATCGAAGTT
* *
3217102 AGATAGAGGATATATATTTTTCAGGTAGGATTAGATC
1 AGATAGAGGATATA-A-ATTTCAGGTAGCATTAGATC
*
3217139 AGATAGAGGATATAAATTTCAGGTCGCATTAGATC
1 AGATAGAGGATATAAATTTCAGGTAGCATTAGATC
* *
3217174 AGCTAAAGGATATAAAATTTC
1 AGATAGAGGATAT-AAATTTC
3217195 GGGTTGAGTC
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
35 28 0.56
36 8 0.16
37 14 0.28
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.31
Consensus pattern (35 bp):
AGATAGAGGATATAAATTTCAGGTAGCATTAGATC
Found at i:3219414 original size:21 final size:21
Alignment explanation
Indices: 3219388--3219427 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3219378 GTTAGGGGGA
*
3219388 CGAACTTGAGCTTATAAAAGG
1 CGAACTTGAACTTATAAAAGG
3219409 CGAACTTGAACTTATAAAA
1 CGAACTTGAACTTATAAAA
3219428 CTCTAGGGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.25
Consensus pattern (21 bp):
CGAACTTGAACTTATAAAAGG
Found at i:3224319 original size:15 final size:15
Alignment explanation
Indices: 3224301--3224336 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
3224291 GCAGATATGG
3224301 GGCGGGCGGATGCGA
1 GGCGGGCGGATGCGA
3224316 GGCGGGCGGATGCGA
1 GGCGGGCGGATGCGA
3224331 GGCGGG
1 GGCGGG
3224337 TAATGTCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.11, C:0.19, G:0.64, T:0.06
Consensus pattern (15 bp):
GGCGGGCGGATGCGA
Found at i:3226074 original size:14 final size:14
Alignment explanation
Indices: 3226055--3226110 Score: 94
Period size: 14 Copynumber: 4.0 Consensus size: 14
3226045 CTAATTTATA
*
3226055 TACATGTATGGATG
1 TACAAGTATGGATG
*
3226069 TACATGTATGGATG
1 TACAAGTATGGATG
3226083 TACAAGTATGGATG
1 TACAAGTATGGATG
3226097 TACAAGTATGGATG
1 TACAAGTATGGATG
3226111 CATGAATTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
14 41 1.00
ACGTcount: A:0.32, C:0.07, G:0.29, T:0.32
Consensus pattern (14 bp):
TACAAGTATGGATG
Found at i:3226938 original size:20 final size:20
Alignment explanation
Indices: 3226870--3226944 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 20
3226860 CGTTATACCA
**
3226870 AAGGGATCAATCCTTTTTGGG
1 AAGGGATCAATCC-TTTTGTC
** *
3226891 AAGGGATTGATCCTTTTCCTC
1 AAGGGATCAATCCTTTT-GTC
*
3226912 GAGGGATCAATCCTTTTGTC
1 AAGGGATCAATCCTTTTGTC
*
3226932 AAGGGATCGATCC
1 AAGGGATCAATCC
3226945 CAAACTCACT
Statistics
Matches: 42, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
20 17 0.40
21 25 0.60
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (20 bp):
AAGGGATCAATCCTTTTGTC
Found at i:3228283 original size:20 final size:20
Alignment explanation
Indices: 3228245--3228294 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
3228235 GCTCAAAATC
*
3228245 GTTTTTCAAAATTTCATTTT
1 GTTTTTCAAAATTCCATTTT
3228265 GTTTTTCAAAA-TCCAATTTT
1 GTTTTTCAAAATTCC-ATTTT
*
3228285 G-CTTTCAAAA
1 GTTTTTCAAAA
3228295 ATCGTTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 10 0.37
20 17 0.63
ACGTcount: A:0.30, C:0.14, G:0.06, T:0.50
Consensus pattern (20 bp):
GTTTTTCAAAATTCCATTTT
Done.