Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 7 of 145
Found at i:2521934 original size:18 final size:18
Alignment explanation
Indices: 2521911--2521945 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2521901 GAAGGAGAGG
2521911 GGAAG-AAGAAGAAAGAAA
1 GGAAGAAAGAA-AAAGAAA
2521929 GGAAGAAAGAAAAAGAA
1 GGAAGAAAGAAAAAGAA
2521946 NNNNNNNNNN
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (18 bp):
GGAAGAAAGAAAAAGAAA
Found at i:2523431 original size:61 final size:62
Alignment explanation
Indices: 2523320--2523437 Score: 161
Period size: 61 Copynumber: 1.9 Consensus size: 62
2523310 CCACTAATCC
* *
2523320 TAATAACTAACACAATAATAATATTAATAATTTTATATACAAAATAATACTAACTAAAATTAT
1 TAATAACTAACACAAAAATAATACTAAT-ATTTTATATACAAAATAATACTAACTAAAATTAT
*
2523383 TAATAACTAACTACAAAAATAATACTAAT-TTTT-TACTA-ACAATAATACTAACTAA
1 TAATAACTAAC-ACAAAAATAATACTAATATTTTATA-TACAAAATAATACTAACTAA
2523438 CATCTTAATA
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
61 18 0.36
62 6 0.12
63 11 0.22
64 15 0.30
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (62 bp):
TAATAACTAACACAAAAATAATACTAATATTTTATATACAAAATAATACTAACTAAAATTAT
Found at i:2523451 original size:3 final size:3
Alignment explanation
Indices: 2523443--2523468 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2523433 ACTAACATCT
2523443 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
2523469 CTATAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2523771 original size:27 final size:27
Alignment explanation
Indices: 2523733--2523827 Score: 154
Period size: 27 Copynumber: 3.5 Consensus size: 27
2523723 ATAACATGAG
*
2523733 TGGTGCCGCCAACAGGGAACCCTTGTT
1 TGGTGCCGCCAACAAGGAACCCTTGTT
*
2523760 TGGTGCCGCCAACAAGGAATCCTTGTT
1 TGGTGCCGCCAACAAGGAACCCTTGTT
**
2523787 TGGTGCCGCCAACAAGGTTCCCTTGTT
1 TGGTGCCGCCAACAAGGAACCCTTGTT
2523814 TGGTGCCGCCAACA
1 TGGTGCCGCCAACA
2523828 GTGTTCCCTT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 63 1.00
ACGTcount: A:0.19, C:0.29, G:0.27, T:0.24
Consensus pattern (27 bp):
TGGTGCCGCCAACAAGGAACCCTTGTT
Found at i:2523923 original size:28 final size:29
Alignment explanation
Indices: 2523891--2523961 Score: 110
Period size: 28 Copynumber: 2.5 Consensus size: 29
2523881 TTAGTTTTTT
*
2523891 TATATATTTTGGTAAAT-AAAAAAATTTA
1 TATATATTTTGGTAAATAAAAAAAATGTA
2523919 TATATATTTTGGTAAATAAAAAAAATGTA
1 TATATATTTTGGTAAATAAAAAAAATGTA
*
2523948 TA-ACATTTTGGTAA
1 TATATATTTTGGTAA
2523962 TTTTTTATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 28 0.70
29 12 0.30
ACGTcount: A:0.48, C:0.01, G:0.10, T:0.41
Consensus pattern (29 bp):
TATATATTTTGGTAAATAAAAAAAATGTA
Found at i:2531414 original size:6 final size:6
Alignment explanation
Indices: 2531403--2531427 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2531393 TTTGGCCTCT
2531403 TAAAAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA TAAAAA TAAAAA TAAAAA T
2531428 CAATTGAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
TAAAAA
Found at i:2532663 original size:2 final size:2
Alignment explanation
Indices: 2532656--2532686 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2532646 ACTCTCAATT
2532656 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 T
2532687 CAAATTGACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2536656 original size:2 final size:2
Alignment explanation
Indices: 2536649--2536682 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2536639 TGATTCAAAG
2536649 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
2536683 GCTAACCTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2536713 original size:37 final size:37
Alignment explanation
Indices: 2536663--2536742 Score: 151
Period size: 37 Copynumber: 2.2 Consensus size: 37
2536653 ATATATATAT
2536663 ATATATATATATATATATATGCTAACCTTGTGCAATA
1 ATATATATATATATATATATGCTAACCTTGTGCAATA
2536700 ATATATATATATATATATATGCTAACCTTGTGCAATA
1 ATATATATATATATATATATGCTAACCTTGTGCAATA
*
2536737 CTATAT
1 ATATAT
2536743 CAAAAGGACC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.41
Consensus pattern (37 bp):
ATATATATATATATATATATGCTAACCTTGTGCAATA
Found at i:2537302 original size:288 final size:288
Alignment explanation
Indices: 2536786--2537364 Score: 1077
Period size: 288 Copynumber: 2.0 Consensus size: 288
2536776 GATCGATTGC
2536786 AACAAACAATATCCCTTTATTCCTGTACCATTTTCAACATGTATACAAAGTTATACAAAAAGATA
1 AACAAACAATATCCCTTTATTCCTGTACCATTTTCAACATGTATACAAAGTTATACAAAAAGATA
2536851 GAAACAGCAAAAAAGGGCTTCATATCAACCATAAAATTCAAGCTTCTCCCCTTATCAAGCTAATA
66 GAAACAGCAAAAAAGGGCTTCATATCAACCATAAAATTCAAGCTTCTCCCCTTATCAAGCTAATA
* * * *
2536916 GAAAAAATGTTAGAATCTAGGAGGTGCTTGTATTATAGGGACTGTATCAAGTAAATCCCCTTTTA
131 GAAAAAAGGTCAGAATCTAGGAGGTGCTTGTAGTATAGGGACTGCATCAAGTAAATCCCCTTTTA
*
2536981 TTAAATGGACCAATTTAATCCCTATAATATTAAAAACAATCAAATAAGTCCAAATAAGATACTAT
196 TTAAATGGACCAATTTAATCCCTATAATATTAAAAACAACCAAATAAGTCCAAATAAGATACTAT
*
2537046 TAACATATAAATATCTTAAATTAATAAT
261 TAACATATAAATATATTAAATTAATAAT
2537074 AACAAACAATATCCCTTTATTCCTGTACCATTTTCAACATGTATACAAAGTTATACAAAAAGATA
1 AACAAACAATATCCCTTTATTCCTGTACCATTTTCAACATGTATACAAAGTTATACAAAAAGATA
* *
2537139 GAAACAGCAAGAAAGGGCTTCATATCAACCGTAAAATTCAAGCTTCTCCCCTTATCAAGCTAATA
66 GAAACAGCAAAAAAGGGCTTCATATCAACCATAAAATTCAAGCTTCTCCCCTTATCAAGCTAATA
2537204 GAAAAAAGGTCAGAATCTAGGAGGTGCTTGTAGTATAGGGACTGCATCAAGTAAATCCCCTTTTA
131 GAAAAAAGGTCAGAATCTAGGAGGTGCTTGTAGTATAGGGACTGCATCAAGTAAATCCCCTTTTA
*
2537269 TTAAATGGACCAATTTAATCCCTATAATATTAAAAACAACCAAATAAGTCCAAATATGATACTAT
196 TTAAATGGACCAATTTAATCCCTATAATATTAAAAACAACCAAATAAGTCCAAATAAGATACTAT
2537334 TAACATATAAATATATTAAATTAATAAT
261 TAACATATAAATATATTAAATTAATAAT
2537362 AAC
1 AAC
2537365 CATAAAATTA
Statistics
Matches: 282, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
288 282 1.00
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (288 bp):
AACAAACAATATCCCTTTATTCCTGTACCATTTTCAACATGTATACAAAGTTATACAAAAAGATA
GAAACAGCAAAAAAGGGCTTCATATCAACCATAAAATTCAAGCTTCTCCCCTTATCAAGCTAATA
GAAAAAAGGTCAGAATCTAGGAGGTGCTTGTAGTATAGGGACTGCATCAAGTAAATCCCCTTTTA
TTAAATGGACCAATTTAATCCCTATAATATTAAAAACAACCAAATAAGTCCAAATAAGATACTAT
TAACATATAAATATATTAAATTAATAAT
Found at i:2540551 original size:2 final size:2
Alignment explanation
Indices: 2540544--2540580 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
2540534 AATCACAAAT
2540544 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
2540581 AAAGGCTAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2541563 original size:2 final size:2
Alignment explanation
Indices: 2541556--2541582 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2541546 TGTCTAATTT
2541556 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 T
2541583 TTAAAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2553625 original size:2 final size:2
Alignment explanation
Indices: 2553620--2553651 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2553610 GAAGAGTGTG
2553620 TA TA TA TA T- 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
2553652 GTTGAAGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2553951 original size:5 final size:5
Alignment explanation
Indices: 2553943--2553968 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2553933 AATTCAATTG
2553943 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
2553969 TTTTAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:2560474 original size:32 final size:31
Alignment explanation
Indices: 2560408--2560476 Score: 104
Period size: 31 Copynumber: 2.2 Consensus size: 31
2560398 TTTGGCCCTT
*
2560408 ATTTTTTTAGCTAAATTTGACTAAAACATTA
1 ATTTTTTTAGCGAAATTTGACTAAAACATTA
2560439 ATTTTTTTAG-GAAATATTGACTAAAACATTA
1 ATTTTTTTAGCGAAAT-TTGACTAAAACATTA
*
2560470 AATTTTT
1 ATTTTTT
2560477 AAATGTGACA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 4 0.11
31 31 0.89
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (31 bp):
ATTTTTTTAGCGAAATTTGACTAAAACATTA
Found at i:2570091 original size:19 final size:20
Alignment explanation
Indices: 2570052--2570091 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
2570042 TCTTTAGGCC
* *
2570052 TTCATTTCATGCATTTGCAT
1 TTCATTACATGCATATGCAT
2570072 TTCATTACAT-CATATGCAT
1 TTCATTACATGCATATGCAT
2570091 T
1 T
2570092 AAACACCGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.47
Consensus pattern (20 bp):
TTCATTACATGCATATGCAT
Found at i:2572004 original size:23 final size:23
Alignment explanation
Indices: 2571961--2572006 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2571951 TGAGCAAATG
*
2571961 TTCTTTCATTCTTTACTATTTTT
1 TTCTTTCATTCTTTACGATTTTT
**
2571984 TTCTTTCATTCTTTTGGATTTTT
1 TTCTTTCATTCTTTACGATTTTT
2572007 CTGCCAAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.11, C:0.15, G:0.04, T:0.70
Consensus pattern (23 bp):
TTCTTTCATTCTTTACGATTTTT
Found at i:2572989 original size:7 final size:7
Alignment explanation
Indices: 2572937--2572983 Score: 69
Period size: 7 Copynumber: 6.7 Consensus size: 7
2572927 AGTGATGTGA
2572937 AAAAATG
1 AAAAATG
2572944 AAAAGATG
1 AAAA-ATG
2572952 -AAAATG
1 AAAAATG
2572958 AAAAATG
1 AAAAATG
2572965 AAAAATG
1 AAAAATG
*
2572972 AGAAATG
1 AAAAATG
2572979 AAAAA
1 AAAAA
2572984 ATAAAATAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
6 3 0.08
7 30 0.83
8 3 0.08
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.13
Consensus pattern (7 bp):
AAAAATG
Found at i:2572989 original size:21 final size:22
Alignment explanation
Indices: 2572934--2572989 Score: 82
Period size: 21 Copynumber: 2.6 Consensus size: 22
2572924 AGAAGTGATG
2572934 TGAAAAAATGAAAAGATGAAAA
1 TGAAAAAATGAAAAGATGAAAA
2572956 TG-AAAAATGAAAA-ATGAGAAA
1 TGAAAAAATGAAAAGATGA-AAA
2572977 TGAAAAAAT-AAAA
1 TGAAAAAATGAAAA
2572990 TAGAGAGGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.12
21 20 0.62
22 8 0.25
ACGTcount: A:0.70, C:0.00, G:0.16, T:0.14
Consensus pattern (22 bp):
TGAAAAAATGAAAAGATGAAAA
Found at i:2574425 original size:43 final size:43
Alignment explanation
Indices: 2574376--2574701 Score: 133
Period size: 44 Copynumber: 7.4 Consensus size: 43
2574366 CCCTGAGGTT
*
2574376 GCAGTGGAGTACATTGAAGCCAGTAATTCTATCTTCCTGGGCA
1 GCAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCA
* * * * **
2574419 GCAGTGGAATAGATTGAAG--ATTACAGATCTTATCTCCCTAAGCA
1 GCAGTGGAGTACATTGAAGCCAGTA-A-TTC-TATCTCCCTGGGCA
** * * * *** * * * **
2574463 ATAGTGGAGCAGATCGAAGATGGTGGATTTTACCTCCCTGAGGTT
1 GCAGTGGAGTACATTGAAGCCAGT-AATTCTATCTCCCTG-GGCA
* *
2574508 GCAGTGGAGTACATTGAAGCCAGTAATTTTATCTTCCTGGGCA
1 GCAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCA
* * **
2574551 GCAGTGG-G-ATCGATTGAAG--ATTACAGATCTTATCTCCCTAAGCA
1 GCAGTGGAGTA-C-ATTGAAGCCAGTA-A-TTC-TATCTCCCTGGGCA
* * * * *** * * * **
2574595 GTAGTGGAGCAGATCGAAGATGGTGGATTTTACCTCCCTGAGGTT
1 GCAGTGGAGTACATTGAAGCCAGT-AATTCTATCTCCCTG-GGCA
2574640 GCAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCA
1 GCAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCA
* * *
2574683 ACAGTGGAATAGATTGAAG
1 GCAGTGGAGTACATTGAAG
2574702 ATTTCAGATC
Statistics
Matches: 196, Mismatches: 69, Indels: 36
0.65 0.23 0.12
Matches are distributed among these distances:
41 7 0.04
42 4 0.02
43 54 0.28
44 88 0.45
45 38 0.19
46 5 0.03
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.28
Consensus pattern (43 bp):
GCAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCA
Found at i:2574474 original size:132 final size:132
Alignment explanation
Indices: 2574311--2576698 Score: 3093
Period size: 132 Copynumber: 17.9 Consensus size: 132
2574301 TGAAGATAGT
* * * * * *
2574311 AGATCTTATCTCTCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGGATTTTACCTCCCTGAGGTT
1 AGATCTTGTCTCCCCAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTT
*
2574376 GCAGTGGAGTACATTGAAGCCAGTAATTCTATCTT-CCTGGGCAGCAGTGGAATAGATTGAAGAT
66 ACAGTGGAGTACATTGAAGCCAGTAATTCTA-CTTCCCTGGGCAGCAGTGGAATAGATTGAAGAT
*
2574440 TAC
130 TTC
* * * * * *
2574443 AGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGATGGTGGATTTTACCTCCCTGAGGTT
1 AGATCTTGTCTCCCCAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTT
* * * *
2574508 GCAGTGGAGTACATTGAAGCCAGTAATTTTATCTT-CCTGGGCAGCAGTGGGATCGATTGAAGAT
66 ACAGTGGAGTACATTGAAGCCAGTAATTCTA-CTTCCCTGGGCAGCAGTGGAATAGATTGAAGAT
*
2574572 TAC
130 TTC
* * * * *
2574575 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGGATTTTACCTCCCTGAGGTT
1 AGATCTTGTCTCCCCAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTT
* *
2574640 GCAGTGGAGTACATTGAAGCCAGTAATTCTA-TCTCCCTGGGCAACAGTGGAATAGATTGAAGAT
66 ACAGTGGAGTACATTGAAGCCAGTAATTCTACT-TCCCTGGGCAGCAGTGGAATAGATTGAAGAT
2574704 TTC
130 TTC
*
2574707 AGATCTTTTCTCCCCAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTT
1 AGATCTTGTCTCCCCAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTT
*
2574772 ACAGTGGAGTACATTGAAGCCAGCAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATT
66 ACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATT
*
2574837 TT
131 TC
* *
2574839 AGATCTTGTCTCCCCAAGCAGTAGTGGAGCAGATCAAATATAGTGAATTTTACCTCCCTGTGGTT
1 AGATCTTGTCTCCCCAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTT
* * * *
2574904 ACAGTAGAGTACATTGAAGCTAGTAATTCTACTTCCCTAGGCAGCAGTAGAATAGATTGAAGATT
66 ACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATT
2574969 TC
131 TC
* * *
2574971 AGATCTTGTCTCCCCAAGCAATAGTTGAGCAGATTAAAGATGGTGAATTTTACCTCCCTGTGGTT
1 AGATCTTGTCTCCCCAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTT
* *
2575036 ACAGTGGAGTACATTGAAGCCAGCAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTAAAGATT
66 ACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATT
2575101 TC
131 TC
* *
2575103 AAATCTTGTCTCCCCAAGCAGTAGTGGAGTAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTT
1 AGATCTTGTCTCCCCAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTT
* * ** *
2575168 ACAGTAGAGTACATTGAAGCCGGTAATTCTACTTCCCTAAGCAACAGTGGAATAGATTGAAGATT
66 ACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATT
2575233 TC
131 TC
* * * *
2575235 ATATATTGTCTCCCTAAACAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTT
1 AGATCTTGTCTCCCCAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTT
* *
2575300 ACAGTGGAGTACATTGAAGCCAGCAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTAAAGATT
66 ACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATT
2575365 TC
131 TC
* *
2575367 AAATCTTGTCTCCCCAAGCAGTAGTGGAGTAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTT
1 AGATCTTGTCTCCCCAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTT
* *
2575432 ACAGTGGAGTACATTGAAGCCAGCAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTAAAGATT
66 ACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATT
2575497 TC
131 TC
* *
2575499 AAATCTTGTCTCCCCAAGCAGTAGTGGAGTAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTT
1 AGATCTTGTCTCCCCAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTT
* *
2575564 ACAGTGGAGTACATTGAAGCCAGCAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTAAAGATT
66 ACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATT
2575629 TC
131 TC
* *
2575631 AAATCTTGTCTCCCCAAGCAGTAGTGGAGTAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTT
1 AGATCTTGTCTCCCCAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTT
* *
2575696 ACAGTGGAGTACATTGAAGCCAGCAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTAAAGATT
66 ACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATT
2575761 TC
131 TC
* *
2575763 AAATCTTGTCTCCCCAAGCAGTAGTGGAGTAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTT
1 AGATCTTGTCTCCCCAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTT
* *
2575828 ACAGTGGAGTACATTGAAGCCAGCAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTAAAGATT
66 ACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATT
2575893 TC
131 TC
* *
2575895 AAATCTTGTCTCCCCAAGCAGTAGTGGAGTAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTT
1 AGATCTTGTCTCCCCAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTT
* * *
2575960 ACAGTGGAGTACATTGAAGCCAG---TTAT-C-TCCCTAGGC-GACAGTGGAATAGATTGGAGAT
66 ACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAG-CAGTGGAATAGATTGAAGAT
2576019 TTC
130 TTC
* * * * * **
2576022 AGATCTTGCCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTT
1 AGATCTTGTCTCCCCAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTT
* * * * *** **
2576087 GCAGTGGAGTATATTGAAGCCAGTAATTCTACCTCCCCGGTTGGC-GT-GAAGTAGATCAAAGAT
66 ACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAA-TAGATTGAAGAT
**
2576150 AAC
130 TTC
* * *
2576153 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCAAATATGGTGGATTT
1 AGATCTTGTCTCCCCA-A------GC--AGTAG-T-G--G--AGCAGATCAAAGATGGTGAATTT
* * * *
2576218 TGCCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAATTCTA-TCTCCCTGGGCAACAGTG
51 TACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACT-TCCCTGGGCAGCAGTG
*
2576282 GAATAGATTGGAGATTTC
115 GAATAGATTGAAGATTTC
* * * ** * * **
2576300 AGATCTTGCCTCCCTAAGTAGTAGTGGAGCAGATTGAAGATGGCGGATTTTACCTCCCTGAAGTT
1 AGATCTTGTCTCCCCAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTT
* * * * * *** **
2576365 GCAGTGGAGTATATTAAAGCCAGTAATTCTACCTCCCCGGTTGGC-GT-GAAGTAGATCAAAGAT
66 ACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAA-TAGATTGAAGAT
**
2576428 AAC
130 TTC
* * *
2576431 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCAAAAATGGTGGATTT
1 AGATCTTGTCTCCCCA-A------GC--AGTAG-T-G--G--AGCAGATCAAAGATGGTGAATTT
* *
2576496 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA-TCTCCCTGGGCAACAGTG
51 TACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACT-TCCCTGGGCAGCAGTG
*
2576560 GAATAGATTGAATATTAT-
115 GAATAGATTGAAGATT-TC
* * * *
2576578 AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTT
1 AGATCTTGTCTCCCCAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTT
*
2576643 ACAGTGGAGTACATTGAAGCCAGTAATTCTA-TCTCCC-GGAGCAACAGTGGAATAGA
66 ACAGTGGAGTACATTGAAGCCAGTAATTCTACT-TCCCTGG-GCAGCAGTGGAATAGA
2576699 CAGAAGAAAT
Statistics
Matches: 2041, Mismatches: 164, Indels: 102
0.88 0.07 0.04
Matches are distributed among these distances:
126 1 0.00
127 106 0.05
128 1 0.00
129 3 0.00
130 10 0.00
131 54 0.03
132 1631 0.80
133 2 0.00
134 2 0.00
136 2 0.00
137 2 0.00
138 13 0.01
140 13 0.01
141 2 0.00
142 2 0.00
144 2 0.00
146 140 0.07
147 49 0.02
148 6 0.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (132 bp):
AGATCTTGTCTCCCCAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTT
ACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATT
TC
Found at i:2574702 original size:88 final size:88
Alignment explanation
Indices: 2574341--2574703 Score: 229
Period size: 88 Copynumber: 4.1 Consensus size: 88
2574331 GTAGTGGAGC
*
2574341 AGATCGAAGATGGTGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAATTCT
1 AGATTGAAGATGGTGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAATTCT
*
2574406 ATCTTCCTGGGCAGCAGTGGAAT
66 ATCTCCCTGGGCAGCAGTGGAAT
**** * * * ** * * * *** *
2574429 AGATTGAAGATTACAGATCTTATCTCCCTAAGCAAT--AGTGGAGCAGATCGAAGATGGTGGATT
1 AGATTGAAGATGGTGGATTTTACCTCCCTGAG-GTTGCAGTGGAGTACATTGAAGCCAGT-AATT
* * ** *
2574492 TTACCTCCCTGAGGTTGCAGTGGAGT
64 CTATCTCCCTG-GGCAGCAGTGGAAT
* *** * * * ** *
2574518 ACATTGAAGCCAGT-AATTTTATCTTCCTG-GGCAGCAGTGG-G-ATCGATTGAAG--ATTACAG
1 AGATTGAAGATGGTGGATTTTACCTCCCTGAGGTTGCAGTGGAGTA-C-ATTGAAGCCAGTA-A-
* ** * **
2574577 ATCTTATCTCCCTAAGCAGTAGTGGAGC
62 TTC-TATCTCCCTGGGCAGCAGTGGAAT
*
2574605 AGATCGAAGATGGTGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAATTCT
1 AGATTGAAGATGGTGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAATTCT
*
2574670 ATCTCCCTGGGCAACAGTGGAAT
66 ATCTCCCTGGGCAGCAGTGGAAT
2574693 AGATTGAAGAT
1 AGATTGAAGAT
2574704 TTCAGATCTT
Statistics
Matches: 190, Mismatches: 69, Indels: 32
0.65 0.24 0.11
Matches are distributed among these distances:
86 3 0.02
87 37 0.19
88 105 0.55
89 38 0.20
90 3 0.02
91 4 0.02
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (88 bp):
AGATTGAAGATGGTGGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAATTCT
ATCTCCCTGGGCAGCAGTGGAAT
Found at i:2575481 original size:88 final size:87
Alignment explanation
Indices: 2575384--2575759 Score: 206
Period size: 88 Copynumber: 4.3 Consensus size: 87
2575374 GTCTCCCCAA
* * *
2575384 GCAGTAGTGGAGTAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGA
1 GCAGCAGTGGAGTAGATTAAAGATGGTGAATTTTACCTCCCTGTGG-TACAGTGGAGTACATTAA
*
2575449 AGCCAGCAATTCTACTTCCCTGG
65 AGACAGCAATTCTACTTCCCTGG
* * * * ** * ** * *
2575472 GCAGCAGTGGAATAGATTAAAGAT-TTCAAATCTTGTCTCCCCAAGCAGT--AGTGGAGTAGATC
1 GCAGCAGTGGAGTAGATTAAAGATGGT-GAATTTTACCT-CCC-TGTGGTACAGTGGAGTACATT
** * * *
2575534 AAAGATGGTGAATTTTACCTCCCTGTG
63 AAAGACAG-CAATTCTACTTCCCTG-G
* * * *** * * * * * *
2575561 GTTA-CAGTGGAGTACATTGAAGCCAG-CAATTCTACTTCCCTG-GGCAGCAGTGGAATAGATTA
1 G-CAGCAGTGGAGTAGATTAAAGATGGTGAATTTTACCTCCCTGTGGTA-CAGTGGAGTACATTA
*** * ** ***
2575623 AAGATTTCAAATCTTGTCTCCCCAA
64 AAGACAGCAATTCTACT-TCCCTGG
* * *
2575648 GCAGTAGTGGAGTAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGA
1 GCAGCAGTGGAGTAGATTAAAGATGGTGAATTTTACCTCCCTGTGG-TACAGTGGAGTACATTAA
*
2575713 AGCCAGCAATTCTACTTCCCTGG
65 AGACAGCAATTCTACTTCCCTGG
*
2575736 GCAGCAGTGGAATAGATTAAAGAT
1 GCAGCAGTGGAGTAGATTAAAGAT
2575760 TTCAAATCTT
Statistics
Matches: 196, Mismatches: 77, Indels: 30
0.65 0.25 0.10
Matches are distributed among these distances:
85 1 0.01
86 2 0.01
87 39 0.20
88 105 0.54
89 45 0.23
90 4 0.02
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (87 bp):
GCAGCAGTGGAGTAGATTAAAGATGGTGAATTTTACCTCCCTGTGGTACAGTGGAGTACATTAAA
GACAGCAATTCTACTTCCCTGG
Found at i:2576539 original size:278 final size:278
Alignment explanation
Indices: 2575925--2576679 Score: 1270
Period size: 278 Copynumber: 2.7 Consensus size: 278
2575915 GTAGTGGAGT
* * *
2575925 AGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAG----T-T
1 AGATCAAAAATGGTGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCT
* *
2575985 ATCTCCCTAGGCGACAGTGGAATAGATTGGAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGA
66 ATCTCCCTGGGCAACAGTGGAATAGATTGGAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGA
2576050 GCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTTGCAGTGGAGTATATTGAAGCCAGTAATT
131 GCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTTGCAGTGGAGTATATTGAAGCCAGTAATT
2576115 CTACCTCCCCGGTTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGCG
196 CTACCTCCCCGGTTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGCG
2576180 AAGTAGATCGAAGAAAGC
261 AAGTAGATCGAAGAAAGC
* * *
2576198 AGATCAAATATGGTGGATTTTGCCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAATTCT
1 AGATCAAAAATGGTGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCT
*
2576263 ATCTCCCTGGGCAACAGTGGAATAGATTGGAGATTTCAGATCTTGCCTCCCTAAGTAGTAGTGGA
66 ATCTCCCTGGGCAACAGTGGAATAGATTGGAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGA
* *
2576328 GCAGATTGAAGATGGCGGATTTTACCTCCCTGAAGTTGCAGTGGAGTATATTAAAGCCAGTAATT
131 GCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTTGCAGTGGAGTATATTGAAGCCAGTAATT
2576393 CTACCTCCCCGGTTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGCG
196 CTACCTCCCCGGTTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGCG
2576458 AAGTAGATCGAAGAAAGC
261 AAGTAGATCGAAGAAAGC
2576476 AGATCAAAAATGGTGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCT
1 AGATCAAAAATGGTGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCT
* * **
2576541 ATCTCCCTGGGCAACAGTGGAATAGATTGAATATTAT-AGATCTTATCTCCCTAAGCAGTAGTGG
66 ATCTCCCTGGGCAACAGTGGAATAGATTGGAGATT-TCAGATCTTGCCTCCCTAAGCAGTAGTGG
* * * * *
2576605 AGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
130 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTTGCAGTGGAGTATATTGAAGCCAGTAAT
*
2576670 TCTATCTCCC
195 TCTACCTCCC
2576680 GGAGCAACAG
Statistics
Matches: 450, Mismatches: 26, Indels: 7
0.93 0.05 0.01
Matches are distributed among these distances:
273 53 0.12
277 1 0.00
278 395 0.88
279 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.27
Consensus pattern (278 bp):
AGATCAAAAATGGTGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCT
ATCTCCCTGGGCAACAGTGGAATAGATTGGAGATTTCAGATCTTGCCTCCCTAAGCAGTAGTGGA
GCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTTGCAGTGGAGTATATTGAAGCCAGTAATT
CTACCTCCCCGGTTGGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGCG
AAGTAGATCGAAGAAAGC
Found at i:2576679 original size:44 final size:44
Alignment explanation
Indices: 2576499--2576679 Score: 104
Period size: 44 Copynumber: 4.1 Consensus size: 44
2576489 TGGATTTTAC
2576499 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTAT
1 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTAT
** * * * * *
2576543 CTCCCTG-GGCAACAGTGGAATAGATTGAA--TATTATAGATCTTAT
1 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTA-A-TTC-TAT
* * * ** *** * * *
2576587 CTCCCTAAGCAG-T--AGTGGAGCAGATCAAAGATGGTGGATTTTAC
1 CTCCCTGAG--GTTACAGTGGAGTACATTGAAGCCAGT-AATTCTAT
2576631 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTAT
1 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTAT
2576675 CTCCC
1 CTCCC
2576680 GGAGCAACAG
Statistics
Matches: 95, Mismatches: 30, Indels: 24
0.64 0.20 0.16
Matches are distributed among these distances:
41 3 0.03
42 2 0.02
43 21 0.22
44 48 0.51
45 17 0.18
46 3 0.03
47 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (44 bp):
CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTAT
Found at i:2579828 original size:9 final size:9
Alignment explanation
Indices: 2579814--2579840 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
2579804 ATAAACTAAA
2579814 AAAATATTT
1 AAAATATTT
2579823 AAAATATTT
1 AAAATATTT
2579832 AAAATATTT
1 AAAATATTT
2579841 TTATAAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
AAAATATTT
Found at i:2583892 original size:2 final size:2
Alignment explanation
Indices: 2583885--2583909 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2583875 TTGAATTTAT
2583885 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 T
2583910 CACAAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2585602 original size:11 final size:11
Alignment explanation
Indices: 2585582--2585678 Score: 50
Period size: 11 Copynumber: 9.4 Consensus size: 11
2585572 TAAAAATTAA
2585582 AAAAAGTATTTT
1 AAAAA-TATTTT
2585594 AAAAATATTTT
1 AAAAATATTTT
2585605 --AAA-A--TT
1 AAAAATATTTT
* * *
2585611 AAAAAAAATTA
1 AAAAATATTTT
2585622 AAAAAGTATTTT
1 AAAAA-TATTTT
*
2585634 AAAAA-AATTT
1 AAAAATATTTT
*
2585644 -AAAA-A-TTA
1 AAAAATATTTT
2585652 AAAAACTATTTT
1 AAAAA-TATTTT
*
2585664 AAAAGTATTTT
1 AAAAATATTTT
2585675 AAAA
1 AAAA
2585679 TTAAAAAAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 21
0.70 0.08 0.22
Matches are distributed among these distances:
6 2 0.03
8 6 0.09
9 13 0.19
10 4 0.06
11 23 0.34
12 19 0.28
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:2585625 original size:41 final size:40
Alignment explanation
Indices: 2585549--2585678 Score: 161
Period size: 40 Copynumber: 3.1 Consensus size: 40
2585539 ATAAATACTA
2585549 AAAAATTATTTTAAAAATTAAAATAAAAATTAAAAAAAGTATTTT
1 AAAAA-TATTTT-AAAATT-AAA-AAAAATT-AAAAAAGTATTTT
2585594 AAAAATATTTTAAAATTAAAAAAAATTAAAAAAGTATTTT
1 AAAAATATTTTAAAATTAAAAAAAATTAAAAAAGTATTTT
* * * **
2585634 AAAAAAATTTAAAAATTAAAAAACTATTTTAAAAGTATTTT
1 AAAAATATTTTAAAATTAAAAAA-AATTAAAAAAGTATTTT
2585675 AAAA
1 AAAA
2585679 TTAAAAAAAA
Statistics
Matches: 79, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
40 34 0.43
41 25 0.32
42 3 0.04
43 6 0.08
44 6 0.08
45 5 0.06
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (40 bp):
AAAAATATTTTAAAATTAAAAAAAATTAAAAAAGTATTTT
Found at i:2585650 original size:30 final size:30
Alignment explanation
Indices: 2585614--2585686 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
2585604 TAAAATTAAA
*
2585614 AAAAATTAAAAAAGTATTTTAAAAAAATTT
1 AAAAATTAAAAAACTATTTTAAAAAAATTT
**
2585644 AAAAATTAAAAAACTATTTTAAAAGTATTT
1 AAAAATTAAAAAACTATTTTAAAAAAATTT
*
2585674 TAAAATTAAAAAA
1 AAAAATTAAAAAA
2585687 AATAAAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (30 bp):
AAAAATTAAAAAACTATTTTAAAAAAATTT
Found at i:2585673 original size:70 final size:72
Alignment explanation
Indices: 2585547--2585696 Score: 223
Period size: 70 Copynumber: 2.1 Consensus size: 72
2585537 AAATAAATAC
* *
2585547 TAAAAAATTATTTTAAAAATTAAAATAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTA
1 TAAAAAAGTATTTTAAAAA-TAAAATAAAAATTAAAAAAACTATTTTAAAAATATTTTAAAATTA
2585612 AAAAAAAT
65 AAAAAAAT
** *
2585620 TAAAAAAGTATTTTAAAAA-AATTTAAAAATT-AAAAAACTATTTTAAAAGTATTTTAAAATTAA
1 TAAAAAAGTATTTTAAAAATAAAATAAAAATTAAAAAAACTATTTTAAAAATATTTTAAAATTAA
2585683 AAAAAAT
66 AAAAAAT
*
2585690 AAAAAAA
1 TAAAAAA
2585697 TAAAAATATT
Statistics
Matches: 71, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
70 43 0.61
71 10 0.14
73 18 0.25
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.33
Consensus pattern (72 bp):
TAAAAAAGTATTTTAAAAATAAAATAAAAATTAAAAAAACTATTTTAAAAATATTTTAAAATTAA
AAAAAAT
Found at i:2586119 original size:17 final size:18
Alignment explanation
Indices: 2586097--2586130 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2586087 TGGGTCCCTA
2586097 AATATAAAAGA-ATTAAT
1 AATATAAAAGACATTAAT
2586114 AATATAAAAGACATTAA
1 AATATAAAAGACATTAA
2586131 AAAAAACAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.26
Consensus pattern (18 bp):
AATATAAAAGACATTAAT
Found at i:2586635 original size:20 final size:20
Alignment explanation
Indices: 2586610--2586647 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2586600 TTTTTTAAAT
2586610 AAAAAAATGAGACAAAAAGC
1 AAAAAAATGAGACAAAAAGC
2586630 AAAAAAATGAGACAAAAA
1 AAAAAAATGAGACAAAAA
2586648 AAACAGAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.74, C:0.08, G:0.13, T:0.05
Consensus pattern (20 bp):
AAAAAAATGAGACAAAAAGC
Found at i:2587731 original size:100 final size:100
Alignment explanation
Indices: 2587546--2587905 Score: 453
Period size: 100 Copynumber: 3.6 Consensus size: 100
2587536 GCCATTGTGA
* *
2587546 CTTCAATCTATTCCACTACACCGCCAGGGAAGTAAGAT-TCGCCG-T-TGGCTTCAATCTTTTTA
1 CTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATCT-GCCGTTGTGGCTTCAATCTTTTTA
* * *
2587608 ATTGCAATGTCTAGGAAACAAGATCTACCATCGTAG
65 ATTGCAATGTCTGGGAAATAAGATCTACCGTCGTAG
* * * * **
2587644 CTTCAATCTGTTCCATTGCCCCACTAGGGAAGTAAGATCTGTTGTTGTGGCTTCAATCTTTTTAA
1 CTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATCTGCCGTTGTGGCTTCAATCTTTTTAA
*
2587709 TTGCAATGTCTGGGAAATAAGATCCACCGTCGTAG
66 TTGCAATGTCTGGGAAATAAGATCTACCGTCGTAG
* * *
2587744 CTTTAATTTGTTCCACTGCACCGCCAGGG-AGATAAGATCTGCCGTTGTGGCTTCAATCTTTTAA
1 CTTCAATCTGTTCCACTGCACCGCCAGGGAAG-TAAGATCTGCCGTTGTGGCTTCAATCTTTTTA
* * *
2587808 ATTGCAATGTCGGGGAAATAAGAT-TCGCCGTCGTGG
65 ATTGCAATGTCTGGGAAATAAGATCT-ACCGTCGTAG
* * *
2587844 CTTCAATCTGTTCCACTGCACTGCCAGGGAAGTAAGAT-TCACCGCTGTGGCTTCAATCTTTT
1 CTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATCT-GCCGTTGTGGCTTCAATCTTTT
2587906 CCACTGTAAT
Statistics
Matches: 225, Mismatches: 30, Indels: 12
0.84 0.11 0.04
Matches are distributed among these distances:
98 34 0.15
99 5 0.02
100 184 0.82
101 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (100 bp):
CTTCAATCTGTTCCACTGCACCGCCAGGGAAGTAAGATCTGCCGTTGTGGCTTCAATCTTTTTAA
TTGCAATGTCTGGGAAATAAGATCTACCGTCGTAG
Found at i:2587874 original size:50 final size:50
Alignment explanation
Indices: 2587522--2587911 Score: 229
Period size: 50 Copynumber: 7.8 Consensus size: 50
2587512 TGCAATGTCG
* * * * * * *
2587522 GGGAAACAAGATTCGCCATTGTGACTTCAATCTATTCCACTACACCGCCA
1 GGGAAATAAGATTCGCCGTCGTGGCTTCAATCTTTTCCACTGCACTGCCA
* ** * * *
2587572 GGGAAGTAAGATTCGCCGT--TGGCTTCAATCTTTTTAATTGCAATGTCTA
1 GGGAAATAAGATTCGCCGTCGTGGCTTCAATCTTTTCCACTGCACTG-CCA
* * * * * * * ** *
2587621 -GGAAACAAGA-TCTACCATCGTAGCTTCAATCTGTTCCATTGCCCCACTA
1 GGGAAATAAGATTC-GCCGTCGTGGCTTCAATCTTTTCCACTGCACTGCCA
* ** * ** * * * *
2587670 GGGAAGTAAGA-TCTGTTGTTGTGGCTTCAATCTTTTTAATTGCAATGTCT
1 GGGAAATAAGATTC-GCCGTCGTGGCTTCAATCTTTTCCACTGCACTGCCA
* * * * *
2587720 GGGAAATAAGATCCACCGTCGTAGCTTTAAT-TTGTTCCACTGCACCGCCA
1 GGGAAATAAGATTCGCCGTCGTGGCTTCAATCTT-TTCCACTGCACTGCCA
* * ** * * * *
2587770 GGGAGATAAGA-TCTGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCG
1 GGGAAATAAGATTC-GCCGTCGTGGCTTCAATCTTTTCCACTGCACTGCCA
*
2587820 GGGAAATAAGATTCGCCGTCGTGGCTTCAATCTGTTCCACTGCACTGCCA
1 GGGAAATAAGATTCGCCGTCGTGGCTTCAATCTTTTCCACTGCACTGCCA
* *
2587870 GGGAAGTAAGATTCACCG-CTGTGGCTTCAATCTTTTCCACTG
1 GGGAAATAAGATTCGCCGTC-GTGGCTTCAATCTTTTCCACTG
2587912 TAATACCAAA
Statistics
Matches: 247, Mismatches: 82, Indels: 22
0.70 0.23 0.06
Matches are distributed among these distances:
47 2 0.01
48 29 0.12
49 9 0.04
50 202 0.82
51 5 0.02
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (50 bp):
GGGAAATAAGATTCGCCGTCGTGGCTTCAATCTTTTCCACTGCACTGCCA
Found at i:2588164 original size:100 final size:100
Alignment explanation
Indices: 2588033--2588271 Score: 343
Period size: 100 Copynumber: 2.4 Consensus size: 100
2588023 CGCTGTGACG
* * * * *
2588033 CCAGGAAAATAAGATCCGCTATTGTGGCTTCAATCTTTTTAATTGCAATGTCTGGGAAATAAGAT
1 CCAGGGAAGTAAGATCCGCCATTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAATAAGAT
*
2588098 CCACCGTCATAGCTTCAATCTGTTCCACTGCACCG
66 CCACCGTCATAGCTTCAATCTGTTCCACTGCACCA
* *
2588133 CCAGGGAGGTAAGATCTGCCATTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAATAAGAT
1 CCAGGGAAGTAAGATCCGCCATTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAATAAGAT
* * * *
2588198 TCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTA
66 CCACCGTCATAGCTTCAATCTGTTCCACTGCACCA
* **
2588233 CCAGGGAAGTAAGATCCGTCGCTGTGGCTTCAATCTTTT
1 CCAGGGAAGTAAGATCCGCCATTGTGGCTTCAATCTTTT
2588272 CCACTGTAAT
Statistics
Matches: 122, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
100 122 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (100 bp):
CCAGGGAAGTAAGATCCGCCATTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAATAAGAT
CCACCGTCATAGCTTCAATCTGTTCCACTGCACCA
Found at i:2588274 original size:50 final size:49
Alignment explanation
Indices: 2588005--2588277 Score: 161
Period size: 50 Copynumber: 5.5 Consensus size: 49
2587995 GACTTGCCCT
* * * * * * **
2588005 TGTGGCTTCAATTTGCTCCGCTGTGAC-GCCAGGAAAATAAGATCCGCTAT
1 TGTGGCTTCAATCTGTTCCACTG-CACTGCCAGGGAAGTAAGATCCGC-CG
* ** * * * * * *
2588055 TGTGGCTTCAATCTTTTTAATTGCAATGTCTGGGAAATAAGATCCACCG
1 TGTGGCTTCAATCTGTTCCACTGCACTGCCAGGGAAGTAAGATCCGCCG
* * * * * *
2588104 TCATAGCTTCAATCTGTTCCACTGCACCGCCAGGGAGGTAAGATCTGCCAT
1 T-GTGGCTTCAATCTGTTCCACTGCACTGCCAGGGAAGTAAGATCCGCC-G
* ** * * * * * *
2588155 TGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAATAAGATTCGCCG
1 TGTGGCTTCAATCTGTTCCACTGCACTGCCAGGGAAGTAAGATCCGCCG
* * *
2588204 TCGTAGCTTCAATCTGTTCCACTGCACTACCAGGGAAGTAAGATCCGTCG
1 T-GTGGCTTCAATCTGTTCCACTGCACTGCCAGGGAAGTAAGATCCGCCG
*
2588254 CTGTGGCTTCAATCTTTTCCACTG
1 -TGTGGCTTCAATCTGTTCCACTG
2588278 TAATACCAAA
Statistics
Matches: 159, Mismatches: 59, Indels: 10
0.70 0.26 0.04
Matches are distributed among these distances:
49 3 0.02
50 154 0.97
51 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (49 bp):
TGTGGCTTCAATCTGTTCCACTGCACTGCCAGGGAAGTAAGATCCGCCG
Found at i:2588582 original size:88 final size:88
Alignment explanation
Indices: 2588460--2588686 Score: 346
Period size: 88 Copynumber: 2.6 Consensus size: 88
2588450 TCATGGCGAT
* * * *
2588460 AAGACTGATGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCAATATCTGCCATTTTCAACCC
1 AAGACTGGTATCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAATATCTGCCATTTTCAACCC
* *
2588525 ACTCCACTGCTGCCTAGGGAGAC
66 ACTCCACTACTGCCCAGGGAGAC
* * * * *
2588548 AAGGCTGGTATCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAAGCT
1 AAGACTGGTATCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAATATCTGCCATTTTCAACCC
2588613 ACTCCACTACTGCCCAGGGAGAC
66 ACTCCACTACTGCCCAGGGAGAC
*
2588636 AAGACTGGTATCTTCGGTCTGCTTCTCTGTCAGTACAGGAAGGCAATATCT
1 AAGACTGGTATCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAATATCT
2588687 ACTATCTTCA
Statistics
Matches: 125, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 125 1.00
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.27
Consensus pattern (88 bp):
AAGACTGGTATCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAATATCTGCCATTTTCAACCC
ACTCCACTACTGCCCAGGGAGAC
Found at i:2589891 original size:42 final size:42
Alignment explanation
Indices: 2589829--2589929 Score: 157
Period size: 42 Copynumber: 2.4 Consensus size: 42
2589819 CCCCATTCCA
** *
2589829 ATCAAAAGCTGAGCCACTCTGATCACCTCCAACCCTATTCTG
1 ATCAAAATTTGAGCCGCTCTGATCACCTCCAACCCTATTCTG
* *
2589871 ATCAAAATTTGAGCCGCTCTGATCACCTCTAGCCCTATTCTG
1 ATCAAAATTTGAGCCGCTCTGATCACCTCCAACCCTATTCTG
2589913 ATCAAAATTTGAGCCGC
1 ATCAAAATTTGAGCCGC
2589930 CCTTTTCGAG
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.28, C:0.32, G:0.14, T:0.27
Consensus pattern (42 bp):
ATCAAAATTTGAGCCGCTCTGATCACCTCCAACCCTATTCTG
Found at i:2590573 original size:16 final size:15
Alignment explanation
Indices: 2590542--2590591 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
2590532 TCGGTAGAAG
2590542 TTTTTTTTCTTTTTC
1 TTTTTTTTCTTTTTC
2590557 TTTTTGTTT-TTTGTTC
1 TTTTT-TTTCTTT-TTC
2590573 TTTTTTATTCTTTTT-
1 TTTTTT-TTCTTTTTC
2590588 TTTT
1 TTTT
2590592 GCATTGAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
15 13 0.42
16 15 0.48
17 3 0.10
ACGTcount: A:0.02, C:0.08, G:0.04, T:0.86
Consensus pattern (15 bp):
TTTTTTTTCTTTTTC
Found at i:2597918 original size:16 final size:16
Alignment explanation
Indices: 2597887--2597919 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
2597877 GTTTCAACCC
2597887 ATAATAGATGCGAAAA
1 ATAATAGATGCGAAAA
2597903 ATAA-AGATGCGAAAA
1 ATAATAGATGCGAAAA
2597918 AT
1 AT
2597920 CAAATAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.58, C:0.06, G:0.18, T:0.18
Consensus pattern (16 bp):
ATAATAGATGCGAAAA
Found at i:2604766 original size:18 final size:19
Alignment explanation
Indices: 2604743--2604779 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2604733 TTTACAAAAT
*
2604743 ATGTATAAA-TTATATAAA
1 ATGTATAAACATATATAAA
2604761 ATGTATAAACATATATAAA
1 ATGTATAAACATATATAAA
2604780 TTATATAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (19 bp):
ATGTATAAACATATATAAA
Found at i:2604967 original size:3 final size:3
Alignment explanation
Indices: 2604959--2605029 Score: 62
Period size: 3 Copynumber: 25.3 Consensus size: 3
2604949 TATATGTAAG
* * *
2604959 ATA ATA ATA AAA AT- ATA AT- ATA ACA ATA ATA GTA ATA ATA A-A A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
2605003 ATA ATA ATA ACA ATA TTA ATA A-A ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2605030 ACTAAAAAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
2 10 0.19
3 44 0.81
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:2604998 original size:31 final size:31
Alignment explanation
Indices: 2604959--2605030 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
2604949 TATATGTAAG
2604959 ATAATAATAAAAATATAAT-ATAACAATAATA
1 ATAATAATAAAAA-ATAATAATAACAATAATA
* *
2604990 GTAATAATAAAAAATAATAATAACAATATTA
1 ATAATAATAAAAAATAATAATAACAATAATA
2605021 ATAA-AATAAA
1 ATAATAATAAA
2605031 CTAAAAAAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 11 0.30
31 26 0.70
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (31 bp):
ATAATAATAAAAAATAATAATAACAATAATA
Found at i:2605008 original size:22 final size:23
Alignment explanation
Indices: 2604959--2605029 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 23
2604949 TATATGTAAG
* *
2604959 ATAATAATAAAAAT-ATAATATA
1 ATAATAATAACAATAATAATAAA
* **
2604981 ACAATAATAGTAATAATAA-AAA
1 ATAATAATAACAATAATAATAAA
*
2605003 ATAATAATAACAATATTAATAAA
1 ATAATAATAACAATAATAATAAA
2605026 ATAA
1 ATAA
2605030 ACTAAAAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
22 28 0.72
23 11 0.28
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (23 bp):
ATAATAATAACAATAATAATAAA
Found at i:2609300 original size:19 final size:19
Alignment explanation
Indices: 2609276--2609316 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2609266 TAGCAATCTA
2609276 AATAAAA-AAGAAAGCTACT
1 AATAAAACAAGAAAG-TACT
*
2609295 AATAAAACAAGAACGTACT
1 AATAAAACAAGAAAGTACT
2609314 AAT
1 AAT
2609317 TAGCAAGCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.61, C:0.12, G:0.10, T:0.17
Consensus pattern (19 bp):
AATAAAACAAGAAAGTACT
Found at i:2632040 original size:260 final size:259
Alignment explanation
Indices: 2631570--2632092 Score: 915
Period size: 260 Copynumber: 2.0 Consensus size: 259
2631560 TCAGAGCTAG
* *
2631570 TAACTCTAAATTTTCTTTCATTAGAAAGACTACGATCTAGTAAGAAGAGAGTTTAGAATCATGGA
1 TAACTCCAAATTTTCTTTCATTAGAAAGACTACAATCTAGTAAGAAGAGAGTTTAGAATCATGGA
* * * *
2631635 ATCCTCTAGATTATCTACCACAAAAGTACCTCTCTCATTACCTGAATCCCCATTTTGCTCTCACT
66 ATCCTCTAGATTATCCACCACAAAAGCACCTCTCTCATTACCTGAATCCACATTTCGCTCTCACT
2631700 CTGCTAGAAAGATTTCTTCTCTTTATGAAGAATATTTTACTGAAGAAGAGAAAGTACAAGCTACT
131 CTGCTAGAAAGA-TTCTTCTCTTTATGAAGAATATTTTACTGAAGAAGAGAAAGTACAAGCTACT
2631765 AATCTTCCTCTTGTAAATCCATATTCTACCTATCAAAAACCTTCATTCTCTCCCATAAAAAGTAT
195 AATCTTCCTCTTGTAAATCCATATTCTACCTATCAAAAACCTTCATTCTCTCCCATAAAAAGTAT
* *
2631830 TAACTCCAGATTTTCTTTCATTAGAAATACTACAATCTAGTAAGAAGAGAGTTTAGAATCATGGA
1 TAACTCCAAATTTTCTTTCATTAGAAAGACTACAATCTAGTAAGAAGAGAGTTTAGAATCATGGA
*
2631895 ATCCTCTAGATTATCCACCACAAAAGCACCTCTCTCATTACCTGAATCCACGTTTCGCTCTCACT
66 ATCCTCTAGATTATCCACCACAAAAGCACCTCTCTCATTACCTGAATCCACATTTCGCTCTCACT
2631960 CTGCTAGAAAGA-T-TTCTCTTTATGAAGTAGAATATTTTACTGAAGAAGAGAAAGTACAAGCTA
131 CTGCTAGAAAGATTCTTCTCTTTATG-A--AGAATATTTTACTGAAGAAGAGAAAGTACAAGCTA
2632023 CTAATCTTCCTCTTGTAAATCCATATTCTACCTATCAAAAACCTTCATTCTCTCCCATAAAAAGT
193 CTAATCTTCCTCTTGTAAATCCATATTCTACCTATCAAAAACCTTCATTCTCTCCCATAAAAAGT
2632088 AT
258 AT
2632090 TAA
1 TAA
2632093 GTCTCTTATT
Statistics
Matches: 251, Mismatches: 9, Indels: 6
0.94 0.03 0.02
Matches are distributed among these distances:
257 11 0.04
258 2 0.01
260 238 0.95
ACGTcount: A:0.34, C:0.22, G:0.11, T:0.33
Consensus pattern (259 bp):
TAACTCCAAATTTTCTTTCATTAGAAAGACTACAATCTAGTAAGAAGAGAGTTTAGAATCATGGA
ATCCTCTAGATTATCCACCACAAAAGCACCTCTCTCATTACCTGAATCCACATTTCGCTCTCACT
CTGCTAGAAAGATTCTTCTCTTTATGAAGAATATTTTACTGAAGAAGAGAAAGTACAAGCTACTA
ATCTTCCTCTTGTAAATCCATATTCTACCTATCAAAAACCTTCATTCTCTCCCATAAAAAGTAT
Found at i:2636768 original size:535 final size:535
Alignment explanation
Indices: 2635759--2636794 Score: 1892
Period size: 535 Copynumber: 1.9 Consensus size: 535
2635749 TTGATGGTTC
2635759 TCCGGCTTCAGTCATCTCTTCATCTGATGGTTCTTCAACTTTCACACCAGGTGTGGCCATTACTT
1 TCCGGCTTCAGTCATCTCTTCATCTGATGGTTCTTCAACTTTCACACCAGGTGTGGCCATTACTT
2635824 CTGGCAAATCCTCAATTCCTTCTTCTGAGAAATTATTGGTTTCTCCAATTGATTCTGAATCATAA
66 CTGGCAAATCCTCAATTCCTTCTTCTGAGAAATTATTGGTTTCTCCAATTGATTCTGAATCATAA
* *
2635889 GAATTTGCTGATCTTTCTGATTTCCCTGAAAATGATACTGAATCATCTTATTCTGGGATTTGTTC
131 GAATTTGCTGATCTTTCTGATTCCCCTGAAAAAGATACTGAATCATCTTATTCTGGGATTTGTTC
*
2635954 CAAATCTGGAATTGGGGTTGTTTCTGATTCATGTCGTTCAGCTACAGATATCTTTGGTAGTATCT
196 CAAATCTGGAACTGGGGTTGTTTCTGATTCATGTCGTTCAGCTACAGATATCTTTGGTAGTATCT
*
2636019 TATGACTGTAATCCTTTAAAAACCTTGTTAAGGGATTAGAAGGATTTTTATAATTTTGCATCATA
261 TATGACTGTAATCCTTTAAAAACCCTGTTAAGGGATTAGAAGGATTTTTATAATTTTGCATCATA
2636084 AGAGACTTTAACATCAGTTTTGGTGGTAGAGATGTTGGTGGTGAAGAGAATTAGCTTTCTTCATC
326 AGAGACTTTAACATCAGTTTTGGTGGTAGAGATGTTGGTGGTGAAGAGAATTAGCTTTCTTCATC
* *
2636149 TTCTTGTTTCTCCACTGGTCTTTTGCCTCTAACCTTTTCTCTTTTTCTTTTTTCTTCTGCAGCTT
391 TTCCTGTTTCTCCACTGGTCTTTTGCCTCTAACCTTTTCTCTTTTTCTTTTTCCTTCTGCAGCTT
2636214 TTCTTTTTTCTTCCTCCTTTTGTGCCTTGATTTGTTGACACAATTCTTAGTAAATAATATGTCCT
456 TTCTTTTTTCTTCCTCCTTTTGTGCCTTGATTTGTTGACACAATTCTTAGTAAATAATATGTCCT
2636279 TTCATAGTAAATTGA
521 TTCATAGTAAATTGA
2636294 TCCGGCTTCAGTCATCTCTTCATCTGATGGTTCTTCAACTTTCACACCAGGTGTGGCCATTACTT
1 TCCGGCTTCAGTCATCTCTTCATCTGATGGTTCTTCAACTTTCACACCAGGTGTGGCCATTACTT
*
2636359 CTGGCAAATCCTCAATTCCTTCTTCTGAGGAATTATTGGTTTCTCCAATTGATTCTGAATCATAA
66 CTGGCAAATCCTCAATTCCTTCTTCTGAGAAATTATTGGTTTCTCCAATTGATTCTGAATCATAA
* * *
2636424 GGATTTGCTGATCTTTCTGATTCCCCTGAAAAAGATACTGAATCATCTTCTTTTGGGATTTGTTC
131 GAATTTGCTGATCTTTCTGATTCCCCTGAAAAAGATACTGAATCATCTTATTCTGGGATTTGTTC
* *
2636489 CCAATCTGGAACTGGGGTTGTTTCTGATTTATGTCGTTCAGCTACAGATATCTTTGGTAGTATCT
196 CAAATCTGGAACTGGGGTTGTTTCTGATTCATGTCGTTCAGCTACAGATATCTTTGGTAGTATCT
* * *
2636554 TATGACTGTAATCCTTTAAAAGCCCTGTTAAGGGATTAGAATGATTTTTATCATTTTGCATCATA
261 TATGACTGTAATCCTTTAAAAACCCTGTTAAGGGATTAGAAGGATTTTTATAATTTTGCATCATA
* * *
2636619 AGAGACTTTGACATCAGTTTTGGTGGTGGAGATGTTGGTGGTGAAGAGAATTGGCTTTCTTCATC
326 AGAGACTTTAACATCAGTTTTGGTGGTAGAGATGTTGGTGGTGAAGAGAATTAGCTTTCTTCATC
* *
2636684 TTCCTGTTTCTCCACTGGTCTTTTGCCTCTAGCCTTTTCTCTTTTTCTTTTTCCTTCTGCAGTTT
391 TTCCTGTTTCTCCACTGGTCTTTTGCCTCTAACCTTTTCTCTTTTTCTTTTTCCTTCTGCAGCTT
2636749 TTCTTTTTTCTTCCTCCTTTTGTGCCTTGATTTGTTGACACAATTC
456 TTCTTTTTTCTTCCTCCTTTTGTGCCTTGATTTGTTGACACAATTC
2636795 ATAGACTGTG
Statistics
Matches: 481, Mismatches: 20, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
535 481 1.00
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.42
Consensus pattern (535 bp):
TCCGGCTTCAGTCATCTCTTCATCTGATGGTTCTTCAACTTTCACACCAGGTGTGGCCATTACTT
CTGGCAAATCCTCAATTCCTTCTTCTGAGAAATTATTGGTTTCTCCAATTGATTCTGAATCATAA
GAATTTGCTGATCTTTCTGATTCCCCTGAAAAAGATACTGAATCATCTTATTCTGGGATTTGTTC
CAAATCTGGAACTGGGGTTGTTTCTGATTCATGTCGTTCAGCTACAGATATCTTTGGTAGTATCT
TATGACTGTAATCCTTTAAAAACCCTGTTAAGGGATTAGAAGGATTTTTATAATTTTGCATCATA
AGAGACTTTAACATCAGTTTTGGTGGTAGAGATGTTGGTGGTGAAGAGAATTAGCTTTCTTCATC
TTCCTGTTTCTCCACTGGTCTTTTGCCTCTAACCTTTTCTCTTTTTCTTTTTCCTTCTGCAGCTT
TTCTTTTTTCTTCCTCCTTTTGTGCCTTGATTTGTTGACACAATTCTTAGTAAATAATATGTCCT
TTCATAGTAAATTGA
Found at i:2637339 original size:94 final size:94
Alignment explanation
Indices: 2637178--2637365 Score: 358
Period size: 94 Copynumber: 2.0 Consensus size: 94
2637168 ATTGCAGCAT
*
2637178 TCTGGGCTACAGCATTTTTTGACTGCCAGTTCAGGGTGGCTTCTACTGCTGCTATCTTGATTTGT
1 TCTGGGCTACAGCATTTTCTGACTGCCAGTTCAGGGTGGCTTCTACTGCTGCTATCTTGATTTGT
2637243 TTTCCTTCTGCATCTGTCTGAAGTTTTGA
66 TTTCCTTCTGCATCTGTCTGAAGTTTTGA
*
2637272 TCTGGGCTACAGCATTTTCTGACTGCCAGTTCAGGGTGGCTTCTGCTGCTGCTATCTTGATTTGT
1 TCTGGGCTACAGCATTTTCTGACTGCCAGTTCAGGGTGGCTTCTACTGCTGCTATCTTGATTTGT
2637337 TTTCCTTCTGCATCTGTCTGAAGTTTTGA
66 TTTCCTTCTGCATCTGTCTGAAGTTTTGA
2637366 AGAGATTTTT
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 92 1.00
ACGTcount: A:0.13, C:0.22, G:0.23, T:0.42
Consensus pattern (94 bp):
TCTGGGCTACAGCATTTTCTGACTGCCAGTTCAGGGTGGCTTCTACTGCTGCTATCTTGATTTGT
TTTCCTTCTGCATCTGTCTGAAGTTTTGA
Found at i:2642511 original size:500 final size:498
Alignment explanation
Indices: 2641496--2642524 Score: 1754
Period size: 497 Copynumber: 2.1 Consensus size: 498
2641486 TAATCCTACA
* *
2641496 ATATTGATGCCCTAAATGAAGGTTAGAACCCCCCTTCACATCATAATTATTTCTATCCTTGGAAA
1 ATATTGTTGCCCTAAATGAAGGTTAG-AGCCCCCTTCACATCATAATTATTTCTATCCTTGGAAA
*
2641561 GTGACTGATTATGCATTTTCCAATGCTGCTTGTCATTATATTTGGTTTGCTCTAAATGAAGGTTA
65 GTGACTGATTATGCATTTGCCAATGCTGCTTGTCATTATATTTGGTTTGCTCTAAATGAAGGTTA
* * * ** * *
2641626 GTGCTATCATAATTATTCCTACCCTTGTAAATTGACTTACTTTTCATTTGCTTGTACTGGTTGTC
130 GTGCCATCATAATTATTCCTACCCTTGTAAATTCACTGACTTTTCATTTGCCAGTAATGCTTGTC
* * *
2641691 ATTGCATTTTGTTTGCTCTTGTTGTCACTAAGAAGCTGATAATGAGCCTTGAACTTCTTGTATAG
195 ATTGCATTTTGTTTGCTCTTGTTGTCACTAAGAAGCTGATAATGAGCCTTGAACTACCTGTATAA
*
2641756 AACTTGAGTAATGCTAAGGTACAAAGAAGTCGAGTCATGTGTAAATGTCTTCCTTTTTCCAAGAT
260 AACTTGAGTAATGCTAAGGTACAAAGAAGTCAAGTCATGTGTAAATGTCTTCCTTTTTCCAAGAT
*
2641821 GAATGAGTGGACTCAGTTTTGTTAGGACTGTGTGTCGTGCTCTGCTTGTTGTTTTGAATGGGTAC
325 GAATGAGTGGACTCAGTTTTGTTAGGACTATGTGTCGTGCTCTGCTTGTTGTTTTGAATGGGTAC
* * *
2641886 GAATCTCCTAGCACCTTTAGGGAACTAGAATTGAAGTTTGTTAGCTTTGGGCAGAGAATTTTAAC
390 GAAGCTCCTAGCACCTTTAGGGAACTAGAACTGAAGTTCGTTAGCTTTGGGCAGAGAATTTTAAC
2641951 CAAAGGCTTGCTTTACCCCAAATAGTTGCTTCTATTTTGATGAT
455 CAAAGGCTTGCTTTACCCCAAATAGTTGCTTCTATTTTGATGAT
**
2641995 ATATTGTTGCCCTAAATGAAGGTTAGAGCCCCCTTCACATGGTAATTATTT-TATCCTTGGAAAG
1 ATATTGTTGCCCTAAATGAAGGTTAGAGCCCCCTTCACATCATAATTATTTCTATCCTTGGAAAG
*
2642059 TGACTGATTATGCATTTGCCAATGTTGCTTGTCATTATATTTGGTTTGCTCTAAATGAAGGTTAG
66 TGACTGATTATGCATTTGCCAATGCTGCTTGTCATTATATTTGGTTTGCTCTAAATGAAGGTTAG
* *
2642124 TGCCATCATAATTATTCCTATCCTTGTAAATTCACTGATTTTTCATTTGCCAGTAATGCTTGTCA
131 TGCCATCATAATTATTCCTACCCTTGTAAATTCACTGACTTTTCATTTGCCAGTAATGCTTGTCA
2642189 TTGCATTTTGTTTGCTCTTGTTGTCACTAAGAAGCTGATAATGAGCCTTGAACTACCTGTATAAA
196 TTGCATTTTGTTTGCTCTTGTTGTCACTAAGAAGCTGATAATGAGCCTTGAACTACCTGTATAAA
*
2642254 ACTTGAGTAATGCTAAGGTACAAAGAAGTCAAGTCGTTGTGTGAAAATGTCTTCCTTTTTCCAAG
261 ACTTGAGTAATGCTAAGGTACAAAGAAGTCAAGTC-ATGTGT--AAATGTCTTCCTTTTTCCAAG
* *
2642319 ATGAATGAGTGGACTCAGTTTTGTTAGGACTATGTGTCGTGCTTTTCTTGTTGTTTTGAATGGGT
323 ATGAATGAGTGGACTCAGTTTTGTTAGGACTATGTGTCGTGCTCTGCTTGTTGTTTTGAATGGGT
* *
2642384 ATGAGGCTCCTAGCACCTTTAGGGAACTAGAACTGAAGTTCGTTAGCTTTGGGCAGAGAATTTTA
388 ACGAAGCTCCTAGCACCTTTAGGGAACTAGAACTGAAGTTCGTTAGCTTTGGGCAGAGAATTTTA
*
2642449 ACCAAAGGCTTGTTTTACCCCAAATAGTTGCTTCTATTTTGATGAT
453 ACCAAAGGCTTGCTTTACCCCAAATAGTTGCTTCTATTTTGATGAT
2642495 ATATTGTTGCCCTAAATGAAGGTTAGAGCC
1 ATATTGTTGCCCTAAATGAAGGTTAGAGCC
2642525 TCCTGTATAA
Statistics
Matches: 498, Mismatches: 29, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
497 228 0.46
498 27 0.05
499 25 0.05
500 218 0.44
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (498 bp):
ATATTGTTGCCCTAAATGAAGGTTAGAGCCCCCTTCACATCATAATTATTTCTATCCTTGGAAAG
TGACTGATTATGCATTTGCCAATGCTGCTTGTCATTATATTTGGTTTGCTCTAAATGAAGGTTAG
TGCCATCATAATTATTCCTACCCTTGTAAATTCACTGACTTTTCATTTGCCAGTAATGCTTGTCA
TTGCATTTTGTTTGCTCTTGTTGTCACTAAGAAGCTGATAATGAGCCTTGAACTACCTGTATAAA
ACTTGAGTAATGCTAAGGTACAAAGAAGTCAAGTCATGTGTAAATGTCTTCCTTTTTCCAAGATG
AATGAGTGGACTCAGTTTTGTTAGGACTATGTGTCGTGCTCTGCTTGTTGTTTTGAATGGGTACG
AAGCTCCTAGCACCTTTAGGGAACTAGAACTGAAGTTCGTTAGCTTTGGGCAGAGAATTTTAACC
AAAGGCTTGCTTTACCCCAAATAGTTGCTTCTATTTTGATGAT
Found at i:2647006 original size:14 final size:14
Alignment explanation
Indices: 2646987--2647013 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2646977 AAATTATAAT
2646987 ATCTAGATGTCTTA
1 ATCTAGATGTCTTA
2647001 ATCTAGATGTCTT
1 ATCTAGATGTCTT
2647014 CATCAAGCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (14 bp):
ATCTAGATGTCTTA
Found at i:2651818 original size:18 final size:18
Alignment explanation
Indices: 2651795--2651831 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2651785 AAATGTTTTT
*
2651795 AAATTTTAATATAATTAA
1 AAATTTAAATATAATTAA
*
2651813 AAATTTAAATTTAATTAA
1 AAATTTAAATATAATTAA
2651831 A
1 A
2651832 TATATAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATTTAAATATAATTAA
Found at i:2651839 original size:18 final size:18
Alignment explanation
Indices: 2651806--2651841 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2651796 AATTTTAATA
*
2651806 TAATTAAAAATTTAAATT
1 TAATTAAAAATATAAATT
*
2651824 TAATTAAATATATAAATT
1 TAATTAAAAATATAAATT
2651842 ATTTAAAGTT
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAATTAAAAATATAAATT
Found at i:2655673 original size:19 final size:18
Alignment explanation
Indices: 2655638--2655673 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2655628 TGTTTATATA
*
2655638 TTTTTTTTCTTTAAATAC
1 TTTTTTTTCTTAAAATAC
2655656 TTTTTTTTCTTAATAATA
1 TTTTTTTTCTTAA-AATA
2655674 AAAAGTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTTTTTCTTAAAATAC
Found at i:2655861 original size:19 final size:20
Alignment explanation
Indices: 2655823--2655861 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
2655813 AATTTATATA
*
2655823 TTTAATTTAAATTTAAATTT
1 TTTAATTTAAATTGAAATTT
*
2655843 TTTAA-TTATATTGAAATTT
1 TTTAATTTAAATTGAAATTT
2655862 AAAAATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
TTTAATTTAAATTGAAATTT
Found at i:2658933 original size:162 final size:163
Alignment explanation
Indices: 2658744--2659068 Score: 643
Period size: 162 Copynumber: 2.0 Consensus size: 163
2658734 TATATTCGGG
2658744 CCGGGCCAAAAAAGTGGTGCCCGAGGCCCGGCCCGTTTTCTAAACGGGCCTAGTTTTTTTGGCCA
1 CCGGGCCAAAAAAGTGGTGCCCGAGGCCCGGCCCGTTTTCTAAACGGGCCTAGTTTTTTTGGCCA
2658809 AACCTATATTTTGGGCCTATATTTTTACCCGAACACTCCCATATTTCGGGCGAGCCGTCGGGCCG
66 AACCTATATTTTGGGCCTATATTTTTACCCGAACACTCCCATATTTCGGGCGAGCCGTCGGGCCG
2658874 AGCCAGGCCGCTCGACCCATGGGCACCTCTACT
131 AGCCAGGCCGCTCGACCCATGGGCACCTCTACT
2658907 CCGGGCC-AAAAAGTGGTGCCCGAGGCCCGGCCCGTTTTCTAAACGGGCCTAGTTTTTTTGGCCA
1 CCGGGCCAAAAAAGTGGTGCCCGAGGCCCGGCCCGTTTTCTAAACGGGCCTAGTTTTTTTGGCCA
2658971 AACCTATATTTTGGGCCTATATTTTTACCCGAACACTCCCATATTTCGGGCGAGCCGTCGGGCCG
66 AACCTATATTTTGGGCCTATATTTTTACCCGAACACTCCCATATTTCGGGCGAGCCGTCGGGCCG
2659036 AGCCAGGCCGCTCGACCCATGGGCACCTCTACT
131 AGCCAGGCCGCTCGACCCATGGGCACCTCTACT
2659069 TCTGTTCCTT
Statistics
Matches: 162, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
162 155 0.96
163 7 0.04
ACGTcount: A:0.19, C:0.32, G:0.25, T:0.24
Consensus pattern (163 bp):
CCGGGCCAAAAAAGTGGTGCCCGAGGCCCGGCCCGTTTTCTAAACGGGCCTAGTTTTTTTGGCCA
AACCTATATTTTGGGCCTATATTTTTACCCGAACACTCCCATATTTCGGGCGAGCCGTCGGGCCG
AGCCAGGCCGCTCGACCCATGGGCACCTCTACT
Found at i:2659371 original size:14 final size:14
Alignment explanation
Indices: 2659352--2659380 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2659342 TCTTGTCATG
2659352 TTATTGATGTAATT
1 TTATTGATGTAATT
2659366 TTATTGATGTAATT
1 TTATTGATGTAATT
2659380 T
1 T
2659381 CTGTTTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.59
Consensus pattern (14 bp):
TTATTGATGTAATT
Found at i:2662053 original size:17 final size:20
Alignment explanation
Indices: 2662019--2662055 Score: 53
Period size: 17 Copynumber: 2.0 Consensus size: 20
2662009 TTTACTTTTA
2662019 AAAAATATATAATATGAAAT
1 AAAAATATATAATATGAAAT
2662039 AAAAA-ATA-AAT-TGAAAT
1 AAAAATATATAATATGAAAT
2662056 TGAAAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.35
18 3 0.18
19 3 0.18
20 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (20 bp):
AAAAATATATAATATGAAAT
Found at i:2675134 original size:25 final size:25
Alignment explanation
Indices: 2675106--2675153 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
2675096 AAAAGGAATC
2675106 TTTATGTTTTT-TTAATAATTATTTT
1 TTTA-GTTTTTCTTAATAATTATTTT
*
2675131 TTTAGTTTTTCTTAATTATTATT
1 TTTAGTTTTTCTTAATAATTATT
2675154 ATTCTTTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.71
Consensus pattern (25 bp):
TTTAGTTTTTCTTAATAATTATTTT
Found at i:2678388 original size:30 final size:30
Alignment explanation
Indices: 2678354--2678418 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
2678344 TGTAATGAAC
* ** *
2678354 TTAAAAT-TAACAAATAATTGGATCTGAATT
1 TTAAAATCTAAAAAATAAAGGGA-CTAAATT
2678384 TTAAAATCTAAAAAATAAAGGGACTAAATT
1 TTAAAATCTAAAAAATAAAGGGACTAAATT
2678414 TTAAA
1 TTAAA
2678419 TTTATAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 18 0.60
31 12 0.40
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.32
Consensus pattern (30 bp):
TTAAAATCTAAAAAATAAAGGGACTAAATT
Found at i:2679350 original size:4 final size:4
Alignment explanation
Indices: 2679341--2679373 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
2679331 ATGTTATGTA
2679341 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
2679374 GAGAAAAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:2682793 original size:2 final size:2
Alignment explanation
Indices: 2682786--2682812 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2682776 AGATTCATGC
2682786 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 A
2682813 AACAAACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2682883 original size:4 final size:4
Alignment explanation
Indices: 2682876--2682905 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
2682866 TGCATGCATG
2682876 CATA CATA CATA CATA CATA CATA CATA CA
1 CATA CATA CATA CATA CATA CATA CATA CA
2682906 AACAAATCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (4 bp):
CATA
Found at i:2682959 original size:16 final size:17
Alignment explanation
Indices: 2682938--2682973 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2682928 TTATATAAAT
*
2682938 TTTGACAT-ATTATTTA
1 TTTGACATAATTATATA
2682954 TTTGACATAATTATATA
1 TTTGACATAATTATATA
2682971 TTT
1 TTT
2682974 TTATTATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.56
Consensus pattern (17 bp):
TTTGACATAATTATATA
Found at i:2683446 original size:31 final size:31
Alignment explanation
Indices: 2683392--2683452 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
2683382 AAATAATCAC
* *
2683392 TGAACTATTCGAAAGTTTTCATTTATGTCAT
1 TGAACTATTCGAAAGTTTCCATTTAAGTCAT
*
2683423 TGAACTTTTC-AAATGTTTCCATTTAAGTCA
1 TGAACTATTCGAAA-GTTTCCATTTAAGTCA
2683453 CTGATTGTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 3 0.12
31 23 0.88
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.44
Consensus pattern (31 bp):
TGAACTATTCGAAAGTTTCCATTTAAGTCAT
Found at i:2685877 original size:24 final size:22
Alignment explanation
Indices: 2685827--2685877 Score: 52
Period size: 24 Copynumber: 2.2 Consensus size: 22
2685817 GCAGAAAACT
2685827 AATA-CTAGAATTTAACCTAAA
1 AATATCTAGAATTTAACCTAAA
2685848 ATATATCTA-AATTTGAACCCTAATA
1 A-ATATCTAGAATTT-AA-CCTAA-A
2685873 AATAT
1 AATAT
2685878 GAAAATAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
21 1 0.04
22 8 0.32
23 5 0.20
24 9 0.36
25 2 0.08
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.33
Consensus pattern (22 bp):
AATATCTAGAATTTAACCTAAA
Found at i:2693666 original size:40 final size:40
Alignment explanation
Indices: 2693621--2693697 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
2693611 TTTAAAATTT
*
2693621 ATAATATTT-TTTCTTGTAGGTAACTGTCGATAAGATTTTC
1 ATAATATTTCTTT-TTGTAGGTAACTATCGATAAGATTTTC
*
2693661 ATAATATTTCTTTTTGTAGGTAATTATCGATAAGATT
1 ATAATATTTCTTTTTGTAGGTAACTATCGATAAGATT
2693698 AAAAATTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 31 0.91
41 3 0.09
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.48
Consensus pattern (40 bp):
ATAATATTTCTTTTTGTAGGTAACTATCGATAAGATTTTC
Found at i:2695556 original size:21 final size:20
Alignment explanation
Indices: 2695510--2695559 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
2695500 TCAGTTTTTC
*
2695510 TATAATTGACATTTTAACAA
1 TATAATTGTCATTTTAACAA
* **
2695530 TTTAATTGTCATATTTATTAA
1 TATAATTGTCAT-TTTAACAA
2695551 TATAATTGT
1 TATAATTGT
2695560 ATTCGTTATG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (20 bp):
TATAATTGTCATTTTAACAA
Found at i:2700069 original size:190 final size:191
Alignment explanation
Indices: 2699737--2700118 Score: 757
Period size: 190 Copynumber: 2.0 Consensus size: 191
2699727 CATCAAATAA
2699737 TTATTTTTAAAATTTTATTATAATAATATTTTATCCGGTCAATATAACAATCGACAAACCAAAAT
1 TTATTTTTAAAATTTTATTATAATAATATTTTATCCGGTCAATATAACAATCGACAAACCAAAAT
2699802 GACGAAGAAAGTTGATGTATTCCTTTCCTTTAACAAATTTCCTATATCCAATTACTACAGTTTTT
66 GACGAAGAAAGTTGATGTATTCCTTTCCTTTAACAAATTTCCTATATCCAATTACTACAGTTTTT
2699867 GCATTTTTGAAGGGCCACTTTCGTCATTTAGTGAAAAAATATTATAAAGGTAAAAGGATAT
131 GCATTTTTGAAGGGCCACTTTCGTCATTTAGTGAAAAAATATTATAAAGGTAAAAGGATAT
2699928 TTATTTTT-AAATTTTATTATAATAATATTTTATCCGGTCAATATAACAATCGACAAACCAAAAT
1 TTATTTTTAAAATTTTATTATAATAATATTTTATCCGGTCAATATAACAATCGACAAACCAAAAT
2699992 GACGAAGAAAGTTGATGTATTCCTTTCCTTTAACAAATTTCCTATATCCAATTACTACAGTTTTT
66 GACGAAGAAAGTTGATGTATTCCTTTCCTTTAACAAATTTCCTATATCCAATTACTACAGTTTTT
2700057 GCATTTTTGAAGGGCCACTTTCGTCATTTAGTGAAAAAATATTATAAAGGTAAAAGGATAT
131 GCATTTTTGAAGGGCCACTTTCGTCATTTAGTGAAAAAATATTATAAAGGTAAAAGGATAT
2700118 T
1 T
2700119 AAAAAATGAA
Statistics
Matches: 191, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
190 183 0.96
191 8 0.04
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.38
Consensus pattern (191 bp):
TTATTTTTAAAATTTTATTATAATAATATTTTATCCGGTCAATATAACAATCGACAAACCAAAAT
GACGAAGAAAGTTGATGTATTCCTTTCCTTTAACAAATTTCCTATATCCAATTACTACAGTTTTT
GCATTTTTGAAGGGCCACTTTCGTCATTTAGTGAAAAAATATTATAAAGGTAAAAGGATAT
Found at i:2704032 original size:30 final size:31
Alignment explanation
Indices: 2703998--2704066 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
2703988 TTACCCAAGA
* **
2703998 GTAAATACT-AAAAAATTGAGGGGTTAA-AGT
1 GTAAATA-TGAAAAAATTGAAGGACTAATAGT
*
2704028 GTAAATATGAAAAAGTTGAAGGACTAATAGT
1 GTAAATATGAAAAAATTGAAGGACTAATAGT
2704059 GTAAATAT
1 GTAAATAT
2704067 TTTAAGGGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 1 0.03
30 21 0.64
31 11 0.33
ACGTcount: A:0.48, C:0.03, G:0.22, T:0.28
Consensus pattern (31 bp):
GTAAATATGAAAAAATTGAAGGACTAATAGT
Found at i:2705776 original size:34 final size:34
Alignment explanation
Indices: 2705718--2705783 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
2705708 CAAACACCAG
* *
2705718 AAAATATTTTCCAGTAAATTATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTAC-GAAAAGT
*
2705753 AAAACATTTTTCAG-AAATCATTTTACGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACGAAAA
2705784 ACATTTTACT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 5 0.18
34 11 0.39
35 12 0.43
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.35
Consensus pattern (34 bp):
AAAACATTTTCCAGTAAATCATTTTACGAAAAGT
Found at i:2707619 original size:14 final size:14
Alignment explanation
Indices: 2707600--2707630 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2707590 ATCCAAACAA
2707600 TAACAACAAAATAG
1 TAACAACAAAATAG
*
2707614 TAACAACATAATAG
1 TAACAACAAAATAG
2707628 TAA
1 TAA
2707631 AATGACAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.13, G:0.06, T:0.19
Consensus pattern (14 bp):
TAACAACAAAATAG
Found at i:2709400 original size:30 final size:30
Alignment explanation
Indices: 2709364--2709425 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
2709354 TAATAAGTGA
2709364 TTACCAATTTAGGGTCTTATTAAATGGAAC
1 TTACCAATTTAGGGTCTTATTAAATGGAAC
2709394 TTACCAATTTAGGGTCTTATTAAATGGAAC
1 TTACCAATTTAGGGTCTTATTAAATGGAAC
2709424 TT
1 TT
2709426 GATCTTGTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (30 bp):
TTACCAATTTAGGGTCTTATTAAATGGAAC
Found at i:2723034 original size:9 final size:9
Alignment explanation
Indices: 2723017--2723053 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
2723007 TGAGTTTTCG
2723017 AATTCGAAT
1 AATTCGAAT
*
2723026 AACTCGAAT
1 AATTCGAAT
2723035 AATTCGAAT
1 AATTCGAAT
2723044 AATTCGAAT
1 AATTCGAAT
2723053 A
1 A
2723054 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:2723273 original size:30 final size:31
Alignment explanation
Indices: 2723237--2723296 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
2723227 AAACCTTTTA
*
2723237 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
2723267 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
2723297 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:2726196 original size:31 final size:31
Alignment explanation
Indices: 2726140--2726200 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
2726130 GTTAATAGTT
*
2726140 AGACTTAAATTTTGAAATTTAAAAAGTACAG
1 AGACTTAAATTTTGAAATTAAAAAAGTACAG
2726171 AGAC-TAAATTCTT-AAATTAAGAAAAGTACA
1 AGACTTAAATT-TTGAAATTAA-AAAAGTACA
2726201 TAGATTTATG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 12 0.44
31 15 0.56
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (31 bp):
AGACTTAAATTTTGAAATTAAAAAAGTACAG
Found at i:2728207 original size:21 final size:23
Alignment explanation
Indices: 2728162--2728211 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 23
2728152 AAAAAAGTTG
*
2728162 TTTTTATTTTTAAATTTTAATTA
1 TTTTTATTTTTAAATATTAATTA
*
2728185 TTTTTA-TTTTAAA-ATTGATTA
1 TTTTTATTTTTAAATATTAATTA
2728206 TTTTTA
1 TTTTTA
2728212 ACTCACATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 12 0.48
22 7 0.28
23 6 0.24
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (23 bp):
TTTTTATTTTTAAATATTAATTA
Found at i:2728580 original size:27 final size:26
Alignment explanation
Indices: 2728548--2728656 Score: 101
Period size: 27 Copynumber: 3.7 Consensus size: 26
2728538 AATCTAAGTT
2728548 TTAAATTTATTAATTAATTTCAATAGC
1 TTAAATTTA-TAATTAATTTCAATAGC
*
2728575 TTAAATTTATAATTAATTTATATGCAATCTAAGTT
1 TTAAATTTATAATTAA--T-T-T-CAA--T-AG-C
2728610 TTAAATTTATTAATTAATTTCAATAGC
1 TTAAATTTA-TAATTAATTTCAATAGC
2728637 TTAAATTTATAATTATATTT
1 TTAAATTTATAATTA-ATTT
2728657 TAATTTAAAA
Statistics
Matches: 69, Mismatches: 2, Indels: 22
0.74 0.02 0.24
Matches are distributed among these distances:
26 13 0.19
27 22 0.32
28 3 0.04
29 2 0.03
30 1 0.01
31 6 0.09
32 1 0.01
33 2 0.03
34 3 0.04
35 9 0.13
36 7 0.10
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.50
Consensus pattern (26 bp):
TTAAATTTATAATTAATTTCAATAGC
Found at i:2728617 original size:62 final size:63
Alignment explanation
Indices: 2728520--2728656 Score: 251
Period size: 62 Copynumber: 2.2 Consensus size: 63
2728510 AATACATTCA
2728520 TATAATT-ATTTATATGCAAATCTAAGTTTTAAATTTATTAATTAATTTCAATAGCTTAAATT
1 TATAATTAATTTATATGCAAATCTAAGTTTTAAATTTATTAATTAATTTCAATAGCTTAAATT
2728582 TATAATTAATTTATATGC-AATCTAAGTTTTAAATTTATTAATTAATTTCAATAGCTTAAATT
1 TATAATTAATTTATATGCAAATCTAAGTTTTAAATTTATTAATTAATTTCAATAGCTTAAATT
2728644 TATAATTATATTT
1 TATAATTA-ATTT
2728657 TAATTTAAAA
Statistics
Matches: 73, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
62 59 0.81
63 14 0.19
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.50
Consensus pattern (63 bp):
TATAATTAATTTATATGCAAATCTAAGTTTTAAATTTATTAATTAATTTCAATAGCTTAAATT
Found at i:2732161 original size:6 final size:6
Alignment explanation
Indices: 2732150--2732178 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2732140 NNNNNNNNTT
2732150 TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
2732179 TCCCTTCTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTC
Found at i:2734077 original size:18 final size:18
Alignment explanation
Indices: 2734054--2734089 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2734044 CAATTAAACC
2734054 ATTTGATTGATATATTTA
1 ATTTGATTGATATATTTA
* *
2734072 ATTTGATTTATTTATTTA
1 ATTTGATTGATATATTTA
2734090 TAAATAAATT
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:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (18 bp):
ATTTGATTGATATATTTA
Found at i:2734289 original size:20 final size:20
Alignment explanation
Indices: 2734264--2734303 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2734254 AATATTTTCA
2734264 GTAAATCATTTTCCAGAAAT
1 GTAAATCATTTTCCAGAAAT
*
2734284 GTAAATCATTTTCTAGAAAT
1 GTAAATCATTTTCCAGAAAT
2734304 CGTTTTCCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (20 bp):
GTAAATCATTTTCCAGAAAT
Found at i:2734304 original size:34 final size:33
Alignment explanation
Indices: 2734253--2734316 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
2734243 AAACACCAGA
2734253 AAATATTTTCAGTAAATCATTTTCCAGAAATGT
1 AAATATTTTCAGTAAATCATTTTCCAGAAATGT
* *
2734286 AAATCATTTTCTAG-AAATCGTTTTCCGGAAA
1 AAAT-ATTTTC-AGTAAATCATTTTCCAGAAA
2734317 ACATTTTACT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 4 0.15
34 21 0.78
35 2 0.07
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.38
Consensus pattern (33 bp):
AAATATTTTCAGTAAATCATTTTCCAGAAATGT
Found at i:2737054 original size:20 final size:20
Alignment explanation
Indices: 2737029--2737066 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2737019 ATTATAAAAA
2737029 TTAAAATATATATATTTTAC
1 TTAAAATATATATATTTTAC
* *
2737049 TTAAAATTTATTTATTTT
1 TTAAAATATATATATTTT
2737067 TTCTATGATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (20 bp):
TTAAAATATATATATTTTAC
Found at i:2738268 original size:83 final size:84
Alignment explanation
Indices: 2738125--2738292 Score: 275
Period size: 83 Copynumber: 2.0 Consensus size: 84
2738115 CCAAGTATAA
* *
2738125 GAAAGAAGAAGAGGGATAAGGGGGGGGGGGAGAAAGACAAGTGGCATAGGTTTAGTGAAATTAGG
1 GAAAGAAGAAGAGGGATAA---GGGGGAGGAGAAAGACAAGTGGCATAGATTTAGTGAAATTAGG
*
2738190 TAGCTGTTATCGTTAAAGTGGT
63 TAGCTGTTATCATTAAAGTGGT
2738212 GAAAGAAGAAGAGGGATAA-GGGGAGGAGAAAGACAAGTGGCATAGATTTAGTGAAATTAGGTAG
1 GAAAGAAGAAGAGGGATAAGGGGGAGGAGAAAGACAAGTGGCATAGATTTAGTGAAATTAGGTAG
2738276 CTGTTATCATTAAAGTG
66 CTGTTATCATTAAAGTG
2738293 ATGATGTGAA
Statistics
Matches: 78, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
83 59 0.76
87 19 0.24
ACGTcount: A:0.38, C:0.05, G:0.37, T:0.21
Consensus pattern (84 bp):
GAAAGAAGAAGAGGGATAAGGGGGAGGAGAAAGACAAGTGGCATAGATTTAGTGAAATTAGGTAG
CTGTTATCATTAAAGTGGT
Found at i:2740120 original size:23 final size:23
Alignment explanation
Indices: 2740081--2740131 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
2740071 GGATATAATT
* *
2740081 GCAATGCATTTTGGCACTTTGAA
1 GCAATGCATCTTGGCACTTCGAA
*
2740104 GCAATGCACTCTT-GCACTTCGAT
1 GCAATGCA-TCTTGGCACTTCGAA
2740127 GCAAT
1 GCAAT
2740132 TAATTCAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 21 0.88
24 3 0.12
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (23 bp):
GCAATGCATCTTGGCACTTCGAA
Found at i:2742272 original size:22 final size:22
Alignment explanation
Indices: 2742240--2742288 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
2742230 GCTTCATGTA
2742240 TTTT-AATTTA-TAAATATGTGT
1 TTTTAAATTTATTAAATAT-TGT
2742261 TTTTAAATTTATTAAATATTGT
1 TTTTAAATTTATTAAATATTGT
*
2742283 ATTTAA
1 TTTTAA
2742289 TAAAATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 4 0.16
22 14 0.56
23 7 0.28
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (22 bp):
TTTTAAATTTATTAAATATTGT
Found at i:2745211 original size:6 final size:6
Alignment explanation
Indices: 2745190--2745229 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
2745180 ACCCTCTCTG
*
2745190 GAAGAC GAAGA- AAAGAC GAAGAC GAAGAC GAAGAC GAAGA
1 GAAGAC GAAGAC GAAGAC GAAGAC GAAGAC GAAGAC GAAGA
2745230 GCCCTTTACT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 4 0.13
6 27 0.87
ACGTcount: A:0.55, C:0.12, G:0.33, T:0.00
Consensus pattern (6 bp):
GAAGAC
Found at i:2753067 original size:4 final size:4
Alignment explanation
Indices: 2753058--2753121 Score: 56
Period size: 4 Copynumber: 15.0 Consensus size: 4
2753048 TATACATTTG
* * * *
2753058 TACA TACA TACA TACA TACA TCGCCA TGCACA TACA TGCA TGCA TGCA
1 TACA TACA TACA TACA TACA T--ACA T--ACA TACA TACA TACA TACA
2753106 TACA TACA TACA TACA
1 TACA TACA TACA TACA
2753122 CATACGTGCA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
4 46 0.88
6 6 0.12
ACGTcount: A:0.41, C:0.28, G:0.08, T:0.23
Consensus pattern (4 bp):
TACA
Found at i:2753118 original size:28 final size:27
Alignment explanation
Indices: 2753087--2753183 Score: 72
Period size: 28 Copynumber: 3.4 Consensus size: 27
2753077 ATCGCCATGC
2753087 ACATACATGCATGCATGCATACATACAT
1 ACATACAT-CATGCATGCATACATACAT
* * *
2753115 ACATACA-CATACGTGCATGCACATACAC
1 ACATACATCATGCATGCAT--ACATACAT
* * *
2753143 ACATACACATCACGCACGCATCCATACAT
1 ACAT--ACATCATGCATGCATACATACAT
2753172 A-ATACATGCATG
1 ACATACAT-CATG
2753184 AAATGGAAAG
Statistics
Matches: 53, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
26 13 0.25
27 3 0.06
28 20 0.38
29 7 0.13
30 3 0.06
31 7 0.13
ACGTcount: A:0.39, C:0.30, G:0.10, T:0.21
Consensus pattern (27 bp):
ACATACATCATGCATGCATACATACAT
Found at i:2753151 original size:14 final size:14
Alignment explanation
Indices: 2753107--2753152 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
2753097 ATGCATGCAT
2753107 ACATACATACATAC
1 ACATACATACATAC
* * *
2753121 ACATACGTGCATGC
1 ACATACATACATAC
*
2753135 ACATACACACATAC
1 ACATACATACATAC
2753149 ACAT
1 ACAT
2753153 CACGCACGCA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.43, C:0.30, G:0.07, T:0.20
Consensus pattern (14 bp):
ACATACATACATAC
Found at i:2760330 original size:139 final size:140
Alignment explanation
Indices: 2760164--2760442 Score: 551
Period size: 139 Copynumber: 2.0 Consensus size: 140
2760154 TAAATTTTTA
2760164 TTTGATTTTAAAAATAAAAATAAAATATTAAAAAAATTGATTATATAAAAAAATCAAACCGGTGA
1 TTTGATTTTAAAAATAAAAATAAAATATTAAAAAAATTGATTATATAAAAAAATCAAACCGGTGA
2760229 TATTACTAGTTAATTGATTATATATAGAAGGGACCTTAAAAGAAGTGAATAATAGTGAAATGACT
66 TATTACTAGTTAATTGATTATATATAGAAGGGACCTTAAAAGAAGTGAATAATAGTGAAATGACT
2760294 GTAAAATGAG
131 GTAAAATGAG
2760304 TTTGATTTT-AAAATAAAAATAAAATATTAAAAAAATTGATTATATAAAAAAATCAAACCGGTGA
1 TTTGATTTTAAAAATAAAAATAAAATATTAAAAAAATTGATTATATAAAAAAATCAAACCGGTGA
2760368 TATTACTAGTTAATTGATTATATATAGAAGGGACCTTAAAAGAAGTGAATAATAGTGAAATGACT
66 TATTACTAGTTAATTGATTATATATAGAAGGGACCTTAAAAGAAGTGAATAATAGTGAAATGACT
2760433 GTAAAATGAG
131 GTAAAATGAG
2760443 AACAGTATAT
Statistics
Matches: 139, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
139 130 0.94
140 9 0.06
ACGTcount: A:0.50, C:0.05, G:0.14, T:0.31
Consensus pattern (140 bp):
TTTGATTTTAAAAATAAAAATAAAATATTAAAAAAATTGATTATATAAAAAAATCAAACCGGTGA
TATTACTAGTTAATTGATTATATATAGAAGGGACCTTAAAAGAAGTGAATAATAGTGAAATGACT
GTAAAATGAG
Found at i:2761794 original size:81 final size:81
Alignment explanation
Indices: 2761665--2761820 Score: 294
Period size: 81 Copynumber: 1.9 Consensus size: 81
2761655 GCCGGGCCAA
* *
2761665 AAAAGTGTTGCCTGAGACCCGGCCCGTTTTCTAAACGGGCCTCATTTTTTTGCCCAAACCCATAT
1 AAAAGTGGTGCCCGAGACCCGGCCCGTTTTCTAAACGGGCCTCATTTTTTTGCCCAAACCCATAT
2761730 TTCGGGCCTACGGGCC
66 TTCGGGCCTACGGGCC
2761746 AAAAGTGGTGCCCGAGACCCGGCCCGTTTTCTAAACGGGCCTCATTTTTTTGCCCAAACCCATAT
1 AAAAGTGGTGCCCGAGACCCGGCCCGTTTTCTAAACGGGCCTCATTTTTTTGCCCAAACCCATAT
2761811 TTCGGGCCTA
66 TTCGGGCCTA
2761821 TATTTTTACC
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
81 73 1.00
ACGTcount: A:0.21, C:0.31, G:0.22, T:0.27
Consensus pattern (81 bp):
AAAAGTGGTGCCCGAGACCCGGCCCGTTTTCTAAACGGGCCTCATTTTTTTGCCCAAACCCATAT
TTCGGGCCTACGGGCC
Found at i:2764055 original size:30 final size:30
Alignment explanation
Indices: 2764019--2764076 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
2764009 TTTTTTTGTT
2764019 AAAGTGTCAAATTATCTGTCAAACTTCTCA
1 AAAGTGTCAAATTATCTGTCAAACTTCTCA
2764049 AAAGTGTCAAATTATCTGTCAAACTTCT
1 AAAGTGTCAAATTATCTGTCAAACTTCT
2764077 TGACTTTGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.34
Consensus pattern (30 bp):
AAAGTGTCAAATTATCTGTCAAACTTCTCA
Found at i:2767674 original size:21 final size:22
Alignment explanation
Indices: 2767650--2767695 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
2767640 ACAATATATA
*
2767650 AAAAAAC-TTAAAATGAATAAT
1 AAAAAACATTAAAATAAATAAT
2767671 AAAAAACAGTTTAAAATAAATAAT
1 AAAAAACA--TTAAAATAAATAAT
2767695 A
1 A
2767696 TATAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
24 14 0.67
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.24
Consensus pattern (22 bp):
AAAAAACATTAAAATAAATAAT
Found at i:2768506 original size:12 final size:13
Alignment explanation
Indices: 2768489--2768517 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2768479 TTCGTATGTA
2768489 AAAAAATG-AAAT
1 AAAAAATGAAAAT
2768501 AAAAAATGAAAAT
1 AAAAAATGAAAAT
2768514 AAAA
1 AAAA
2768518 TCAAACTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (13 bp):
AAAAAATGAAAAT
Found at i:2770564 original size:41 final size:39
Alignment explanation
Indices: 2770438--2770577 Score: 133
Period size: 40 Copynumber: 3.6 Consensus size: 39
2770428 ACAAACTAGT
* * * *
2770438 TTGATACCCAGTACCTCATCGGATAATTCGAAGTAATAA
1 TTGACACCCAGTGCCTCATCGAATAATCCGAAGTAATAA
* ** * *
2770477 GTTGACACTCAGTGTCC-CATCGGCTAAACTGAAGT-A-AA
1 -TTGACACCCAGTG-CCTCATCGAATAATCCGAAGTAATAA
2770515 TTGACACCCAGTGCCTCATCGAATTAATCCGAAGTAATAGA
1 TTGACACCCAGTGCCTCATCGAA-TAATCCGAAGTAATA-A
*
2770556 TTGACACCCAGTGTCTCATCGA
1 TTGACACCCAGTGCCTCATCGA
2770578 CTCCAAGACG
Statistics
Matches: 81, Mismatches: 13, Indels: 11
0.77 0.12 0.10
Matches are distributed among these distances:
36 2 0.02
37 17 0.21
38 11 0.14
39 2 0.02
40 25 0.31
41 24 0.30
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (39 bp):
TTGACACCCAGTGCCTCATCGAATAATCCGAAGTAATAA
Found at i:2771021 original size:22 final size:21
Alignment explanation
Indices: 2770996--2771070 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 21
2770986 AACCCTTAGC
*
2770996 TTTTCTTTCTCCTTTCCTTTTT
1 TTTTCTTTCT-CTTTCCTTTCT
* *
2771018 TTTTCTTTCTTTTTCCCTTCT
1 TTTTCTTTCTCTTTCCTTTCT
* *
2771039 ATTTCGTTTCACTTTCTCTTTCT
1 TTTTC-TTTCTCTTTC-CTTTCT
2771062 TTTTCTTTC
1 TTTTCTTTC
2771071 ATTTATTTGT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
21 12 0.28
22 22 0.51
23 9 0.21
ACGTcount: A:0.03, C:0.27, G:0.01, T:0.69
Consensus pattern (21 bp):
TTTTCTTTCTCTTTCCTTTCT
Found at i:2789455 original size:9 final size:9
Alignment explanation
Indices: 2789443--2789479 Score: 74
Period size: 9 Copynumber: 4.1 Consensus size: 9
2789433 TATATCAAAT
2789443 TATTAATTG
1 TATTAATTG
2789452 TATTAATTG
1 TATTAATTG
2789461 TATTAATTG
1 TATTAATTG
2789470 TATTAATTG
1 TATTAATTG
2789479 T
1 T
2789480 TGTAACAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:2797510 original size:16 final size:16
Alignment explanation
Indices: 2797489--2797520 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2797479 AAACAAAACG
2797489 TGAAAGGGAATGGGAA
1 TGAAAGGGAATGGGAA
2797505 TGAAAGGGAATGGGAA
1 TGAAAGGGAATGGGAA
2797521 AGAAGTTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.44, T:0.12
Consensus pattern (16 bp):
TGAAAGGGAATGGGAA
Found at i:2801210 original size:140 final size:140
Alignment explanation
Indices: 2800958--2801242 Score: 471
Period size: 140 Copynumber: 2.0 Consensus size: 140
2800948 GAAGTCAAAG
* *
2800958 AAACTTATCTAAATTCATTTGTAAATGATAAATTTAAGTTTTGGACATCAGCCTTCCTTTAAAAT
1 AAACTTATCTAAATTCATTTGTAAATGATAAATTTAAGATTTGGACATCAACCTTCCTTTAAAAT
* *
2801023 TTTGAACACTCCTCGAAGTACAAACTCCAACATCCCTCATGTTCCGATAGCGTTCCTCCTCTAAA
66 TTCGAACACTCCTCGAAGTACAAACTCCAACATCCCTCATGTTCCGATAGCGTTCCTCCTCAAAA
2801088 GACTATCAAC
131 GACTATCAAC
* * *
2801098 AAACTTATCTAAATTCATTTGTAAATGATAAATTTAAGATTTGGACATCAACTTTTCTTTGAAAT
1 AAACTTATCTAAATTCATTTGTAAATGATAAATTTAAGATTTGGACATCAACCTTCCTTTAAAAT
* * * *
2801163 TTCGAACGCTTCTCGAAGTACAAACTCCGACATCCCTCATGTTCCGATAGTGTTCCTCCTCAAAA
66 TTCGAACACTCCTCGAAGTACAAACTCCAACATCCCTCATGTTCCGATAGCGTTCCTCCTCAAAA
2801228 GACTATCAAC
131 GACTATCAAC
2801238 AAACT
1 AAACT
2801243 GCATAATTAT
Statistics
Matches: 134, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
140 134 1.00
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.33
Consensus pattern (140 bp):
AAACTTATCTAAATTCATTTGTAAATGATAAATTTAAGATTTGGACATCAACCTTCCTTTAAAAT
TTCGAACACTCCTCGAAGTACAAACTCCAACATCCCTCATGTTCCGATAGCGTTCCTCCTCAAAA
GACTATCAAC
Found at i:2803732 original size:277 final size:278
Alignment explanation
Indices: 2803228--2803783 Score: 1105
Period size: 277 Copynumber: 2.0 Consensus size: 278
2803218 AAAACACATT
2803228 ATTCTAATCAAATATCAAATAGAAGAAGTAAACTTCTATATGGATTCCACTTGTGTAGCCCTCGG
1 ATTCTAATCAAATATCAAATAGAAGAAGTAAACTTCTATATGGATTCCACTTGTGTAGCCCTCGG
2803293 CCTTTGCCCTCATAGATCTCCCTATTTTGGCACTTATATTTTATTTTAATAGGAATTTAAGCCAC
66 CCTTTGCCCTCATAGATCTCCCTATTTTGGCACTTATATTTTATTTTAATAGGAATTTAAGCCAC
2803358 ATAACTCTAACAATGATCATTATCTATTCTTATTTTGCAATCACAATTTCATTTAAACCCAACTA
131 ATAACTCTAACAATGATCATTATCTATTCTTATTTTGCAATCACAATTTCATTTAAACCCAACTA
2803423 CATATCTTATCATTAATTTTGATGATGCAGATATAAAACTTAACGTCACCATTATAGTAATTAAT
196 CATATCTTATCATTAATTTTGATGATGCAGATATAAAACTTAACGTCACCATTATAGTAATTAAT
2803488 TTCACTGAAAACCAAGCA
261 TTCACTGAAAACCAAGCA
2803506 ATTCTAATC-AATATCAAATAGAAGAAGTAAACTTCTATATGGATTCCACTTGTGTAGCCCTCGG
1 ATTCTAATCAAATATCAAATAGAAGAAGTAAACTTCTATATGGATTCCACTTGTGTAGCCCTCGG
2803570 CCTTTGCCCTCATAGATCTCCCTATTTTGGCACTTATATTTTATTTTAATAGGAATTTAAGCCAC
66 CCTTTGCCCTCATAGATCTCCCTATTTTGGCACTTATATTTTATTTTAATAGGAATTTAAGCCAC
2803635 ATAACTCTAACAATGATCATTATCTATTCTTATTTTGCAATCACAATTTCATTTAAACCCAACTA
131 ATAACTCTAACAATGATCATTATCTATTCTTATTTTGCAATCACAATTTCATTTAAACCCAACTA
2803700 CATATCTTATCATTAATTTTGATGATGCAGATATAAAACTTAACGTCACCATTATAGTAATTAAT
196 CATATCTTATCATTAATTTTGATGATGCAGATATAAAACTTAACGTCACCATTATAGTAATTAAT
2803765 TTCACTGAAAACCAAGCA
261 TTCACTGAAAACCAAGCA
2803783 A
1 A
2803784 CGAATTTCTC
Statistics
Matches: 278, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
277 269 0.97
278 9 0.03
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.36
Consensus pattern (278 bp):
ATTCTAATCAAATATCAAATAGAAGAAGTAAACTTCTATATGGATTCCACTTGTGTAGCCCTCGG
CCTTTGCCCTCATAGATCTCCCTATTTTGGCACTTATATTTTATTTTAATAGGAATTTAAGCCAC
ATAACTCTAACAATGATCATTATCTATTCTTATTTTGCAATCACAATTTCATTTAAACCCAACTA
CATATCTTATCATTAATTTTGATGATGCAGATATAAAACTTAACGTCACCATTATAGTAATTAAT
TTCACTGAAAACCAAGCA
Found at i:2804392 original size:170 final size:171
Alignment explanation
Indices: 2804194--2804534 Score: 675
Period size: 170 Copynumber: 2.0 Consensus size: 171
2804184 CACATTTAAA
2804194 ATATTAAAAATTAAAAATTTAATTGAAATTAAACATTAAAATACCTTATTAAAATCTGAGTTTAT
1 ATATTAAAAATTAAAAATTTAATTGAAATTAAACATTAAAATACCTTATTAAAATCTGAGTTTAT
2804259 TTTTCAAGAATTTTAAATTAAATTAAAATTTCATTACATATGTTTTAATAATTGGTTATTTATTA
66 TTTTCAAGAATTTTAAATTAAATTAAAATTTCATTACATATGTTTTAATAATTGGTTATTTATTA
2804324 AACATTAAAATACTTAAATATTTTTATTTTATTATTTAAGT
131 AACATTAAAATACTTAAATATTTTTATTTTATTATTTAAGT
2804365 ATATTAAAAA-TAAAAATTTAATTGAAATTAAACATTAAAATACCTTATTAAAATCTGAGTTTAT
1 ATATTAAAAATTAAAAATTTAATTGAAATTAAACATTAAAATACCTTATTAAAATCTGAGTTTAT
2804429 TTTTCAAGAATTTTAAATTAAATTAAAATTTCATTACATATGTTTTAATAATTGGTTATTTATTA
66 TTTTCAAGAATTTTAAATTAAATTAAAATTTCATTACATATGTTTTAATAATTGGTTATTTATTA
2804494 AACATTAAAATACTTAAATATTTTTATTTTATTATTTAAGT
131 AACATTAAAATACTTAAATATTTTTATTTTATTATTTAAGT
2804535 TTTAAGTCAT
Statistics
Matches: 170, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
170 160 0.94
171 10 0.06
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (171 bp):
ATATTAAAAATTAAAAATTTAATTGAAATTAAACATTAAAATACCTTATTAAAATCTGAGTTTAT
TTTTCAAGAATTTTAAATTAAATTAAAATTTCATTACATATGTTTTAATAATTGGTTATTTATTA
AACATTAAAATACTTAAATATTTTTATTTTATTATTTAAGT
Found at i:2813462 original size:23 final size:23
Alignment explanation
Indices: 2813427--2813472 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2813417 GGCTAGCTTA
*
2813427 TTTTTTTATTTAATATTAAATAT
1 TTTTTTTATTTAAAATTAAATAT
*
2813450 TTTTATTTA-TTAAAATTATATAT
1 TTTT-TTTATTTAAAATTAAATAT
2813473 ATGCAACTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
TTTTTTTATTTAAAATTAAATAT
Found at i:2821053 original size:236 final size:236
Alignment explanation
Indices: 2820640--2821111 Score: 926
Period size: 236 Copynumber: 2.0 Consensus size: 236
2820630 CACATTCAAA
2820640 GGCCCAATTTCAGCCCAACCAGATATATTTTTTTAAGTATGTAATATGTTATTTTATTAAAATTT
1 GGCCCAATTTCAGCCCAACCAGATATATTTTTTTAAGTATGTAATATGTTATTTTATTAAAATTT
2820705 TAATAAATGATTATATATAAAATTATTAAATGTTAAATTAAAAATAATATAAAATTATTCTTTTG
66 TAATAAATGATTATATATAAAATTATTAAATGTTAAATTAAAAATAATATAAAATTATTCTTTTG
2820770 AATTTAAAAATAATATGTACAAGCTTAAAACAATTTAGGTTAATCATTTATAAATATGGATACAT
131 AATTTAAAAATAATATGTACAAGCTTAAAACAATTTAGGTTAATCATTTATAAATATGGATACAT
* *
2820835 TTATCAAATTTTGAGGTTTATATTTTTAATCAATTTAGTTT
196 TTATCAAATTTTGAGGTTTATATTTTGAATCAATCTAGTTT
2820876 GGCCCAATTTCAGCCCAACCAGATATATTTTTTTAAGTATGTAATATGTTATTTTATTAAAATTT
1 GGCCCAATTTCAGCCCAACCAGATATATTTTTTTAAGTATGTAATATGTTATTTTATTAAAATTT
2820941 TAATAAATGATTATATATAAAATTATTAAATGTTAAATTAAAAATAATATAAAATTATTCTTTTG
66 TAATAAATGATTATATATAAAATTATTAAATGTTAAATTAAAAATAATATAAAATTATTCTTTTG
2821006 AATTTAAAAATAATATGTACAAGCTTAAAACAATTTAGGTTAATCATTTATAAATATGGATACAT
131 AATTTAAAAATAATATGTACAAGCTTAAAACAATTTAGGTTAATCATTTATAAATATGGATACAT
2821071 TTATCAAATTTTGAGGTTTATATTTTGAATCAATCTAGTTT
196 TTATCAAATTTTGAGGTTTATATTTTGAATCAATCTAGTTT
2821112 AAGCAGACAT
Statistics
Matches: 234, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
236 234 1.00
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (236 bp):
GGCCCAATTTCAGCCCAACCAGATATATTTTTTTAAGTATGTAATATGTTATTTTATTAAAATTT
TAATAAATGATTATATATAAAATTATTAAATGTTAAATTAAAAATAATATAAAATTATTCTTTTG
AATTTAAAAATAATATGTACAAGCTTAAAACAATTTAGGTTAATCATTTATAAATATGGATACAT
TTATCAAATTTTGAGGTTTATATTTTGAATCAATCTAGTTT
Found at i:2828929 original size:26 final size:28
Alignment explanation
Indices: 2828883--2828945 Score: 94
Period size: 26 Copynumber: 2.3 Consensus size: 28
2828873 GAGATCATGG
2828883 AAGATGATCTCATAGGAGATGATCAACT
1 AAGATGATCTCATAGGAGATGATCAACT
*
2828911 AAGATGA-C-CATAGGAGATGATCAAGT
1 AAGATGATCTCATAGGAGATGATCAACT
*
2828937 GAGATGATC
1 AAGATGATC
2828946 CAGACGAGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
26 23 0.72
27 2 0.06
28 7 0.22
ACGTcount: A:0.40, C:0.13, G:0.25, T:0.22
Consensus pattern (28 bp):
AAGATGATCTCATAGGAGATGATCAACT
Found at i:2828944 original size:13 final size:13
Alignment explanation
Indices: 2828898--2828945 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
2828888 GATCTCATAG
*
2828898 GAGATGATCAACT
1 GAGATGATCAAGT
* *
2828911 AAGATGACCATAG-
1 GAGATGATCA-AGT
2828924 GAGATGATCAAGT
1 GAGATGATCAAGT
2828937 GAGATGATC
1 GAGATGATC
2828946 CAGACGAGGC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
12 2 0.07
13 25 0.89
14 1 0.04
ACGTcount: A:0.40, C:0.12, G:0.27, T:0.21
Consensus pattern (13 bp):
GAGATGATCAAGT
Found at i:2831236 original size:64 final size:62
Alignment explanation
Indices: 2831092--2831343 Score: 396
Period size: 62 Copynumber: 4.0 Consensus size: 62
2831082 AATTTGGATT
* *
2831092 ATATTGTGGCACATTATACTTTTTAAGCCTAAAATGCAACTCCATTTCCTCAAAATTGGACC
1 ATATTGTGGCACATTATACTTTTAAAGCCTAAAATGCAACCCCATTTCCTCAAAATTGGACC
* *
2831154 CTATTGTGGCACATTATACTTTTAAAGCCTAAAATGCAACTCCATATTTCCTCAAAATTGGACC
1 ATATTGTGGCACATTATACTTTTAAAGCCTAAAATGCAAC-CC-CATTTCCTCAAAATTGGACC
*
2831218 ATATTGTGGCACATTATACTTTTAAAGCCTAAATTGCAACCCCATTTCCTCAAAATTGGACC
1 ATATTGTGGCACATTATACTTTTAAAGCCTAAAATGCAACCCCATTTCCTCAAAATTGGACC
* * * * *
2831280 ATATTGTGGCACATTATGCTTTTGAAGTCTAAAATGCAACCCCATCTCCTCAAGATTGGACC
1 ATATTGTGGCACATTATACTTTTAAAGCCTAAAATGCAACCCCATTTCCTCAAAATTGGACC
2831342 AT
1 AT
2831344 GATGGCCTTG
Statistics
Matches: 175, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
62 115 0.66
63 3 0.02
64 57 0.33
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (62 bp):
ATATTGTGGCACATTATACTTTTAAAGCCTAAAATGCAACCCCATTTCCTCAAAATTGGACC
Found at i:2831238 original size:126 final size:124
Alignment explanation
Indices: 2831092--2831343 Score: 396
Period size: 126 Copynumber: 2.0 Consensus size: 124
2831082 AATTTGGATT
* * *
2831092 ATATTGTGGCACATTATACTTTTTAAGCCTAAAATGCAACTCCATTTCCTCAAAATTGGACCCTA
1 ATATTGTGGCACATTATACTTTTAAAGCCTAAAATGCAACCCCATTTCCTCAAAATTGGACCATA
* *
2831157 TTGTGGCACATTATACTTTTAAAGCCTAAAATGCAACTCCATATTTCCTCAAAATTGGACC
66 TTGTGGCACATTATACTTTTAAAGCCTAAAATGCAAC-CC-CATCTCCTCAAAATTGGACC
*
2831218 ATATTGTGGCACATTATACTTTTAAAGCCTAAATTGCAACCCCATTTCCTCAAAATTGGACCATA
1 ATATTGTGGCACATTATACTTTTAAAGCCTAAAATGCAACCCCATTTCCTCAAAATTGGACCATA
* * * *
2831283 TTGTGGCACATTATGCTTTTGAAGTCTAAAATGCAACCCCATCTCCTCAAGATTGGACC
66 TTGTGGCACATTATACTTTTAAAGCCTAAAATGCAACCCCATCTCCTCAAAATTGGACC
2831342 AT
1 AT
2831344 GATGGCCTTG
Statistics
Matches: 116, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
124 19 0.16
125 2 0.02
126 95 0.82
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (124 bp):
ATATTGTGGCACATTATACTTTTAAAGCCTAAAATGCAACCCCATTTCCTCAAAATTGGACCATA
TTGTGGCACATTATACTTTTAAAGCCTAAAATGCAACCCCATCTCCTCAAAATTGGACC
Found at i:2831925 original size:6 final size:6
Alignment explanation
Indices: 2831914--2831942 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2831904 TATAATCTTA
2831914 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
2831943 GGGTGTGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:2844511 original size:22 final size:20
Alignment explanation
Indices: 2844465--2844513 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
2844455 AGCTCTGTTA
*
2844465 CCAAAAATTGTATATAAGTT
1 CCAAAAATTGTATAGAAGTT
*
2844485 CCAAAAATTGTATGTAGAATTT
1 CCAAAAATTGTA--TAGAAGTT
2844507 CCAAAAA
1 CCAAAAA
2844514 GAAAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 12 0.48
22 13 0.52
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.31
Consensus pattern (20 bp):
CCAAAAATTGTATAGAAGTT
Found at i:2846856 original size:31 final size:32
Alignment explanation
Indices: 2846813--2846878 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
2846803 TTAGGCTATT
* *
2846813 AAAAATTTTAATTAGA-CTTCTAAATTATTTG
1 AAAAATTCTAATTAGACCTTCAAAATTATTTG
*
2846844 AAAAATTCTAATTAGACCCTTCAAAATTTTTTG
1 AAAAATTCTAATTAGA-CCTTCAAAATTATTTG
2846877 AA
1 AA
2846879 TTCTCATTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 15 0.50
33 15 0.50
ACGTcount: A:0.42, C:0.11, G:0.06, T:0.41
Consensus pattern (32 bp):
AAAAATTCTAATTAGACCTTCAAAATTATTTG
Found at i:2846888 original size:30 final size:30
Alignment explanation
Indices: 2846847--2846905 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
2846837 TTATTTGAAA
2846847 AATTCTAATTAGACCCTTCAAAATTTTTTG
1 AATTCTAATTAGACCCTTCAAAATTTTTTG
* **
2846877 AATTCTCATTAGATTCTTCAAAATTTTTT
1 AATTCTAATTAGACCCTTCAAAATTTTTT
2846906 TTTAAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.32, C:0.15, G:0.05, T:0.47
Consensus pattern (30 bp):
AATTCTAATTAGACCCTTCAAAATTTTTTG
Found at i:2854079 original size:2 final size:2
Alignment explanation
Indices: 2854072--2854100 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2854062 CAAAGCAACG
2854072 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
2854101 CTGTCATTCT
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:2856044 original size:17 final size:17
Alignment explanation
Indices: 2856023--2856059 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
2856013 GAATTTATGT
*
2856023 AAAAAATATATATTTATA
1 AAAAAAT-TATATTAATA
2856041 AAAAAATTATATTAATA
1 AAAAAATTATATTAATA
2856058 AA
1 AA
2856060 TTAATATCCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAAAATTATATTAATA
Found at i:2856617 original size:22 final size:22
Alignment explanation
Indices: 2856568--2856618 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
2856558 GTTAGTGAAT
2856568 AAAAATATATAAATATAAATAA
1 AAAAATATATAAATATAAATAA
* * *
2856590 ACAAATATTTATATATAAA-AA
1 AAAAATATATAAATATAAATAA
2856611 ATAAAATA
1 A-AAAATA
2856619 AATTGAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAAATATATAAATATAAATAA
Found at i:2857609 original size:125 final size:125
Alignment explanation
Indices: 2857370--2857904 Score: 684
Period size: 125 Copynumber: 4.3 Consensus size: 125
2857360 ATTAATGCAG
* * * * *
2857370 TCGCGGCCACGTGAACGCGCTTTTGGTACAGTAGGTCCTGAA-AAATTTATTTCGAGTTGATGTT
1 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAGAAA-TAATTTCGAGTTGACGTT
* * * * *
2857434 TCTGAGCAAATAGTATAAAAAACACTTCAAGCAGGGTGCTATATGCGAAGAATTTGTGAAA
65 TCTGAGCAAATAGTATAAAAATCGCTTCAAGCAGGATGCTTTATGAGAAGAATTTGTGAAA
* * *
2857495 TCGCGCCCTCGTGGACGCGCTTTTGCTACAGTTGGTCCTGGAAGGAATAATTTCGAGTTGACGTT
1 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCT-GAAGAAATAATTTCGAGTTGACGTT
* **
2857560 TCTAAGCAAATAGTAT-AAAATCGCTTC-TCCTAGGATGCTTTATGAGAAGAATTTGTGAAA
65 TCTGAGCAAATAGTATAAAAATCGCTTCAAGC-AGGATGCTTTATGAGAAGAATTTGTGAAA
* * * *
2857620 TCGCACCCACGTGGACGTGCTTTTGCTACAGTAGGTCCTGAAAAAATTATTTCGAGTTGACGTTT
1 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAGAAATAATTTCGAGTTGACGTTT
* * *
2857685 CTGAGCAAATAGTATAAAAAAGCGCTTCAAGCAGGATG-TTATTTGCGAAGAATTTGTGAAA
66 CTGAGCAAATAGTAT-AAAAATCGCTTCAAGCAGGATGCTT-TATGAGAAGAATTTGTGAAA
* * * * *
2857746 TCGCGGCCTCATGGACGCGCTTTTGCTACAATTGGTCCTGGAAGAAATAATTTCGAGTTGACGTT
1 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCT-GAAGAAATAATTTCGAGTTGACGTT
* * * **
2857811 TCTGAGCAAATAGTAT-AAAATTGCTTCTATCAGGATGCTTTATGAGGGGAATTTGTGAAA
65 TCTGAGCAAATAGTATAAAAATCGCTTCAAGCAGGATGCTTTATGAGAAGAATTTGTGAAA
2857871 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAG
1 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAG
2857905 CATGTTTGGG
Statistics
Matches: 350, Mismatches: 51, Indels: 18
0.84 0.12 0.04
Matches are distributed among these distances:
124 38 0.11
125 168 0.48
126 102 0.29
127 42 0.12
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (125 bp):
TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAGAAATAATTTCGAGTTGACGTTT
CTGAGCAAATAGTATAAAAATCGCTTCAAGCAGGATGCTTTATGAGAAGAATTTGTGAAA
Found at i:2857821 original size:251 final size:250
Alignment explanation
Indices: 2857376--2857904 Score: 862
Period size: 251 Copynumber: 2.1 Consensus size: 250
2857366 GCAGTCGCGG
* * * *
2857376 CCACGTGAACGCGCTTTTGGTACAGTAGGTCCTGAAAAATTTATTTCGAGTTGATGTTTCTGAGC
1 CCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATTATTTCGAGTTGACGTTTCTGAGC
* *
2857441 AAATAGTATAAAAAACACTTCAAGCAGGGTGCTATATGCGAAGAATTTGTGAAATCGCGCCCTCG
66 AAATAGTATAAAAAACACTTCAAGCAGGATGCTATATGCGAAGAATTTGTGAAATCGCGCCCTCA
* *
2857506 TGGACGCGCTTTTGCTACAGTTGGTCCTGGAAGGAATAATTTCGAGTTGACGTTTCTAAGCAAAT
131 TGGACGCGCTTTTGCTACAATTGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTAAGCAAAT
*
2857571 AGTATAAAATCGCTTCT-CCTAGGATGCTTTATGAGAAGAATTTGTGAAATCGCAC
196 AGTATAAAATCGCTTCTATC-AGGATGCTTTATGAGAAGAATTTGTGAAATCGCAC
*
2857626 CCACGTGGACGTGCTTTTGCTACAGTAGGTCCTGAAAAAATTATTTCGAGTTGACGTTTCTGAGC
1 CCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATTATTTCGAGTTGACGTTTCTGAGC
* * * *
2857691 AAATAGTATAAAAAAGCGCTTCAAGCAGGATGTTATTTGCGAAGAATTTGTGAAATCGCGGCCTC
66 AAATAGTATAAAAAA-CACTTCAAGCAGGATGCTATATGCGAAGAATTTGTGAAATCGCGCCCTC
*
2857756 ATGGACGCGCTTTTGCTACAATTGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAA
130 ATGGACGCGCTTTTGCTACAATTGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTAAGCAAA
* ** *
2857821 TAGTATAAAATTGCTTCTATCAGGATGCTTTATGAGGGGAATTTGTGAAATCGCGC
195 TAGTATAAAATCGCTTCTATCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCAC
2857877 CCACGTGGACGCGCTTTTGCTACAGTAG
1 CCACGTGGACGCGCTTTTGCTACAGTAG
2857905 CATGTTTGGG
Statistics
Matches: 257, Mismatches: 20, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
250 75 0.29
251 181 0.70
252 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (250 bp):
CCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATTATTTCGAGTTGACGTTTCTGAGC
AAATAGTATAAAAAACACTTCAAGCAGGATGCTATATGCGAAGAATTTGTGAAATCGCGCCCTCA
TGGACGCGCTTTTGCTACAATTGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTAAGCAAAT
AGTATAAAATCGCTTCTATCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCAC
Found at i:2859443 original size:24 final size:23
Alignment explanation
Indices: 2859412--2859456 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
2859402 TATACATACC
* *
2859412 TTATTATATATCTTTATATCTTA
1 TTATTATATATATCTATATCTTA
2859435 TTATGTATATATATCTATATCT
1 TTAT-TATATATATCTATATCT
2859457 CTTCTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.31, C:0.09, G:0.02, T:0.58
Consensus pattern (23 bp):
TTATTATATATATCTATATCTTA
Found at i:2867626 original size:6 final size:6
Alignment explanation
Indices: 2867615--2867655 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
2867605 TAGTAGTGTT
* *
2867615 ATATAA ATATAA ATACAA ATACAA ATATAA ATATAA A-ATAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
2867656 GTATGTATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
5 4 0.12
6 29 0.88
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (6 bp):
ATATAA
Done.