Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 65 of 205
Found at i:19411672 original size:78 final size:77
Alignment explanation
Indices: 19411171--19412341 Score: 1327
Period size: 78 Copynumber: 15.2 Consensus size: 77
19411161 CTAAATTTCT
* * * * ** *
19411171 TTTTTGAAAAACAGAAA-TAAAAAATAGCTCAGGGTACGACCCGAAGCTCAACTCACCTCTCAG-
1 TTTTTGAAAAACATAAATTGAAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTC-GC
19411234 ATTATGAGTTG-A
65 ATTATGAGTTGAA
* * * * * *
19411246 TCTTTGAAAAACAGAAATT-AAAAATACCTCAGCGTGCGACCCAAAGCTCAACTCACCTCTCGGA
1 TTTTTGAAAAACATAAATTGAAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCA
19411310 TTATGAGTTG-A
66 TTATGAGTTGAA
* * * * *
19411321 TCTTTGAAGAACAGAAATTG-AAAAT-CCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGGA
1 TTTTTGAAAAACATAAATTGAAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCA
*
19411384 TTATGAGTTGATT
66 TTATGAGTTGA-A
* * * * **
19411397 TTTTTGAAAAACATAAATTAAAAAATACCTCGGCATTTG-CCCGAGGCTCAACTCACCTCTCATA
1 TTTTTGAAAAACATAAATTGAAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCA
19411461 TTATGAGTTG-A
66 TTATGAGTTGAA
* * *
19411472 TTTTTGAAAGA-ATGGAAATTGAAAAATACCTCGGCATGTG-CCCGAGGCTCAACTCACCTCTCG
1 TTTTTGAAAAACAT--AAATTGAAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCG
19411535 CATTATGAGTT-AA
64 CATTATGAGTTGAA
* * * *
19411548 TTTTTGAAAAACAGAAATTGAAAAATACCTCAACGTGCGGCCCGAGGCAT-AACTCACCTCTCGC
1 TTTTTGAAAAACATAAATTGAAAAATACCTCAGCGTGTGACCCGAGGC-TCAACTCACCTCTCGC
19411612 ATTATGAGTTGATA
65 ATTATGAGTTGA-A
* * * * * * *
19411626 TTTTTCAAAAACATAAATTCAAAAATACCTCGGTGTGTGACTCGAGGCTCAACTCACATCTCACA
1 TTTTTGAAAAACATAAATTGAAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCA
*
19411691 TTATGAGTTAAA
66 TTATGAGTTGAA
* * *
19411703 TTTTTTTGAAAAACATAAATTGAAAAATACCTCGGCGTGCGACCCGAGGCTTAACTCACCTCTCG
1 --TTTTTGAAAAACATAAATTGAAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCG
*
19411768 CATTATGAGTTGATT
64 CATTATGAGTTGA-A
* *
19411783 TTTTTGAAAAACATAAATTGAATAATACCTCAGCGTGCGACCCGAGGCTCAACTCACCTCTCGCA
1 TTTTTGAAAAACATAAATTGAAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCA
19411848 TTATGAGTTG-A
66 TTATGAGTTGAA
* *
19411859 TTTTTGAAAAAAACAGAAATTGAAAAATACCTCAGGGTGTGACCCGAGGCTCAACTCACCTCTCG
1 TTTTTG--AAAAACATAAATTGAAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCG
*
19411924 CATTATAAGTTG-A
64 CATTATGAGTTGAA
* * * ** *
19411937 TTTTTGAAAAATATAGAAATTGAAAAATACCTTAGTGTGTGACCTTAGTCTCAACTCACCTCTCG
1 TTTTTGAAAAACAT--AAATTGAAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCG
*
19412002 CATTATGAGTTGATT
64 CATTATGAGTTGA-A
* * * *
19412017 TTTTTGAAAAACATAAATTGAAAAATACATCAGCGTGTGACCCGTGGCTCAACTCACCTTTGGCA
1 TTTTTGAAAAACATAAATTGAAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCA
*
19412082 TTATGAGTTGAG
66 TTATGAGTTGAA
** * * * * **
19412094 TTTTAAAAAAATAGAAATTGAAAAATACTTC-GACGTGTGACCCGAGGCTCAACTTATTTCTCGC
1 TTTTTGAAAAACATAAATTGAAAAATACCTCAG-CGTGTGACCCGAGGCTCAACTCACCTCTCGC
19412158 ATTATGAGTTG-A
65 ATTATGAGTTGAA
* * * * *
19412170 TTTTTGAAAAATAGAAATTGAAAAGTACCTCAGCGTGCGATCCGAGGCTCAACTCACCTCTCGCA
1 TTTTTGAAAAACATAAATTGAAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCA
19412235 TTATGAGTTG-A
66 TTATGAGTTGAA
* * * * * *
19412246 GTTTTGAAAAAAAATAGAAATTGAAAAAAACCTCGGCGTGTGACCCGAGGCTCAACTCACATCTT
1 TTTTTG-AAAAACAT--AAATTGAAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTC
19412311 GCATTATGAGTTG-A
63 GCATTATGAGTTGAA
19412325 TTTTTGAAAAACATAAA
1 TTTTTGAAAAACATAAA
19412342 AAGAAATGGT
Statistics
Matches: 951, Mismatches: 115, Indels: 59
0.85 0.10 0.05
Matches are distributed among these distances:
74 49 0.05
75 120 0.13
76 201 0.21
77 112 0.12
78 329 0.35
79 127 0.13
80 13 0.01
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.28
Consensus pattern (77 bp):
TTTTTGAAAAACATAAATTGAAAAATACCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCA
TTATGAGTTGAA
Found at i:19416773 original size:26 final size:25
Alignment explanation
Indices: 19416743--19416793 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 25
19416733 AGATACATGT
*
19416743 AGGGAAAGGCTGTGAGAAGAGGAAA
1 AGGGAAAGGCTATGAGAAGAGGAAA
19416768 NAGGGAAAGGCTATGAGAAGAGGAAA
1 -AGGGAAAGGCTATGAGAAGAGGAAA
19416794 TAATTATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.45, C:0.04, G:0.41, T:0.08
Consensus pattern (25 bp):
AGGGAAAGGCTATGAGAAGAGGAAA
Found at i:19421430 original size:28 final size:28
Alignment explanation
Indices: 19421395--19421448 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
19421385 TGGGCTGTTG
* *
19421395 GCTGTTGGGCCAAGTGCTAGCCTGCTGT
1 GCTGTTGGGCCAAGCGCAAGCCTGCTGT
*
19421423 GCTGTTGGGCCAGGCGCAAGCCTGCT
1 GCTGTTGGGCCAAGCGCAAGCCTGCT
19421449 AGTTTGGGCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.11, C:0.28, G:0.37, T:0.24
Consensus pattern (28 bp):
GCTGTTGGGCCAAGCGCAAGCCTGCTGT
Found at i:19421701 original size:10 final size:10
Alignment explanation
Indices: 19421688--19421730 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
19421678 CCTTTTTTTC
19421688 CTTCTTCTTT
1 CTTCTTCTTT
19421698 CTTCTTCTTT
1 CTTCTTCTTT
* *
19421708 TTTCCTTCATT
1 CTT-CTTCTTT
19421719 CTTCTTCTTT
1 CTTCTTCTTT
19421729 CT
1 CT
19421731 CCTTGCTCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
10 20 0.71
11 8 0.29
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.67
Consensus pattern (10 bp):
CTTCTTCTTT
Found at i:19421708 original size:24 final size:24
Alignment explanation
Indices: 19421681--19421727 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
19421671 ATTTTTTCCT
19421681 TTTTTTCCTTC-TTCTTTCTTCTTC
1 TTTTTTCCTTCATTC-TTCTTCTTC
19421705 TTTTTTCCTTCATTCTTCTTCTT
1 TTTTTTCCTTCATTCTTCTTCTT
19421728 TCTCCTTGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (24 bp):
TTTTTTCCTTCATTCTTCTTCTTC
Found at i:19421792 original size:17 final size:17
Alignment explanation
Indices: 19421772--19421811 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
19421762 ACGCCGCCAC
*
19421772 CTCCTTCACGTTGTCGT
1 CTCCTTCACGTCGTCGT
*
19421789 CTCCTTTACGTCGTCGT
1 CTCCTTCACGTCGTCGT
*
19421806 CCCCTT
1 CTCCTT
19421812 TCTACTTTCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.05, C:0.40, G:0.15, T:0.40
Consensus pattern (17 bp):
CTCCTTCACGTCGTCGT
Found at i:19422177 original size:30 final size:29
Alignment explanation
Indices: 19422102--19422198 Score: 124
Period size: 30 Copynumber: 3.3 Consensus size: 29
19422092 AGGGCTAATG
* *
19422102 TGTAATTTTTGGAAAATTTAGGGTCAAAA
1 TGTAATTTTTAGAAAGTTTAGGGTCAAAA
19422131 TGTAA-TTTTAGAAAGTTTAGGGGTCAAAA
1 TGTAATTTTTAGAAAGTTTA-GGGTCAAAA
* * *
19422160 TGTAATTTTTTGAAAGTTTAAAGGTTAAAA
1 TGTAATTTTTAGAAAGTTT-AGGGTCAAAA
19422190 TGTAATTTT
1 TGTAATTTT
19422199 AAAAAAAATA
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
28 12 0.20
29 19 0.32
30 28 0.47
31 1 0.02
ACGTcount: A:0.37, C:0.02, G:0.20, T:0.41
Consensus pattern (29 bp):
TGTAATTTTTAGAAAGTTTAGGGTCAAAA
Found at i:19430494 original size:15 final size:15
Alignment explanation
Indices: 19430469--19430503 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
19430459 AACTCTATTT
*
19430469 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
19430483 TAATTAATATTAAGA
1 TAATTAATATTAAGA
19430498 TAATTA
1 TAATTA
19430504 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:19432054 original size:15 final size:15
Alignment explanation
Indices: 19432036--19432086 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
19432026 ATGTGTTTTT
19432036 TATTTTTAAAAATAA
1 TATTTTTAAAAATAA
* **
19432051 TATTTTTTAATTTAA
1 TATTTTTAAAAATAA
* *
19432066 AATTTTAAAAAATAA
1 TATTTTTAAAAATAA
19432081 TATTTT
1 TATTTT
19432087 ATTTGGTGGA
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTTTTAAAAATAA
Found at i:19435567 original size:41 final size:42
Alignment explanation
Indices: 19435466--19435624 Score: 130
Period size: 41 Copynumber: 3.7 Consensus size: 42
19435456 ATATCGAACA
* * **
19435466 ATGCCAACGTCCCAGAC-GTGGTCTTACATGCT-ATCTCATATCG
1 ATGCCAATGTCCCAGACAG-GGTCTTACACG-TAATCAAATA-CG
*
19435509 ATGCCACTGTCCCAGACAGGGTCTTACACG-AATCAAATACG
1 ATGCCAATGTCCCAGACAGGGTCTTACACGTAATCAAATACG
* * *
19435550 ATGCCAATGTCCTAGACATGGTCTTACACGTAATCACATATATCA
1 ATGCCAATGTCCCAGACAGGGTCTTACACGTAATCA-A-ATA-CG
*
19435595 ATGCC-ATCTTCCCAGAC-GTGGTCTTACACG
1 ATGCCAAT-GTCCCAGACAG-GGTCTTACACG
19435625 AGAACACATA
Statistics
Matches: 96, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
41 29 0.30
42 11 0.11
43 26 0.27
44 6 0.06
45 24 0.25
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.26
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACAGGGTCTTACACGTAATCAAATACG
Found at i:19436549 original size:28 final size:31
Alignment explanation
Indices: 19436517--19436575 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 31
19436507 TGTTTTGTTT
19436517 TTATTATAATAA-CATTAT-AAT-ATATAAA
1 TTATTATAATAACCATTATAAATAATATAAA
* *
19436545 TTATTATTATAACCTTTATAAATAATATAAA
1 TTATTATAATAACCATTATAAATAATATAAA
19436576 AACTATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 11 0.42
29 5 0.19
30 3 0.12
31 7 0.27
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (31 bp):
TTATTATAATAACCATTATAAATAATATAAA
Found at i:19437441 original size:354 final size:354
Alignment explanation
Indices: 19436792--19437500 Score: 1418
Period size: 354 Copynumber: 2.0 Consensus size: 354
19436782 CATAATAAAC
19436792 ACAGAAAATAATTTTAAAATATTTTTCTAACTCAGATTCATGGTCCCGAAACCACCGTTCCGATT
1 ACAGAAAATAATTTTAAAATATTTTTCTAACTCAGATTCATGGTCCCGAAACCACCGTTCCGATT
19436857 AGGATCAAAATCGGGCTGTTACAGCCAAGCTCTTTGGCTCCACCAATTTTTACTGTAGATTTCAG
66 AGGATCAAAATCGGGCTGTTACAGCCAAGCTCTTTGGCTCCACCAATTTTTACTGTAGATTTCAG
19436922 GTAATTTACGTGTAAAATAAAAAAGTGAATCATTTTCGTAATTAATCAAAATTTTAGGGTTATTT
131 GTAATTTACGTGTAAAATAAAAAAGTGAATCATTTTCGTAATTAATCAAAATTTTAGGGTTATTT
19436987 ATATAAAAGGGCCATGCTTTGACCGGAAGGCACCTCTGCCTCGTTTACATTGGGGAACTTTATCC
196 ATATAAAAGGGCCATGCTTTGACCGGAAGGCACCTCTGCCTCGTTTACATTGGGGAACTTTATCC
19437052 TTTCCCTTCGAAAATGTTGAGAGGATACTAACTATTTGATTTTATGAATAAAAAAGTTATTAATT
261 TTTCCCTTCGAAAATGTTGAGAGGATACTAACTATTTGATTTTATGAATAAAAAAGTTATTAATT
19437117 AAAAATGAATTAAAAAATAAAAAATATAT
326 AAAAATGAATTAAAAAATAAAAAATATAT
19437146 ACAGAAAATAATTTTAAAATATTTTTCTAACTCAGATTCATGGTCCCGAAACCACCGTTCCGATT
1 ACAGAAAATAATTTTAAAATATTTTTCTAACTCAGATTCATGGTCCCGAAACCACCGTTCCGATT
19437211 AGGATCAAAATCGGGCTGTTACAGCCAAGCTCTTTGGCTCCACCAATTTTTACTGTAGATTTCAG
66 AGGATCAAAATCGGGCTGTTACAGCCAAGCTCTTTGGCTCCACCAATTTTTACTGTAGATTTCAG
19437276 GTAATTTACGTGTAAAATAAAAAAGTGAATCATTTTCGTAATTAATCAAAATTTTAGGGTTATTT
131 GTAATTTACGTGTAAAATAAAAAAGTGAATCATTTTCGTAATTAATCAAAATTTTAGGGTTATTT
19437341 ATATAAAAGGGCCATGCTTTGACCGGAAGGCACCTCTGCCTCGTTTACATTGGGGAACTTTATCC
196 ATATAAAAGGGCCATGCTTTGACCGGAAGGCACCTCTGCCTCGTTTACATTGGGGAACTTTATCC
19437406 TTTCCCTTCGAAAATGTTGAGAGGATACTAACTATTTGATTTTATGAATAAAAAAGTTATTAATT
261 TTTCCCTTCGAAAATGTTGAGAGGATACTAACTATTTGATTTTATGAATAAAAAAGTTATTAATT
19437471 AAAAATGAATTAAAAAATAAAAAATATAT
326 AAAAATGAATTAAAAAATAAAAAATATAT
19437500 A
1 A
19437501 TTTATTAATT
Statistics
Matches: 355, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
354 355 1.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (354 bp):
ACAGAAAATAATTTTAAAATATTTTTCTAACTCAGATTCATGGTCCCGAAACCACCGTTCCGATT
AGGATCAAAATCGGGCTGTTACAGCCAAGCTCTTTGGCTCCACCAATTTTTACTGTAGATTTCAG
GTAATTTACGTGTAAAATAAAAAAGTGAATCATTTTCGTAATTAATCAAAATTTTAGGGTTATTT
ATATAAAAGGGCCATGCTTTGACCGGAAGGCACCTCTGCCTCGTTTACATTGGGGAACTTTATCC
TTTCCCTTCGAAAATGTTGAGAGGATACTAACTATTTGATTTTATGAATAAAAAAGTTATTAATT
AAAAATGAATTAAAAAATAAAAAATATAT
Found at i:19437592 original size:39 final size:39
Alignment explanation
Indices: 19437538--19437616 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
19437528 ACATGAAGTA
*
19437538 AAAATTACAAATATGTTTAGAAAAGGAGGATTGAACCTG
1 AAAATTACAAATATGTTTAGAAAAGGAGAATTGAACCTG
*
19437577 AAAATTACAAATATGTTTATAAAAGGAGAATTGAACCTG
1 AAAATTACAAATATGTTTAGAAAAGGAGAATTGAACCTG
19437616 A
1 A
19437617 GTCTTAAGGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.48, C:0.08, G:0.18, T:0.27
Consensus pattern (39 bp):
AAAATTACAAATATGTTTAGAAAAGGAGAATTGAACCTG
Found at i:19441787 original size:3 final size:3
Alignment explanation
Indices: 19441779--19441920 Score: 284
Period size: 3 Copynumber: 47.3 Consensus size: 3
19441769 TTCCACTAAC
19441779 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
19441827 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
19441875 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
19441921 GTTTTATAAT
Statistics
Matches: 139, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 139 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:19444485 original size:16 final size:16
Alignment explanation
Indices: 19444464--19444494 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19444454 AAGAAACGAT
*
19444464 AAATATGTATATATAA
1 AAATATGTACATATAA
19444480 AAATATGTACATATA
1 AAATATGTACATATA
19444495 TATGGGTGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.35
Consensus pattern (16 bp):
AAATATGTACATATAA
Found at i:19445047 original size:3 final size:3
Alignment explanation
Indices: 19445039--19445094 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
19445029 AACAAATAGG
19445039 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
19445087 TAA TAA TA
1 TAA TAA TA
19445095 GTTAGTGGAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:19452831 original size:22 final size:24
Alignment explanation
Indices: 19452797--19452876 Score: 82
Period size: 22 Copynumber: 3.5 Consensus size: 24
19452787 CATAAACTAA
*
19452797 TTCTCTCTCAAATTTTCTCTCAAT
1 TTCTCTCTCAAATTTCCTCTCAAT
19452821 TTCT-TCT-AAATTTCCTCTCAAT
1 TTCTCTCTCAAATTTCCTCTCAAT
* *
19452843 TT-GCTCTCAAA-TTCCT-TCAAAA
1 TTCTCTCTCAAATTTCCTCTC-AAT
19452865 TT-TCTCTCAAAT
1 TTCTCTCTCAAAT
19452877 CCATATTTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
21 2 0.04
22 36 0.75
23 6 0.12
24 4 0.08
ACGTcount: A:0.25, C:0.28, G:0.01, T:0.46
Consensus pattern (24 bp):
TTCTCTCTCAAATTTCCTCTCAAT
Found at i:19452850 original size:33 final size:33
Alignment explanation
Indices: 19452795--19452874 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 33
19452785 TTCATAAACT
* * *
19452795 AATTCTCTCTCAAATTTTCTCTC-AATTTCTTCTA
1 AATT-TCTCTC-AATTTGCTCTCAAATTCCTTCAA
19452829 AATTTCCTCTCAATTTGCTCTCAAATTCCTTCAA
1 AATTT-CTCTCAATTTGCTCTCAAATTCCTTCAA
19452863 AATTTCTCTCAA
1 AATTTCTCTCAA
19452875 ATCCATATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
33 18 0.44
34 23 0.56
ACGTcount: A:0.26, C:0.28, G:0.01, T:0.45
Consensus pattern (33 bp):
AATTTCTCTCAATTTGCTCTCAAATTCCTTCAA
Found at i:19452876 original size:11 final size:11
Alignment explanation
Indices: 19452795--19452876 Score: 73
Period size: 11 Copynumber: 7.3 Consensus size: 11
19452785 TTCATAAACT
19452795 AATTCTCTCTCA
1 AATT-TCTCTCA
19452807 AATTTTCTCTC-
1 AA-TTTCTCTCA
19452818 AATTTCT-TCTA
1 AATTTCTCTC-A
19452829 AATTTCCTCTC-
1 AATTT-CTCTCA
19452840 AATTTGCTCTCA
1 AATTT-CTCTCA
*
19452852 AATTCCT-TCAA
1 AATTTCTCTC-A
19452863 AATTTCTCTCA
1 AATTTCTCTCA
19452874 AAT
1 AAT
19452877 CCATATTTAT
Statistics
Matches: 59, Mismatches: 3, Indels: 17
0.75 0.04 0.22
Matches are distributed among these distances:
9 2 0.03
10 7 0.12
11 30 0.51
12 16 0.27
13 4 0.07
ACGTcount: A:0.27, C:0.27, G:0.01, T:0.45
Consensus pattern (11 bp):
AATTTCTCTCA
Found at i:19455330 original size:22 final size:21
Alignment explanation
Indices: 19455315--19455790 Score: 542
Period size: 22 Copynumber: 22.0 Consensus size: 21
19455305 TAAAAACCCT
*
19455315 AACCCTAACCCTTAAATTAAA
1 AACCCTAACCCTTAACTTAAA
* *
19455336 AATCCTAAACCCTTAACCTAAA
1 AACCCT-AACCCTTAACTTAAA
*
19455358 AACCCTAAACCCTTAATTTAAA
1 AACCCT-AACCCTTAACTTAAA
* *
19455380 AACCCTAACCTATTAACCTAAA
1 AACCCTAACC-CTTAACTTAAA
* *
19455402 AACCCTAACCTTTAACTTTAA
1 AACCCTAACCCTTAACTTAAA
* *
19455423 AACCCTAAACCTTTAAATTAAA
1 AACCCT-AACCCTTAACTTAAA
19455445 AACCCTAAACCCTTAACTT-AA
1 AACCCT-AACCCTTAACTTAAA
** *
19455466 AACCCATAAACTATTAACCTAAA
1 AACCC-T-AACCCTTAACTTAAA
19455489 AACCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
19455510 AACCCTAACCCCTTAACTTAAA
1 AACCCTAA-CCCTTAACTTAAA
*
19455532 AATCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
*
19455553 AAACCTAACCCTTTAACTTAAA
1 AACCCTAACCC-TTAACTTAAA
19455575 AACCCTAAACCCTTAACTTAAA
1 AACCCT-AACCCTTAACTTAAA
* ** *
19455597 AACACTAACTTTTAACTTTAA
1 AACCCTAACCCTTAACTTAAA
*
19455618 AACCCTAAACCCTTAAATTAAA
1 AACCCT-AACCCTTAACTTAAA
*
19455640 AACCCTAAACCCTTAAATTAAA
1 AACCCT-AACCCTTAACTTAAA
*
19455662 AACCCTAACCCCTTAAATT-AA
1 AACCCTAA-CCCTTAACTTAAA
*
19455683 AACCCATAAACCCTTAACCTAAA
1 AACCC-T-AACCCTTAACTTAAA
*
19455706 AACCTTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
*
19455727 AACCCTAACCCTTAACTTTAA
1 AACCCTAACCCTTAACTTAAA
* *
19455748 AACCCTAAACCATTAAATTAAA
1 AACCCT-AACCCTTAACTTAAA
*
19455770 AACCCTAACCATTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
19455791 TATAATTTGA
Statistics
Matches: 397, Mismatches: 44, Indels: 28
0.85 0.09 0.06
Matches are distributed among these distances:
21 152 0.38
22 225 0.57
23 20 0.05
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.25
Consensus pattern (21 bp):
AACCCTAACCCTTAACTTAAA
Found at i:19455386 original size:65 final size:64
Alignment explanation
Indices: 19455315--19455790 Score: 573
Period size: 65 Copynumber: 7.3 Consensus size: 64
19455305 TAAAAACCCT
* * * * *
19455315 AACCCTAACCCTTAAATTAAAAATCCTAAACCCTTAACCTAAAAACCCTAAACCCTTAATTTAAA
1 AACCCTAACCCTTAACTTAAAAACCCT-AACCCTTAACTTTAAAACCCTAAACCCTTAAATTAAA
* * * *
19455380 AACCCTAACCTATTAACCTAAAAACCCTAACCTTTAACTTTAAAACCCTAAACCTTTAAATTAAA
1 AACCCTAACC-CTTAACTTAAAAACCCTAACCCTTAACTTTAAAACCCTAAACCCTTAAATTAAA
** * * *
19455445 AACCCTAAACCCTTAACTT-AAAACCCATAAACTATTAACCTAAAAACCCT-AACCCTTAACTTA
1 AACCCT-AACCCTTAACTTAAAAACCC-T-AACCCTTAACTTTAAAACCCTAAACCCTTAAATTA
19455508 AA
63 AA
* * * *
19455510 AACCCTAACCCCTTAACTTAAAAATCCTAACCCTTAACTTAAAAAACCT-AACCCTTTAACTTAA
1 AACCCTAA-CCCTTAACTTAAAAACCCTAACCCTTAACTTTAAAACCCTAAACCC-TTAAATTAA
19455574 A
64 A
* **
19455575 AACCCTAAACCCTTAACTTAAAAACACTAACTTTTAACTTTAAAACCCTAAACCCTTAAATTAAA
1 AACCCT-AACCCTTAACTTAAAAACCCTAACCCTTAACTTTAAAACCCTAAACCCTTAAATTAAA
* * **
19455640 AACCCTAAACCCTTAAATTAAAAACCCTAACCCCTTAA-ATTAAAACCCATAAACCCTTAACCTA
1 AACCCT-AACCCTTAACTTAAAAACCCTAA-CCCTTAACTTTAAAACCC-TAAACCCTTAAATTA
19455704 AA
63 AA
* *
19455706 AACCTTAACCCTTAACTTAAAAACCCTAACCCTTAACTTTAAAACCCTAAACCATTAAATTAAA
1 AACCCTAACCCTTAACTTAAAAACCCTAACCCTTAACTTTAAAACCCTAAACCCTTAAATTAAA
*
19455770 AACCCTAACCATTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
19455791 TATAATTTGA
Statistics
Matches: 355, Mismatches: 44, Indels: 25
0.84 0.10 0.06
Matches are distributed among these distances:
64 71 0.20
65 212 0.60
66 72 0.20
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.25
Consensus pattern (64 bp):
AACCCTAACCCTTAACTTAAAAACCCTAACCCTTAACTTTAAAACCCTAAACCCTTAAATTAAA
Found at i:19455445 original size:43 final size:43
Alignment explanation
Indices: 19455315--19455790 Score: 552
Period size: 43 Copynumber: 11.0 Consensus size: 43
19455305 TAAAAACCCT
* * *
19455315 AACCCTAACCCTTAAATTAAAAATCCTAAACCCTTAACCTAAA
1 AACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAA
* * *
19455358 AACCCTAAACCCTTAATTTAAAAACCCT-AACCTATTAACCTAAA
1 AACCCT-AACCCTTAACTTAAAAACCCTAAACC-CTTAACTTAAA
* * * *
19455402 AACCCTAACCTTTAACTTTAAAACCCTAAACCTTTAAATTAAA
1 AACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAA
** *
19455445 AACCCTAAACCCTTAACTT-AAAACCCATAAACTATTAACCTAAA
1 AACCCT-AACCCTTAACTTAAAAACCC-TAAACCCTTAACTTAAA
*
19455489 AACCCTAACCCTTAACTTAAAAACCCTAACCCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAA
* *
19455532 AATCCTAACCCTTAACTTAAAAAACCT-AACCCTTTAACTTAAA
1 AACCCTAACCCTTAACTTAAAAACCCTAAACCC-TTAACTTAAA
* ** *
19455575 AACCCTAAACCCTTAACTTAAAAACACT-AACTTTTAACTTTAA
1 AACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAA
* *
19455618 AACCCTAAACCCTTAAATTAAAAACCCTAAACCCTTAAATTAAA
1 AACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAA
* *
19455662 AACCCTAACCCCTTAAATT-AAAACCCATAAACCCTTAACCTAAA
1 AACCCTAA-CCCTTAACTTAAAAACCC-TAAACCCTTAACTTAAA
* *
19455706 AACCTTAACCCTTAACTTAAAAACCCT-AACCCTTAACTTTAA
1 AACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAA
* * *
19455748 AACCCTAAACCATTAAATTAAAAACCCT-AACCATTAACTTAAA
1 AACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAA
19455791 TATAATTTGA
Statistics
Matches: 376, Mismatches: 44, Indels: 26
0.84 0.10 0.06
Matches are distributed among these distances:
42 22 0.06
43 200 0.53
44 154 0.41
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.25
Consensus pattern (43 bp):
AACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAA
Found at i:19459537 original size:125 final size:124
Alignment explanation
Indices: 19458957--19459522 Score: 720
Period size: 124 Copynumber: 4.5 Consensus size: 124
19458947 CCTAAACATG
* * * *
19458957 CTACTGTAGCAAAAACGTGTCCACGTGGGCACGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGACTTCACAAATTCTTCTCATAAAGCATCCTGC
* * * * * * *
19459022 TAGAAGTGATTTTATACTATTTGCTCAGAAACGTCAAGTCAAAATTATTTTTCCAAGAC
66 TTGAAGCGTTTTTAAACTATTTGCTCAAAAACGTCAACTCAAAATTATTTTTCCAGGAC
* * * *
19459081 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAACTCTTCTCA-AATAGCATGCTG
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGACTTCACAAATTCTTCTCATAA-AGCATCCTG
* ** * * *
19459145 CTTGCAGCGTTGTTTTATGCTATTTGTTCAAGAACGTCAACTCAAAATTATTTTTTCAGGAC
65 CTTGAAGCG-T-TTTTAAACTATTTGCTCAAAAACGTCAACTCAAAATTATTTTTCCAGGAC
* * * *
19459207 CCACTGTAGCAAAAGCGCGTCCACGTGGGCGCGACTTCTCAAATTCTTCTTATAAATCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGACTTCACAAATTCTTCTCATAAAGCATCCTGC
* *
19459272 TTGAAGCGTTTTTAAACTATTTGCTCAAAAATGTCAACTCGAAATTATTTCTTCCAGGAC
66 TTGAAGCGTTTTTAAACTATTTGCTCAAAAACGTCAACTCAAAATTATTT-TTCCAGGAC
* * *
19459332 CAACTGTAGCAAAAGCGCGTCCACGAGGGCGCGAATTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGACTTCACAAATTCTTCTCATAAAGCATCCTGC
* ** *
19459397 TTGAAGCGTTTTTAAACTATTTGCTCAAAAACGTCAAGTTGAAATTATTTTTCTAGGAC
66 TTGAAGCGTTTTTAAACTATTTGCTCAAAAACGTCAACTCAAAATTATTTTTCCAGGAC
* * * * * * *
19459456 CTATTGTAGCAAAAGCGCGTACACGTGGCCGCGACTTCAAAAATCCTTCTGATAAATCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGACTTCACAAATTCTTCTCATAAAGCATCCTGC
19459521 TT
66 TT
19459523 TGATTTTATC
Statistics
Matches: 384, Mismatches: 53, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
123 2 0.01
124 161 0.42
125 115 0.30
126 104 0.27
127 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGACTTCACAAATTCTTCTCATAAAGCATCCTGC
TTGAAGCGTTTTTAAACTATTTGCTCAAAAACGTCAACTCAAAATTATTTTTCCAGGAC
Found at i:19464858 original size:30 final size:30
Alignment explanation
Indices: 19464824--19464883 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
19464814 CGAGTGTGAG
19464824 CTCGAACCAATTGAACCAAAACACAGAACT
1 CTCGAACCAATTGAACCAAAACACAGAACT
*
19464854 CTCGAACCAATTGAATCAAAACACAGAACT
1 CTCGAACCAATTGAACCAAAACACAGAACT
19464884 AGAAAAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.47, C:0.28, G:0.10, T:0.15
Consensus pattern (30 bp):
CTCGAACCAATTGAACCAAAACACAGAACT
Found at i:19465383 original size:25 final size:25
Alignment explanation
Indices: 19465355--19465425 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
19465345 TCTCATCACA
19465355 ATTTTACACCGATAAAATTTTGACG
1 ATTTTACACCGATAAAATTTTGACG
* *
19465380 ATTTT-CCCCTAGTAAAATTTTGACG
1 ATTTTACACCGA-TAAAATTTTGACG
* *
19465405 ATTTTACCATCGGTAAAATTT
1 ATTTTA-CACCGATAAAATTT
19465426 CGAGAAAATT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
24 4 0.11
25 23 0.62
26 8 0.22
27 2 0.05
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.39
Consensus pattern (25 bp):
ATTTTACACCGATAAAATTTTGACG
Found at i:19466695 original size:18 final size:17
Alignment explanation
Indices: 19466643--19466695 Score: 79
Period size: 18 Copynumber: 3.0 Consensus size: 17
19466633 TTATTATTAA
19466643 ATATAATTTAATAAAAAT
1 ATATAATTTAAT-AAAAT
19466661 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
*
19466678 ATATGAATTTACTAAAAT
1 ATAT-AATTTAATAAAAT
19466696 CATAATGTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
17 9 0.27
18 24 0.73
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:19470290 original size:29 final size:28
Alignment explanation
Indices: 19470246--19470342 Score: 90
Period size: 29 Copynumber: 3.5 Consensus size: 28
19470236 ATAATATATG
*
19470246 TAAATTAAAATATTAAAACAAATTTAAA
1 TAAATTAAAATATTAAAACAAATTGAAA
* *
19470274 TAAATTAACAATATTAAAATAAGTTGAAA
1 TAAATTAA-AATATTAAAACAAATTGAAA
* * * *
19470303 TGAATTAAAGATGTTAAAA-TATTTGAAA
1 TAAATTAAA-ATATTAAAACAAATTGAAA
*
19470331 GAAA-TAAAATAT
1 TAAATTAAAATAT
19470343 CTATATAACA
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
26 3 0.05
27 4 0.07
28 18 0.32
29 32 0.56
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (28 bp):
TAAATTAAAATATTAAAACAAATTGAAA
Found at i:19470686 original size:21 final size:21
Alignment explanation
Indices: 19470653--19470700 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
19470643 TAATATTAAT
** *
19470653 AATAATGAAAATAGTAATAAC
1 AATAATGAAAATAACAACAAC
* *
19470674 AATAATTATAATAACAACAAC
1 AATAATGAAAATAACAACAAC
19470695 AATAAT
1 AATAAT
19470701 CTTAATATTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.62, C:0.08, G:0.04, T:0.25
Consensus pattern (21 bp):
AATAATGAAAATAACAACAAC
Found at i:19474986 original size:21 final size:21
Alignment explanation
Indices: 19474960--19475001 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
19474950 TTAAATGTTG
19474960 ACCTGTCATCTACGTGGCAAT
1 ACCTGTCATCTACGTGGCAAT
19474981 ACCTGTCATCTACGTGGCAAT
1 ACCTGTCATCTACGTGGCAAT
19475002 CCATGTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.29
Consensus pattern (21 bp):
ACCTGTCATCTACGTGGCAAT
Found at i:19476315 original size:55 final size:55
Alignment explanation
Indices: 19476249--19476364 Score: 214
Period size: 55 Copynumber: 2.1 Consensus size: 55
19476239 TATATAAATA
*
19476249 AATAAAACAGAACAACACAAAAATAAATAAATAAATAAAAGCTTGAAACTAAACG
1 AATAATACAGAACAACACAAAAATAAATAAATAAATAAAAGCTTGAAACTAAACG
*
19476304 AATAATACAGAACAACACAAAAATAAATAAATAAATAAATGCTTGAAACTAAACG
1 AATAATACAGAACAACACAAAAATAAATAAATAAATAAAAGCTTGAAACTAAACG
19476359 AATAAT
1 AATAAT
19476365 GATTAAATTG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 59 1.00
ACGTcount: A:0.64, C:0.12, G:0.07, T:0.17
Consensus pattern (55 bp):
AATAATACAGAACAACACAAAAATAAATAAATAAATAAAAGCTTGAAACTAAACG
Found at i:19477369 original size:15 final size:16
Alignment explanation
Indices: 19477351--19477380 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19477341 TGTTTATTAT
19477351 TTCTCT-TTGCTACTG
1 TTCTCTGTTGCTACTG
19477366 TTCTCTGTTGCTACT
1 TTCTCTGTTGCTACT
19477381 TTGCGTGTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.07, C:0.27, G:0.13, T:0.53
Consensus pattern (16 bp):
TTCTCTGTTGCTACTG
Found at i:19477567 original size:18 final size:19
Alignment explanation
Indices: 19477528--19477570 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
19477518 TTTTCTTAAT
*
19477528 TTTTGGGTTTGTAATGTTTA
1 TTTTGGCTTTGTAA-GTTTA
19477548 TTTTGGCTTTGTAA-TTTA
1 TTTTGGCTTTGTAAGTTTA
19477566 TTTTG
1 TTTTG
19477571 TTAGGCTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
20 13 0.59
ACGTcount: A:0.14, C:0.02, G:0.21, T:0.63
Consensus pattern (19 bp):
TTTTGGCTTTGTAAGTTTA
Found at i:19478005 original size:94 final size:94
Alignment explanation
Indices: 19477904--19478081 Score: 275
Period size: 94 Copynumber: 1.9 Consensus size: 94
19477894 GGCTGGTGGT
* *
19477904 TTTAATCTACTTCACTGCATCTTCAGGGAGATAAGATTCGCCATGATGACTTCAATCCATCCCAC
1 TTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTCGCCATGATGACTTCAATCCATCCCAC
*
19477969 TGCAACTTTAGGGGTATAGAATTAGTTGC
66 TGCAACTTCAGGGGTATAGAATTAGTTGC
* * * * *
19477998 TTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTCGTCATGATGGCTTCAATCCATCCCAT
1 TTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTCGCCATGATGACTTCAATCCATCCCAC
*
19478063 TGTAACTTCAGGGGTATAG
66 TGCAACTTCAGGGGTATAG
19478082 GATTTGTGGT
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
94 75 1.00
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (94 bp):
TTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATTCGCCATGATGACTTCAATCCATCCCAC
TGCAACTTCAGGGGTATAGAATTAGTTGC
Found at i:19482244 original size:64 final size:64
Alignment explanation
Indices: 19482168--19482295 Score: 247
Period size: 64 Copynumber: 2.0 Consensus size: 64
19482158 TGATAAAGTT
*
19482168 ATAATAACAACACCAAATAATAATAACAATAATCATATTAACTACTATTTTAATATTAAAAATA
1 ATAATAACAACACCAAATAATAATAACAATAATCATATTAACTACTATTCTAATATTAAAAATA
19482232 ATAATAACAACACCAAATAATAATAACAATAATCATATTAACTACTATTCTAATATTAAAAATA
1 ATAATAACAACACCAAATAATAATAACAATAATCATATTAACTACTATTCTAATATTAAAAATA
19482296 GTAAAAGTGA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.30
Consensus pattern (64 bp):
ATAATAACAACACCAAATAATAATAACAATAATCATATTAACTACTATTCTAATATTAAAAATA
Found at i:19483669 original size:20 final size:18
Alignment explanation
Indices: 19483646--19483688 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
19483636 TTTTTTTAAT
*
19483646 TTTTGGGTTTCTAATGTTTA
1 TTTTGGCTTTCTAA--TTTA
*
19483666 TTTTGGCTTTGTAATTTA
1 TTTTGGCTTTCTAATTTA
19483684 TTTTG
1 TTTTG
19483689 TTGGGCCTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 9 0.43
20 12 0.57
ACGTcount: A:0.14, C:0.05, G:0.19, T:0.63
Consensus pattern (18 bp):
TTTTGGCTTTCTAATTTA
Found at i:19484153 original size:143 final size:143
Alignment explanation
Indices: 19483976--19484568 Score: 644
Period size: 143 Copynumber: 4.2 Consensus size: 143
19483966 TTTTAATCTA
* * * * *
19483976 CTCCACTGCAACTTCAGGAAGAT-AGGATTGGTGGCTTCAATATGCTCCACTGCAACTTCAAGTA
1 CTCCACTGCAATTTCAGGGAGATAAGG-CTGGTGGCTTCAATCTGCTCCACTGCAACTTCAAGAA
* * * * *
19484040 GATAAGATCCTCCATAATTTGTAACTCTAATCTGTTCCATTGCAACGTCAGGGAAATAAGATTCG
65 GATAAGATCCGCCATAATTTGTAGCTTTAATTTGTTCCATTGCAACGCCAGGGAAATAAGATTCG
*
19484105 CTGTTTTCAGTCTG
130 CTGTCTTCAGTCTG
* * * * *
19484119 CTCCACTACAATTTCAGGGAGATAAGGCTAGTGGCTTGAATCTGCTCCACTGCAACTTTAGGAAG
1 CTCCACTGCAATTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAAGAAG
*
19484184 ATAAGATCCGCCATAATTTGTAGCTTTAATTTGTTCCACTGCAACGCCAGGGAAATAAGATTCGC
66 ATAAGATCCGCCATAATTTGTAGCTTTAATTTGTTCCATTGCAACGCCAGGGAAATAAGATTCGC
19484249 TGTCTTCAGTCTG
131 TGTCTTCAGTCTG
* * * * * * * *
19484262 CTCCACTGCAACTTCAGGGATATAAGGTTGGTGGCTTCAGTCTGCTACACTACAGCTTGAAGAAG
1 CTCCACTGCAATTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAAGAAG
* *
19484327 ATGAGATCCGCCATAATTTGTAGCTTTAATTTGTTCCATTGCAACGCCAGGGAAATAAGATTCTC
66 ATAAGATCCGCCATAATTTGTAGCTTTAATTTGTTCCATTGCAACGCCAGGGAAATAAGATTCGC
* * *
19484392 TATCTTAAATCTG
131 TGTCTTCAGTCTG
* * * * * * *
19484405 CTCCGCTGCAACTTT-AAGGAGAAAAGGCTGGTGGCTTCAATCTGTTCCACTGCATCTTCAGGGA
1 CTCCACTGCAA-TTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAAGAA
* * *** * ** ** * *
19484469 GATAAGATTCGCCATGA--TG-A-CTTTAATCCATCCCATTGCAACTTCAGGGGTATAGGATTAG
65 GATAAGATCCGCCATAATTTGTAGCTTTAATTTGTTCCATTGCAACGCCAGGGAAATAAGATTCG
* *
19484530 -TGGCTTCAATCTG
130 CTGTCTTCAGTCTG
19484543 CTCCACTGCAACTTT-AGGGAGATAAG
1 CTCCACTGCAA-TTTCAGGGAGATAAG
19484569 ATTCGCCATG
Statistics
Matches: 379, Mismatches: 69, Indels: 9
0.83 0.15 0.02
Matches are distributed among these distances:
138 33 0.09
139 30 0.08
140 1 0.00
141 2 0.01
143 308 0.81
144 5 0.01
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (143 bp):
CTCCACTGCAATTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAAGAAG
ATAAGATCCGCCATAATTTGTAGCTTTAATTTGTTCCATTGCAACGCCAGGGAAATAAGATTCGC
TGTCTTCAGTCTG
Found at i:19484287 original size:45 final size:44
Alignment explanation
Indices: 19484218--19484312 Score: 118
Period size: 45 Copynumber: 2.1 Consensus size: 44
19484208 TTTAATTTGT
*
19484218 TCCACTGCAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGC
1 TCCACTGCAACGCCAGGGAAATAAGATT-GCTGGCTTCAGTCTGC
** * * *
19484263 TCCACTGCAACTTCAGGGATATAAGGTTGGTGGCTTCAGTCTGC
1 TCCACTGCAACGCCAGGGAAATAAGATTGCTGGCTTCAGTCTGC
*
19484307 TACACT
1 TCCACT
19484313 ACAGCTTGAA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 19 0.44
45 24 0.56
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.27
Consensus pattern (44 bp):
TCCACTGCAACGCCAGGGAAATAAGATTGCTGGCTTCAGTCTGC
Found at i:19484542 original size:94 final size:94
Alignment explanation
Indices: 19484435--19484621 Score: 311
Period size: 94 Copynumber: 2.0 Consensus size: 94
19484425 GAAAAGGCTG
* *
19484435 GTGGCTTCAATCTGTTCCACTGCATCTTCAGGGAGATAAGATTCGCCATGATGACTTTAATCCAT
1 GTGGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATGATGACTTTAATCCAT
*
19484500 CCCATTGCAACTTCAGGGGTATAGGATTA
66 CCCACTGCAACTTCAGGGGTATAGGATTA
* * *
19484529 GTGGCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTCGCCATGATGGCTTTAATTCAT
1 GTGGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATGATGACTTTAATCCAT
*
19484594 CCCACTGTAACTTCAGGGGTATAGGATT
66 CCCACTGCAACTTCAGGGGTATAGGATT
19484622 TATGGTTTTA
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
94 86 1.00
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (94 bp):
GTGGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATGATGACTTTAATCCAT
CCCACTGCAACTTCAGGGGTATAGGATTA
Found at i:19484606 original size:50 final size:50
Alignment explanation
Indices: 19484451--19484611 Score: 160
Period size: 50 Copynumber: 3.3 Consensus size: 50
19484441 TCAATCTGTT
* * *
19484451 CCACTGCATCTTCAGGGAGATAAGATTCGCCATGATGACTTTAATCCATC
1 CCACTGCAACTTCAGGGAGATAAGATTCGCCATGATGGCTTTAATTCATC
* * *
19484501 CCATTGCAACTTCAGGG-GTATAGGATT----A-G-TGGCTTCAA-TC-TGC
1 CCACTGCAACTTCAGGGAG-ATAAGATTCGCCATGATGGCTTTAATTCAT-C
*
19484544 TCCACTGCAACTTTAGGGAGATAAGATTCGCCATGATGGCTTTAATTCATC
1 -CCACTGCAACTTCAGGGAGATAAGATTCGCCATGATGGCTTTAATTCATC
*
19484595 CCACTGTAACTTCAGGG
1 CCACTGCAACTTCAGGG
19484612 GTATAGGATT
Statistics
Matches: 87, Mismatches: 12, Indels: 24
0.71 0.10 0.20
Matches are distributed among these distances:
42 1 0.01
43 2 0.02
44 29 0.33
45 2 0.02
46 1 0.01
48 1 0.01
49 2 0.02
50 45 0.52
51 3 0.03
52 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (50 bp):
CCACTGCAACTTCAGGGAGATAAGATTCGCCATGATGGCTTTAATTCATC
Found at i:19485302 original size:20 final size:18
Alignment explanation
Indices: 19485277--19485319 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
19485267 TTTTTTTAAT
19485277 TTTTGGGCTTGTAATGTTTA
1 TTTTGGGCTTGTAA--TTTA
**
19485297 TTTTGGTTTTGTAATTTA
1 TTTTGGGCTTGTAATTTA
19485315 TTTTG
1 TTTTG
19485320 TTGGGCCCGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 9 0.43
20 12 0.57
ACGTcount: A:0.14, C:0.02, G:0.21, T:0.63
Consensus pattern (18 bp):
TTTTGGGCTTGTAATTTA
Found at i:19488717 original size:33 final size:33
Alignment explanation
Indices: 19488696--19488758 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
19488686 GTAAAATAAT
19488696 AAAAAACAAAACTAATGAAAATAAAACAAAATA
1 AAAAAACAAAACTAATGAAAATAAAACAAAATA
19488729 AAAAAACAAAACTAATGAAAATAAAACAAA
1 AAAAAACAAAACTAATGAAAATAAAACAAA
19488759 CTTATGTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.76, C:0.10, G:0.03, T:0.11
Consensus pattern (33 bp):
AAAAAACAAAACTAATGAAAATAAAACAAAATA
Found at i:19488754 original size:15 final size:15
Alignment explanation
Indices: 19488698--19488755 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
19488688 AAAATAATAA
19488698 AAAACAAAACTAATG
1 AAAACAAAACTAATG
* * *
19488713 AAAATAAAACAAAATAAA
1 AAAACAAAAC-TAAT--G
19488731 AAAACAAAACTAATG
1 AAAACAAAACTAATG
*
19488746 AAAATAAAAC
1 AAAACAAAAC
19488756 AAACTTATGT
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
15 18 0.55
16 3 0.09
17 3 0.09
18 9 0.27
ACGTcount: A:0.74, C:0.10, G:0.03, T:0.12
Consensus pattern (15 bp):
AAAACAAAACTAATG
Found at i:19489908 original size:54 final size:54
Alignment explanation
Indices: 19489796--19489916 Score: 127
Period size: 54 Copynumber: 2.2 Consensus size: 54
19489786 CACGGGCTGT
* * ** * *
19489796 CACACGGCCTGGCTACACGGTCGTGTGTACCAAGTCAGTGTGTTACACGGCCCAG
1 CACACGG-CTTGCGACACGGTCGTGTGTACCAAGTCAAAGAGTTACACGGACCAG
* * **
19489851 CACATGGCTTGCGACACGGTCGTGTGT-CGCAAGTCAAAGAGTTACATGGACTGG
1 CACACGGCTTGCGACACGGTCGTGTGTAC-CAAGTCAAAGAGTTACACGGACCAG
19489905 CACACGGCTTGC
1 CACACGGCTTGC
19489917 AACATAATCG
Statistics
Matches: 54, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
53 1 0.02
54 47 0.87
55 6 0.11
ACGTcount: A:0.21, C:0.28, G:0.30, T:0.21
Consensus pattern (54 bp):
CACACGGCTTGCGACACGGTCGTGTGTACCAAGTCAAAGAGTTACACGGACCAG
Found at i:19492871 original size:14 final size:15
Alignment explanation
Indices: 19492846--19492881 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
19492836 ATTCTCCAAT
19492846 ATGATCATTTGTTAA
1 ATGATCATTTGTTAA
19492861 ATGAT-ATTTGTTAA
1 ATGATCATTTGTTAA
*
19492875 ATAATCA
1 ATGATCA
19492882 CAACTCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.44
Consensus pattern (15 bp):
ATGATCATTTGTTAA
Found at i:19505829 original size:26 final size:26
Alignment explanation
Indices: 19505792--19505842 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
19505782 ACTTTATGAT
* *
19505792 TTCATGAGTGTATAAATATAAACCAC
1 TTCATGAGTGTAAAAAGATAAACCAC
19505818 TTCATGCA-TGTAAAAAGATAAACCA
1 TTCATG-AGTGTAAAAAGATAAACCA
19505843 AACTTCAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 21 0.95
27 1 0.05
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.27
Consensus pattern (26 bp):
TTCATGAGTGTAAAAAGATAAACCAC
Found at i:19508256 original size:13 final size:12
Alignment explanation
Indices: 19508226--19508269 Score: 56
Period size: 13 Copynumber: 3.8 Consensus size: 12
19508216 TATTCCTAGA
19508226 AAAATA-ATTAT
1 AAAATATATTAT
19508237 AAAATATATCTAT
1 AAAATATAT-TAT
*
19508250 AATATATATTAT
1 AAAATATATTAT
19508262 AAAA-ATAT
1 AAAATATAT
19508270 GAATTTGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 10 0.34
12 8 0.28
13 11 0.38
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (12 bp):
AAAATATATTAT
Found at i:19513679 original size:21 final size:22
Alignment explanation
Indices: 19513635--19513681 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
19513625 TCCTGGGAGT
* *
19513635 TCTACAATGCCCAACTACAGTC
1 TCTAAAATGCCCAACTAAAGTC
*
19513657 TCTAAAATGCGCAA-TAAAGTC
1 TCTAAAATGCCCAACTAAAGTC
19513678 TCTA
1 TCTA
19513682 CCAAGCCTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.36, C:0.28, G:0.11, T:0.26
Consensus pattern (22 bp):
TCTAAAATGCCCAACTAAAGTC
Found at i:19519841 original size:28 final size:27
Alignment explanation
Indices: 19519801--19519855 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 27
19519791 AGCGAGTGAA
19519801 CCGCTCAGAGAGGATCTCTAATGTAGT
1 CCGCTCAGAGAGGATCTCTAATGTAGT
*
19519828 NCCGCTCAGAGAGGTTCTCTAATGTAGT
1 -CCGCTCAGAGAGGATCTCTAATGTAGT
19519856 AGCAAAAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.27
Consensus pattern (27 bp):
CCGCTCAGAGAGGATCTCTAATGTAGT
Found at i:19521292 original size:45 final size:43
Alignment explanation
Indices: 19521241--19521324 Score: 116
Period size: 45 Copynumber: 1.9 Consensus size: 43
19521231 CTAAAGAAAA
19521241 TAATAAGAATAATAAGAAT-AAATAGAAAATAAAAACAAAAAATAT
1 TAATAAGAATAATAA-AATAAAAT-G-AAATAAAAACAAAAAATAT
* *
19521286 TAATAAGAATAATAAAGTAAAATGAAATAAAAATAAAAA
1 TAATAAGAATAATAAAATAAAATGAAATAAAAACAAAAA
19521325 TAAAGAACTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
43 14 0.39
44 3 0.08
45 19 0.53
ACGTcount: A:0.71, C:0.01, G:0.07, T:0.20
Consensus pattern (43 bp):
TAATAAGAATAATAAAATAAAATGAAATAAAAACAAAAAATAT
Found at i:19533544 original size:17 final size:17
Alignment explanation
Indices: 19533518--19533556 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
19533508 AGAAAATTAG
* *
19533518 AAAATAAAAATTAAACTA
1 AAAACAAAAA-TAAAATA
19533536 AAAACAAAAATAAAATA
1 AAAACAAAAATAAAATA
19533553 AAAA
1 AAAA
19533557 AAGGCTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.15
Consensus pattern (17 bp):
AAAACAAAAATAAAATA
Found at i:19533812 original size:21 final size:21
Alignment explanation
Indices: 19533788--19533827 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
19533778 TTTTTAATCT
19533788 AAAATTACTAAACTAATTTTC
1 AAAATTACTAAACTAATTTTC
19533809 AAAATTACTAAACTAATTT
1 AAAATTACTAAACTAATTT
19533828 ATCTAAGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAATTACTAAACTAATTTTC
Found at i:19545086 original size:4 final size:4
Alignment explanation
Indices: 19545077--19545103 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
19545067 GGATACTGAT
19545077 ATGA ATGA ATGA ATGA ATGA ATGA ATG
1 ATGA ATGA ATGA ATGA ATGA ATGA ATG
19545104 CATACTCGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.26, T:0.26
Consensus pattern (4 bp):
ATGA
Found at i:19552047 original size:19 final size:20
Alignment explanation
Indices: 19552007--19552050 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
19551997 GTCTCTTTAG
* *
19552007 GCATT-CATTTCATGCATTT
1 GCATTACATTGCATGCATAT
19552026 GCATTACATTGCAT-CATAT
1 GCATTACATTGCATGCATAT
19552045 GCATTA
1 GCATTA
19552051 GATTTTCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (20 bp):
GCATTACATTGCATGCATAT
Found at i:19554581 original size:20 final size:19
Alignment explanation
Indices: 19554556--19554619 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 19
19554546 AAAATCAAAG
19554556 TCAAAATGAAAATGAAAAAA
1 TCAAAAT-AAAATGAAAAAA
19554576 TCAAAAATAAAAAT-AAAAAA
1 TC-AAAAT-AAAATGAAAAAA
* *
19554596 ACAAAA-AGAA-GAAAAAA
1 TCAAAATAAAATGAAAAAA
19554613 TCAAAAT
1 TCAAAAT
19554620 CAAGATCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
17 14 0.38
19 4 0.11
20 9 0.24
21 10 0.27
ACGTcount: A:0.75, C:0.06, G:0.06, T:0.12
Consensus pattern (19 bp):
TCAAAATAAAATGAAAAAA
Found at i:19554588 original size:21 final size:20
Alignment explanation
Indices: 19554558--19554602 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
19554548 AATCAAAGTC
* *
19554558 AAAATGAAAATGAAAAAATCA
1 AAAATAAAAAT-AAAAAAACA
19554579 AAAATAAAAATAAAAAAACA
1 AAAATAAAAATAAAAAAACA
19554599 AAAA
1 AAAA
19554603 GAAGAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.80, C:0.04, G:0.04, T:0.11
Consensus pattern (20 bp):
AAAATAAAAATAAAAAAACA
Found at i:19555572 original size:15 final size:16
Alignment explanation
Indices: 19555552--19555581 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
19555542 GAAGAAGAAG
19555552 ATGAAAAA-TAAAAAA
1 ATGAAAAAGTAAAAAA
19555567 ATGAAAAAGTAAAAA
1 ATGAAAAAGTAAAAA
19555582 TGGAGAGGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (16 bp):
ATGAAAAAGTAAAAAA
Found at i:19556910 original size:44 final size:44
Alignment explanation
Indices: 19556862--19557088 Score: 135
Period size: 44 Copynumber: 5.2 Consensus size: 44
19556852 AGACACAAAC
19556862 CTTGCCTCTCTCGGTTATGATGGAGCTGGTTGAAGACAAAAGAT
1 CTTGCCTCTCTCGGTTATGATGGAGCTGGTTGAAGACAAAAGAT
* * * * * * *
19556906 CTTGCCT-TC-CTG-CATTGACAGCGAAGCAGGTCGAAGACACAA-AC
1 CTTGCCTCTCTCGGTTA-TGA-TG-G-AGCTGGTTGAAGACAAAAGAT
* * * *
19556950 CTTTCCTCTCTTGGTTGTGATGGAGCTGGTTGAAGACAAAGGAT
1 CTTGCCTCTCTCGGTTATGATGGAGCTGGTTGAAGACAAAAGAT
* * ** * * * * *
19556994 CTTGCATTTCT-GCAT-TGATAGCGAAGCAGATCGAAGACACAA-AC
1 CTTGCCTCTCTCGGTTATGAT-G-G-AGCTGGTTGAAGACAAAAGAT
* * *
19557038 CTTGCCTCTTTCGGTTGTGATAGAGCTGGTTGAAGACAAAAGAT
1 CTTGCCTCTCTCGGTTATGATGGAGCTGGTTGAAGACAAAAGAT
19557082 CTTGCCT
1 CTTGCCT
19557089 TCCTGCATTG
Statistics
Matches: 129, Mismatches: 40, Indels: 28
0.65 0.20 0.14
Matches are distributed among these distances:
41 1 0.01
42 9 0.07
43 34 0.26
44 44 0.34
45 33 0.26
46 8 0.06
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (44 bp):
CTTGCCTCTCTCGGTTATGATGGAGCTGGTTGAAGACAAAAGAT
Found at i:19556971 original size:88 final size:88
Alignment explanation
Indices: 19556814--19557283 Score: 621
Period size: 88 Copynumber: 5.4 Consensus size: 88
19556804 ATGAAGTTGC
*
19556814 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTA
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
19556879 TGATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
* *
19556902 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTTCCTCTCTTGGTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
19556967 TGATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
* * * * * *
19556990 GGATCTTGCATTTCTGCATTGATAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
*
19557055 TGATAGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
*
19557078 AGATCTTGCCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
* **
19557143 T-AGTGGAGCTGGTTAAAGA-AGC
66 TGA-TGGAGCTGGTTGAAGACAAA
* * * * *
19557165 AGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAA-A-ACAAAGCCTTGCATC-CATCGAT
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAA-CCTTGCCTCTC-TCGGT
* * * **
19557227 TG-CAGTGGAGCTAGTTAAAGA-AGC
64 TGTGA-TGGAGCTGGTTGAAGACAAA
* *
19557251 AGATCTTGCCTTCCTGCATTAACAGCAAAGCAG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAG
19557284 ATCAAAAAAA
Statistics
Matches: 346, Mismatches: 32, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
85 6 0.02
86 66 0.19
87 37 0.11
88 237 0.68
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (88 bp):
AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
TGATGGAGCTGGTTGAAGACAAA
Found at i:19559161 original size:3 final size:3
Alignment explanation
Indices: 19559149--19559184 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
19559139 ATTATTTTGT
*
19559149 TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA CTTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TT
19559185 TGTTTATGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:19559161 original size:9 final size:9
Alignment explanation
Indices: 19559136--19559178 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
19559126 TTTTTTCCAC
19559136 TTTATTATT
1 TTTATTATT
19559145 TTGT-TTATT
1 TT-TATTATT
19559154 TTTATTATT
1 TTTATTATT
*
19559163 ATTATTATT
1 TTTATTATT
*
19559172 ATTATTA
1 TTTATTA
19559179 CTTATTTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
8 1 0.03
9 29 0.94
10 1 0.03
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (9 bp):
TTTATTATT
Found at i:19560748 original size:3 final size:3
Alignment explanation
Indices: 19560742--19560803 Score: 56
Period size: 3 Copynumber: 21.0 Consensus size: 3
19560732 TTTAGCCATT
* *
19560742 TTA TTA TT- TTG TTTA TT- TTA TTA TTA TTA TTA TTA TTA TTA CTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
19560786 CTA CTA TTG TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
19560804 CCTATTTATT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
2 4 0.08
3 45 0.88
4 2 0.04
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:19573717 original size:76 final size:76
Alignment explanation
Indices: 19573634--19573787 Score: 263
Period size: 76 Copynumber: 2.0 Consensus size: 76
19573624 AATACTTATA
*
19573634 ATTTTTTAAAATCTAGCAGTAAGAAATTTAAATATTAACATAAATAATATGTATCTTTATTAGGT
1 ATTTTTTAAAATCTAGCAGTAAGAAATTTAAATATCAACATAAATAATATGTATCTTTATTAGGT
* *
19573699 TCATGATTCAC
66 TCACGATTAAC
* *
19573710 ATTTTTTAAAATCTAGCGGTAAGAAATTTAAATATCAACATAAATAATATTTATCTTTATTAGGT
1 ATTTTTTAAAATCTAGCAGTAAGAAATTTAAATATCAACATAAATAATATGTATCTTTATTAGGT
19573775 TCACGATTAAC
66 TCACGATTAAC
19573786 AT
1 AT
19573788 AAATTATTGT
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 73 1.00
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.40
Consensus pattern (76 bp):
ATTTTTTAAAATCTAGCAGTAAGAAATTTAAATATCAACATAAATAATATGTATCTTTATTAGGT
TCACGATTAAC
Found at i:19574409 original size:16 final size:17
Alignment explanation
Indices: 19574381--19574414 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
19574371 TGACAATTCA
19574381 TTCCAATCTATTTATTT
1 TTCCAATCTATTTATTT
19574398 TTCCAA-CTATTTATTT
1 TTCCAATCTATTTATTT
19574414 T
1 T
19574415 CTCCCCTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.24, C:0.18, G:0.00, T:0.59
Consensus pattern (17 bp):
TTCCAATCTATTTATTT
Found at i:19581592 original size:22 final size:23
Alignment explanation
Indices: 19581561--19581603 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
19581551 AAAAAAAATC
*
19581561 TGCTAATTTTATTTTTGTTTTTA
1 TGCTAATTTTATTGTTGTTTTTA
*
19581584 TGCT-ATTTTCTTGTTGTTTT
1 TGCTAATTTTATTGTTGTTTT
19581604 CTCCTTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.12, C:0.07, G:0.12, T:0.70
Consensus pattern (23 bp):
TGCTAATTTTATTGTTGTTTTTA
Found at i:19582208 original size:22 final size:23
Alignment explanation
Indices: 19582183--19582243 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 23
19582173 TATATATGGC
*
19582183 AAATATA-TTTTTTCACTATTCA
1 AAATATATTTTTTTCAATATTCA
*
19582205 AAATTTATTTTTTTCAATATTC-
1 AAATATATTTTTTTCAATATTCA
*
19582227 --ATATTTTTTTTTCAATA
1 AAATATATTTTTTTCAATA
19582244 GCCAATAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 15 0.44
22 6 0.18
23 13 0.38
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (23 bp):
AAATATATTTTTTTCAATATTCA
Found at i:19582238 original size:23 final size:23
Alignment explanation
Indices: 19582190--19582243 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
19582180 GGCAAATATA
*
19582190 TTTTTTCACTATTCAAAATTTAT
1 TTTTTTCAATATTCAAAATTTAT
*
19582213 TTTTTTCAATATTC-ATA-TT-T
1 TTTTTTCAATATTCAAAATTTAT
19582233 TTTTTTCAATA
1 TTTTTTCAATA
19582244 GCCAATAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 12 0.41
21 2 0.07
22 2 0.07
23 13 0.45
ACGTcount: A:0.28, C:0.11, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTTTTCAATATTCAAAATTTAT
Found at i:19601047 original size:23 final size:23
Alignment explanation
Indices: 19601016--19601081 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 23
19601006 TATTGGATTT
19601016 ATATATTTTAAAATTTTATAAAAA
1 ATAT-TTTTAAAATTTTATAAAAA
* *
19601040 ATATTTTTAAAACTTTTTTAAAAT
1 ATATTTTTAAAA-TTTTATAAAAA
* *
19601064 A-ATTTTTACATTTTTATA
1 ATATTTTTAAAATTTTATA
19601082 TTTTTATAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 6 0.17
23 16 0.44
24 14 0.39
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (23 bp):
ATATTTTTAAAATTTTATAAAAA
Found at i:19601151 original size:16 final size:15
Alignment explanation
Indices: 19601132--19601162 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
19601122 CACTATCCCT
19601132 TTTTTAGTAAATTTTA
1 TTTTTA-TAAATTTTA
19601148 TTTTTATAAATTTTA
1 TTTTTATAAATTTTA
19601163 ATAAATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (15 bp):
TTTTTATAAATTTTA
Found at i:19602902 original size:23 final size:24
Alignment explanation
Indices: 19602865--19602927 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 24
19602855 AAAATAATGA
*
19602865 AAAACAATA-AGAAAATAA-CAAC
1 AAAACAATATAAAAAATAAGCAAC
* *
19602887 AAAATAATATAAAAAA-AAGCAAG
1 AAAACAATATAAAAAATAAGCAAC
*
19602910 AAAACAGTA-AAAAAATAA
1 AAAACAATATAAAAAATAA
19602928 TAGTTTCTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
22 16 0.48
23 17 0.52
ACGTcount: A:0.75, C:0.08, G:0.06, T:0.11
Consensus pattern (24 bp):
AAAACAATATAAAAAATAAGCAAC
Found at i:19604519 original size:25 final size:25
Alignment explanation
Indices: 19604491--19604542 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
19604481 GCCGTATGTT
19604491 TGTTTCTTCTGATTCTGAATGTCCA
1 TGTTTCTTCTGATTCTGAATGTCCA
19604516 TGTTTCTTCTGATTCTGAATGTCCA
1 TGTTTCTTCTGATTCTGAATGTCCA
19604541 TG
1 TG
19604543 GACCATCATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.15, C:0.19, G:0.17, T:0.48
Consensus pattern (25 bp):
TGTTTCTTCTGATTCTGAATGTCCA
Found at i:19614883 original size:52 final size:48
Alignment explanation
Indices: 19614864--19615066 Score: 265
Period size: 46 Copynumber: 4.3 Consensus size: 48
19614854 TGACAAGTGG
* *
19614864 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
19614910 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-A---A
* *
19614962 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
** *
19615008 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
19615054 AAAGTGATAAGTG
1 AAAGTGATAAGTG
19615067 GCTACACTTA
Statistics
Matches: 144, Mismatches: 7, Indels: 12
0.88 0.04 0.07
Matches are distributed among these distances:
46 100 0.69
52 44 0.31
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
Found at i:19614918 original size:98 final size:98
Alignment explanation
Indices: 19614798--19615066 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
19614788 TTTGAGTACT
*
19614798 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
19614863 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
19614896 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
19614961 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
19614994 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGT
*
19615059 GATAAGTG
65 GAAAAGTG
19615067 GCTACACTTA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 149 0.93
99 11 0.07
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:19615074 original size:37 final size:37
Alignment explanation
Indices: 19615030--19615175 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
19615020 GATAGCTTTA
*
19615030 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
19615067 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
19615104 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
19615141 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
19615176 ATCATACGTA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 89 0.86
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:19619103 original size:82 final size:82
Alignment explanation
Indices: 19619015--19619177 Score: 317
Period size: 82 Copynumber: 2.0 Consensus size: 82
19619005 ACCATAAACA
*
19619015 TAATTAAAATAACTACTAAAACACTCTCAATCACTCTTAACTTGAATGAAATAAAAGCTTAAAAG
1 TAATTAAAATAACTACTAAAACACTCTCAATCACTCTGAACTTGAATGAAATAAAAGCTTAAAAG
19619080 TAATAAAATAACTCTAG
66 TAATAAAATAACTCTAG
19619097 TAATTAAAATAACTACTAAAACACTCTCAATCACTCTGAACTTGAATGAAATAAAAGCTTAAAAG
1 TAATTAAAATAACTACTAAAACACTCTCAATCACTCTGAACTTGAATGAAATAAAAGCTTAAAAG
19619162 TAATAAAATAACTCTA
66 TAATAAAATAACTCTA
19619178 TATCCTAGAG
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 80 1.00
ACGTcount: A:0.50, C:0.16, G:0.06, T:0.28
Consensus pattern (82 bp):
TAATTAAAATAACTACTAAAACACTCTCAATCACTCTGAACTTGAATGAAATAAAAGCTTAAAAG
TAATAAAATAACTCTAG
Found at i:19621651 original size:5 final size:5
Alignment explanation
Indices: 19621643--19621669 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
19621633 AAATAAAAGA
19621643 AATCT AATCT AATCT AATCT AATCT AA
1 AATCT AATCT AATCT AATCT AATCT AA
19621670 AAATATGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.37
Consensus pattern (5 bp):
AATCT
Found at i:19621981 original size:16 final size:16
Alignment explanation
Indices: 19621960--19621990 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19621950 GAGATTAAAA
*
19621960 AATTAAATTAATTAAT
1 AATTAAATCAATTAAT
19621976 AATTAAATCAATTAA
1 AATTAAATCAATTAA
19621991 ATTAGTATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
AATTAAATCAATTAAT
Found at i:19623498 original size:17 final size:17
Alignment explanation
Indices: 19623476--19623508 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
19623466 ATATTTTTTA
19623476 TTTTTAATCAAATATAC
1 TTTTTAATCAAATATAC
19623493 TTTTTAATCAAATATA
1 TTTTTAATCAAATATA
19623509 TATATTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTTAATCAAATATAC
Found at i:19636453 original size:28 final size:28
Alignment explanation
Indices: 19636410--19636465 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
19636400 ACGTATTCCC
19636410 AATTCATAAATGTCAGCTTGTGTGAGCA
1 AATTCATAAATGTCAGCTTGTGTGAGCA
*
19636438 AATTCATAAATTTCAGCTTGTGTGAGCA
1 AATTCATAAATGTCAGCTTGTGTGAGCA
19636466 CTATAATCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (28 bp):
AATTCATAAATGTCAGCTTGTGTGAGCA
Found at i:19640755 original size:20 final size:21
Alignment explanation
Indices: 19640726--19640774 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 21
19640716 TATAAACAAT
19640726 TATAT-ATATATTAGGTCGAA
1 TATATCATATATTAGGTCGAA
19640746 TATATCTATATATTAGGTCGAA
1 TATATC-ATATATTAGGTCGAA
19640768 TATATCA
1 TATATCA
19640775 GAAATATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.19
21 1 0.04
22 21 0.78
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.41
Consensus pattern (21 bp):
TATATCATATATTAGGTCGAA
Found at i:19640758 original size:22 final size:22
Alignment explanation
Indices: 19640730--19640773 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
19640720 AACAATTATA
19640730 TATATATTAGGTCGAATATATC
1 TATATATTAGGTCGAATATATC
19640752 TATATATTAGGTCGAATATATC
1 TATATATTAGGTCGAATATATC
19640774 AGAAATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (22 bp):
TATATATTAGGTCGAATATATC
Found at i:19646617 original size:16 final size:17
Alignment explanation
Indices: 19646585--19646619 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
19646575 TTTCTACTTA
*
19646585 ACATGTTTAAGTTCATT
1 ACATGATTAAGTTCATT
19646602 ACATGATTAA-TTCATT
1 ACATGATTAAGTTCATT
19646618 AC
1 AC
19646620 TTACACATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (17 bp):
ACATGATTAAGTTCATT
Found at i:19650199 original size:14 final size:14
Alignment explanation
Indices: 19650180--19650209 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19650170 TTTTTGAATT
19650180 TTGAGTTAATCGAA
1 TTGAGTTAATCGAA
*
19650194 TTGAGTTATTCGAA
1 TTGAGTTAATCGAA
19650208 TT
1 TT
19650210 ATTCAAGTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.43
Consensus pattern (14 bp):
TTGAGTTAATCGAA
Found at i:19650433 original size:18 final size:19
Alignment explanation
Indices: 19650399--19650434 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
19650389 AATAATTTTC
19650399 AAAATTCTAAATATTTATT
1 AAAATTCTAAATATTTATT
19650418 AAAATTCTAAAT-TTTAT
1 AAAATTCTAAATATTTAT
19650435 ATTTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (19 bp):
AAAATTCTAAATATTTATT
Found at i:19650445 original size:24 final size:24
Alignment explanation
Indices: 19650409--19650457 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
19650399 AAAATTCTAA
* *
19650409 ATATTTATTAAAATTCTAAATTTT
1 ATATTTATTAAAATTATAAAATTT
19650433 ATATTT-TTAAAAATTATAAAATTT
1 ATATTTATT-AAAATTATAAAATTT
19650457 A
1 A
19650458 AAAAAATCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 2 0.09
24 20 0.91
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
ATATTTATTAAAATTATAAAATTT
Found at i:19653301 original size:35 final size:36
Alignment explanation
Indices: 19653262--19653329 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
19653252 ATTAGGTTAC
*
19653262 TTATTTTTT-AAATTTTAAACTAAATTAAATTACTG
1 TTATTTTTTAAAACTTTAAACTAAATTAAATTACTG
* *
19653297 TTATTTTTTAAAACTTTACATTAAATTAAATTA
1 TTATTTTTTAAAACTTTAAACTAAATTAAATTA
19653330 TTAAAGGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 9 0.31
36 20 0.69
ACGTcount: A:0.41, C:0.06, G:0.01, T:0.51
Consensus pattern (36 bp):
TTATTTTTTAAAACTTTAAACTAAATTAAATTACTG
Found at i:19653569 original size:21 final size:21
Alignment explanation
Indices: 19653543--19653582 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
19653533 AAAAAAATCA
*
19653543 ATTTTCATTTTAG-TTTGTTTT
1 ATTTTC-TTATAGATTTGTTTT
19653564 ATTTTCTTATAGATTTGTT
1 ATTTTCTTATAGATTTGTT
19653583 CCAATGGGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.17, C:0.05, G:0.10, T:0.68
Consensus pattern (21 bp):
ATTTTCTTATAGATTTGTTTT
Found at i:19677693 original size:12 final size:11
Alignment explanation
Indices: 19677676--19677709 Score: 52
Period size: 10 Copynumber: 3.1 Consensus size: 11
19677666 TTCACACACG
19677676 AAAAAAAAGCAA
1 AAAAAAAAG-AA
19677688 AAAAAAAAG-A
1 AAAAAAAAGAA
19677698 AAAAAAAAGAA
1 AAAAAAAAGAA
19677709 A
1 A
19677710 GGGGAGAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.48
11 2 0.10
12 9 0.43
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:19678011 original size:22 final size:20
Alignment explanation
Indices: 19677965--19678017 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
19677955 AGGCCGGAGA
19677965 AGAGAAAGGGGGTGAGATAG
1 AGAGAAAGGGGGTGAGATAG
*
19677985 AGAGAAATGGGGTGAGATAG
1 AGAGAAAGGGGGTGAGATAG
*
19678005 AGAGAGAGGGGGT
1 AGAGAAAGGGGGT
19678018 TCAGCCTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.38, C:0.00, G:0.51, T:0.11
Consensus pattern (20 bp):
AGAGAAAGGGGGTGAGATAG
Found at i:19678495 original size:3 final size:3
Alignment explanation
Indices: 19678467--19678632 Score: 120
Period size: 3 Copynumber: 55.3 Consensus size: 3
19678457 TTTAGTCCTG
* *
19678467 TTA TTG TTA TTG TTA TT- TTCA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
19678512 TTA TTA TTA TTA TTA TTA TCA TCA TTA CTA GTA TTA TTA TTA GTT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
* * * ** ** * * *
19678557 TTA TTG CTA TTT TTA ACA TTA TTA TTA GAA TTA TTA TTA ATG TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * **
19678605 CTA TTA ATA TTA TTA TTA CCA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
19678633 ATACATATAT
Statistics
Matches: 122, Mismatches: 37, Indels: 8
0.73 0.22 0.05
Matches are distributed among these distances:
2 4 0.03
3 114 0.93
4 4 0.03
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:19680750 original size:16 final size:16
Alignment explanation
Indices: 19680711--19680743 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
19680701 CGTTTGGTTC
19680711 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
19680727 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
19680743 G
1 G
19680744 GCGTAATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.33, T:0.24
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:19680783 original size:45 final size:44
Alignment explanation
Indices: 19680732--19680823 Score: 141
Period size: 44 Copynumber: 2.1 Consensus size: 44
19680722 ATAGAGCTGT
19680732 AATGGAATAGAGGCGTAATAGTAATTCAAT-TGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGT-ATT-AATGTGTTTGGTTGAATGG
* *
19680777 AATGGAATGGAGGCGTAATAGTATTATTGTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGTATTAATGTGTTTGGTTGAATGG
19680821 AAT
1 AAT
19680824 AATGTTGTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
43 2 0.05
44 21 0.48
45 21 0.48
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.35
Consensus pattern (44 bp):
AATGGAATAGAGGCGTAATAGTATTAATGTGTTTGGTTGAATGG
Found at i:19681063 original size:37 final size:36
Alignment explanation
Indices: 19681001--19681184 Score: 106
Period size: 37 Copynumber: 4.7 Consensus size: 36
19680991 TTAATAATAA
*
19681001 TATATAATTTAATAAAATTCTTAATATTAAATATTCT
1 TATATAATTTAATAAAA-TCATAATATTAAATATTCT
* *
19681038 TATATGAATTTACTAAAATCATAATA-TATAATATTAT
1 TATAT-AATTTAATAAAATCATAATATTA-AATATTCT
* * *
19681075 AAAATATAATTTAA-AATAAT-A-ATTATTAAATATAATTT
1 --TATATAATTTAATAA-AATCATAATATTAAATAT--TCT
*
19681113 AATAAAAAGGTATAATTTAATAAAATTCTTAATATTAAATATTCT
1 --T----A--TATAATTTAATAAAA-TCATAATATTAAATATTCT
*
19681158 TATATGAATTTACTAAAATCATAATAT
1 TATAT-AATTTAATAAAATCATAATAT
19681185 ATAATGCTAT
Statistics
Matches: 115, Mismatches: 13, Indels: 38
0.69 0.08 0.23
Matches are distributed among these distances:
36 10 0.09
37 35 0.30
38 35 0.30
39 5 0.04
42 1 0.01
43 1 0.01
44 12 0.10
45 5 0.04
47 11 0.10
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (36 bp):
TATATAATTTAATAAAATCATAATATTAAATATTCT
Found at i:19681083 original size:22 final size:24
Alignment explanation
Indices: 19681038--19681084 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
19681028 TAAATATTCT
19681038 TATATGAATTTACTAAAATCATAA
1 TATATGAATTTACTAAAATCATAA
19681062 TATAT-AATATTA-TAAAAT-ATAA
1 TATATGAAT-TTACTAAAATCATAA
19681084 T
1 T
19681085 TTAAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 5 0.23
23 9 0.41
24 8 0.36
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (24 bp):
TATATGAATTTACTAAAATCATAA
Found at i:19681098 original size:13 final size:13
Alignment explanation
Indices: 19681070--19681111 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
19681060 AATATATAAT
19681070 ATTATAAAATATA
1 ATTATAAAATATA
19681083 ATT-TAAAATAATA
1 ATTATAAAAT-ATA
*
19681096 ATTATTAAATATA
1 ATTATAAAATATA
19681109 ATT
1 ATT
19681112 TAATAAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 6 0.23
13 15 0.58
14 5 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATTATAAAATATA
Found at i:19681105 original size:26 final size:25
Alignment explanation
Indices: 19681065--19681114 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 25
19681055 ATCATAATAT
19681065 ATAATATTATAAAATATAATTTAAA
1 ATAATATTATAAAATATAATTTAAA
*
19681090 ATAATAATTATTAAATATAATTTAA
1 ATAAT-ATTATAAAATATAATTTAA
19681115 TAAAAAGGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
ATAATATTATAAAATATAATTTAAA
Found at i:19681137 original size:120 final size:120
Alignment explanation
Indices: 19680964--19681239 Score: 471
Period size: 120 Copynumber: 2.3 Consensus size: 120
19680954 TTAATCATAT
* * *
19680964 TTTAACATAATTATTATTAAATATAATTTAATAATAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAAGATATAATTTAATAAAATTCTTAATATT
*
19681029 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATATTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
* *
19681084 TTTAAAATAATAATTATTAAATATAATTTAATAAAAAGGTATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAAGATATAATTTAATAAAATTCTTAATATT
*
19681149 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATGCTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
* *
19681204 TTCAAAATAATTATTATTAAATATAGTTTAATAAAA
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAA
19681240 TTCAATATAA
Statistics
Matches: 146, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
120 146 1.00
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.42
Consensus pattern (120 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAAGATATAATTTAATAAAATTCTTAATATT
AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
Found at i:19681199 original size:61 final size:61
Alignment explanation
Indices: 19680997--19681189 Score: 216
Period size: 61 Copynumber: 3.2 Consensus size: 61
19680987 TAATTTAATA
19680997 ATAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATC
1 ATAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATC
* ** * * * ** *
19681058 ATAATATATAATATT-ATAAAA-T-ATAAT-TTAAAATAATAATTAT-TAAATATAATTTAATA
1 ATAATATATAAT-TTAATAAAATTCTTAATATT-AAAT-ATTCTTATATGAATTTACTAAAATC
* **
19681117 AAAAGGTATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATC
1 ATAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATC
19681178 ATAATATATAAT
1 ATAATATATAAT
19681190 GCTATAAAAT
Statistics
Matches: 100, Mismatches: 24, Indels: 16
0.71 0.17 0.11
Matches are distributed among these distances:
58 4 0.04
59 33 0.33
60 14 0.14
61 45 0.45
62 4 0.04
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.42
Consensus pattern (61 bp):
ATAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATC
Found at i:19682527 original size:23 final size:23
Alignment explanation
Indices: 19682501--19682546 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
19682491 TGCATTAATG
19682501 TAAATAGCTATTT-AAATAAAAAA
1 TAAATA-CTATTTGAAATAAAAAA
* *
19682524 TAAATATTTTTTGAAATAAAAAA
1 TAAATACTATTTGAAATAAAAAA
19682547 AATATTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (23 bp):
TAAATACTATTTGAAATAAAAAA
Found at i:19683702 original size:6 final size:6
Alignment explanation
Indices: 19683691--19683717 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
19683681 ATTTATTATT
19683691 AATGTG AATGTG AATGTG AATGTG AAT
1 AATGTG AATGTG AATGTG AATGTG AAT
19683718 ATCAATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.30, T:0.33
Consensus pattern (6 bp):
AATGTG
Found at i:19683944 original size:18 final size:18
Alignment explanation
Indices: 19683921--19683960 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
19683911 TTTTTTCGAG
*
19683921 ATTTTGATATTTACACTC
1 ATTTTGATATTTACACTA
19683939 ATTTTGATATTTACACTA
1 ATTTTGATATTTACACTA
19683957 ATTT
1 ATTT
19683961 ACTGTCAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.30, C:0.12, G:0.05, T:0.53
Consensus pattern (18 bp):
ATTTTGATATTTACACTA
Found at i:19696460 original size:16 final size:16
Alignment explanation
Indices: 19696436--19696473 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
19696426 TTTGGTTCGC
* *
19696436 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
19696452 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
19696468 TGTAAT
1 TGTAAT
19696474 AGCAAATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:19696518 original size:45 final size:44
Alignment explanation
Indices: 19696452--19696542 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 44
19696442 GGATTAGAGG
*
19696452 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATCAACTGTTTGGTTGAA
* ***
19696497 TGTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
19696541 TG
1 TG
19696543 AAATAGAGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 18 0.44
45 23 0.56
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:19696728 original size:18 final size:17
Alignment explanation
Indices: 19696707--19696741 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
19696697 TTATTATTAA
*
19696707 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
19696725 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
19696742 TCTTAATACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:19696795 original size:157 final size:157
Alignment explanation
Indices: 19696601--19696906 Score: 576
Period size: 157 Copynumber: 1.9 Consensus size: 157
19696591 CCCTTAACAT
*
19696601 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTATCAA
1 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
*
19696666 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAA
66 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
19696731 TTTAATAAAATTCTTAATACTTAGCAG
131 TTTAATAAAATTCTTAATACTTAGCAG
*
19696758 AAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
1 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
*
19696823 TAATAAATAATTTAATCGTATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
66 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
19696888 TTTAATAAAATTCTTAATA
131 TTTAATAAAATTCTTAATA
19696907 ATTAATATTC
Statistics
Matches: 145, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 145 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.47
Consensus pattern (157 bp):
AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
TTTAATAAAATTCTTAATACTTAGCAG
Found at i:19696881 original size:16 final size:16
Alignment explanation
Indices: 19696844--19696885 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
19696834 TTAATCGTAT
*
19696844 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
19696860 TT-AAATATATTATAA
1 TTAAAATATATTATAA
19696875 TTAAAATATAT
1 TTAAAATATAT
19696886 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:19696892 original size:14 final size:15
Alignment explanation
Indices: 19696853--19696894 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
19696843 TTTAAACATA
*
19696853 ATTATTATTAAATAT
1 ATTATAATTAAATAT
19696868 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
19696882 A-TATAATTTAATA
1 ATTATAATTAAATA
19696895 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:19696987 original size:120 final size:120
Alignment explanation
Indices: 19696847--19697109 Score: 481
Period size: 120 Copynumber: 2.2 Consensus size: 120
19696837 ATCGTATTTA
19696847 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
19696912 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
* *
19696967 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
* **
19697032 TATTCTTATATTAATTTACTTGAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
19697087 AACATAATTATTATTAAATATAT
1 AACATAATTATTATTAAATATAT
19697110 AACTTGAAAA
Statistics
Matches: 138, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 138 1.00
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:19700570 original size:25 final size:25
Alignment explanation
Indices: 19700542--19700616 Score: 102
Period size: 25 Copynumber: 3.1 Consensus size: 25
19700532 TTAATAAAAT
19700542 ATTAAAGTCCTTATTTTAATTATTG
1 ATTAAAGTCCTTATTTTAATTATTG
* *
19700567 ATT--AGTCCTTATTTTAATGAAAT-
1 ATTAAAGTCCTTATTTTAAT-TATTG
19700590 ATTAAAGTCCTTATTTTAATTATTG
1 ATTAAAGTCCTTATTTTAATTATTG
19700615 AT
1 AT
19700617 GTAATTATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
23 18 0.43
24 4 0.10
25 20 0.48
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.51
Consensus pattern (25 bp):
ATTAAAGTCCTTATTTTAATTATTG
Found at i:19700577 original size:23 final size:24
Alignment explanation
Indices: 19700546--19700616 Score: 92
Period size: 23 Copynumber: 3.0 Consensus size: 24
19700536 TAAAATATTA
19700546 AAGTCCTTATTTTAATTATTGATT
1 AAGTCCTTATTTTAATTATTGATT
* *
19700570 -AGTCCTTATTTTAATGAAAT-ATT
1 AAGTCCTTATTTTAAT-TATTGATT
19700593 AAAGTCCTTATTTTAATTATTGAT
1 -AAGTCCTTATTTTAATTATTGAT
19700617 GTAATTATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
23 18 0.46
24 4 0.10
25 17 0.44
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.51
Consensus pattern (24 bp):
AAGTCCTTATTTTAATTATTGATT
Found at i:19701859 original size:23 final size:23
Alignment explanation
Indices: 19701804--19701876 Score: 87
Period size: 23 Copynumber: 3.2 Consensus size: 23
19701794 TAAACAAATT
* *
19701804 CAATTTCCAACAGACAATCATAA
1 CAATTTCCAGCAGACAATCAAAA
*
19701827 CAATTTCCAGCAGACAATTAAAA
1 CAATTTCCAGCAGACAATCAAAA
19701850 CAATTTCCAG-A-ACAAATCAAGAA
1 CAATTTCCAGCAGAC-AATCAA-AA
19701873 CAAT
1 CAAT
19701877 ATCAAAACAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
21 2 0.05
22 6 0.14
23 36 0.82
ACGTcount: A:0.49, C:0.23, G:0.07, T:0.21
Consensus pattern (23 bp):
CAATTTCCAGCAGACAATCAAAA
Found at i:19702641 original size:17 final size:17
Alignment explanation
Indices: 19702619--19702654 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
19702609 ACTCAAAGGG
19702619 AAATAAACAGCAATAGA
1 AAATAAACAGCAATAGA
19702636 AAATAAACAGCAATAGA
1 AAATAAACAGCAATAGA
19702653 AA
1 AA
19702655 CATGCAATCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.67, C:0.11, G:0.11, T:0.11
Consensus pattern (17 bp):
AAATAAACAGCAATAGA
Found at i:19702890 original size:5 final size:5
Alignment explanation
Indices: 19702880--19702905 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
19702870 AAAGAGAGTT
19702880 AGAAA AGAAA AGAAA AGAAA AGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA A
19702906 AAGAGAGTTG
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:0.19, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:19705097 original size:19 final size:20
Alignment explanation
Indices: 19705071--19705116 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
19705061 AAAAAAAGAA
*
19705071 TCAAAATAATTATTAAAATT
1 TCAAAATAATTATAAAAATT
*
19705091 T-AAAATATTTATAAAAATT
1 TCAAAATAATTATAAAAATT
19705110 TCAAAAT
1 TCAAAAT
19705117 TCATATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (20 bp):
TCAAAATAATTATAAAAATT
Found at i:19705144 original size:9 final size:10
Alignment explanation
Indices: 19705130--19705174 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
19705120 TATTTTTAAG
19705130 AAAAATTAT-
1 AAAAATTATA
*
19705139 AAAAATTTTA
1 AAAAATTATA
*
19705149 AAAAATTCTA
1 AAAAATTATA
19705159 AAAAATATATA
1 AAAAAT-TATA
19705170 AAAAA
1 AAAAA
19705175 GTTAAAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
9 8 0.26
10 15 0.48
11 8 0.26
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (10 bp):
AAAAATTATA
Found at i:19705190 original size:9 final size:9
Alignment explanation
Indices: 19705130--19705194 Score: 51
Period size: 10 Copynumber: 7.0 Consensus size: 9
19705120 TATTTTTAAG
*
19705130 AAAAATTAT
1 AAAAATTTT
19705139 AAAAATTTT
1 AAAAATTTT
*
19705148 AAAAAATTCTA
1 -AAAAATT-TT
*
19705159 AAAAATATAT
1 AAAAAT-TTT
**
19705169 AAAAAAGTT
1 AAAAATTTT
19705178 -AAAATTTT
1 AAAAATTTT
19705186 AAAAATTTT
1 AAAAATTTT
19705195 CTAAAATAAT
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
8 6 0.14
9 17 0.40
10 18 0.42
11 2 0.05
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (9 bp):
AAAAATTTT
Found at i:19706040 original size:6 final size:6
Alignment explanation
Indices: 19705981--19706021 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
19705971 ATTTTTCAAG
* *
19705981 AAAACG AAAACG AAAACA AAAACA AAAACA AAAACA AAAAC
1 AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAAAC
19706022 GACTATTTCC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.78, C:0.17, G:0.05, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:19717437 original size:16 final size:18
Alignment explanation
Indices: 19717416--19717459 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
19717406 TTTAATATGT
19717416 TATAAAT-T-ACATAATA
1 TATAAATATAACATAATA
*
19717432 TATAAATATAATATAATA
1 TATAAATATAACATAATA
*
19717450 TATTAATATA
1 TATAAATATA
19717460 TTATAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 7 0.29
17 1 0.04
18 16 0.67
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
TATAAATATAACATAATA
Found at i:19717449 original size:18 final size:18
Alignment explanation
Indices: 19717426--19717465 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
19717416 TATAAATTAC
19717426 ATAATATATAAATATAAT
1 ATAATATATAAATATAAT
* *
19717444 ATAATATATTAATATATT
1 ATAATATATAAATATAAT
19717462 ATAA
1 ATAA
19717466 ATTTAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATAATATATAAATATAAT
Found at i:19719420 original size:32 final size:32
Alignment explanation
Indices: 19719381--19719448 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
19719371 TTATATAAAT
* * *
19719381 GTTACATTTTTGTCACTTATCTATTAACTTCC
1 GTTACATTTTGGCCACTTATCCATTAACTTCC
*
19719413 GTTACATTTTGGCCACTTATCCGTTAACTTCC
1 GTTACATTTTGGCCACTTATCCATTAACTTCC
19719445 GTTA
1 GTTA
19719449 AGATGGTGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.21, C:0.24, G:0.10, T:0.46
Consensus pattern (32 bp):
GTTACATTTTGGCCACTTATCCATTAACTTCC
Found at i:19731877 original size:20 final size:20
Alignment explanation
Indices: 19731852--19731891 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
19731842 CCCCTATAGA
*
19731852 ACACTTGTCAACTCTTTACT
1 ACACTTGCCAACTCTTTACT
19731872 ACACTTGCCAACTCTTTACT
1 ACACTTGCCAACTCTTTACT
19731892 CTGCTTTTGG
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:0.25, C:0.33, G:0.05, T:0.38
Consensus pattern (20 bp):
ACACTTGCCAACTCTTTACT
Done.