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 93 of 145
Found at i:31100380 original size:31 final size:32
Alignment explanation
Indices: 31100342--31100430 Score: 119
Period size: 31 Copynumber: 2.8 Consensus size: 32
31100332 AACTTTGGAC
31100342 ATAGGTATCGATACCCAGATCAGGTACT-GAT
1 ATAGGTATCGATACCCAGATCAGGTACTCGAT
*
31100373 ATAGGTATCGATACACAGATCAGGTA-TCGAT
1 ATAGGTATCGATACCCAGATCAGGTACTCGAT
* * * *
31100404 ATCGGTATCGATAGCCAAATCAAGTAC
1 ATAGGTATCGATACCCAGATCAGGTAC
31100431 CAATATCGTC
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
30 1 0.02
31 49 0.98
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (32 bp):
ATAGGTATCGATACCCAGATCAGGTACTCGAT
Found at i:31100599 original size:20 final size:19
Alignment explanation
Indices: 31100557--31100604 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
31100547 AAGTCAATTC
*
31100557 GTATTGATACCTTTATAAA
1 GTATTGATACCTTGATAAA
31100576 GTATTGAT-CCTTGATGATAA
1 GTATTGATACCTTGAT-A-AA
*
31100596 GTATCGATA
1 GTATTGATA
31100605 TTGTATACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 6 0.25
19 9 0.38
20 9 0.38
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (19 bp):
GTATTGATACCTTGATAAA
Found at i:31105981 original size:23 final size:23
Alignment explanation
Indices: 31105955--31106005 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
31105945 TTTGTTGAAG
*
31105955 TTAAATGAAAATATTCGTGAACA
1 TTAAATGAAAATATTCGTAAACA
* * *
31105978 TTAAATTAATATGTTCGTAAACA
1 TTAAATGAAAATATTCGTAAACA
31106001 TTAAA
1 TTAAA
31106006 CAAATATGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.35
Consensus pattern (23 bp):
TTAAATGAAAATATTCGTAAACA
Found at i:31106011 original size:23 final size:23
Alignment explanation
Indices: 31105968--31106015 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
31105958 AATGAAAATA
* **
31105968 TTCGTGAACATTAAATTAATATG
1 TTCGTAAACATTAAACAAATATG
31105991 TTCGTAAACATTAAACAAATATG
1 TTCGTAAACATTAAACAAATATG
31106014 TT
1 TT
31106016 TAGTAACATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (23 bp):
TTCGTAAACATTAAACAAATATG
Found at i:31106024 original size:23 final size:23
Alignment explanation
Indices: 31105974--31106021 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
31105964 AATATTCGTG
** *
31105974 AACATTAAATTAATATGTTCGTA
1 AACATTAAACAAATATGTTAGTA
31105997 AACATTAAACAAATATGTTTAGTA
1 AACATTAAACAAATATG-TTAGTA
31106021 A
1 A
31106022 CATATTCATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.35
Consensus pattern (23 bp):
AACATTAAACAAATATGTTAGTA
Found at i:31115097 original size:59 final size:59
Alignment explanation
Indices: 31115014--31115577 Score: 589
Period size: 59 Copynumber: 9.7 Consensus size: 59
31115004 AACAGAGGTA
*
31115014 GCCACGAAA-GCTTT-CTTTTCAGAGATTTGCCACAAAGGCATCATTTTTATTCAGTACTC
1 GCCAC-AAAGGCTTTCCTTTT-AGAGATTTGCCACAAAGGCATCATTTTCATTCAGTACTC
* * * * *
31115073 ACTAAAAAGGCTTCCCTTTTAGAGATTTGCCACAAAGGCATCATTTTCATCCAGTACTC
1 GCCACAAAGGCTTTCCTTTTAGAGATTTGCCACAAAGGCATCATTTTCATTCAGTACTC
* * *
31115132 GCGAAAAAGGCTTTCCTTTTAGAGATTTGCCACAAAGGCATCATTTTCATTCAATACTC
1 GCCACAAAGGCTTTCCTTTTAGAGATTTGCCACAAAGGCATCATTTTCATTCAGTACTC
* * * * * *
31115191 CCCACAAAGGCTTT-CTTTTAAGTGATTTTCCACAAAATGCATCATTTTTATTTAGTACTC
1 GCCACAAAGGCTTTCCTTTT-AGAGATTTGCCAC-AAAGGCATCATTTTCATTCAGTACTC
* * * * *
31115251 GTCACAAAGGCTTTCCTTTAAGAGATTTTCCACAAAGGTATCCTTTTCATTCAGTACTC
1 GCCACAAAGGCTTTCCTTTTAGAGATTTGCCACAAAGGCATCATTTTCATTCAGTACTC
* * *
31115310 GCCACAAAGGCTTTCCTTTCA-ATGATTTTCCACAAAGGCATCCTTTTCATTCAGTACTC
1 GCCACAAAGGCTTTCCTTTTAGA-GATTTGCCACAAAGGCATCATTTTCATTCAGTACTC
* * * *
31115369 GCCACAAAGGCTTTCCTTTAAGAGATTCT-CCACAAAGGCATCCTTTTCATTCAATATTC
1 GCCACAAAGGCTTTCCTTTTAGAGATT-TGCCACAAAGGCATCATTTTCATTCAGTACTC
* * * * * *
31115428 GCCACAAAGGCTCTCCTTTCAAAGATTTGCCACAAAGACATCCTTTTCATTCAGTACTT
1 GCCACAAAGGCTTTCCTTTTAGAGATTTGCCACAAAGGCATCATTTTCATTCAGTACTC
* * * * *
31115487 GCCACAAA-G--TT-C----A-ATGATTTTCTACAAATGAATCATTTTCTTTCAGTACTC
1 GCCACAAAGGCTTTCCTTTTAGA-GATTTGCCACAAAGGCATCATTTTCATTCAGTACTC
* * *
31115538 GCCAAAAAGGCTTTCCTTTTTGTAGGTTTGCCACAAAGGC
1 GCCACAAAGGCTTTCCTTTTAG-AGATTTGCCACAAAGGC
31115578 TTTCCTTTTC
Statistics
Matches: 427, Mismatches: 58, Indels: 39
0.81 0.11 0.07
Matches are distributed among these distances:
50 1 0.00
51 36 0.08
52 1 0.00
54 2 0.00
55 2 0.00
56 1 0.00
58 11 0.03
59 304 0.71
60 64 0.15
61 5 0.01
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (59 bp):
GCCACAAAGGCTTTCCTTTTAGAGATTTGCCACAAAGGCATCATTTTCATTCAGTACTC
Found at i:31115285 original size:28 final size:29
Alignment explanation
Indices: 31115253--31115464 Score: 116
Period size: 28 Copynumber: 7.2 Consensus size: 29
31115243 TAGTACTCGT
* *
31115253 CACAAAGGCTTTCCTTT-AAGAGATTTTC
1 CACAAAGGCTTTCCTTTCAACAGATTCTC
* * * *
31115281 CACAAAGG-TATCCTTTTCATTCAGTACTCGC
1 CACAAAGGCTTTCC-TTTCA-ACAG-ATTCTC
* *
31115312 CACAAAGGCTTTCCTTTCAA-TGATTTTC
1 CACAAAGGCTTTCCTTTCAACAGATTCTC
* * * *
31115340 CACAAAGGC-ATCCTTTTCATTCAGTACTCGC
1 CACAAAGGCTTTCC-TTTCA-ACAG-ATTCTC
*
31115371 CACAAAGGCTTTCCTTT-AAGAGATTCTC
1 CACAAAGGCTTTCCTTTCAACAGATTCTC
* * * *
31115399 CACAAAGGC-ATCCTTTTCATTCAATATTCGC
1 CACAAAGGCTTTCC-TTTCA-AC-AGATTCTC
*
31115430 CACAAAGGCTCTCCTTTCAA-AGATT-TGC
1 CACAAAGGCTTTCCTTTCAACAGATTCT-C
31115458 CACAAAG
1 CACAAAG
31115465 ACATCCTTTT
Statistics
Matches: 136, Mismatches: 32, Indels: 32
0.68 0.16 0.16
Matches are distributed among these distances:
27 10 0.07
28 56 0.41
29 5 0.04
30 4 0.03
31 51 0.38
32 10 0.07
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.32
Consensus pattern (29 bp):
CACAAAGGCTTTCCTTTCAACAGATTCTC
Found at i:31115316 original size:31 final size:31
Alignment explanation
Indices: 31115280--31115495 Score: 143
Period size: 31 Copynumber: 7.3 Consensus size: 31
31115270 AAGAGATTTT
*
31115280 CCACAAAGGTATCCTTTTCATTCAGTACTCG
1 CCACAAAGGTATCCTTTTCATTCAGTATTCG
* * **
31115311 CCACAAAGGCTTTCC-TTTCAAT--G-ATTTT
1 CCACAAAGG-TATCCTTTTCATTCAGTATTCG
* *
31115339 CCACAAAGGCATCCTTTTCATTCAGTACTCG
1 CCACAAAGGTATCCTTTTCATTCAGTATTCG
* ** *
31115370 CCACAAAGGCTTTCC-TTT-A-AGAG-ATTCT
1 CCACAAAGG-TATCCTTTTCATTCAGTATTCG
* *
31115398 CCACAAAGGCATCCTTTTCATTCAATATTCG
1 CCACAAAGGTATCCTTTTCATTCAGTATTCG
* * *
31115429 CCACAAAGGCTCTCC-TTTCA--AAG-ATTTG
1 CCACAAAGG-TATCCTTTTCATTCAGTATTCG
**
31115457 CCACAAAGACATCCTTTTCATTCAGTACTT-G
1 CCACAAAGGTATCCTTTTCATTCAGTA-TTCG
31115488 CCACAAAG
1 CCACAAAG
31115496 TTCAATGATT
Statistics
Matches: 137, Mismatches: 32, Indels: 32
0.68 0.16 0.16
Matches are distributed among these distances:
27 9 0.07
28 49 0.36
29 5 0.04
30 5 0.04
31 57 0.42
32 12 0.09
ACGTcount: A:0.28, C:0.29, G:0.12, T:0.31
Consensus pattern (31 bp):
CCACAAAGGTATCCTTTTCATTCAGTATTCG
Found at i:31115463 original size:237 final size:237
Alignment explanation
Indices: 31115023--31115463 Score: 618
Period size: 237 Copynumber: 1.9 Consensus size: 237
31115013 AGCCACGAAA
* * * *
31115023 GCTTTCTTTTCAGAGATTTGCCACAAAGGCATCATTTTTATTCAGTACTCACTAAAAAGGCTTCC
1 GCTTTCCTTTAAGAGATTTGCCACAAAGGCATCATTTTCATTCAGTACTCACCAAAAAGGCTTCC
* * *
31115088 CTTTTAGAGATTTGCCACAAAGGCATCATTTTCATCCAGTACTCGCGAAAAAGGCTTTCCTTTTA
66 CTTTCAGAGATTTGCCACAAAGGCATCATTTTCATCCAGTACTCGCCAAAAAGGCTTTCCTTTAA
* * *
31115153 GAGATTTGCCACAAAGGCATCATTTTCATTCAATACTCCCCACAAAGGCTTTCTTTTAAGTGATT
131 GAGATTTGCCACAAAGGCATCATTTTCATTCAATACTCCCCACAAAGGCTTCCTTTCAAGAGATT
*
31115218 TTCCACAAAATGCATCATTTTTATTTAGTACTCGTCACAAAG
196 TGCCACAAAATGCATCATTTTTATTTAGTACTCGTCACAAAG
* * * * * *
31115260 GCTTTCCTTTAAGAGATTTTCCACAAAGGTATCCTTTTCATTCAGTACTCGCCACAAAGGCTTTC
1 GCTTTCCTTTAAGAGATTTGCCACAAAGGCATCATTTTCATTCAGTACTCACCAAAAAGGCTTCC
* * * *
31115325 CTTTCA-ATGATTTTCCACAAAGGCATCCTTTTCATTCAGTACTCGCCACAAAGGCTTTCCTTTA
66 CTTTCAGA-GATTTGCCACAAAGGCATCATTTTCATCCAGTACTCGCCAAAAAGGCTTTCCTTTA
* * *
31115389 AGAGATTCT-CCACAAAGGCATCCTTTTCATTCAATATTCGCCACAAAGGCTCTCCTTTCAA-AG
130 AGAGATT-TGCCACAAAGGCATCATTTTCATTCAATACTCCCCACAAAGGCT-TCCTTTCAAGAG
31115452 ATTTGCCACAAA
193 ATTTGCCACAAA
31115464 GACATCCTTT
Statistics
Matches: 177, Mismatches: 24, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
236 1 0.01
237 168 0.95
238 8 0.05
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (237 bp):
GCTTTCCTTTAAGAGATTTGCCACAAAGGCATCATTTTCATTCAGTACTCACCAAAAAGGCTTCC
CTTTCAGAGATTTGCCACAAAGGCATCATTTTCATCCAGTACTCGCCAAAAAGGCTTTCCTTTAA
GAGATTTGCCACAAAGGCATCATTTTCATTCAATACTCCCCACAAAGGCTTCCTTTCAAGAGATT
TGCCACAAAATGCATCATTTTTATTTAGTACTCGTCACAAAG
Found at i:31115475 original size:28 final size:29
Alignment explanation
Indices: 31115280--31115477 Score: 122
Period size: 28 Copynumber: 6.7 Consensus size: 29
31115270 AAGAGATTTT
* * *
31115280 CCACAAAGGTATCCTTTTCATTCAGTACTCG
1 CCACAAAGGCATCCTTTTCA-TAAG-ATTCG
* * **
31115311 CCACAAAGGCTTTCC-TTTCA-ATGATTTT
1 CCACAAAGGC-ATCCTTTTCATAAGATTCG
* *
31115339 CCACAAAGGCATCCTTTTCATTCAGTACTCG
1 CCACAAAGGCATCCTTTTCA-TAAG-ATTCG
* *
31115370 CCACAAAGGCTTTCC-TTT-A-AGAGATTCT
1 CCACAAAGGC-ATCCTTTTCATA-AGATTCG
*
31115398 CCACAAAGGCATCCTTTTCATTCAATATTCG
1 CCACAAAGGCATCCTTTTCA-T-AAGATTCG
* *
31115429 CCACAAAGGC-TCTCCTTTCA-AAGATTTG
1 CCACAAAGGCATC-CTTTTCATAAGATTCG
*
31115457 CCACAAAGACATCCTTTTCAT
1 CCACAAAGGCATCCTTTTCAT
31115478 TCAGTACTTG
Statistics
Matches: 127, Mismatches: 25, Indels: 32
0.69 0.14 0.17
Matches are distributed among these distances:
27 6 0.05
28 54 0.43
29 6 0.05
30 4 0.03
31 50 0.39
32 7 0.06
ACGTcount: A:0.28, C:0.29, G:0.12, T:0.32
Consensus pattern (29 bp):
CCACAAAGGCATCCTTTTCATAAGATTCG
Found at i:31115526 original size:51 final size:51
Alignment explanation
Indices: 31115445--31115546 Score: 125
Period size: 51 Copynumber: 2.0 Consensus size: 51
31115435 AGGCTCTCCT
* * *
31115445 TTCAAAGATTTGCCACAAAGACATCCTTTTCATTCAGTACTTGCCACAAAG
1 TTCAAAGATTTGCCACAAAGACATCATTTTCATTCAGTACTCGCCAAAAAG
* * * *
31115496 TTCAATGATTTTCTACAAATGA-ATCATTTTCTTTCAGTACTCGCCAAAAAG
1 TTCAAAGATTTGCCACAAA-GACATCATTTTCATTCAGTACTCGCCAAAAAG
31115547 GCTTTCCTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
51 41 0.95
52 2 0.05
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.33
Consensus pattern (51 bp):
TTCAAAGATTTGCCACAAAGACATCATTTTCATTCAGTACTCGCCAAAAAG
Found at i:31115600 original size:29 final size:29
Alignment explanation
Indices: 31115543--31115616 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 29
31115533 TACTCGCCAA
** * **
31115543 AAAGGCTTTCCTTTTTGTAGGTTTGCCAC
1 AAAGGCTTTCCTTTTCATAAGTTCACCAC
31115572 AAAGGCTTTCCTTTTCATAAGTTCACCAC
1 AAAGGCTTTCCTTTTCATAAGTTCACCAC
* *
31115601 AAAGGTTTTTCTTTTC
1 AAAGGCTTTCCTTTTC
31115617 TGACATGTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.42
Consensus pattern (29 bp):
AAAGGCTTTCCTTTTCATAAGTTCACCAC
Found at i:31116007 original size:15 final size:15
Alignment explanation
Indices: 31115986--31116040 Score: 101
Period size: 15 Copynumber: 3.7 Consensus size: 15
31115976 TTATTAGAAT
31115986 CATCAGATTTCAAGC
1 CATCAGATTTCAAGC
*
31116001 TATCAGATTTCAAGC
1 CATCAGATTTCAAGC
31116016 CATCAGATTTCAAGC
1 CATCAGATTTCAAGC
31116031 CATCAGATTT
1 CATCAGATTT
31116041 TAGTCTTCAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.31
Consensus pattern (15 bp):
CATCAGATTTCAAGC
Found at i:31117667 original size:261 final size:262
Alignment explanation
Indices: 31117190--31117713 Score: 861
Period size: 261 Copynumber: 2.0 Consensus size: 262
31117180 GCAGCCTTAT
* * *
31117190 TTTGAAAGCAGTTAAAGATACAATTTCATATCAAGCATTTATTAGTATTGAGGGTATATCAACCA
1 TTTGAAAGAAGTTAAAGATACAATTTCATATCAAGCATTTATTAGTATCGAGGGCATATCAACCA
31117255 TAAAGTGCACGTATTTTAGCCTATAAATAAGAGCTTCCTATATAGATTTAGACATAGAAGTGCAG
66 TAAAGTGCACGTATTTTAGCCTATAAATAAGAGCTTCCTATATAGATTTAGACATAGAAGTGCAG
*
31117320 GCGTAGATAGAAAATTTTTCCTATTCAGATTTTAGTTTTCGTTTCTTTTCATGCTCGTGTATTCG
131 ACGTAGATAGAAAATTTTTCCTATTCAGATTTTAGTTTTCGTTTCTTTTCATGCTCGTGTATTCG
* * ** *
31117385 AAACTTTTCTATTCCAATGTGAAGATAATTGCGAGTGAAGATTGCTCTAGATTCGCGCTTCAATA
196 AAACTTTTCTATTCCAATGTGAAGACAATTACGAGCAAAGATTGCTCTAGATTCACGCTTCAATA
31117450 TA
261 TA
* *
31117452 TTTGAAAGAAGTTAAAGATACAATTTGATATCAAGCATTTATTAGTATCGAGGGCATATCAAGCA
1 TTTGAAAGAAGTTAAAGATACAATTTCATATCAAGCATTTATTAGTATCGAGGGCATATCAACCA
* *
31117517 T-AAGTGCACGTATTTTAGCCTATAAATAAGAGCTTCCTGTATAGATTTAGACATAGAAGTTCAG
66 TAAAGTGCACGTATTTTAGCCTATAAATAAGAGCTTCCTATATAGATTTAGACATAGAAGTGCAG
* * * *
31117581 ATGTAGATAGAAAATTTTTCCTATTCAGATTTTAGTTTTCTTTTCTTTTCATGTTCGTGTATTTG
131 ACGTAGATAGAAAATTTTTCCTATTCAGATTTTAGTTTTCGTTTCTTTTCATGCTCGTGTATTCG
* * *
31117646 AAACTTTTTTATTCGAATGTGAAGACAATTACGAGCAAAGATTGCTCTCGATTCACGCTTCAATA
196 AAACTTTTCTATTCCAATGTGAAGACAATTACGAGCAAAGATTGCTCTAGATTCACGCTTCAATA
31117711 TA
261 TA
31117713 T
1 T
31117714 ATATTCATGA
Statistics
Matches: 242, Mismatches: 20, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
261 181 0.75
262 61 0.25
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (262 bp):
TTTGAAAGAAGTTAAAGATACAATTTCATATCAAGCATTTATTAGTATCGAGGGCATATCAACCA
TAAAGTGCACGTATTTTAGCCTATAAATAAGAGCTTCCTATATAGATTTAGACATAGAAGTGCAG
ACGTAGATAGAAAATTTTTCCTATTCAGATTTTAGTTTTCGTTTCTTTTCATGCTCGTGTATTCG
AAACTTTTCTATTCCAATGTGAAGACAATTACGAGCAAAGATTGCTCTAGATTCACGCTTCAATA
TA
Found at i:31123518 original size:111 final size:112
Alignment explanation
Indices: 31123311--31123535 Score: 425
Period size: 111 Copynumber: 2.0 Consensus size: 112
31123301 TTTTGTTTTA
31123311 AATAAGGAGATAAAGAGCTCCTTATCATTTAATATAGAACACTTTCAATTCTTTTTATTTTATTT
1 AATAAGGAGAT-AAGAGCTCCTTATCATTTAATATAGAACACTTTCAATTCTTTTTATTTTATTT
31123376 CTTTTAACATTATCCTTTAAATGCTTTATCTTTATAATTTTCAAAATT
65 CTTTTAACATTATCCTTTAAATGCTTTATCTTTATAATTTTCAAAATT
*
31123424 AATAAGGAGAT-AGAGCTCCTTATCATTTAATATGGAACACTTTCAATTCTTTTTATTTTATTTC
1 AATAAGGAGATAAGAGCTCCTTATCATTTAATATAGAACACTTTCAATTCTTTTTATTTTATTTC
31123488 TTTTAACATTATCCTTTAAATGCTTTATCTTTATAATTTTCAAAATT
66 TTTTAACATTATCCTTTAAATGCTTTATCTTTATAATTTTCAAAATT
31123535 A
1 A
31123536 CATTTATCAA
Statistics
Matches: 111, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
111 100 0.90
113 11 0.10
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.47
Consensus pattern (112 bp):
AATAAGGAGATAAGAGCTCCTTATCATTTAATATAGAACACTTTCAATTCTTTTTATTTTATTTC
TTTTAACATTATCCTTTAAATGCTTTATCTTTATAATTTTCAAAATT
Found at i:31124075 original size:21 final size:21
Alignment explanation
Indices: 31124050--31124090 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
31124040 GGGAGCAGTT
31124050 TTTCAATCAATTTAAAAATGG
1 TTTCAATCAATTTAAAAATGG
31124071 TTTCAATCAATTTAAAAATG
1 TTTCAATCAATTTAAAAATG
31124091 CTTTGGACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.39
Consensus pattern (21 bp):
TTTCAATCAATTTAAAAATGG
Found at i:31135384 original size:45 final size:44
Alignment explanation
Indices: 31135242--31135397 Score: 170
Period size: 44 Copynumber: 3.5 Consensus size: 44
31135232 GATCCATTCT
* * * *
31135242 ACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCC
1 ACTGCAACTTCAGAGAGATAAGATTTATCACTTCAATCTGCTCC
* * * *
31135286 ACTACAACTTCAGGGAGATAGGA-TTATCGGCTTCAATCTGCTCC
1 ACTGCAACTTCAGAGAGATAAGATTTATC-ACTTCAATCTGCTCC
* * * *
31135330 ACTGTAACTTCAGAGAGATAAGATTTACCATCTTCGATCTGCCCC
1 ACTGCAACTTCAGAGAGATAAGATTTATCA-CTTCAATCTGCTCC
*
31135375 ACTGCAACTTCAGAGGGATAAGA
1 ACTGCAACTTCAGAGAGATAAGA
31135398 CCTGCTTGCT
Statistics
Matches: 91, Mismatches: 18, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
43 3 0.03
44 51 0.56
45 37 0.41
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (44 bp):
ACTGCAACTTCAGAGAGATAAGATTTATCACTTCAATCTGCTCC
Found at i:31135586 original size:131 final size:131
Alignment explanation
Indices: 31135449--31135928 Score: 775
Period size: 131 Copynumber: 3.7 Consensus size: 131
31135439 AGACCTGCCA
* * * *
31135449 TCTTCGATCTGCTCCGCTACT-GCTTAGGGAGACAAGATCTGTAATTTCCATCCTATTCCACTGC
1 TCTTCGATCTGCTCCACTA-TAGCTTAGGGAGATAAGATCTGTAGTTTCCAACCTATTCCACTGC
* * * *
31135513 TGAC-CAGGGACATTGGACTTGTGGCTTGAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCG
65 TG-CTCAGGGAAATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCG
31135577 CCG
129 CCG
**
31135580 TCTTCGATCTGCTCCACTATTTCTTAGGGAGATAAGATCTGTAGTTTCCAACCTATTCCACTGCT
1 TCTTCGATCTGCTCCACTATAGCTTAGGGAGATAAGATCTGTAGTTTCCAACCTATTCCACTGCT
* * *
31135645 GCTCAGGGAAATAGGAATTGTGGCTTAAATCTATTTCCCTACTCCTGGGGAAGATAAGATTCACC
66 GCTCAGGGAAATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCC
31135710 G
131 G
*
31135711 TCTTCAATCTGCTCCACTATAGCTTAGGGAGATAAGATCTGTAGTTTCCAACCTATTCCACTGCT
1 TCTTCGATCTGCTCCACTATAGCTTAGGGAGATAAGATCTGTAGTTTCCAACCTATTCCACTGCT
*
31135776 GCTCAGGGAAATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGAC
66 GCTCAGGGAAATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCC
31135841 G
131 G
* *
31135842 TCTTCGATCTGCTCCACTATAGCTTAGAGAGATAAGATCTGTAGTGTCCAACCTATTCCACTGCT
1 TCTTCGATCTGCTCCACTATAGCTTAGGGAGATAAGATCTGTAGTTTCCAACCTATTCCACTGCT
31135907 GCTCAGGGAAATAGGACTTGTG
66 GCTCAGGGAAATAGGACTTGTG
31135929 ATTTCACCGA
Statistics
Matches: 325, Mismatches: 22, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
130 2 0.01
131 323 0.99
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (131 bp):
TCTTCGATCTGCTCCACTATAGCTTAGGGAGATAAGATCTGTAGTTTCCAACCTATTCCACTGCT
GCTCAGGGAAATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCC
G
Found at i:31135653 original size:44 final size:42
Alignment explanation
Indices: 31135605--31135784 Score: 98
Period size: 44 Copynumber: 4.1 Consensus size: 42
31135595 ACTATTTCTT
31135605 AGGGAGATAAGATCTGTAGTTTCCAACCTATTCCACTGCTGCTC
1 AGGGAGATAAGAT-TGTAGTTT-CAACCTATTCCACTGCTGCTC
* * * * * * * *
31135649 AGGGAAATAGGAATTGTGGCTTAAATCTATTTCC-CTACTCCT-
1 AGGGAGATAAG-ATTGTAGTTTCAACCTA-TTCCACTGCTGCTC
* * * ** * *
31135691 GGGGAAGATAAGATT-CACCGTCTTCAATCTGCTCCACT-ATAGCTT
1 AGGG-AGATAAGATTGTA--GT-TTCAACCTATTCCACTGCT-GCTC
31135736 AGGGAGATAAGATCTGTAGTTTCCAACCTATTCCACTGCTGCTC
1 AGGGAGATAAGAT-TGTAGTTT-CAACCTATTCCACTGCTGCTC
31135780 AGGGA
1 AGGGA
31135785 AATAGGACTT
Statistics
Matches: 97, Mismatches: 26, Indels: 26
0.65 0.17 0.17
Matches are distributed among these distances:
42 6 0.06
43 23 0.24
44 60 0.62
45 7 0.07
46 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (42 bp):
AGGGAGATAAGATTGTAGTTTCAACCTATTCCACTGCTGCTC
Found at i:31137042 original size:21 final size:21
Alignment explanation
Indices: 31137018--31137067 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
31137008 CCTTAACCTC
*
31137018 TTCATTTTTACTTTTTCA-TTT
1 TTCATTTTT-CATTTTCATTTT
31137039 TTCATTTTTCATTTTCATTTT
1 TTCATTTTTCATTTTCATTTT
31137060 TTCATTTT
1 TTCATTTT
31137068 CTCACATCAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 7 0.26
21 20 0.74
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (21 bp):
TTCATTTTTCATTTTCATTTT
Found at i:31137068 original size:6 final size:7
Alignment explanation
Indices: 31137018--31137067 Score: 68
Period size: 7 Copynumber: 7.1 Consensus size: 7
31137008 CCTTAACCTC
31137018 TTCATTT
1 TTCATTT
31137025 TT-ACTTT
1 TTCA-TTT
31137032 TTCATTT
1 TTCATTT
31137039 TTCATTT
1 TTCATTT
31137046 TTCA-TT
1 TTCATTT
31137052 TTCATTTT
1 TTCA-TTT
31137060 TTCATTT
1 TTCATTT
31137067 T
1 T
31137068 CTCACATCAC
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
6 7 0.18
7 25 0.64
8 7 0.18
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (7 bp):
TTCATTT
Found at i:31147010 original size:28 final size:29
Alignment explanation
Indices: 31146965--31147039 Score: 102
Period size: 28 Copynumber: 2.7 Consensus size: 29
31146955 TTCAATATAA
* *
31146965 ATTTTT-ATTTTTACTTTTTCA-TTTTTC
1 ATTTTTCATTTTCATTTTTTCATTTTTTC
31146992 ATTTTTCATTTTCATTTTTTCATTTTTTC
1 ATTTTTCATTTTCATTTTTTCATTTTTTC
*
31147021 ATTTTTCA-TTTCTTTTTTT
1 ATTTTTCATTTTCATTTTTT
31147040 TTGACTCAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 6 0.14
28 23 0.53
29 14 0.33
ACGTcount: A:0.13, C:0.12, G:0.00, T:0.75
Consensus pattern (29 bp):
ATTTTTCATTTTCATTTTTTCATTTTTTC
Found at i:31147017 original size:7 final size:7
Alignment explanation
Indices: 31146965--31147031 Score: 86
Period size: 7 Copynumber: 9.6 Consensus size: 7
31146955 TTCAATATAA
31146965 ATTTTT-
1 ATTTTTC
31146971 ATTTTT-
1 ATTTTTC
31146977 ACTTTTTC
1 A-TTTTTC
31146985 ATTTTTC
1 ATTTTTC
31146992 ATTTTTC
1 ATTTTTC
31146999 A-TTTTC
1 ATTTTTC
31147005 ATTTTTTC
1 A-TTTTTC
31147013 ATTTTTTC
1 A-TTTTTC
31147021 ATTTTTC
1 ATTTTTC
31147028 ATTT
1 ATTT
31147032 CTTTTTTTTT
Statistics
Matches: 57, Mismatches: 0, Indels: 7
0.89 0.00 0.11
Matches are distributed among these distances:
6 13 0.23
7 29 0.51
8 15 0.26
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (7 bp):
ATTTTTC
Found at i:31147039 original size:14 final size:13
Alignment explanation
Indices: 31146966--31147040 Score: 62
Period size: 14 Copynumber: 5.4 Consensus size: 13
31146956 TCAATATAAA
*
31146966 TTTTT-ATTTTTAC
1 TTTTTCATTTTT-T
*
31146979 TTTTTCATTTTTCA
1 TTTTTCATTTTT-T
*
31146993 TTTTTCATTTTCAT
1 TTTTTCATTTT-TT
31147007 TTTTTCATTTTTT
1 TTTTTCATTTTTT
31147020 CATTTTTCATTTCTTT
1 --TTTTTCATTT-TTT
31147036 TTTTT
1 TTTTT
31147041 TGACTCAAAG
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
13 6 0.12
14 33 0.63
15 10 0.19
16 3 0.06
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTCATTTTTT
Found at i:31147903 original size:120 final size:120
Alignment explanation
Indices: 31147769--31148020 Score: 348
Period size: 120 Copynumber: 2.1 Consensus size: 120
31147759 TTGGGTTGGG
* * *
31147769 CCGGG-CCGGGCCGGGCTCGGGCTTATTATTTTTTTCCCGGGCCGGG-TCTAGGCAAAATTTTAA
1 CCGGGCCCGGCCCGGGCTCGGGCTTACTATTTTTTTCCCGGGCCGGGCT-TAGGCAAAATTTCAA
*
31147832 GCCCATATTTCGGGCCGGGCCGGGCCCAGTCCTAAGAGTCGGGC-AAAAATTTTTTT
65 GCCCATATTTCGGGCCGGGCCGGGCCCAGGCCTAAGAGTCGGGCTAAAAA-TTTTTT
* * * * *
31147888 CCGGGCCCGGCCCGGGCTCGGGCTTACTCTTTTTTTCCCGGGTCGGGCTTGGGTAAAATTTCAGG
1 CCGGGCCCGGCCCGGGCTCGGGCTTACTATTTTTTTCCCGGGCCGGGCTTAGGCAAAATTTCAAG
* * *
31147953 CCCATATTTCGGGTCGGGCCGGGCCCGGGCCTAAGAGTCGGGCTGAAAATTTTTT
66 CCCATATTTCGGGCCGGGCCGGGCCCAGGCCTAAGAGTCGGGCTAAAAATTTTTT
*
31148008 CCGGGCCCAGCCC
1 CCGGGCCCGGCCC
31148021 ATGGACAGCT
Statistics
Matches: 117, Mismatches: 13, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
119 5 0.04
120 107 0.91
121 5 0.04
ACGTcount: A:0.14, C:0.29, G:0.32, T:0.25
Consensus pattern (120 bp):
CCGGGCCCGGCCCGGGCTCGGGCTTACTATTTTTTTCCCGGGCCGGGCTTAGGCAAAATTTCAAG
CCCATATTTCGGGCCGGGCCGGGCCCAGGCCTAAGAGTCGGGCTAAAAATTTTTT
Found at i:31148412 original size:7 final size:7
Alignment explanation
Indices: 31148402--31148496 Score: 50
Period size: 7 Copynumber: 12.7 Consensus size: 7
31148392 TTCATCTAGA
31148402 TTTTTTC
1 TTTTTTC
31148409 TTTTTTC
1 TTTTTTC
*
31148416 TTCGTTTC
1 TT-TTTTC
*
31148424 TTCTTTC
1 TTTTTTC
31148431 TTTTTCTCTC
1 -TTTT-T-TC
*
31148441 ATTTTTTA
1 -TTTTTTC
*
31148449 TTTTTTA
1 TTTTTTC
31148456 TTTTGATT-
1 TTTT--TTC
31148464 TTTTTTC
1 TTTTTTC
31148471 TTTTTT-
1 TTTTTTC
**
31148477 TTCCTTC
1 TTTTTTC
31148484 TTTTTTTC
1 -TTTTTTC
31148492 TTTTT
1 TTTTT
31148497 ATTGAATCTA
Statistics
Matches: 70, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
6 6 0.09
7 35 0.50
8 19 0.27
9 4 0.06
10 6 0.09
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.79
Consensus pattern (7 bp):
TTTTTTC
Found at i:31148474 original size:20 final size:19
Alignment explanation
Indices: 31148441--31148478 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
31148431 TTTTTCTCTC
31148441 ATTTTTTATTTTTTATTTTG
1 ATTTTTTATTTTTT-TTTTG
31148461 ATTTTTT-TTCTTTTTTTT
1 ATTTTTTATT-TTTTTTTT
31148479 CCTTCTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.11, C:0.03, G:0.03, T:0.84
Consensus pattern (19 bp):
ATTTTTTATTTTTTTTTTG
Found at i:31148474 original size:21 final size:21
Alignment explanation
Indices: 31148402--31148499 Score: 62
Period size: 21 Copynumber: 4.7 Consensus size: 21
31148392 TTCATCTAGA
*
31148402 TTTTTTCTTTTT-TCTT-CGTT
1 TTTTTTCTTTTTAT-TTCCATT
* *
31148422 TCTTCTTTCTTTTTCTCT-CATT
1 T-TT-TTTCTTTTTATTTCCATT
* **
31148444 TTTTAT-TTTTTATTTTGATT
1 TTTTTTCTTTTTATTTCCATT
*
31148464 TTTTTTCTTTTT-TTTCCTTCT
1 TTTTTTCTTTTTATTTCCAT-T
31148485 TTTTTTCTTTTTATT
1 TTTTTTCTTTTTATT
31148500 GAATCTAAAC
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
19 7 0.11
20 15 0.25
21 22 0.36
22 16 0.26
23 1 0.02
ACGTcount: A:0.05, C:0.14, G:0.02, T:0.79
Consensus pattern (21 bp):
TTTTTTCTTTTTATTTCCATT
Found at i:31154779 original size:30 final size:30
Alignment explanation
Indices: 31154632--31154819 Score: 121
Period size: 30 Copynumber: 6.3 Consensus size: 30
31154622 GACATGTCCG
**
31154632 TTTTCATAATTTGATAGCCGAAGTTATCCC
1 TTTTCATAATTTGATAGCCGAAGCCATCCC
** * ** *
31154662 TTAACATAGTTTGATAATCGAAGCAATCCC
1 TTTTCATAATTTGATAGCCGAAGCCATCCC
* * * * *
31154692 TTTTTATAATTTGATGGTCGTCA-CCATCCT
1 TTTTCATAATTTGATAGCCG-AAGCCATCCC
** * *** *
31154722 TTTTCATAATTCAATGGTCTTCA-CCATCCG
1 TTTTCATAATTTGATAG-CCGAAGCCATCCC
*
31154752 TTTTCATAATTTGATGGCCGAAGCCATCCC
1 TTTTCATAATTTGATAGCCGAAGCCATCCC
* *
31154782 TTTTCA-AAGATTGATAGCCAAAGCCATCCC
1 TTTTCATAA-TTTGATAGCCGAAGCCATCCC
31154812 TTTTCATA
1 TTTTCATA
31154820 GTTCAATGGT
Statistics
Matches: 121, Mismatches: 32, Indels: 9
0.75 0.20 0.06
Matches are distributed among these distances:
29 4 0.03
30 115 0.95
31 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (30 bp):
TTTTCATAATTTGATAGCCGAAGCCATCCC
Found at i:31154839 original size:30 final size:30
Alignment explanation
Indices: 31154687--31154846 Score: 128
Period size: 30 Copynumber: 5.3 Consensus size: 30
31154677 AATCGAAGCA
* *
31154687 ATCCCTTTTTATAATTTGATGGTCGTCACC
1 ATCCCTTTTCATAATTCGATGGTCGTCACC
* * *
31154717 ATCCTTTTTCATAATTCAATGGTCTTCACC
1 ATCCCTTTTCATAATTCGATGGTCGTCACC
* * * *
31154747 ATCCGTTTTCATAATTTGATGGCCG-AAGCC
1 ATCCCTTTTCATAATTCGATGGTCGTCA-CC
* * ***
31154777 ATCCCTTTTCAAAGATT-GATAG-CCAAAGCC
1 ATCCCTTTTCATA-ATTCGATGGTCGTCA-CC
* *
31154807 ATCCCTTTTCATAGTTCAATGGTCGTCACC
1 ATCCCTTTTCATAATTCGATGGTCGTCACC
31154837 ATCCCTTTTC
1 ATCCCTTTTC
31154847 TTGATCGATA
Statistics
Matches: 103, Mismatches: 22, Indels: 10
0.76 0.16 0.07
Matches are distributed among these distances:
29 4 0.04
30 94 0.91
31 5 0.05
ACGTcount: A:0.23, C:0.27, G:0.12, T:0.38
Consensus pattern (30 bp):
ATCCCTTTTCATAATTCGATGGTCGTCACC
Found at i:31164303 original size:25 final size:25
Alignment explanation
Indices: 31164269--31164330 Score: 106
Period size: 25 Copynumber: 2.5 Consensus size: 25
31164259 TTTAGGCATT
31164269 CATTTCATGCATTTGCATTACATGA
1 CATTTCATGCATTTGCATTACATGA
31164294 CATTTCATGCATTTGCATTACATGA
1 CATTTCATGCATTTGCATTACATGA
**
31164319 CATCACATGCAT
1 CATTTCATGCAT
31164331 AAATCCATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (25 bp):
CATTTCATGCATTTGCATTACATGA
Found at i:31167923 original size:129 final size:129
Alignment explanation
Indices: 31167688--31168169 Score: 802
Period size: 129 Copynumber: 3.7 Consensus size: 129
31167678 ATGAAGATAG
* * *
31167688 CAGATCTTGTCACCCTAAGCAGTAGCGGAGCAGATCGAAGATGGGGAAATCTTATCTTCAAGTGT
1 CAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGA-CGGCAAATCTTATCTTCAAGTGT
* * * *
31167753 AAGGAAGCAAATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGAGAAATTA
65 AAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTAGTCAGCAGCGGAATAGGTTGGGAAATTA
* *
31167818 CAAATCTTGCCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGTGTA
1 CAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGTGTA
*
31167883 AGGAAGCAGATTTAAGCCATAAGTCCTATATCCCTAGTCAGCAGCGGAATAGGTTGGGAAATTA
66 AGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTAGTCAGCAGCGGAATAGGTTGGGAAATTA
*
31167947 CAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGTGTA
1 CAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGTGTA
* *
31168012 AGAAAGGAGATTTAAGCCACAAGTCCTATATCCCTAGTCAGCAGCGGAATAGGTTGGGAAATTA
66 AGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTAGTCAGCAGCGGAATAGGTTGGGAAATTA
* **
31168076 CAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAGACGGTGAATCTTATCTTCAAGTGTA
1 CAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGTGTA
*
31168141 AGGAAGCAGATTTAAGCCACAAATCCTAT
66 AGGAAGCAGATTTAAGCCACAAGTCCTAT
31168170 CTCCTTGAAG
Statistics
Matches: 331, Mismatches: 21, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
129 293 0.89
130 38 0.11
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.24
Consensus pattern (129 bp):
CAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGTGTA
AGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTAGTCAGCAGCGGAATAGGTTGGGAAATTA
Found at i:31168344 original size:44 final size:44
Alignment explanation
Indices: 31168167--31168402 Score: 182
Period size: 44 Copynumber: 5.5 Consensus size: 44
31168157 CCACAAATCC
* * * *
31168167 TATCTCCTTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATTT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGCAATAGATCT
* * * * * *
31168211 TATCTCACTGAAGTTGCAGTAGAGTGGA-T--CGCATTAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGCAATAGATCT
* * * * *
31168252 TATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGATA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAG-CAATAGATCT
* * *
31168296 TATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATTT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGCAATAGATCT
* * * * *
31168340 TATCTCACTGAAGTTGCAGTAGAGTGGA-T--CGC-ATCAGGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGCAAT-AGATCT
*
31168381 TATCTCCCTGAGGTTGCAGTGG
1 TATCTCCCTGAAGTTGCAGTGG
31168403 TGCACACTGA
Statistics
Matches: 148, Mismatches: 38, Indels: 15
0.74 0.19 0.07
Matches are distributed among these distances:
40 2 0.01
41 54 0.36
42 1 0.01
43 5 0.03
44 83 0.56
45 3 0.02
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGCAATAGATCT
Found at i:31168382 original size:129 final size:129
Alignment explanation
Indices: 31168145--31168402 Score: 446
Period size: 129 Copynumber: 2.0 Consensus size: 129
31168135 AGTGTAAGGA
* *
31168145 AGCAGATTTAAGCCACAAATCCTATCTCCTTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATT
1 AGCAGATTGAAGCCACAAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATT
*
31168210 TTATCTCACTGAAGTTGCAGTAGAGTGGATCGCATTAAATCTTATCTCCCTGAGGTTGCAGTGG
66 TTATCTCACTGAAGTTGCAGTAGAGTGGATCGCATCAAATCTTATCTCCCTGAGGTTGCAGTGG
*
31168274 AGCAGATTGAAGCCGA-TAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGAT
1 AGCAGATTGAAGCC-ACAAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGAT
**
31168338 TTTATCTCACTGAAGTTGCAGTAGAGTGGATCGCATCAGGTCTTATCTCCCTGAGGTTGCAGTGG
65 TTTATCTCACTGAAGTTGCAGTAGAGTGGATCGCATCAAATCTTATCTCCCTGAGGTTGCAGTGG
31168403 TGCACACTGA
Statistics
Matches: 122, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
129 121 0.99
130 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (129 bp):
AGCAGATTGAAGCCACAAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATT
TTATCTCACTGAAGTTGCAGTAGAGTGGATCGCATCAAATCTTATCTCCCTGAGGTTGCAGTGG
Found at i:31168434 original size:129 final size:129
Alignment explanation
Indices: 31168162--31168439 Score: 414
Period size: 129 Copynumber: 2.2 Consensus size: 129
31168152 TTAAGCCACA
* *
31168162 AATCCTATCTCCTTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATTTTATCTCACTGAAGTTG
1 AATCCTATCCCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATTTTATCTCACTGAAGTTG
* * * *** *
31168227 CAGTAGAGTGGATCGCATTAAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGAT
66 CAGTAGAGTGGATCGCATCAAATCTTATCTCCCTGAGGTTGCAGTGGAGCACACTGAAGAAAAC
*
31168291 AATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATTTTATCTCACTGAAGTTG
1 AATCCTATCCCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATTTTATCTCACTGAAGTTG
** *
31168356 CAGTAGAGTGGATCGCATCAGGTCTTATCTCCCTGAGGTTGCAGTGGTGCACACTG-AGAAAAC
66 CAGTAGAGTGGATCGCATCAAATCTTATCTCCCTGAGGTTGCAGTGGAGCACACTGAAGAAAAC
*
31168419 AAGTCTTATCCCCCTGAAGTT
1 AA-TCCTATCCCCCTGAAGTT
31168440 ACAGTGTGGC
Statistics
Matches: 135, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
128 5 0.04
129 130 0.96
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.30
Consensus pattern (129 bp):
AATCCTATCCCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATTTTATCTCACTGAAGTTG
CAGTAGAGTGGATCGCATCAAATCTTATCTCCCTGAGGTTGCAGTGGAGCACACTGAAGAAAAC
Found at i:31176541 original size:106 final size:107
Alignment explanation
Indices: 31175913--31176541 Score: 721
Period size: 106 Copynumber: 5.9 Consensus size: 107
31175903 TGTGTTTCTA
* * * * * * *
31175913 GTAGGTCATCGAGCCGTTTTAGAATTTTCGATATTAAATCAGCTAACT-AAAAAAAGCTTGGGTT
1 GTAGGTCATCGAGCTGTTTTAGGAGTTGCGATCTTAAATCAGCTAACTCAAAGAAA-CTTAGGTT
* * *
31175977 GCAATCTTAAATCAACTAAACTTTATAATATCAGTTA-TGAAT
65 GCGATCTTAAATCAACTAACCTTTATAATATCAGCTAGTGAAT
*
31176019 GTAGGTCATCGAGCTGTTTTAGGAGTTGCGATCTTAAATTAGCTAACTCAAAGAAACTTAGGTTG
1 GTAGGTCATCGAGCTGTTTTAGGAGTTGCGATCTTAAATCAGCTAACTCAAAGAAACTTAGGTTG
* * **
31176084 CGATATTAAACCAACTAACCTTTATAATATCAATTA-TGAAT
66 CGATCTTAAATCAACTAACCTTTATAATATCAGCTAGTGAAT
** * * *
31176125 GTAGGTCATCGATTTGTTTTAGGAGTTGCAATCTTAAATCAGTTAACTCAATGAAACTTAGGTTG
1 GTAGGTCATCGAGCTGTTTTAGGAGTTGCGATCTTAAATCAGCTAACTCAAAGAAACTTAGGTTG
* * * **
31176190 AGATCTTAAATCAGCTAACCTTTATAATATCAACT-GTGAGC
66 CGATCTTAAATCAACTAACCTTTATAATATCAGCTAGTGAAT
* * * * * * * *
31176231 ATAGGTCATTGAACTGTTTTTGGATTTGCGATCTTAAATTAGTTACCTCAAAGAAACTTAGGTTG
1 GTAGGTCATCGAGCTGTTTTAGGAGTTGCGATCTTAAATCAGCTAACTCAAAGAAACTTAGGTTG
* * * * * *
31176296 CGATCCTAAATTAGCTAACCCTTATAATATCAG-TTGTGAAC
66 CGATCTTAAATCAACTAACCTTTATAATATCAGCTAGTGAAT
* * * * * * *
31176337 ATGGGTCATCAAGTTGTTTTAGGAGTTACGATATTAAATCAGCTAACTCAAAGAAACTTAGGTTA
1 GTAGGTCATCGAGCTGTTTTAGGAGTTGCGATCTTAAATCAGCTAACTCAAAGAAACTTAGGTTG
*** *
31176402 CGATCTTCGGTCAACTAAACTTTATAATATCAGCTAGT-AAT
66 CGATCTTAAATCAACTAACCTTTATAATATCAGCTAGTGAAT
* * *
31176443 GTAGATCATCGAGCTATTTTAGGAGTTGCGATCTTAAATCAACTAACTCAAAGAAACTTAGGTTG
1 GTAGGTCATCGAGCTGTTTTAGGAGTTGCGATCTTAAATCAGCTAACTCAAAGAAACTTAGGTTG
*
31176508 CGATCTTAAATCAACTAACTTTTATAATATCAGC
66 CGATCTTAAATCAACTAACCTTTATAATATCAGC
31176542 ACTTTTAAAT
Statistics
Matches: 439, Mismatches: 80, Indels: 8
0.83 0.15 0.02
Matches are distributed among these distances:
105 1 0.00
106 429 0.98
107 9 0.02
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (107 bp):
GTAGGTCATCGAGCTGTTTTAGGAGTTGCGATCTTAAATCAGCTAACTCAAAGAAACTTAGGTTG
CGATCTTAAATCAACTAACCTTTATAATATCAGCTAGTGAAT
Found at i:31187985 original size:13 final size:13
Alignment explanation
Indices: 31187967--31187995 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
31187957 TACAATTTTA
31187967 CATTACGGTGATT
1 CATTACGGTGATT
31187980 CATTACGGTGATT
1 CATTACGGTGATT
31187993 CAT
1 CAT
31187996 AAAAGATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (13 bp):
CATTACGGTGATT
Found at i:31197028 original size:25 final size:25
Alignment explanation
Indices: 31196956--31197063 Score: 69
Period size: 25 Copynumber: 4.3 Consensus size: 25
31196946 AAACCAAATG
* **
31196956 AAGCCTTTGTGG-AAAGTTATTTGTG
1 AAGCC-TTGTGGCGAAGTTATTTGAA
* * *
31196981 AAGCCCTTGGGGCGAA-ATCTTTGAA
1 AAG-CCTTGTGGCGAAGTTATTTGAA
*
31197006 AAGCCTATGTGGCG-TGTTATTTGAA
1 AAGCCT-TGTGGCGAAGTTATTTGAA
* * *
31197031 AATCCTTAGTGGCGAAGTTATCTGGA
1 AAGCCTT-GTGGCGAAGTTATTTGAA
31197057 AAGCCTT
1 AAGCCTT
31197064 TGTGTCAAGT
Statistics
Matches: 62, Mismatches: 15, Indels: 11
0.70 0.17 0.12
Matches are distributed among these distances:
24 4 0.06
25 40 0.65
26 18 0.29
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (25 bp):
AAGCCTTGTGGCGAAGTTATTTGAA
Found at i:31197144 original size:71 final size:72
Alignment explanation
Indices: 31197062--31197200 Score: 199
Period size: 72 Copynumber: 1.9 Consensus size: 72
31197052 CTGGAAAGCC
* * * *
31197062 TTTGTGTCAAGTCATTTGGAAAACC-GTATGGCAAATTCTGCGATGCCTAAGTGGCGAGTTGTTA
1 TTTGTGGCAAGTCATTTGCAAAACCTGTATGGCAAATTCTACAATGCCTAAGTGGCGAGTTGTTA
31197126 CTCCACA
66 CTCCACA
* ** *
31197133 TTTGTGGCAAGTCATTTGCAAAGCCTGTATGGTGAATTCTACAATGCGTAAGTGGCGAGTTGTTA
1 TTTGTGGCAAGTCATTTGCAAAACCTGTATGGCAAATTCTACAATGCCTAAGTGGCGAGTTGTTA
31197198 CTC
66 CTC
31197201 TGCCTTTGTA
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
71 22 0.37
72 37 0.63
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.32
Consensus pattern (72 bp):
TTTGTGGCAAGTCATTTGCAAAACCTGTATGGCAAATTCTACAATGCCTAAGTGGCGAGTTGTTA
CTCCACA
Found at i:31199668 original size:18 final size:19
Alignment explanation
Indices: 31199634--31199669 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
31199624 TTCTAATTAG
*
31199634 TTTTAAATGTTAATTATTC
1 TTTTAAATGTAAATTATTC
31199653 TTTTAAA-GTAAATTATT
1 TTTTAAATGTAAATTATT
31199670 AGCCATTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.56
Consensus pattern (19 bp):
TTTTAAATGTAAATTATTC
Found at i:31203397 original size:39 final size:39
Alignment explanation
Indices: 31203335--31203472 Score: 154
Period size: 39 Copynumber: 3.5 Consensus size: 39
31203325 AACATGTTTT
* *
31203335 TGAGTATTACGATATATGGTTGAATGTTATGTGATTATA
1 TGAGTATTGCGATATATGCTTGAATGTTATGTGATTATA
* * *
31203374 TGAGTATTGTGATATGTGCTTGAACGTTATGT-ACTTATA
1 TGAGTATTGCGATATATGCTTGAATGTTATGTGA-TTATA
* * *
31203413 TGAGTATTGCAATATATGCTTAAATGTTATATGATTATA
1 TGAGTATTGCGATATATGCTTGAATGTTATGTGATTATA
* *
31203452 TGTGTCA-TGTGATATATGCTT
1 TGAGT-ATTGCGATATATGCTT
31203473 AAAAGTGAAT
Statistics
Matches: 82, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
38 1 0.01
39 79 0.96
40 2 0.02
ACGTcount: A:0.29, C:0.06, G:0.21, T:0.44
Consensus pattern (39 bp):
TGAGTATTGCGATATATGCTTGAATGTTATGTGATTATA
Found at i:31204875 original size:23 final size:21
Alignment explanation
Indices: 31204814--31204881 Score: 55
Period size: 23 Copynumber: 3.0 Consensus size: 21
31204804 CCTAGAATAA
*
31204814 TTTTGTATTAATTTATTTTTCT
1 TTTTGTATTAAGTTATTTTT-T
* *
31204836 TTTTATATTTAGTGTTATTTTTT
1 TTTTGTA-TTA-AGTTATTTTTT
*
31204859 TCTTTGTATTGAAGTTATATTTT
1 T-TTTGTATT-AAGTTATTTTTT
31204882 CTCGAGTAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
22 6 0.17
23 16 0.44
24 14 0.39
ACGTcount: A:0.19, C:0.03, G:0.09, T:0.69
Consensus pattern (21 bp):
TTTTGTATTAAGTTATTTTTT
Found at i:31209205 original size:48 final size:45
Alignment explanation
Indices: 31209110--31209218 Score: 110
Period size: 48 Copynumber: 2.3 Consensus size: 45
31209100 GTGTAGGTTC
* * * *
31209110 AACCCTAACGGTGACCAGGCACTATTATTCGATTCGTGTAGGCTT
1 AACCCTAACGGTAACCAGGCACTATAATTCGATTCGTGCACGCTT
** *
31209155 AACCCTAACGGGTAACCAGGCACTATAATTAATTATTCGTGCACGTTT
1 AACCCTAAC-GGTAACCAGGCACTATAATT--CGATTCGTGCACGCTT
*
31209203 AACCCAAACAGGTAAC
1 AACCCTAAC-GGTAAC
31209219 TAAACACTAT
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
45 9 0.17
46 18 0.35
48 25 0.48
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (45 bp):
AACCCTAACGGTAACCAGGCACTATAATTCGATTCGTGCACGCTT
Found at i:31216068 original size:14 final size:14
Alignment explanation
Indices: 31216049--31216076 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
31216039 TTACACTCAA
31216049 AATTTAAAGTAGGG
1 AATTTAAAGTAGGG
31216063 AATTTAAAGTAGGG
1 AATTTAAAGTAGGG
31216077 GTTTAGGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (14 bp):
AATTTAAAGTAGGG
Found at i:31222838 original size:7 final size:7
Alignment explanation
Indices: 31222826--31222852 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
31222816 TTTATCTTTA
31222826 ATTTATT
1 ATTTATT
31222833 ATTTATT
1 ATTTATT
31222840 ATTTATT
1 ATTTATT
31222847 ATTTAT
1 ATTTAT
31222853 CTTTAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
ATTTATT
Found at i:31224331 original size:19 final size:19
Alignment explanation
Indices: 31224287--31224331 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
31224277 TTATTTCAGA
31224287 ATTAT-AAAATATTAAAAT
1 ATTATAAAAATATTAAAAT
*
31224305 ATTA-AAAAAGTATTATAAT
1 ATTATAAAAA-TATTAAAAT
31224324 -TTATAAAA
1 ATTATAAAA
31224332 GTGTTCAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
ATTATAAAAATATTAAAAT
Found at i:31224332 original size:18 final size:19
Alignment explanation
Indices: 31224287--31224333 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
31224277 TTATTTCAGA
31224287 ATTATAAAA-TATTAAAAT
1 ATTATAAAAGTATTAAAAT
* *
31224305 ATTAAAAAAGTATTATAAT
1 ATTATAAAAGTATTAAAAT
31224324 -TTATAAAAGT
1 ATTATAAAAGT
31224334 GTTCAATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (19 bp):
ATTATAAAAGTATTAAAAT
Found at i:31225686 original size:22 final size:22
Alignment explanation
Indices: 31225644--31225684 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
31225634 AAAATGAAAA
31225644 TAATTTTTAAAAATATTTTTAT
1 TAATTTTTAAAAATATTTTTAT
*
31225666 TAATTTTT-AATATATTTTT
1 TAATTTTTAAAAATATTTTT
31225685 TAGATTATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TAATTTTTAAAAATATTTTTAT
Found at i:31228381 original size:24 final size:24
Alignment explanation
Indices: 31228354--31228405 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
31228344 TTAGTAAGTC
*
31228354 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* * *
31228378 AAATATATTATGCTAATAAATACT
1 AAATAAACTATACTAATAAATACT
31228402 AAAT
1 AAAT
31228406 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:31232334 original size:25 final size:25
Alignment explanation
Indices: 31232278--31232395 Score: 82
Period size: 25 Copynumber: 4.8 Consensus size: 25
31232268 GCTCTCTCTT
* *
31232278 GAGCCATATAATGGGAAGCTCATAT
1 GAGCCATATAACGGGAAGCTCATAA
* * *
31232303 GAACCATGTAACGGGAAGCTTATAA
1 GAGCCATATAACGGGAAGCTCATAA
* ** **
31232328 GAGCCATA-ATCAAGAAGCTCATGC
1 GAGCCATATAACGGGAAGCTCATAA
* *
31232352 GAGCCA-ATAATGGGTAGCTC-TGAA
1 GAGCCATATAACGGGAAGCTCAT-AA
31232376 GAGCCAT-TAATCGGGAAGCT
1 GAGCCATATAA-CGGGAAGCT
31232396 TTGGATAGCC
Statistics
Matches: 67, Mismatches: 22, Indels: 8
0.69 0.23 0.08
Matches are distributed among these distances:
23 2 0.03
24 32 0.48
25 33 0.49
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.20
Consensus pattern (25 bp):
GAGCCATATAACGGGAAGCTCATAA
Found at i:31247723 original size:37 final size:38
Alignment explanation
Indices: 31247682--31247803 Score: 153
Period size: 37 Copynumber: 3.3 Consensus size: 38
31247672 TCCATCTGAA
*
31247682 AACACGCCAAATGCTCAT-AAGAACTCATCCACCCGAT
1 AACACGCCAAATGCTCATCAAGAGCTCATCCACCCGAT
* * * * *
31247719 AACACGCCAATTGCTC-TGAAGAGCT-AGTGCAACCGAA
1 AACACGCCAAATGCTCATCAAGAGCTCA-TCCACCCGAT
31247756 AACACGCCAAATGCTCATCAA-AGCTCATCCACCCGAT
1 AACACGCCAAATGCTCATCAAGAGCTCATCCACCCGAT
31247793 AACACGCCAAA
1 AACACGCCAAA
31247804 ACAAGGAGTA
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
36 2 0.03
37 65 0.92
38 4 0.06
ACGTcount: A:0.38, C:0.34, G:0.14, T:0.15
Consensus pattern (38 bp):
AACACGCCAAATGCTCATCAAGAGCTCATCCACCCGAT
Found at i:31251951 original size:9 final size:9
Alignment explanation
Indices: 31251937--31251986 Score: 82
Period size: 9 Copynumber: 5.6 Consensus size: 9
31251927 TTTTGGTTAA
31251937 AATTAACCG
1 AATTAACCG
31251946 AATTAACCG
1 AATTAACCG
*
31251955 AATTACCCG
1 AATTAACCG
31251964 AATTAACCG
1 AATTAACCG
*
31251973 AATTACCCG
1 AATTAACCG
31251982 AATTA
1 AATTA
31251987 TATGTTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.42, C:0.24, G:0.10, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:31251964 original size:18 final size:18
Alignment explanation
Indices: 31251937--31251986 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
31251927 TTTTGGTTAA
*
31251937 AATTAACCGAATTAACCG
1 AATTACCCGAATTAACCG
31251955 AATTACCCGAATTAACCG
1 AATTACCCGAATTAACCG
31251973 AATTACCCGAATTA
1 AATTACCCGAATTA
31251987 TATGTTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.42, C:0.24, G:0.10, T:0.24
Consensus pattern (18 bp):
AATTACCCGAATTAACCG
Found at i:31252037 original size:26 final size:25
Alignment explanation
Indices: 31251994--31252043 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
31251984 TTATATGTTT
*
31251994 TTTTATTTTTAAACTTTATTTTTAG
1 TTTTAGTTTTAAACTTTATTTTTAG
*
31252019 TTTTAGTTTTAGAATTTTATTTTTA
1 TTTTAGTTTTA-AACTTTATTTTTA
31252044 TTTATTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.24, C:0.02, G:0.06, T:0.68
Consensus pattern (25 bp):
TTTTAGTTTTAAACTTTATTTTTAG
Found at i:31252041 original size:13 final size:14
Alignment explanation
Indices: 31251994--31252043 Score: 61
Period size: 12 Copynumber: 3.8 Consensus size: 14
31251984 TTATATGTTT
31251994 TTTTATTTTTA-AA
1 TTTTATTTTTAGAA
*
31252007 CTTTATTTTTAG--
1 TTTTATTTTTAGAA
*
31252019 TTTTAGTTTTAGAA
1 TTTTATTTTTAGAA
31252033 TTTTATTTTTA
1 TTTTATTTTTA
31252044 TTTATTAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
12 10 0.33
13 10 0.33
14 10 0.33
ACGTcount: A:0.24, C:0.02, G:0.06, T:0.68
Consensus pattern (14 bp):
TTTTATTTTTAGAA
Found at i:31252094 original size:18 final size:18
Alignment explanation
Indices: 31252071--31252124 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
31252061 AATTTTTATG
31252071 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGGGTA
*
31252089 ATTGGGTTGGGTTGGATA
1 ATTGGGTTGGGTTGGGTA
* *
31252107 CTTGGGTTTGGATTGGGT
1 ATTGGG-TTGGGTTGGGT
31252125 TTAGGTGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 22 0.71
19 9 0.29
ACGTcount: A:0.11, C:0.02, G:0.46, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGGGTA
Found at i:31252891 original size:43 final size:44
Alignment explanation
Indices: 31252786--31252894 Score: 150
Period size: 43 Copynumber: 2.5 Consensus size: 44
31252776 AATTGCCGCA
* * *
31252786 AAAGATCATGTTCTTTAGCAGC-ATTTGTAGTAAAAGCGCCGTT
1 AAAGATCATGTTCTATAGCGGCGATTTGTAATAAAAGCGCCGTT
* **
31252829 AAATATCATGTTCTATAGCGGCGA-TTGTAATAAAAGCGTTGTT
1 AAAGATCATGTTCTATAGCGGCGATTTGTAATAAAAGCGCCGTT
31252872 AAAGATCATGTTCTATAGCGGCG
1 AAAGATCATGTTCTATAGCGGCG
31252895 TTTTCCCACA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
43 57 0.98
44 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (44 bp):
AAAGATCATGTTCTATAGCGGCGATTTGTAATAAAAGCGCCGTT
Found at i:31255707 original size:24 final size:24
Alignment explanation
Indices: 31255679--31255730 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
31255669 ATGGGAAAGA
*
31255679 AAAAATTAAGTTAGGGAATTGGGG
1 AAAAACTAAGTTAGGGAATTGGGG
*
31255703 AAAAACTAAGTTAGGGATTTGGGG
1 AAAAACTAAGTTAGGGAATTGGGG
31255727 AAAA
1 AAAA
31255731 TGATTTGGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.44, C:0.02, G:0.31, T:0.23
Consensus pattern (24 bp):
AAAAACTAAGTTAGGGAATTGGGG
Found at i:31255863 original size:41 final size:42
Alignment explanation
Indices: 31255803--31255912 Score: 125
Period size: 41 Copynumber: 2.6 Consensus size: 42
31255793 AAAAATATTC
* *
31255803 GTGGCGTTTATGGGCAAAACGCCGCTATTG-CTTT-ACCTTTA
1 GTGGCGTTTAT-GGAAAAACGCCGCTATCGTCTTTAACCTTTA
* * *
31255844 GTGGCATTTATGAGAAAAACGCCGCTATCGTTTTTAACCTTTT
1 GTGGCGTTTATG-GAAAAACGCCGCTATCGTCTTTAACCTTTA
* *
31255887 GCGGCGTTTATGCAAAAACGCCGCTA
1 GTGGCGTTTATGGAAAAACGCCGCTA
31255913 ACGTTGCTCC
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
40 1 0.02
41 25 0.43
42 16 0.28
43 16 0.28
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.32
Consensus pattern (42 bp):
GTGGCGTTTATGGAAAAACGCCGCTATCGTCTTTAACCTTTA
Found at i:31258619 original size:44 final size:44
Alignment explanation
Indices: 31258598--31258914 Score: 256
Period size: 44 Copynumber: 7.4 Consensus size: 44
31258588 ATCTGTAATT
*
31258598 TTCAACCTATTTCACTGCTGCTCAGAGAGATAAGATTCACAATC
1 TTCAACCTATTCCACTGCTGCTCAGAGAGATAAGATTCACAATC
* *
31258642 TTCAACCTATTCCACTGCTGACTAAG-GAGATAGGATT--C-A-C
1 TTCAACCTATTCCACTGCTG-CTCAGAGAGATAAGATTCACAATC
* *
31258682 --C-A---ATTCCACTGCTGAC-CAGGGAGATAGGACTT-ACAATC
1 TTCAACCTATTCCACTGCTG-CTCAGAGAGATAAGA-TTCACAATC
* * *
31258720 TTCAACCTATTCCACTGTTGAC-CAGGGAGATAGGATTCACAATC
1 TTCAACCTATTCCACTGCTG-CTCAGAGAGATAAGATTCACAATC
* * *
31258764 TTCAACCTATTCTACTGCTGACT-AGGGAGATAGGATTCACAATC
1 TTCAACCTATTCCACTGCTG-CTCAGAGAGATAAGATTCACAATC
* * * * *
31258808 TTCAACCTATTCCACTACTGAC-CAGGGGGATAGGACTCACAATC
1 TTCAACCTATTCCACTGCTG-CTCAGAGAGATAAGATTCACAATC
* * * *
31258852 TTCAACCTATTCCATTGCTGAC-CAGGGAGATAGGACTT-ATAATC
1 TTCAACCTATTCCACTGCTG-CTCAGAGAGATAAGA-TTCACAATC
31258896 TTCAACCTATTCCACTGCT
1 TTCAACCTATTCCACTGCT
31258915 TTCCAGGGAG
Statistics
Matches: 240, Mismatches: 17, Indels: 32
0.83 0.06 0.11
Matches are distributed among these distances:
33 2 0.01
34 23 0.10
35 2 0.01
36 1 0.00
37 2 0.01
38 2 0.01
40 2 0.01
41 2 0.01
42 1 0.00
43 2 0.01
44 196 0.82
45 5 0.02
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (44 bp):
TTCAACCTATTCCACTGCTGCTCAGAGAGATAAGATTCACAATC
Found at i:31258921 original size:44 final size:44
Alignment explanation
Indices: 31258684--31258932 Score: 376
Period size: 44 Copynumber: 5.7 Consensus size: 44
31258674 GGATTCACCA
31258684 ATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCAACCT
1 ATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCAACCT
*
31258728 ATTCCACTGTTGACCAGGGAGATAGGA-TTCACAATCTTCAACCT
1 ATTCCACTGCTGACCAGGGAGATAGGACTT-ACAATCTTCAACCT
* *
31258772 ATTCTACTGCTGACTAGGGAGATAGGA-TTCACAATCTTCAACCT
1 ATTCCACTGCTGACCAGGGAGATAGGACTT-ACAATCTTCAACCT
* * *
31258816 ATTCCACTACTGACCAGGGGGATAGGACTCACAATCTTCAACCT
1 ATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCAACCT
* *
31258860 ATTCCATTGCTGACCAGGGAGATAGGACTTATAATCTTCAACCT
1 ATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCAACCT
**
31258904 ATTCCACTGCTTTCCAGGGAGATAGGACT
1 ATTCCACTGCTGACCAGGGAGATAGGACT
31258933 AGTCTCTTCG
Statistics
Matches: 186, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
43 2 0.01
44 183 0.98
45 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (44 bp):
ATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCAACCT
Found at i:31261800 original size:9 final size:9
Alignment explanation
Indices: 31261781--31261813 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
31261771 ATGCAAAGCT
31261781 AATGC-ATG
1 AATGCAATG
31261789 AATGCAATG
1 AATGCAATG
*
31261798 AATGCCATG
1 AATGCAATG
31261807 AATGCAA
1 AATGCAA
31261814 AAGAAGAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 5 0.23
9 17 0.77
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.21
Consensus pattern (9 bp):
AATGCAATG
Found at i:31263538 original size:19 final size:20
Alignment explanation
Indices: 31263495--31263548 Score: 83
Period size: 19 Copynumber: 2.6 Consensus size: 20
31263485 NNNNNNNNNN
31263495 AAGATTGCATATCATATCTTCT
1 AAGATTGCATATCATA--TTCT
31263517 AAGATTGCATATCATA-TCT
1 AAGATTGCATATCATATTCT
31263536 AAGATTGCATATC
1 AAGATTGCATATC
31263549 CTTGAAGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 16 0.50
22 16 0.50
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (20 bp):
AAGATTGCATATCATATTCT
Found at i:31265473 original size:31 final size:31
Alignment explanation
Indices: 31265438--31265496 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
31265428 AACAGCCTTA
31265438 TGACTTAAATAAAAACTTTTGAATAATTTAG
1 TGACTTAAATAAAAACTTTTGAATAATTTAG
* *
31265469 TGACTTAAATGAAATCTTTTGAATAATT
1 TGACTTAAATAAAAACTTTTGAATAATT
31265497 CAATGATCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.41
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTTGAATAATTTAG
Found at i:31267390 original size:29 final size:28
Alignment explanation
Indices: 31267336--31267393 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
31267326 CCTACAAAAA
*
31267336 TTTTAATTTTTTTAACTTTATATATATT
1 TTTTAATTTTTTTAAATTTATATATATT
*
31267364 TTTTATATTTTTTTAGAATTTCT-TATATT
1 TTTTA-ATTTTTTTA-AATTTATATATATT
31267393 T
1 T
31267394 AAAAAAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 5 0.19
29 16 0.62
30 5 0.19
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.69
Consensus pattern (28 bp):
TTTTAATTTTTTTAAATTTATATATATT
Found at i:31268844 original size:14 final size:15
Alignment explanation
Indices: 31268811--31268846 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
31268801 CACTTGTTTT
*
31268811 TTTTAATTTTATATA
1 TTTTAGTTTTATATA
31268826 TTTTAGTTTTATA-A
1 TTTTAGTTTTATATA
31268840 TTTTAGT
1 TTTTAGT
31268847 CACTTGTAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.67
Consensus pattern (15 bp):
TTTTAGTTTTATATA
Found at i:31270323 original size:10 final size:10
Alignment explanation
Indices: 31270308--31270341 Score: 68
Period size: 10 Copynumber: 3.4 Consensus size: 10
31270298 TTCCCCTGTT
31270308 TAAATAAAAA
1 TAAATAAAAA
31270318 TAAATAAAAA
1 TAAATAAAAA
31270328 TAAATAAAAA
1 TAAATAAAAA
31270338 TAAA
1 TAAA
31270342 AGTTGAATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
TAAATAAAAA
Found at i:31275683 original size:24 final size:25
Alignment explanation
Indices: 31275637--31275684 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
31275627 TAATAAATAT
*
31275637 ATATATTTAAAATTTTTAATTTTAAA
1 ATATATTTAAAATTCTT-ATTTTAAA
*
31275663 ATATTTTTAAAATTCTT-TTTTA
1 ATATATTTAAAATTCTTATTTTA
31275685 TTTTTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
26 15 0.75
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (25 bp):
ATATATTTAAAATTCTTATTTTAAA
Found at i:31280112 original size:27 final size:26
Alignment explanation
Indices: 31280082--31280170 Score: 71
Period size: 24 Copynumber: 3.5 Consensus size: 26
31280072 AATTGTAAAA
31280082 ATTATAATTATTTTTAAATGTATAACT
1 ATTATAATTATTTTTAAATGTATAA-T
* *
31280109 ATTA-CA--ATTTTTAAAT-TA-AAA
1 ATTATAATTATTTTTAAATGTATAAT
* *
31280130 ATTCTAATTATTTTTAATTGTATAAGT
1 ATTATAATTATTTTTAAATGTATAA-T
* *
31280157 ATTACAAGTATTTT
1 ATTATAATTATTTT
31280171 ACTTCAGCAC
Statistics
Matches: 47, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
21 3 0.06
22 3 0.06
23 2 0.04
24 19 0.40
25 2 0.04
26 3 0.06
27 15 0.32
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (26 bp):
ATTATAATTATTTTTAAATGTATAAT
Found at i:31303385 original size:2 final size:2
Alignment explanation
Indices: 31303378--31303420 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
31303368 TTTGAATAGA
*
31303378 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC T- TC -C TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
31303418 TC T
1 TC T
31303421 TGAACATACA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:31306029 original size:12 final size:12
Alignment explanation
Indices: 31306012--31306046 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
31306002 TAGGAGTGAT
31306012 TGTTTGTTTTTC
1 TGTTTGTTTTTC
31306024 TGTTTGTTTTTC
1 TGTTTGTTTTTC
*
31306036 TTTTTGTTTTT
1 TGTTTGTTTTT
31306047 GTTTTAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.06, G:0.14, T:0.80
Consensus pattern (12 bp):
TGTTTGTTTTTC
Found at i:31306051 original size:12 final size:12
Alignment explanation
Indices: 31306014--31306051 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
31306004 GGAGTGATTG
*
31306014 TTTGTTTTTCTG
1 TTTGTTTTTCTT
31306026 TTTGTTTTTCTT
1 TTTGTTTTTCTT
*
31306038 TTTGTTTTTGTT
1 TTTGTTTTTCTT
31306050 TT
1 TT
31306052 AAGAAACCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.00, C:0.05, G:0.13, T:0.82
Consensus pattern (12 bp):
TTTGTTTTTCTT
Found at i:31306170 original size:28 final size:27
Alignment explanation
Indices: 31306113--31306171 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 27
31306103 AAAAGCCCTT
31306113 TTTTTTAAATTTACCGAAATAGGCCGA
1 TTTTTTAAATTTACCGAAATAGGCCGA
* *
31306140 TTTTTTAATTATTTACCGGAATGGGCC-A
1 TTTTTTAA--ATTTACCGAAATAGGCCGA
31306168 TTTT
1 TTTT
31306172 CCCCGAAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 8 0.29
28 5 0.18
29 15 0.54
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (27 bp):
TTTTTTAAATTTACCGAAATAGGCCGA
Found at i:31306577 original size:52 final size:51
Alignment explanation
Indices: 31306515--31306670 Score: 258
Period size: 52 Copynumber: 3.0 Consensus size: 51
31306505 GGGTTTTAGG
*
31306515 GTTTAGGGTGCAAGCTTTTTTAGGGTTTAGAGGTCCCAAAAAAAATTATTTC
1 GTTTAGGGTGCAGGCTTTTTTAGGGTTTAG-GGTCCCAAAAAAAATTATTTC
* *
31306567 GTTTAGGGTGCAGGCTTTTTTAGGGTTTAGGGTGCCGAAAAAAATTATTTC
1 GTTTAGGGTGCAGGCTTTTTTAGGGTTTAGGGTCCCAAAAAAAATTATTTC
*
31306618 GTTTAGGGTGCAGGCTTTTTTAGGGTTTAGGGGTCCCAAAAAAATTTATTTC
1 GTTTAGGGTGCAGGCTTTTTTAGGGTTTA-GGGTCCCAAAAAAAATTATTTC
31306670 G
1 G
31306671 AGTTGACGTT
Statistics
Matches: 97, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
51 48 0.49
52 49 0.51
ACGTcount: A:0.25, C:0.11, G:0.27, T:0.37
Consensus pattern (51 bp):
GTTTAGGGTGCAGGCTTTTTTAGGGTTTAGGGTCCCAAAAAAAATTATTTC
Found at i:31312547 original size:21 final size:21
Alignment explanation
Indices: 31312521--31312581 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
31312511 AGTGTCAAAT
31312521 TTTTTAAATTAGGGTTATT-GG
1 TTTTTAAATTAGGGTT-TTGGG
**
31312542 TTTTTAGGGTTAGGGTTTTGGG
1 TTTTTA-AATTAGGGTTTTGGG
* *
31312564 TATTTAAAGTAGGGTTTT
1 TTTTTAAATTAGGGTTTT
31312582 TTTAGTTTAG
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
21 17 0.53
22 15 0.47
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.51
Consensus pattern (21 bp):
TTTTTAAATTAGGGTTTTGGG
Found at i:31322889 original size:17 final size:17
Alignment explanation
Indices: 31322867--31322904 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
31322857 AACATTGAAA
31322867 AAAAAAATA-ATTAACTC
1 AAAAAAATATA-TAACTC
31322884 AAAAAAATATATAACTC
1 AAAAAAATATATAACTC
31322901 AAAA
1 AAAA
31322905 CATGCATAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 19 0.95
18 1 0.05
ACGTcount: A:0.68, C:0.11, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAAAAATATATAACTC
Found at i:31325570 original size:38 final size:38
Alignment explanation
Indices: 31325519--31325595 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
31325509 GCCAAACTAG
*
31325519 CCATCTTCCCAATTGAAATTGTAGACGACATAATAATC
1 CCATCTCCCCAATTGAAATTGTAGACGACATAATAATC
* *
31325557 CCATCTCCCCAATTGGAATTGTGGACGACATAATAATC
1 CCATCTCCCCAATTGAAATTGTAGACGACATAATAATC
31325595 C
1 C
31325596 TTCTCAATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.27
Consensus pattern (38 bp):
CCATCTCCCCAATTGAAATTGTAGACGACATAATAATC
Found at i:31330773 original size:24 final size:24
Alignment explanation
Indices: 31330726--31330773 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
31330716 TAAGAATTTG
* *
31330726 AAAAATATATTATAAAATGTAATA
1 AAAAATAAATTATAAAATGAAATA
31330750 AAAAATAAATTATATAAAT-AAATA
1 AAAAATAAATTATA-AAATGAAATA
31330774 TAAATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (24 bp):
AAAAATAAATTATAAAATGAAATA
Found at i:31333196 original size:9 final size:9
Alignment explanation
Indices: 31333182--31333214 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
31333172 GATTTAATTC
31333182 TTTTTTTTG
1 TTTTTTTTG
*
31333191 TTTTTTTTA
1 TTTTTTTTG
31333200 TTTTTTTTG
1 TTTTTTTTG
31333209 TTTTTT
1 TTTTTT
31333215 CATTAATTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.03, C:0.00, G:0.06, T:0.91
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:31337280 original size:18 final size:17
Alignment explanation
Indices: 31337254--31337287 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
31337244 GTTACTCTTG
31337254 TAAAATATTAAATTAAAA
1 TAAAATATT-AATTAAAA
*
31337272 TAAATTATTAATTAAA
1 TAAAATATTAATTAAA
31337288 TTCCAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAATATTAATTAAAA
Found at i:31337590 original size:18 final size:20
Alignment explanation
Indices: 31337567--31337604 Score: 53
Period size: 18 Copynumber: 1.9 Consensus size: 20
31337557 TTACATGTAC
31337567 AAATAA-TTGAAA-AATAAA
1 AAATAACTTGAAACAATAAA
31337585 AAATAACCTTGAAACAATAA
1 AAATAA-CTTGAAACAATAA
31337605 TATTATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
20 6 0.35
21 5 0.29
ACGTcount: A:0.66, C:0.08, G:0.05, T:0.21
Consensus pattern (20 bp):
AAATAACTTGAAACAATAAA
Found at i:31345357 original size:109 final size:110
Alignment explanation
Indices: 31345165--31345384 Score: 433
Period size: 109 Copynumber: 2.0 Consensus size: 110
31345155 TTAATACATA
31345165 ATATAATTATTTTAATTATATCCAATTTATTTTGGGTAAAAAAATTATTATTAATTATATTATGA
1 ATATAATTATTTTAATTATATCCAATTTATTTTGGGTAAAAAAATTATTATTAATTATATTATGA
31345230 AAGGAGGCCTATTTGTGCTAAACCGAAAGACTGATCCAATCGAGC
66 AAGGAGGCCTATTTGTGCTAAACCGAAAGACTGATCCAATCGAGC
31345275 ATATAATTA-TTTAATTATATCCAATTTATTTTGGGTAAAAAAATTATTATTAATTATATTATGA
1 ATATAATTATTTTAATTATATCCAATTTATTTTGGGTAAAAAAATTATTATTAATTATATTATGA
31345339 AAGGAGGCCTATTTGTGCTAAACCGAAAGACTGATCCAATCGAGC
66 AAGGAGGCCTATTTGTGCTAAACCGAAAGACTGATCCAATCGAGC
31345384 A
1 A
31345385 AATAGGCTGT
Statistics
Matches: 110, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
109 101 0.92
110 9 0.08
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.37
Consensus pattern (110 bp):
ATATAATTATTTTAATTATATCCAATTTATTTTGGGTAAAAAAATTATTATTAATTATATTATGA
AAGGAGGCCTATTTGTGCTAAACCGAAAGACTGATCCAATCGAGC
Found at i:31351744 original size:23 final size:22
Alignment explanation
Indices: 31351671--31351744 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 22
31351661 AATGCCTAAT
*
31351671 AAATCTGAAATAATAATACATAA
1 AAATCT-AAGTAATAATACATAA
* * *
31351694 TAAATTTAAG-AATAAATATATCAT
1 -AAATCTAAGTAAT-AATACAT-AA
31351718 AAATCTAAGCTAATAATACATAA
1 AAATCTAAG-TAATAATACATAA
31351741 AAAT
1 AAAT
31351745 TTATGATGTT
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
22 3 0.08
23 21 0.54
24 12 0.31
25 3 0.08
ACGTcount: A:0.58, C:0.08, G:0.04, T:0.30
Consensus pattern (22 bp):
AAATCTAAGTAATAATACATAA
Found at i:31353690 original size:13 final size:13
Alignment explanation
Indices: 31353672--31353696 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31353662 AGCTAGATGA
31353672 TTGGTTATTAAAT
1 TTGGTTATTAAAT
31353685 TTGGTTATTAAA
1 TTGGTTATTAAA
31353697 CAGGACTATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (13 bp):
TTGGTTATTAAAT
Found at i:31356841 original size:13 final size:13
Alignment explanation
Indices: 31356823--31356848 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31356813 ATTGAATCAA
31356823 GTAATAAAGTGAT
1 GTAATAAAGTGAT
31356836 GTAATAAAGTGAT
1 GTAATAAAGTGAT
31356849 AAGTAAGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (13 bp):
GTAATAAAGTGAT
Found at i:31368605 original size:23 final size:23
Alignment explanation
Indices: 31368575--31368621 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
31368565 TTTTGAGAAG
31368575 TATGTTGAGATATGTTATGCATT
1 TATGTTGAGATATGTTATGCATT
31368598 TATGTTGAGATATGTTATGCATT
1 TATGTTGAGATATGTTATGCATT
31368621 T
1 T
31368622 GAACAACTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.04, G:0.21, T:0.49
Consensus pattern (23 bp):
TATGTTGAGATATGTTATGCATT
Found at i:31375416 original size:14 final size:14
Alignment explanation
Indices: 31375397--31375423 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31375387 AAACCTCTAG
31375397 ACTTGGTTAATTGA
1 ACTTGGTTAATTGA
31375411 ACTTGGTTAATTG
1 ACTTGGTTAATTG
31375424 TTTGTAGTTA
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:0.07, G:0.22, T:0.44
Consensus pattern (14 bp):
ACTTGGTTAATTGA
Found at i:31384158 original size:51 final size:51
Alignment explanation
Indices: 31384031--31384177 Score: 190
Period size: 50 Copynumber: 2.9 Consensus size: 51
31384021 AGTGAAAGTG
* *
31384031 ATGGTCACGTGTGTAGTACTATGTGCAGACTACTACGTGTACCGAAATGAT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAATGAT
* * * * *
31384082 A-GGTCGCAAGTGTAGTACTATGTGCAGGCTACTACGTGTATCG-GATGGT
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAATGAT
* *
31384131 AATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGAACCGAA
1 -ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAA
31384178 CCTCATTGAT
Statistics
Matches: 80, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
49 4 0.05
50 38 0.47
51 38 0.47
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.29
Consensus pattern (51 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAAATGAT
Found at i:31384170 original size:26 final size:26
Alignment explanation
Indices: 31384091--31384170 Score: 62
Period size: 26 Copynumber: 3.1 Consensus size: 26
31384081 TAGGTCGCAA
*
31384091 GTGTAGTACTATGTGCAGGCTACTAC
1 GTGTAGTACTATGTGCAGGCTACTAT
* *
31384117 GTGTA-T-CGGATG-GTAATGG-TCAC-AT
1 GTGTAGTAC-TATGTG-CA-GGCT-ACTAT
31384142 GTGTAGTACTATGTGCAGGCTACTAT
1 GTGTAGTACTATGTGCAGGCTACTAT
31384168 GTG
1 GTG
31384171 AACCGAACCT
Statistics
Matches: 40, Mismatches: 5, Indels: 18
0.63 0.08 0.29
Matches are distributed among these distances:
24 2 0.05
25 16 0.40
26 20 0.50
27 2 0.05
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (26 bp):
GTGTAGTACTATGTGCAGGCTACTAT
Found at i:31384231 original size:45 final size:45
Alignment explanation
Indices: 31384180--31384265 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
31384170 GAACCGAACC
* * *
31384180 TCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCCACCGGACA
1 TCATTGATTAATAAGGTGGTTACTATGTGCTGAATCCACCGGACA
31384225 TCATTGATTAATAAGGTGGTTACTATGTGCTGAATCCACCG
1 TCATTGATTAATAAGGTGGTTACTATGTGCTGAATCCACCG
31384266 AGTATCTGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (45 bp):
TCATTGATTAATAAGGTGGTTACTATGTGCTGAATCCACCGGACA
Found at i:31391513 original size:26 final size:26
Alignment explanation
Indices: 31391484--31391536 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
31391474 CACACAATCT
*
31391484 TGAAAAGAGTATGCTCATATGAGCTG
1 TGAAAAGAGTATGCTCACATGAGCTG
* * *
31391510 TGAAATGGGTCTGCTCACATGAGCTG
1 TGAAAAGAGTATGCTCACATGAGCTG
31391536 T
1 T
31391537 TGGTCAGAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.28
Consensus pattern (26 bp):
TGAAAAGAGTATGCTCACATGAGCTG
Found at i:31398364 original size:29 final size:29
Alignment explanation
Indices: 31398302--31398401 Score: 175
Period size: 29 Copynumber: 3.5 Consensus size: 29
31398292 AAAAATAAAA
* *
31398302 ATTTACTAAAATATTAC-ACCTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTTT
31398330 ATTTACCAAAATATTACAACTTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTTT
31398359 ATTTACCAAAATATTACAACTTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTTT
31398388 ATTTACCAAAATAT
1 ATTTACCAAAATAT
31398402 ATCAAAAAAA
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
28 16 0.23
29 53 0.77
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (29 bp):
ATTTACCAAAATATTACAACTTTTTTTTT
Found at i:31398512 original size:27 final size:27
Alignment explanation
Indices: 31398482--31398548 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
31398472 CGCCAATGGT
31398482 ATTGGCGGCACCAAAGGTGCCAAAACC
1 ATTGGCGGCACCAAAGGTGCCAAAACC
* **
31398509 ATTGGCGGCACCAATGGTGCCAATGCC
1 ATTGGCGGCACCAAAGGTGCCAAAACC
31398536 ATTGGCGGCACCA
1 ATTGGCGGCACCA
31398549 CTCGTATTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.27, C:0.30, G:0.28, T:0.15
Consensus pattern (27 bp):
ATTGGCGGCACCAAAGGTGCCAAAACC
Found at i:31398713 original size:19 final size:21
Alignment explanation
Indices: 31398675--31398713 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
31398665 AATAATTGAT
*
31398675 TATATTATTGTTATTATTTTG
1 TATATTATTGTTAATATTTTG
31398696 TATATT-TTG-TAATATTTT
1 TATATTATTGTTAATATTTT
31398714 TTGTTGTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.67
Consensus pattern (21 bp):
TATATTATTGTTAATATTTTG
Found at i:31398902 original size:28 final size:29
Alignment explanation
Indices: 31398848--31398916 Score: 95
Period size: 28 Copynumber: 2.4 Consensus size: 29
31398838 AACTTAGTAA
*
31398848 TATTATTGTTAGCAAAAAACTAGTATTAT
1 TATTATAGTTAGCAAAAAACTAGTATTAT
* * *
31398877 TATTATGGTTA-CGAAAAATTAGTATTAT
1 TATTATAGTTAGCAAAAAACTAGTATTAT
31398905 TATTATAGTTAG
1 TATTATAGTTAG
31398917 TTTTTTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 25 0.71
29 10 0.29
ACGTcount: A:0.39, C:0.04, G:0.13, T:0.43
Consensus pattern (29 bp):
TATTATAGTTAGCAAAAAACTAGTATTAT
Found at i:31399026 original size:12 final size:12
Alignment explanation
Indices: 31399009--31399039 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
31398999 ATAATTTTAG
31399009 TGTGTATTATTT
1 TGTGTATTATTT
31399021 TGTGTATTATTT
1 TGTGTATTATTT
*
31399033 TGAGTAT
1 TGTGTAT
31399040 AAATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.61
Consensus pattern (12 bp):
TGTGTATTATTT
Found at i:31405245 original size:19 final size:19
Alignment explanation
Indices: 31405210--31405247 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
31405200 TTTAAACACA
31405210 CAAATATTACAAAAAAATT
1 CAAATATTACAAAAAAATT
*
31405229 CAAAT-TTATAAATAAAATT
1 CAAATATTACAAA-AAAATT
31405248 ACCTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.32
Consensus pattern (19 bp):
CAAATATTACAAAAAAATT
Found at i:31405290 original size:22 final size:22
Alignment explanation
Indices: 31405265--31405340 Score: 68
Period size: 22 Copynumber: 3.4 Consensus size: 22
31405255 TTTCCCTTTT
*
31405265 TTTTCTTTCTTCCCTCTTCTTC
1 TTTTCTTTCTTCCCTCTCCTTC
*
31405287 TTTT-TTT-TTCTCTTCTCCTTTCC
1 TTTTCTTTCTTC-CCTCTCC-TT-C
*
31405310 TTTTCTTTCTTTCCTCTCCTT-
1 TTTTCTTTCTTCCCTCTCCTTC
31405331 TCTTTCTTTC
1 T-TTTCTTTC
31405341 CCTCCTTCTG
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
20 3 0.07
21 9 0.20
22 14 0.32
23 7 0.16
24 9 0.20
25 2 0.05
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTCTTTCTTCCCTCTCCTTC
Found at i:31405301 original size:18 final size:18
Alignment explanation
Indices: 31405278--31405320 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
31405268 TCTTTCTTCC
**
31405278 CTCTTCTTCTTTTTTTTT
1 CTCTTCTTCTTTCCTTTT
*
31405296 CTCTTCTCCTTTCCTTTT
1 CTCTTCTTCTTTCCTTTT
31405314 CT-TTCTT
1 CTCTTCTT
31405321 TCCTCTCCTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (18 bp):
CTCTTCTTCTTTCCTTTT
Found at i:31405418 original size:27 final size:27
Alignment explanation
Indices: 31405378--31405448 Score: 115
Period size: 27 Copynumber: 2.6 Consensus size: 27
31405368 CCCATAAAAC
*
31405378 CCATTGGTGTCGCCAATGGTATTGGCA
1 CCATTGGTGCCGCCAATGGTATTGGCA
*
31405405 CCATTGGTGCCGCCAATGGTTTTGGCA
1 CCATTGGTGCCGCCAATGGTATTGGCA
*
31405432 CCTTTGGTGCCGCCAAT
1 CCATTGGTGCCGCCAAT
31405449 ACCATTGGCG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.15, C:0.27, G:0.28, T:0.30
Consensus pattern (27 bp):
CCATTGGTGCCGCCAATGGTATTGGCA
Found at i:31405456 original size:27 final size:27
Alignment explanation
Indices: 31405378--31405457 Score: 79
Period size: 27 Copynumber: 3.0 Consensus size: 27
31405368 CCCATAAAAC
* ***
31405378 CCATTGGTGTCGCCAATGGTATTGGCA
1 CCATTGGTGCCGCCAATACCATTGGCA
****
31405405 CCATTGGTGCCGCCAATGGTTTTGGCA
1 CCATTGGTGCCGCCAATACCATTGGCA
*
31405432 CCTTTGGTGCCGCCAATACCATTGGC
1 CCATTGGTGCCGCCAATACCATTGGC
31405458 GTCACCAGTA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.29
Consensus pattern (27 bp):
CCATTGGTGCCGCCAATACCATTGGCA
Found at i:31405564 original size:22 final size:22
Alignment explanation
Indices: 31405536--31405588 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 22
31405526 TTGGTAAATA
31405536 AAAAAAAGTT-TATATATTTTGGT
1 AAAAAAA-TTGTA-ATATTTTGGT
31405559 AAAAAAATTGTAATATTTTGGT
1 AAAAAAATTGTAATATTTTGGT
31405581 AAATAAAA
1 AAA-AAAA
31405589 AAAAAGTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 15 0.54
23 13 0.46
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (22 bp):
AAAAAAATTGTAATATTTTGGT
Found at i:31405598 original size:29 final size:28
Alignment explanation
Indices: 31405521--31405613 Score: 119
Period size: 29 Copynumber: 3.5 Consensus size: 28
31405511 GTTTTTTTAT
31405521 ATATTTTGGTAAATAAAAAAAAGTT-TA
1 ATATTTTGGTAAATAAAAAAAAGTTGTA
31405548 TATATTTTGG----T-AAAAAAA-TTGTA
1 -ATATTTTGGTAAATAAAAAAAAGTTGTA
31405571 ATATTTTGGTAAATAAAAAAAAAGTTGTA
1 ATATTTTGGTAAAT-AAAAAAAAGTTGTA
31405600 ATATTTTGGTAAAT
1 ATATTTTGGTAAAT
31405614 TTTTATTTTT
Statistics
Matches: 57, Mismatches: 0, Indels: 15
0.79 0.00 0.21
Matches are distributed among these distances:
22 11 0.19
23 9 0.16
24 1 0.02
26 1 0.02
28 16 0.28
29 19 0.33
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTGTA
Found at i:31406200 original size:23 final size:23
Alignment explanation
Indices: 31406169--31406226 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
31406159 CCAATAGGGG
*
31406169 ACTTTTGTTACTAGTACTCTAGT
1 ACTTATGTTACTAGTACTCTAGT
* * * *
31406192 ACTTCTGTTATTAGTACTTTGGT
1 ACTTATGTTACTAGTACTCTAGT
31406215 ACTTATGTTACT
1 ACTTATGTTACT
31406227 GGCACTACGG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.21, C:0.16, G:0.14, T:0.50
Consensus pattern (23 bp):
ACTTATGTTACTAGTACTCTAGT
Found at i:31407547 original size:32 final size:32
Alignment explanation
Indices: 31407506--31407571 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
31407496 ACAATAAATG
*
31407506 TTTGGATAATTACCCTTGAATTTTTGTAGACA
1 TTTGGATAATTACCCTTGAACTTTTGTAGACA
31407538 TTTGGATAATTACCCTTGAACTTTTGTAGACA
1 TTTGGATAATTACCCTTGAACTTTTGTAGACA
31407570 TT
1 TT
31407572 AATTTATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (32 bp):
TTTGGATAATTACCCTTGAACTTTTGTAGACA
Found at i:31413691 original size:42 final size:42
Alignment explanation
Indices: 31413628--31413764 Score: 188
Period size: 42 Copynumber: 3.3 Consensus size: 42
31413618 GTGTAACACA
* *
31413628 CCCGTGTGCCAGGCTGTGTAACTCTCTGAGTTGCCCCACATG
1 CCCGTGTGCTAGGCCGTGTAACTCTCTGAGTTGCCCCACATG
*
31413670 CCCGTAG-GCTAGGTCC-TGTAACTCTCTAAGTTGCCCCACATG
1 CCCGT-GTGCTAGG-CCGTGTAACTCTCTGAGTTGCCCCACATG
* *
31413712 CTCGTGTGCTAGGCCGTATAACTCTCTGAGTTGCCCCACATG
1 CCCGTGTGCTAGGCCGTGTAACTCTCTGAGTTGCCCCACATG
*
31413754 CCCATGTGCTA
1 CCCGTGTGCTA
31413765 AGCCATGTGT
Statistics
Matches: 83, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
41 3 0.04
42 78 0.94
43 2 0.02
ACGTcount: A:0.17, C:0.33, G:0.23, T:0.27
Consensus pattern (42 bp):
CCCGTGTGCTAGGCCGTGTAACTCTCTGAGTTGCCCCACATG
Found at i:31415407 original size:60 final size:60
Alignment explanation
Indices: 31415309--31415422 Score: 192
Period size: 60 Copynumber: 1.9 Consensus size: 60
31415299 GAAAGGACTG
* * *
31415309 TTCATAATAGACTTCGAGAACAAAGAAATATGGCTCTACCAGGGCACAATGCAGGTACTA
1 TTCAGAATAGACTTCGAGAACAAAGAAATATGACTCTACCAGGGAACAATGCAGGTACTA
*
31415369 TTCAGAATAGACTTCGAGAACAATGAAATATGACTCTACCAGGGAACAATGCAG
1 TTCAGAATAGACTTCGAGAACAAAGAAATATGACTCTACCAGGGAACAATGCAG
31415423 CCATACCCCC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.21
Consensus pattern (60 bp):
TTCAGAATAGACTTCGAGAACAAAGAAATATGACTCTACCAGGGAACAATGCAGGTACTA
Found at i:31421756 original size:18 final size:18
Alignment explanation
Indices: 31421735--31421782 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
31421725 AAGAAGTTGA
*
31421735 TGTTGCAGAAGCA-TAAGT
1 TGTTGCAGAAG-AGGAAGT
*
31421753 TGTTGTAGAAGAGGAAGT
1 TGTTGCAGAAGAGGAAGT
*
31421771 TGTTGCTGAAGA
1 TGTTGCAGAAGA
31421783 AGATAAAGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 1 0.04
18 24 0.96
ACGTcount: A:0.31, C:0.06, G:0.33, T:0.29
Consensus pattern (18 bp):
TGTTGCAGAAGAGGAAGT
Found at i:31421784 original size:39 final size:36
Alignment explanation
Indices: 31421716--31421793 Score: 86
Period size: 39 Copynumber: 2.1 Consensus size: 36
31421706 GAAGACACTA
* *
31421716 TTGTTGAGAAAGAAGTTGATGTTGCAGAAGCAT-AAG
1 TTGTTGAGAAAGAAGTTGATGCTGAAGAAG-ATAAAG
*
31421752 TTGTTGTAGAAGAGGAAGTTGTTGCTGAAGAAGATAAAG
1 TTGTTG-AGAA-A-GAAGTTGATGCTGAAGAAGATAAAG
31421791 TTG
1 TTG
31421794 CTAAAAATGA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
36 6 0.17
37 4 0.11
38 3 0.09
39 22 0.63
ACGTcount: A:0.35, C:0.04, G:0.32, T:0.29
Consensus pattern (36 bp):
TTGTTGAGAAAGAAGTTGATGCTGAAGAAGATAAAG
Found at i:31422253 original size:17 final size:17
Alignment explanation
Indices: 31422231--31422264 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
31422221 GATAAGTATA
*
31422231 CATTGTCATTGCATTTT
1 CATTGTCATTACATTTT
31422248 CATTGTCATTACATTTT
1 CATTGTCATTACATTTT
31422265 AGTGTTAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.18, G:0.09, T:0.53
Consensus pattern (17 bp):
CATTGTCATTACATTTT
Found at i:31425123 original size:20 final size:19
Alignment explanation
Indices: 31425098--31425166 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 19
31425088 TAAATGCGTT
31425098 CAGGGGTACTGAAGTACACA
1 CAGGGGTACTGAAGTACA-A
* * *
31425118 CAGGGGCA-TGTATGTGCAA
1 CAGGGGTACTG-AAGTACAA
*
31425137 TCAGGGGTGCTGAAGTACAAA
1 -CAGGGGTACTGAAGTAC-AA
31425158 CAGGGGTAC
1 CAGGGGTAC
31425167 GTCTATGCAA
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
19 3 0.08
20 30 0.81
21 4 0.11
ACGTcount: A:0.30, C:0.17, G:0.35, T:0.17
Consensus pattern (19 bp):
CAGGGGTACTGAAGTACAA
Found at i:31425176 original size:40 final size:40
Alignment explanation
Indices: 31425097--31425176 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
31425087 GTAAATGCGT
* * *
31425097 TCAGGGGTACTGAAGTACACACAGGGGCATGTATGTGCAA
1 TCAGGGGTACTGAAGTACAAACAGGGGCACGTATATGCAA
* * *
31425137 TCAGGGGTGCTGAAGTACAAACAGGGGTACGTCTATGCAA
1 TCAGGGGTACTGAAGTACAAACAGGGGCACGTATATGCAA
31425177 ATAGGGTATC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.30, C:0.17, G:0.33, T:0.20
Consensus pattern (40 bp):
TCAGGGGTACTGAAGTACAAACAGGGGCACGTATATGCAA
Found at i:31433775 original size:32 final size:32
Alignment explanation
Indices: 31433734--31433806 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
31433724 GTAAACTAAC
*
31433734 TTTCGTGAATATAGCATATAAGCATTCATACT
1 TTTCATGAATATAGCATATAAGCATTCATACT
31433766 TTTCATGAATATAGCATATAAGCATTCATACT
1 TTTCATGAATATAGCATATAAGCATTCATACT
31433798 TTTCATGAA
1 TTTCATGAA
31433807 CATGGCTATA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (32 bp):
TTTCATGAATATAGCATATAAGCATTCATACT
Found at i:31436553 original size:20 final size:20
Alignment explanation
Indices: 31436530--31436590 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
31436520 GGGTATTAAA
31436530 GTACAAACAAGGGCACGTAT
1 GTACAAACAAGGGCACGTAT
* * *
31436550 GTACAATC-AGGGTATCG-AA
1 GTACAAACAAGGGCA-CGTAT
31436569 GTACAAACAAGGGCACGTAT
1 GTACAAACAAGGGCACGTAT
31436589 GT
1 GT
31436591 GCAATCATTC
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.18
Consensus pattern (20 bp):
GTACAAACAAGGGCACGTAT
Found at i:31436574 original size:39 final size:40
Alignment explanation
Indices: 31436440--31436597 Score: 205
Period size: 40 Copynumber: 4.0 Consensus size: 40
31436430 ATGCGTTCAA
*
31436440 GGGTACTGAAGTACAAACAGGGGCACGTATGTGCAATCAG
1 GGGTACTGAAGTACAAACAAGGGCACGTATGTGCAATCAG
*** *
31436480 GGGTACTGAAGTACAAATTGGGGCACATATGTGCAAAT-AG
1 GGGTACTGAAGTACAAACAAGGGCACGTATGTGC-AATCAG
* * *
31436520 GGGTATTAAAGTACAAACAAGGGCACGTATGTACAATCA-
1 GGGTACTGAAGTACAAACAAGGGCACGTATGTGCAATCAG
31436559 GGGTA-TCGAAGTACAAACAAGGGCACGTATGTGCAATCA
1 GGGTACT-GAAGTACAAACAAGGGCACGTATGTGCAATCA
31436598 TTCAATAATT
Statistics
Matches: 103, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
38 1 0.01
39 38 0.37
40 61 0.59
41 3 0.03
ACGTcount: A:0.36, C:0.16, G:0.28, T:0.20
Consensus pattern (40 bp):
GGGTACTGAAGTACAAACAAGGGCACGTATGTGCAATCAG
Found at i:31438845 original size:29 final size:29
Alignment explanation
Indices: 31438812--31439042 Score: 234
Period size: 29 Copynumber: 7.9 Consensus size: 29
31438802 GATGGTTGTC
* * *
31438812 ACCATCTCTTTTCATATTTGATGATCGAA
1 ACCATCCCTTTTCATAGTTGATGGTCGAA
* * *
31438841 ACCATCCCTTTTCATTAATCGATGGTC-ATC
1 ACCATCCCTTTTCA-TAGTTGATGGTCGA-A
* **
31438871 ACCATCCCTTTTCATAGTCGATAATCGAA
1 ACCATCCCTTTTCATAGTTGATGGTCGAA
* *
31438900 ACTATCCCTTTTCATA-TATGATGGTC-ATC
1 ACCATCCCTTTTCATAGT-TGATGGTCGA-A
**
31438929 ACCATCCCTTTTCATAGTTGATGGTCGTC
1 ACCATCCCTTTTCATAGTTGATGGTCGAA
*
31438958 ACCATCCCTTTTCATAGTCGATGGTCGAA
1 ACCATCCCTTTTCATAGTTGATGGTCGAA
* *
31438987 ACTATCCCTTTTCATAGTTGATAGTCGAA
1 ACCATCCCTTTTCATAGTTGATGGTCGAA
* * *
31439016 ACTATCCCTTTTCATAGTGGATAGTCG
1 ACCATCCCTTTTCATAGTTGATGGTCG
31439043 TCGATACATC
Statistics
Matches: 172, Mismatches: 23, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
28 2 0.01
29 145 0.84
30 25 0.15
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.37
Consensus pattern (29 bp):
ACCATCCCTTTTCATAGTTGATGGTCGAA
Found at i:31438978 original size:87 final size:86
Alignment explanation
Indices: 31438819--31439044 Score: 301
Period size: 87 Copynumber: 2.6 Consensus size: 86
31438809 GTCACCATCT
* * *
31438819 CTTTTCATATTTGATGATCGAAACCATCCCTTTTCATTAATCGATGGTCATCACCATCCCTTTTC
1 CTTTTCATA-TTGATGGTCGAAACCATCCCTTTTCA-TAGTCGATGGTCGTCACCATCCCTTTTC
31438884 ATAGTCGATAATCGAAACTATCC
64 ATAGTCGATAATCGAAACTATCC
* *
31438907 CTTTTCATATATGATGGTC-ATCACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTC
1 CTTTTCATAT-TGATGGTCGA-AACCATCCCTTTTCATAGTCGATGGTCGTCACCATCCCTTTTC
**
31438971 ATAGTCGATGGTCGAAACTATCC
64 ATAGTCGATAATCGAAACTATCC
* * * *
31438994 CTTTTCATAGTTGATAGTCGAAACTATCCCTTTTCATAGTGGATAGTCGTC
1 CTTTTCATA-TTGATGGTCGAAACCATCCCTTTTCATAGTCGATGGTCGTC
31439045 GATACATCGT
Statistics
Matches: 122, Mismatches: 12, Indels: 9
0.85 0.08 0.06
Matches are distributed among these distances:
87 90 0.74
88 32 0.26
ACGTcount: A:0.24, C:0.25, G:0.14, T:0.37
Consensus pattern (86 bp):
CTTTTCATATTGATGGTCGAAACCATCCCTTTTCATAGTCGATGGTCGTCACCATCCCTTTTCAT
AGTCGATAATCGAAACTATCC
Found at i:31439032 original size:58 final size:58
Alignment explanation
Indices: 31438801--31439033 Score: 274
Period size: 58 Copynumber: 4.0 Consensus size: 58
31438791 AGTGTGCTAA
** * * *
31438801 CGATGGTTGTCACCATCTCTTTTCATATTTGAT-GATCGAAACCATCCCTTTTCATTAAT
1 CGATGGTCATCACCATCCCTTTTCATAGTTGATAG-TCGAAACCATCCCTTTTCA-TAGT
* * *
31438860 CGATGGTCATCACCATCCCTTTTCATAGTCGATAATCGAAACTATCCCTTTTCATA-T
1 CGATGGTCATCACCATCCCTTTTCATAGTTGATAGTCGAAACCATCCCTTTTCATAGT
* * **
31438917 ATGATGGTCATCACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGT
1 -CGATGGTCATCACCATCCCTTTTCATAGTTGATAGTCGAAACCATCCCTTTTCATAGT
* * *
31438976 CGATGGTCGA-AACTATCCCTTTTCATAGTTGATAGTCGAAACTATCCCTTTTCATAGT
1 CGATGGTC-ATCACCATCCCTTTTCATAGTTGATAGTCGAAACCATCCCTTTTCATAGT
31439034 GGATAGTCGT
Statistics
Matches: 149, Mismatches: 21, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
57 1 0.01
58 100 0.67
59 48 0.32
ACGTcount: A:0.24, C:0.25, G:0.13, T:0.37
Consensus pattern (58 bp):
CGATGGTCATCACCATCCCTTTTCATAGTTGATAGTCGAAACCATCCCTTTTCATAGT
Found at i:31440400 original size:35 final size:36
Alignment explanation
Indices: 31440348--31440417 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 36
31440338 TATTATAATA
* * *
31440348 ACTATCACATGGTATGAA-AACATACTCGCATATTT
1 ACTATCACATGGAATGAATAACATACCCACATATTT
*
31440383 ACTATCATATGGAATGAATAACATACCCACATATT
1 ACTATCACATGGAATGAATAACATACCCACATATT
31440418 CTCTTTCACA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 16 0.53
36 14 0.47
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (36 bp):
ACTATCACATGGAATGAATAACATACCCACATATTT
Found at i:31443497 original size:26 final size:26
Alignment explanation
Indices: 31443467--31443531 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
31443457 ACAAAACATC
* *
31443467 GGCTCAAAGCCTGCTAAATATTCATT
1 GGCTCAAAGCCTGCTAAATATACACT
*
31443493 GGCTCAAAGCATGCTAAATATACACT
1 GGCTCAAAGCCTGCTAAATATACACT
* *
31443519 GACACAAAGCCTG
1 GGCTCAAAGCCTG
31443532 ATACACTCTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (26 bp):
GGCTCAAAGCCTGCTAAATATACACT
Done.