Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
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: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 210 of 250
Found at i:65497539 original size:42 final size:42
Alignment explanation
Indices: 65497491--65497713 Score: 243
Period size: 42 Copynumber: 5.3 Consensus size: 42
65497481 GAAGCTTGTA
* *
65497491 AGCTGAACAGAAACTCTTAAGAGTTGAACAAAAGCTCATAAG
1 AGCTGAACAGAAACTCATAAGAGTTGAATAAAAGCTCATAAG
* * *
65497533 AGCTGAACAAAAACTCATAAGAGTTGAAAAAAAGCTCGTAAG
1 AGCTGAACAGAAACTCATAAGAGTTGAATAAAAGCTCATAAG
* * * * *
65497575 AGCTAAACAGAAACTCGTATGAGTTAAATAGAAGCTCATAAG
1 AGCTGAACAGAAACTCATAAGAGTTGAATAAAAGCTCATAAG
* * * *
65497617 AGCTGAACAGAAACTCTTAAAAGTTGAATAGAAGGTCA-ATAG
1 AGCTGAACAGAAACTCATAAGAGTTGAATAAAAGCTCATA-AG
* * * *
65497659 AGTTGAACGGAAACTCATAAGAGTTAAATAGAAA-CTCGTAAG
1 AGCTGAACAGAAACTCATAAGAGTTGAATA-AAAGCTCATAAG
*
65497701 AGCTAAACAGAAA
1 AGCTGAACAGAAA
65497714 GTAAAACACA
Statistics
Matches: 149, Mismatches: 29, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
41 1 0.01
42 145 0.97
43 3 0.02
ACGTcount: A:0.47, C:0.14, G:0.20, T:0.19
Consensus pattern (42 bp):
AGCTGAACAGAAACTCATAAGAGTTGAATAAAAGCTCATAAG
Found at i:65498974 original size:20 final size:21
Alignment explanation
Indices: 65498927--65498974 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
65498917 ATAATAAAAT
65498927 ATAAA-TAA-ATTTGATTTAA
1 ATAAACTAATATTTGATTTAA
65498946 ATAAACTAATATTT-ATTTAA
1 ATAAACTAATATTTGATTTAA
* *
65498966 TTAATCTAA
1 ATAAACTAA
65498975 AATATCACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 5 0.20
20 16 0.64
21 4 0.16
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (21 bp):
ATAAACTAATATTTGATTTAA
Found at i:65500375 original size:3 final size:3
Alignment explanation
Indices: 65500369--65500638 Score: 109
Period size: 3 Copynumber: 88.3 Consensus size: 3
65500359 TGAATTTCTA
* * * *
65500369 TAT TAT TAT TAT TAT TAT TGT TACT TAT TAT TAT TAC TGT TAT GTACA
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT -TA-T
* * *
65500417 TAT TAT T-T ATAC TA- TACT TAA TAT TAT TAT TAT CAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
65500462 TAT TA- TATT TAC TAT TAT TATT TAT AAA TAT TAGT GTA- TAT T-T TAT
1 TAT TAT TA-T TAT TAT TAT TA-T TAT TAT TAT TA-T -TAT TAT TAT TAT
* *
65500508 T-T TAA TAT CAT TA- TAT TAT GT-T TACT T-T T-T TGAAT T-T CTA-
1 TAT TAT TAT TAT TAT TAT TAT -TAT TA-T TAT TAT T--AT TAT -TAT
* * * *
65500548 TAT TAT TAT TAT TAT TAT TGT TACT TAT TAT TAT TAC TGT TAT GTACA
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT -TA-T
* *
65500596 TAT TAT T-T ATAC TA- TACT TAA TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT -TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT T
65500639 TATAAATATT
Statistics
Matches: 201, Mismatches: 34, Indels: 64
0.67 0.11 0.21
Matches are distributed among these distances:
2 24 0.12
3 146 0.73
4 27 0.13
5 4 0.02
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:65500814 original size:3 final size:3
Alignment explanation
Indices: 65500808--65500847 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
65500798 CTATTATTGC
*
65500808 TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
65500848 ATAGGTACTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:65522202 original size:31 final size:31
Alignment explanation
Indices: 65522159--65522222 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
65522149 CCTTTTCATA
65522159 TTTCATAATTCATAACACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
* **
65522190 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
65522221 TT
1 TT
65522223 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCATAATTCATAACACTGGGCCGAAGCCT
Found at i:65522454 original size:23 final size:24
Alignment explanation
Indices: 65522428--65522569 Score: 240
Period size: 23 Copynumber: 6.1 Consensus size: 24
65522418 GCCTAGCCTC
65522428 TTTAATAACTGGGGCA-AAGCCCT
1 TTTAATAACTGGGGCATAAGCCCT
65522451 TTTAATAACT-GGGCATAAGCCC-
1 TTTAATAACTGGGGCATAAGCCCT
65522473 TTTAATAACTGGGGCATAAGCCCT
1 TTTAATAACTGGGGCATAAGCCCT
65522497 TTT-ATAACTGGGGCATAAGCCCT
1 TTTAATAACTGGGGCATAAGCCCT
*
65522520 TTTGATAACTGGGGCATAAGCCC-
1 TTTAATAACTGGGGCATAAGCCCT
65522543 TTTAATAACTGGGGCATAAGCCCT
1 TTTAATAACTGGGGCATAAGCCCT
65522567 TTT
1 TTT
65522570 GCACTTCCTC
Statistics
Matches: 113, Mismatches: 1, Indels: 9
0.92 0.01 0.07
Matches are distributed among these distances:
22 15 0.13
23 73 0.65
24 25 0.22
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (24 bp):
TTTAATAACTGGGGCATAAGCCCT
Found at i:65522551 original size:47 final size:47
Alignment explanation
Indices: 65522432--65522570 Score: 230
Period size: 47 Copynumber: 3.0 Consensus size: 47
65522422 AGCCTCTTTA
*
65522432 ATAACTGGGGCA-AAGCCCTTTTAATAACT-GGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCATAAGCCCTTTTG
*
65522477 ATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCCTTTTG
65522524 ATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCCTTTTG
65522571 CACTTCCTCC
Statistics
Matches: 88, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
45 21 0.24
46 18 0.20
47 49 0.56
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (47 bp):
ATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCCTTTTG
Found at i:65522553 original size:70 final size:68
Alignment explanation
Indices: 65522422--65522569 Score: 251
Period size: 70 Copynumber: 2.1 Consensus size: 68
65522412 CTGGAGGCCT
*
65522422 AGCCTCTTTAATAACTGGGGCAAAGCCCTTTTAATAACTGGGCATAAGCCCTTTAATAACTGGGG
1 AGCC-CTTTTATAACTGGGGCAAAGCCCTTTTAATAACTGGGCATAAGCCCTTTAATAACTGGGG
65522487 CATA
65 CATA
*
65522491 AGCCCTTTTATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTAATAACTGGG
1 AGCCCTTTTATAACTGGGGCA-AAGCCCTTTTAATAACT-GGGCATAAGCCCTTTAATAACTGGG
65522556 GCATA
64 GCATA
65522561 AGCCCTTTT
1 AGCCCTTTT
65522570 GCACTTCCTC
Statistics
Matches: 75, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
68 16 0.21
69 20 0.27
70 39 0.52
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (68 bp):
AGCCCTTTTATAACTGGGGCAAAGCCCTTTTAATAACTGGGCATAAGCCCTTTAATAACTGGGGC
ATA
Found at i:65522641 original size:9 final size:9
Alignment explanation
Indices: 65522627--65522683 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
65522617 ATCTCATGTG
65522627 CATATCATA
1 CATATCATA
*
65522636 CATATCATGTG
1 CATATCA--TA
65522647 CATATCATA
1 CATATCATA
* *
65522656 CATGTCATGTG
1 CATATCA--TA
65522667 CATATCATA
1 CATATCATA
65522676 CATATCAT
1 CATATCAT
65522684 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:65522643 original size:20 final size:20
Alignment explanation
Indices: 65522615--65522685 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
65522605 GCATTTATGA
*
65522615 ACATCTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
65522635 ACATATCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
*
65522655 ACATGTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
65522675 ACATATCATGT
1 ACATATCATGT
65522686 TTATCAAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.35
Consensus pattern (20 bp):
ACATATCATGTGCATATCAT
Found at i:65522650 original size:11 final size:11
Alignment explanation
Indices: 65522620--65522674 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
65522610 TATGAACATC
65522620 TCATGTGCATA
1 TCATGTGCATA
*
65522631 TCA--TACATA
1 TCATGTGCATA
65522640 TCATGTGCATA
1 TCATGTGCATA
* *
65522651 TCA--TACATG
1 TCATGTGCATA
65522660 TCATGTGCATA
1 TCATGTGCATA
65522671 TCAT
1 TCAT
65522675 ACATATCATG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:65522750 original size:25 final size:25
Alignment explanation
Indices: 65522722--65522769 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
65522712 ATATATAAAC
* * *
65522722 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
65522747 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
65522770 CATTTATAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:65528519 original size:15 final size:14
Alignment explanation
Indices: 65528493--65528528 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
65528483 CCTTTTCTTC
*
65528493 TTTTATTCATTCAT
1 TTTTATTAATTCAT
65528507 TTCTTATTAATTCAT
1 TT-TTATTAATTCAT
65528522 TTTTATT
1 TTTTATT
65528529 TGGATTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTATTAATTCAT
Found at i:65532541 original size:38 final size:39
Alignment explanation
Indices: 65532499--65532592 Score: 111
Period size: 40 Copynumber: 2.4 Consensus size: 39
65532489 CCATCTCCGA
* *
65532499 CCAA-CCTAACACACCA-TCTGGAGATAGAATCGACCCAC
1 CCAACCCT-ACACACCAGTATGGAGATAGAATCAACCCAC
* * *
65532537 CCAACCCTACACACCAAGTATGGGGATATAATCAACCCAT
1 CCAACCCTACACACC-AGTATGGAGATAGAATCAACCCAC
65532577 CCAACCCTACACACCA
1 CCAACCCTACACACCA
65532593 CAAGGTACCG
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
38 11 0.23
39 5 0.10
40 32 0.67
ACGTcount: A:0.37, C:0.38, G:0.11, T:0.14
Consensus pattern (39 bp):
CCAACCCTACACACCAGTATGGAGATAGAATCAACCCAC
Found at i:65538197 original size:24 final size:24
Alignment explanation
Indices: 65538165--65538224 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
65538155 ACTTATTCGC
**
65538165 ACACATAGTGCCACGTTTTCTCGA
1 ACACATAGTGCCACGTAATCTCGA
* *
65538189 ACACATAGTGCCATGTAATCTCGT
1 ACACATAGTGCCACGTAATCTCGA
65538213 ACACATAGTGCC
1 ACACATAGTGCC
65538225 GCATAGCCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (24 bp):
ACACATAGTGCCACGTAATCTCGA
Found at i:65540808 original size:19 final size:19
Alignment explanation
Indices: 65540773--65540809 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
65540763 TTCTATATTA
**
65540773 TTATTATTATTGTTGTTAC
1 TTATTATTATTACTGTTAC
65540792 TTATTATTATTACTGTTA
1 TTATTATTATTACTGTTA
65540810 TGTACATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (19 bp):
TTATTATTATTACTGTTAC
Found at i:65540822 original size:3 final size:3
Alignment explanation
Indices: 65540582--65540803 Score: 97
Period size: 3 Copynumber: 72.7 Consensus size: 3
65540572 TGAATTTCTA
* * *
65540582 TAT TAT TAT TAT TAT TAT TAT TGT TACT TAT TAT TAT TAC TGT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
* * * * *
65540628 GTACA TAT TAT T-T ATAC TA- TACT TAA TAT TAT TAT TAT CAT TAT CAT
1 -TA-T TAT TAT TAT -TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
* * *
65540675 TAT TAT TAT TAT TATT TAC TAT TAT TATT TAT AAA TAT TAGT GTA- TAT
1 TAT TAT TAT TAT TA-T TAT TAT TAT TA-T TAT TAT TAT TA-T -TAT TAT
* *
65540723 T-T TAT T-T TAA TAT CAT TA- TAT TAT GT-T TACT T-T T-T TGAAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA-T TAT TAT T--AT TAT
* *
65540765 CTA- TAT TAT TAT TAT TAT TGT TGT TACT TAT TAT TAT TA
1 -TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TA
65540804 CTGTTATGTA
Statistics
Matches: 167, Mismatches: 27, Indels: 50
0.68 0.11 0.20
Matches are distributed among these distances:
2 19 0.11
3 122 0.73
4 22 0.13
5 4 0.02
ACGTcount: A:0.31, C:0.05, G:0.04, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:65540864 original size:183 final size:186
Alignment explanation
Indices: 65540533--65540867 Score: 572
Period size: 183 Copynumber: 1.8 Consensus size: 186
65540523 TTTTTTAAAT
* *
65540533 TATTTTATTTTAATATTATTATATTATGTTTAGTTTTTTTGAATTTCTATATTATTATTATTATT
1 TATTTTATTTTAATATCATTATATTATGTTTAGCTTTTTTGAATTTC-ATATTATTATTATTATT
65540598 ATTATTGTTACTTATTATTATTACTGTTATGTACATATTATTTATACTATACTTAATATTATTAT
65 ATTATTGTTACTTATTATTATTACTGTTATGTACATATTATTTATACTATACTTAATATTATTAT
*
65540663 TATCATTATCATTATTATTATTATTATTTACTATTATTATTTATAAATATTAGTGTA
130 TATCATTATCACTATTATTATTATTATTTACTATTATTATTTATAAATATTAGTGTA
65540720 TATTTTATTTTAATATCATTATATTATGTTTA-CTTTTTTGAATTTC-TA-TATTATTATTATTA
1 TATTTTATTTTAATATCATTATATTATGTTTAGCTTTTTTGAATTTCATATTATTATTATTATTA
*
65540782 TTGTTGTTACTTATTATTATTACTGTTATGTACATATTATTTATACTATACTTAATATTATTATT
66 TTATTGTTACTTATTATTATTACTGTTATGTACATATTATTTATACTATACTTAATATTATTATT
65540847 ATTACATT-T-ACTATTATTATT
131 A-T-CATTATCACTATTATTATT
65540868 TATAAATATT
Statistics
Matches: 142, Mismatches: 4, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
183 90 0.63
184 4 0.03
185 4 0.03
186 13 0.09
187 31 0.22
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.59
Consensus pattern (186 bp):
TATTTTATTTTAATATCATTATATTATGTTTAGCTTTTTTGAATTTCATATTATTATTATTATTA
TTATTGTTACTTATTATTATTACTGTTATGTACATATTATTTATACTATACTTAATATTATTATT
ATCATTATCACTATTATTATTATTATTTACTATTATTATTTATAAATATTAGTGTA
Found at i:65541044 original size:3 final size:3
Alignment explanation
Indices: 65541038--65541091 Score: 81
Period size: 3 Copynumber: 17.7 Consensus size: 3
65541028 CTATTATTGC
* *
65541038 TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
65541084 TAT TAT TA
1 TAT TAT TA
65541092 ATAGGTACTT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 44 0.96
4 2 0.04
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:65553410 original size:27 final size:27
Alignment explanation
Indices: 65553372--65553424 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
65553362 AGTTGAGCCT
65553372 CAAGACACGTTGAGGTAATTTTTATTG
1 CAAGACACGTTGAGGTAATTTTTATTG
65553399 CAAGACACGTTGAGGTAATTTTTATT
1 CAAGACACGTTGAGGTAATTTTTATT
65553425 TCTATTTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (27 bp):
CAAGACACGTTGAGGTAATTTTTATTG
Found at i:65553516 original size:72 final size:72
Alignment explanation
Indices: 65553399--65553845 Score: 455
Period size: 72 Copynumber: 6.0 Consensus size: 72
65553389 ATTTTTATTG
**
65553399 CAAGACACGTTGAGGTAATTTTTATTTCTATTTTCAAAATTCAACTCATATTGCGAGAAATGAGT
1 CAAGACACGTTGAGGTAATTTCAATTTCTATTTTCAAAATTCAACTCATATTGCGAGAAATGAGT
65553464 TGAGCCT
66 TGAGCCT
* *
65553471 CAAGACACGTTGAGGTAATTTCAATTTTTATTTTCAAAATTCAACTCAGATTGCGAGAAATGAGT
1 CAAGACACGTTGAGGTAATTTCAATTTCTATTTTCAAAATTCAACTCATATTGCGAGAAATGAGT
65553536 TGAGCCT
66 TGAGCCT
* * * * * * * *
65553543 TAAGACATGCTGAGGTATTTTGAATTTCTGTTTTTCAAAAACAACAATCGACTCATATTGCGAGA
1 CAAGACACGTTGAGGTAATTTCAATTTCT-ATTTTC----A-AA-ATTCAACTCATATTGCGAGA
* *
65553608 AGTGAGTTGAGTCT
59 AATGAGTTGAGCCT
* * * * *
65553622 CAGGACAAGCTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGTAATGAGT
1 CAAGACACGTTGAGGTAATTTCAATTTCTATTTTCAAAATTCAACTCATATTGCGAGAAATGAGT
*
65553687 TGAACCT
66 TGAGCCT
* * * * *
65553694 CAAGACACGTTGAGGTATTTTCAATTTATGTTTTCAAAAATCAACTCATATTGCGAGAGATGAGT
1 CAAGACACGTTGAGGTAATTTCAATTTCTATTTTCAAAATTCAACTCATATTGCGAGAAATGAGT
65553759 TGAGCCT
66 TGAGCCT
* * * * * *
65553766 C-GGTTCACATGCTGAGGTATTTTCAATTTCTATCTTTCAAAAAAAATCAACTCATAATGCGAGA
1 CAAG---ACACGTTGAGGTAATTTCAATTTCTAT-TTTC---AAAATTCAACTCATATTGCGAGA
** *
65553830 GGTGAGTTAAGCCT
59 AATGAGTTGAGCCT
65553844 CA
1 CA
65553846 GGGCATGCTG
Statistics
Matches: 315, Mismatches: 45, Indels: 23
0.82 0.12 0.06
Matches are distributed among these distances:
71 1 0.00
72 183 0.58
73 7 0.02
74 24 0.08
75 4 0.01
77 1 0.00
78 42 0.13
79 53 0.17
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (72 bp):
CAAGACACGTTGAGGTAATTTCAATTTCTATTTTCAAAATTCAACTCATATTGCGAGAAATGAGT
TGAGCCT
Found at i:65553667 original size:151 final size:147
Alignment explanation
Indices: 65553434--65554173 Score: 773
Period size: 151 Copynumber: 4.9 Consensus size: 147
65553424 TTCTATTTTC
* * * * *
65553434 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
* * *
65553499 TATTTTCAAAATTCAACTCAGATTGCGAGAAATGAGTTGAGCCTTAAGACATGCTGAGGTATTTT
66 TATTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTT
*
65553564 GAATTTCTGTTTTTCAAAA
131 CAATTTCTGTTTTTC--AA
* * *
65553583 ACAACAATCGACTCATATTGCGAGAAGTGAGTTGAGTCTCAGGACAAGCTGAGGTAATTTCAATT
1 A-AA-AATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
* * * * * *
65553648 TCTGTTTTCAAAATTCAACTCATATTGCGAGTAATGAGTTGAACCTCAAGACACGTTGAGGTATT
64 TCTATTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATT
*
65553713 TTCAATTTATG-TTTTC--
129 TTCAATTTCTGTTTTTCAA
* *
65553729 AAAAATCAACTCATATTGCGAG-AGATGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTTTCAA
1 AAAAATCAACTCATATTGCGAGAAG-TGAGTTGAGCCTCAGG---ACACGCTGAGGTAATTTCAA
* ** * * *
65553792 TTTCTATCTTTCAAAAAAAATCAACTCATAATGCGAGAGGTGAGTTAAGCCTCAGGGCATGCTGA
62 TTTCTAT-TTTC---AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGA
** *
65553857 GGTATTGGCAATTTTTGTTTCTT-AA
123 GGTATTTTCAATTTCTGTTT-TTCAA
* * *
65553882 TTTATGTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAA
1 ---A------AAAA-TCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAA
*
65553947 TTTCAATTTC-ATTTTCAAAAATCAACTCATATTGCAAGAAATGAGTTGAGCCTC-AGACATGCT
56 TTTCAATTTCTATTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCT
* *
65554010 GAGGTA-TTTCAATTTTTGTCTTTCAA
121 GAGGTATTTTCAATTTCTGTTTTTCAA
* * *
65554036 AAAAATCAACTC--ATTGCGAGAGGGGAGTTGAGCCTCAGGACGCGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
* ** * * * *
65554099 TGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCGTCAGGGCACGCTGAGGTATTT
66 T-ATTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTT
65554164 TCAATTTCTG
130 TCAATTTCTG
65554174 CTTTCCAATT
Statistics
Matches: 494, Mismatches: 66, Indels: 65
0.79 0.11 0.10
Matches are distributed among these distances:
142 45 0.09
143 4 0.01
144 76 0.15
145 18 0.04
146 36 0.07
147 4 0.01
149 1 0.00
150 60 0.12
151 122 0.25
152 2 0.00
153 2 0.00
154 14 0.03
155 13 0.03
156 34 0.07
159 4 0.01
160 2 0.00
161 21 0.04
162 4 0.01
163 30 0.06
164 2 0.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (147 bp):
AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
TATTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTT
CAATTTCTGTTTTTCAA
Found at i:65553989 original size:71 final size:72
Alignment explanation
Indices: 65553959--65554171 Score: 209
Period size: 73 Copynumber: 3.0 Consensus size: 72
65553949 TCAATTTCAT
* *
65553959 TTTCAAAAATCAACTCATATTGCAAGAAATGAGTTGAGCCTC-AGACATGCTGAGGT-ATTTCAA
1 TTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAA
**
65554022 TTTTTGTC
66 -TTTCATC
*** * *
65554030 TTTCAAAAAAATCAACTC--ATTGCGAGAGGGGAGTTGAGCCTCAGGACGCGCTGAGGTAATTTC
1 TTTC--AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTC
* *
65554093 AATTTCTGTT
64 AATTTC-ATC
** * * * *
65554103 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCGTCAGGGCACGCTGAGGTATTTTCAA
1 TTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAA
65554168 TTTC
66 TTTC
65554172 TGCTTTCCAA
Statistics
Matches: 121, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
71 36 0.30
72 14 0.12
73 71 0.59
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (72 bp):
TTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAA
TTTCATC
Found at i:65554107 original size:73 final size:72
Alignment explanation
Indices: 65553888--65554173 Score: 339
Period size: 71 Copynumber: 4.0 Consensus size: 72
65553878 TTAATTTATG
* ** * *
65553888 TTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAA
1 TTTCAAAAATCAACTCA-ATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAA
*
65553953 TTTC--AT
65 TTTCTGTT
* ** *
65553959 TTTCAAAAATCAACTCATATTGCAAGAAATGAGTTGAGCCTCA-GACATGCTGAGGT-ATTTCAA
1 TTTCAAAAATCAACTCA-ATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAA
* *
65554022 TTTTTGTC
65 TTTCTGTT
* *
65554030 TTTCAAAAAAATCAACTC-ATTGCGAGAGGGGAGTTGAGCCTCAGGACGCGCTGAGGTAATTTCA
1 TTTC--AAAAATCAACTCAATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCA
65554094 ATTTCTGTT
64 ATTTCTGTT
* * *
65554103 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCGTCAGGGCACGCTGAGGTATTTTCAA
1 TTTCAAAAATCAACTCA-ATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAA
65554168 TTTCTG
65 TTTCTG
65554174 CTTTCCAATT
Statistics
Matches: 187, Mismatches: 20, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
69 10 0.05
70 11 0.06
71 78 0.42
72 11 0.06
73 77 0.41
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.31
Consensus pattern (72 bp):
TTTCAAAAATCAACTCAATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAAT
TTCTGTT
Found at i:65554184 original size:14 final size:15
Alignment explanation
Indices: 65554165--65554193 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
65554155 GAGGTATTTT
65554165 CAATTTCTG-CTTTC
1 CAATTTCTGCCTTTC
65554179 CAATTTCTGCCTTTC
1 CAATTTCTGCCTTTC
65554194 AAAAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.14, C:0.31, G:0.07, T:0.48
Consensus pattern (15 bp):
CAATTTCTGCCTTTC
Found at i:65554380 original size:179 final size:177
Alignment explanation
Indices: 65554037--65554365 Score: 475
Period size: 179 Copynumber: 1.8 Consensus size: 177
65554027 GTCTTTCAAA
* *
65554037 AAAATCAACTCATTGCGAGAGGGGAGTTGAGCCTCAGGACGCGCTGAGGTAATTTCAATTTCTGT
1 AAAATCAACTCATTGCGAGAGGGGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTCCTGT
* * *
65554102 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCGTCAGGGCACGCTGAGGTATTTTCA
66 TTATCAAAAATCAACTCATATTGCGAGAGGTGAGCTGAGCCTCAGGGCACGCTGAGGTATTTTCA
** * *
65554167 ATTTCTGCTTTCCAATTTCTGCCTTTCAAAAAAAAAAAGAAAGAAAG
131 AAGTATGCTTTCCAATTTATGCCTTTCAAAAAAAAAAAGAAAGAAAG
* *
65554214 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTAATTTCAATTCCT
1 AAAATCAACTC--ATTGCGAGAGGGGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTCCT
*
65554279 GTTTATC-AAAATCAACTCATATTGCGAGAGGTGAGCTGAGCCTC-GGGTCACAGTTG-GGTATT
64 GTTTATCAAAAATCAACTCATATTGCGAGAGGTGAGCTGAGCCTCAGGG-CAC-GCTGAGGTATT
*
65554341 TTCAAAGTATGCTTTTTCAATTTAT
127 TTCAAAGTATGC-TTTCCAATTTAT
65554366 TTTTGTCAAA
Statistics
Matches: 134, Mismatches: 13, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
177 14 0.10
178 53 0.40
179 67 0.50
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.30
Consensus pattern (177 bp):
AAAATCAACTCATTGCGAGAGGGGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTCCTGT
TTATCAAAAATCAACTCATATTGCGAGAGGTGAGCTGAGCCTCAGGGCACGCTGAGGTATTTTCA
AAGTATGCTTTCCAATTTATGCCTTTCAAAAAAAAAAAGAAAGAAAG
Found at i:65556397 original size:179 final size:177
Alignment explanation
Indices: 65556161--65556486 Score: 541
Period size: 179 Copynumber: 1.8 Consensus size: 177
65556151 ATTTTTAAAT
* *
65556161 TATTTTATTTTAATATTATTATATATGTTTAGTTTTTTTTGAATTTCTATATTATTATTATTATT
1 TATTTTATTTTAATATCATTATATATGTTTAG-CTTTTTTGAATTTCTATATTATTATTATTATT
65556226 GTTACTTATTATTATTACTGTTATGTACATATTATTTATACTATACTTAATATTATTATTATTAT
65 GTTACTTATTATTATTACTGTTATGTACATATTATTTATACTATACTTAATA-TATTATTATTA-
*
65556291 CATTATTATTATTATTATATATTTACTATTATTATTTATAAATATTAGTGTA
128 CATT-CTATTATTATT-TATATTTACTATTATTATTTATAAATATTAGTGTA
65556343 TATTTTATTTT-ATATCATTATATTATG-TTA-CTTTTTTGAATTTCTATATTATTATTATTATT
1 TATTTTATTTTAATATCATTATA-TATGTTTAGCTTTTTTGAATTTCTATATTATTATTATTATT
*
65556405 GTTACTTATTATTATTACTGTTATGTACATATTATTTATACTATACTTATTATATTATTATTACA
65 GTTACTTATTATTATTACTGTTATGTACATATTATTTATACTATACTTAATATATTATTATTACA
65556470 TTCTATTATTATTTATA
130 TTCTATTATTATTTATA
65556487 AATATTAGTG
Statistics
Matches: 139, Mismatches: 4, Indels: 9
0.91 0.03 0.06
Matches are distributed among these distances:
175 4 0.03
176 10 0.07
177 4 0.03
178 11 0.08
179 82 0.59
181 13 0.09
182 15 0.11
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.60
Consensus pattern (177 bp):
TATTTTATTTTAATATCATTATATATGTTTAGCTTTTTTGAATTTCTATATTATTATTATTATTG
TTACTTATTATTATTACTGTTATGTACATATTATTTATACTATACTTAATATATTATTATTACAT
TCTATTATTATTTATATTTACTATTATTATTTATAAATATTAGTGTA
Found at i:65556415 original size:13 final size:13
Alignment explanation
Indices: 65556389--65556423 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
65556379 TGAATTTCTA
65556389 TATTATTA-TTAT
1 TATTATTACTTAT
*
65556401 TATTGTTACTTAT
1 TATTATTACTTAT
65556414 TATTATTACT
1 TATTATTACT
65556424 GTTATGTACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 7 0.35
13 13 0.65
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.63
Consensus pattern (13 bp):
TATTATTACTTAT
Found at i:65556440 original size:3 final size:3
Alignment explanation
Indices: 65556210--65556421 Score: 88
Period size: 3 Copynumber: 69.7 Consensus size: 3
65556200 TGAATTTCTA
* * * *
65556210 TAT TAT TAT TAT TAT TGT TACT TAT TAT TAT TAC TGT TAT GTACA TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT -TA-T TAT
* * *
65556258 TAT T-T ATAC TA- TACT TAA TAT TAT TAT TAT TAT CAT TAT TAT TAT
1 TAT TAT -TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
65556303 TAT TAT ATATT TAC TAT TAT TATT TAT AAA TAT TAGT GTA- TAT T-T
1 TAT TAT -TA-T TAT TAT TAT TA-T TAT TAT TAT TA-T -TAT TAT TAT
* *
65556348 TAT T-T TA- TAT CAT TA- TAT TA- TGT TACT T-T T-T TGAAT T-T CTA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT T--AT TAT -TAT
*
65556389 TAT TAT TAT TAT TAT TGT TACT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TA
65556422 CTGTTATGTA
Statistics
Matches: 158, Mismatches: 25, Indels: 52
0.67 0.11 0.22
Matches are distributed among these distances:
2 21 0.13
3 110 0.70
4 22 0.14
5 5 0.03
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:65556659 original size:3 final size:3
Alignment explanation
Indices: 65556653--65556712 Score: 65
Period size: 3 Copynumber: 20.7 Consensus size: 3
65556643 CTATTATTGC
*
65556653 TAT TAT TGT TAT TAT TAT TAT T-T TAT TAT TAT TAT TA- TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
65556698 T-T ATAT ATAT TAT TA
1 TAT -TAT -TAT TAT TA
65556713 ATAGGTACTT
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
2 7 0.14
3 38 0.76
4 5 0.10
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:65556680 original size:14 final size:14
Alignment explanation
Indices: 65556653--65556695 Score: 68
Period size: 14 Copynumber: 3.0 Consensus size: 14
65556643 CTATTATTGC
65556653 TATTATTGTTATTAT
1 TATTATT-TTATTAT
65556668 TATTATTTTATTAT
1 TATTATTTTATTAT
*
65556682 TATTATTATATTAT
1 TATTATTTTATTAT
65556696 ATTTATATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
14 20 0.74
15 7 0.26
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (14 bp):
TATTATTTTATTAT
Found at i:65560143 original size:17 final size:17
Alignment explanation
Indices: 65560117--65560164 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
65560107 ACATTATTAG
*
65560117 AAAATTTAAAAATTAAT-
1 AAAATATAAAAATT-ATC
65560134 AAAATATAAAAATT-TC
1 AAAATATAAAAATTATC
65560150 AAAA-ATAAAAATTAT
1 AAAATATAAAAATTAT
65560165 TTAAAAGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 10 0.36
16 5 0.18
17 13 0.46
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAATATAAAAATTATC
Found at i:65560170 original size:17 final size:18
Alignment explanation
Indices: 65560103--65560170 Score: 54
Period size: 17 Copynumber: 3.9 Consensus size: 18
65560093 TACAAATTTT
* *
65560103 TAAAACATTATTAGAAAATT
1 TAAAA-ATTATT-TAAAATA
*
65560123 TAAAAATTA-ATAAAATA
1 TAAAAATTATTTAAAATA
*
65560140 TAAAAA-T-TTCAAAA-A
1 TAAAAATTATTTAAAATA
65560155 TAAAAATTATTTAAAA
1 TAAAAATTATTTAAAA
65560171 GTTAAGTCCA
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
15 7 0.18
16 6 0.15
17 17 0.44
19 4 0.10
20 5 0.13
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.32
Consensus pattern (18 bp):
TAAAAATTATTTAAAATA
Found at i:65566337 original size:15 final size:17
Alignment explanation
Indices: 65566303--65566340 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
65566293 TAATTTATTT
65566303 ATTTTTATTATTTTAGA
1 ATTTTTATTATTTTAGA
*
65566320 ATTTTTA-TA-TTTATA
1 ATTTTTATTATTTTAGA
65566335 ATTTTT
1 ATTTTT
65566341 TTTCCTTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 11 0.55
16 2 0.10
17 7 0.35
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
ATTTTTATTATTTTAGA
Found at i:65567057 original size:27 final size:26
Alignment explanation
Indices: 65567027--65567083 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
65567017 AATTTCGAGG
*
65567027 TTTACAATTTT-TAATTTTTATTAATT
1 TTTA-AATTTTCTAACTTTTATTAATT
* *
65567053 ATTTATATTTTCTCACTTTTATTAATT
1 -TTTAAATTTTCTAACTTTTATTAATT
65567080 TTTA
1 TTTA
65567084 TTATTATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 9 0.35
27 17 0.65
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (26 bp):
TTTAAATTTTCTAACTTTTATTAATT
Found at i:65572836 original size:2 final size:2
Alignment explanation
Indices: 65572825--65572863 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
65572815 AACGTACTCC
65572825 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
65572864 CCATAAAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.91
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:65575267 original size:17 final size:15
Alignment explanation
Indices: 65575229--65575260 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
65575219 TTAGGAAACG
65575229 TACATAAAAAATATA
1 TACATAAAAAATATA
*
65575244 TACATAAAAAATTTA
1 TACATAAAAAATATA
65575259 TA
1 TA
65575261 ACAATAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (15 bp):
TACATAAAAAATATA
Found at i:65575539 original size:11 final size:11
Alignment explanation
Indices: 65575512--65575554 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
65575502 ATGGCATTAA
*
65575512 AAAATATATAC
1 AAAATATATAT
*
65575523 ATAATATATAT
1 AAAATATATAT
*
65575534 AAAATACATAT
1 AAAATATATAT
*
65575545 AATATATATA
1 AAAATATATA
65575555 CGTATTAGAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (11 bp):
AAAATATATAT
Found at i:65576058 original size:11 final size:12
Alignment explanation
Indices: 65576044--65576079 Score: 58
Period size: 11 Copynumber: 3.2 Consensus size: 12
65576034 AAAAAAAAAA
65576044 GAAGAGAG-AGG
1 GAAGAGAGAAGG
65576055 GAAGAGAGAAGG
1 GAAGAGAGAAGG
65576067 G-AGAGAGAAGG
1 GAAGAGAGAAGG
65576078 GA
1 GA
65576080 GGGGGGAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 19 0.83
12 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (12 bp):
GAAGAGAGAAGG
Found at i:65576200 original size:13 final size:13
Alignment explanation
Indices: 65576170--65576223 Score: 54
Period size: 13 Copynumber: 4.0 Consensus size: 13
65576160 GAAAAGGTAA
*
65576170 ATTTTTTATTTTT
1 ATTTTTTATATTT
65576183 ATTTTTTATATTT
1 ATTTTTTATATTT
* *
65576196 GTTTTGTATATATAT
1 ATTTT-T-TATATTT
*
65576211 ATTTATTATATTT
1 ATTTTTTATATTT
65576224 TTTATTATGA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
13 22 0.67
14 2 0.06
15 9 0.27
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (13 bp):
ATTTTTTATATTT
Found at i:65576298 original size:17 final size:17
Alignment explanation
Indices: 65576276--65576314 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
65576266 GGGAAAAATA
*
65576276 AAAATAA-AAATAAGAGT
1 AAAATAATAAAGAAGA-T
65576293 AAAATAATAAAGAAGAT
1 AAAATAATAAAGAAGAT
65576310 AAAAT
1 AAAAT
65576315 CACCTTTAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.18
Consensus pattern (17 bp):
AAAATAATAAAGAAGAT
Found at i:65583070 original size:10 final size:11
Alignment explanation
Indices: 65583051--65583076 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
65583041 AATTTGATTT
65583051 AATTTAAAAAA
1 AATTTAAAAAA
65583062 AATTTAAAAAA
1 AATTTAAAAAA
65583073 AATT
1 AATT
65583077 GAATTTCAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
AATTTAAAAAA
Found at i:65584678 original size:17 final size:17
Alignment explanation
Indices: 65584656--65584689 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
65584646 ATCCACTAAT
*
65584656 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
65584673 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
65584690 AATCCACTAC
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:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:65589317 original size:17 final size:17
Alignment explanation
Indices: 65589295--65589328 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
65589285 ATCCACTAAT
*
65589295 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
65589312 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
65589329 AATCCACTAC
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:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:65592962 original size:3 final size:3
Alignment explanation
Indices: 65592954--65592978 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
65592944 GAGGACATGG
65592954 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
65592979 TGAATGAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:65595394 original size:35 final size:35
Alignment explanation
Indices: 65595332--65595417 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 35
65595322 TTTTATTTGT
*
65595332 TTTA-ATTATATAATTAATGATATTTAAA-TATAA
1 TTTATATTATATAATTAATGATAATTAAATTATAA
*
65595365 TTTATATTATATGAATTTATGATAATTAAATTATAA
1 TTTATATTATAT-AATTAATGATAATTAAATTATAA
* *
65595401 -TGATATTATATTATTAA
1 TTTATATTATATAATTAA
65595418 ATAAATTAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
33 4 0.09
34 11 0.24
35 25 0.56
36 5 0.11
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (35 bp):
TTTATATTATATAATTAATGATAATTAAATTATAA
Found at i:65595403 original size:25 final size:23
Alignment explanation
Indices: 65595359--65595419 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
65595349 TGATATTTAA
*
65595359 ATATAATTTATATTATATGA-ATTT
1 ATATAA-TTAAATTATATGATA-TT
65595383 ATGATAATTAAATTATAATGATATT
1 AT-ATAATTAAATTAT-ATGATATT
*
65595408 ATATTATTAAAT
1 ATATAATTAAAT
65595420 AAATTAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 19 0.59
25 12 0.38
26 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (23 bp):
ATATAATTAAATTATATGATATT
Found at i:65595796 original size:16 final size:15
Alignment explanation
Indices: 65595770--65595800 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
65595760 AATAGAGCAG
65595770 GAAAGAAAAAGGAAA
1 GAAAGAAAAAGGAAA
65595785 GAAAGAAGAAAGGAAA
1 GAAAGAA-AAAGGAAA
65595801 AATTCAGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (15 bp):
GAAAGAAAAAGGAAA
Found at i:65602867 original size:13 final size:13
Alignment explanation
Indices: 65602851--65602916 Score: 62
Period size: 13 Copynumber: 5.1 Consensus size: 13
65602841 CTTAAACCAA
*
65602851 ACTTTTCAAAAGT
1 ACTTTTCAAAAGC
* *
65602864 ACTTCTCAAAATC
1 ACTTTTCAAAAGC
*
65602877 ACTTTTCCACAA-C
1 ACTTTT-CAAAAGC
*
65602890 ACTTTTTAAAAGC
1 ACTTTTCAAAAGC
*
65602903 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
65602916 A
1 A
65602917 ATGCTAAACT
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
12 3 0.07
13 35 0.83
14 4 0.10
ACGTcount: A:0.38, C:0.26, G:0.05, T:0.32
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:65605772 original size:43 final size:44
Alignment explanation
Indices: 65605723--65605869 Score: 192
Period size: 43 Copynumber: 3.4 Consensus size: 44
65605713 GATTACCGAG
* * *
65605723 ATGTGATTACATGTAAGAACATGTCTGGGACATTGGCATTGTAT
1 ATGTGATTACATGTAAGACCATGTCTAGGACATTGGCATCGTAT
*
65605767 -TGTGATTACGTGTAAGACCATGTCTAGGACATTGGCATCGT-T
1 ATGTGATTACATGTAAGACCATGTCTAGGACATTGGCATCGTAT
* * * *
65605809 ATGTGATTTCGTGTAAGACCCTGTCTAGGACAGTGGCATCG-AT
1 ATGTGATTACATGTAAGACCATGTCTAGGACATTGGCATCGTAT
*
65605852 ATGTGATAACATGTAAGA
1 ATGTGATTACATGTAAGA
65605870 TCATATTTGG
Statistics
Matches: 91, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
42 1 0.01
43 90 0.99
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (44 bp):
ATGTGATTACATGTAAGACCATGTCTAGGACATTGGCATCGTAT
Found at i:65614323 original size:30 final size:30
Alignment explanation
Indices: 65614288--65614384 Score: 149
Period size: 30 Copynumber: 3.1 Consensus size: 30
65614278 ACTTATTTTA
*
65614288 TTGTTAATTTTATTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAGAGGCAT
65614318 TTGTTAATTTTGTTATTATTTTAGAGGCATTT
1 TTGTTAATTTTGTTATTATTTTAGAGGCA--T
65614350 GCTTGTTAATTTTGTTATTATTTTAGAGGCAT
1 --TTGTTAATTTTGTTATTATTTTAGAGGCAT
65614382 TTG
1 TTG
65614385 CTTGTTAAGT
Statistics
Matches: 62, Mismatches: 1, Indels: 8
0.87 0.01 0.11
Matches are distributed among these distances:
30 31 0.50
32 2 0.03
34 29 0.47
ACGTcount: A:0.23, C:0.04, G:0.16, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAGAGGCAT
Found at i:65614361 original size:34 final size:34
Alignment explanation
Indices: 65614288--65614392 Score: 173
Period size: 34 Copynumber: 3.2 Consensus size: 34
65614278 ACTTATTTTA
*
65614288 TTGTTAATTTTATTATTATTTTAGAGGCA--T--
1 TTGTTAATTTTGTTATTATTTTAGAGGCATTTGC
65614318 TTGTTAATTTTGTTATTATTTTAGAGGCATTTGC
1 TTGTTAATTTTGTTATTATTTTAGAGGCATTTGC
65614352 TTGTTAATTTTGTTATTATTTTAGAGGCATTTGC
1 TTGTTAATTTTGTTATTATTTTAGAGGCATTTGC
65614386 TTGTTAA
1 TTGTTAA
65614393 GTTGCATCTA
Statistics
Matches: 70, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
30 28 0.40
32 1 0.01
34 41 0.59
ACGTcount: A:0.23, C:0.05, G:0.16, T:0.56
Consensus pattern (34 bp):
TTGTTAATTTTGTTATTATTTTAGAGGCATTTGC
Found at i:65614983 original size:15 final size:15
Alignment explanation
Indices: 65614963--65615005 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
65614953 TAACCCGTCC
65614963 ATATTAATTTTTTTT
1 ATATTAATTTTTTTT
65614978 ATATTATATTGTTTTTT
1 ATATTA-ATT-TTTTTT
*
65614995 ACA-TAATTTTT
1 ATATTAATTTTT
65615006 AAATATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 3 0.12
15 9 0.36
16 5 0.20
17 8 0.32
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (15 bp):
ATATTAATTTTTTTT
Found at i:65615655 original size:20 final size:21
Alignment explanation
Indices: 65615630--65615671 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
65615620 AAAATAACAT
*
65615630 TTAC-GGGCCTTAAAAAGAGC
1 TTACGGGGCCCTAAAAAGAGC
*
65615650 TTACGGGGCCCTAAAAATAGC
1 TTACGGGGCCCTAAAAAGAGC
65615671 T
1 T
65615672 CAGGAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.21
Consensus pattern (21 bp):
TTACGGGGCCCTAAAAAGAGC
Found at i:65615844 original size:19 final size:19
Alignment explanation
Indices: 65615820--65615856 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
65615810 TGTGGCTACC
65615820 CCACACACCTGTATGGTCG
1 CCACACACCTGTATGGTCG
65615839 CCACACACCTGTATGGTC
1 CCACACACCTGTATGGTC
65615857 AGATTGTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.22, C:0.38, G:0.19, T:0.22
Consensus pattern (19 bp):
CCACACACCTGTATGGTCG
Found at i:65621611 original size:19 final size:18
Alignment explanation
Indices: 65621564--65621614 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
65621554 TTGAGTGAGC
* *
65621564 GTATTTTTTTTTCTTTTT
1 GTATTTTTTTTTCATTAT
*
65621582 GTATTCATTTTTTCATTAT
1 GTATT-TTTTTTTCATTAT
65621601 GTAATTTTTTTTTC
1 GT-ATTTTTTTTTC
65621615 TCTTTTAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 5 0.19
19 19 0.70
20 3 0.11
ACGTcount: A:0.14, C:0.08, G:0.06, T:0.73
Consensus pattern (18 bp):
GTATTTTTTTTTCATTAT
Found at i:65622079 original size:21 final size:21
Alignment explanation
Indices: 65622050--65622089 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
65622040 TAATGCCACA
* *
65622050 TCAATATTTTCATCTTGAATT
1 TCAAGATTTTCATCGTGAATT
65622071 TCAAGATTTTCATCGTGAA
1 TCAAGATTTTCATCGTGAA
65622090 AAAAAATCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (21 bp):
TCAAGATTTTCATCGTGAATT
Found at i:65625894 original size:16 final size:16
Alignment explanation
Indices: 65625861--65625913 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 16
65625851 AAACGATCAT
65625861 TTAAAAAAAAGTTATAAAA
1 TTAAAAAAAA--T-TAAAA
65625880 TTAAAAAAAATTAAAA
1 TTAAAAAAAATTAAAA
65625896 -TATAAAAAAATTAAAA
1 TTA-AAAAAAATTAAAA
65625912 TT
1 TT
65625914 CAATGTCATC
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
15 2 0.06
16 18 0.56
17 2 0.06
19 10 0.31
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (16 bp):
TTAAAAAAAATTAAAA
Found at i:65628249 original size:26 final size:26
Alignment explanation
Indices: 65628220--65628280 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
65628210 TATCCCAAGC
** *
65628220 TCCTGATTAAAGGTTCTTCGTGAGCT
1 TCCTGATTAAAAATTCTTCGTGAACT
*
65628246 TCCTGATTAAAAATTCTTTGTGAACT
1 TCCTGATTAAAAATTCTTCGTGAACT
65628272 TCCTGATTA
1 TCCTGATTA
65628281 TGGCTCTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Consensus pattern (26 bp):
TCCTGATTAAAAATTCTTCGTGAACT
Found at i:65634653 original size:53 final size:51
Alignment explanation
Indices: 65634505--65634718 Score: 162
Period size: 52 Copynumber: 4.3 Consensus size: 51
65634495 TGACTGAAAA
* *
65634505 GATGTGATATGTGCTTTCGTATAAGACCATAGT-TGGGCTATGGCATCG-GT
1 GATGTGATATGTGATTCCGTATAAGACCATA-TCTGGGCTATGGCATCGTGT
* * * *
65634555 ACAATGTGATTCATGT--TCCCGTATAAGACTATAGCTGGGCTATGGCATCAGTGT
1 --GATGTGA-T-ATGTGATTCCGTATAAGACCATATCTGGGCTATGGCATC-GTGT
* *
65634609 GATGTGATAATGTGATTCCGTATAAGACCATATCTGAGATATGGCATCG-GT
1 GATGTGAT-ATGTGATTCCGTATAAGACCATATCTGGGCTATGGCATCGTGT
* ** * *
65634660 -ATGT--TATGTGA-TCCGTGTAAGACCATGGCAGGGCTATGGCTTCG-GT
1 GATGTGATATGTGATTCCGTATAAGACCATATCTGGGCTATGGCATCGTGT
*
65634706 G-TGTGATGTGTGA
1 GATGTGATATGTGA
65634719 CAATATGAAA
Statistics
Matches: 132, Mismatches: 20, Indels: 24
0.75 0.11 0.14
Matches are distributed among these distances:
46 31 0.23
47 6 0.05
48 7 0.05
50 4 0.03
51 7 0.05
52 41 0.31
53 30 0.23
54 6 0.05
ACGTcount: A:0.24, C:0.15, G:0.29, T:0.32
Consensus pattern (51 bp):
GATGTGATATGTGATTCCGTATAAGACCATATCTGGGCTATGGCATCGTGT
Found at i:65639492 original size:33 final size:33
Alignment explanation
Indices: 65639450--65639514 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
65639440 TCCCTGACAA
65639450 GATTAAATCATAAAAGCACTTAATTAGCAAGGG
1 GATTAAATCATAAAAGCACTTAATTAGCAAGGG
*
65639483 GATTAAATCATAAAAGCACTTAATTAGTAAGG
1 GATTAAATCATAAAAGCACTTAATTAGCAAGG
65639515 TTCAGTTCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.46, C:0.11, G:0.17, T:0.26
Consensus pattern (33 bp):
GATTAAATCATAAAAGCACTTAATTAGCAAGGG
Found at i:65645829 original size:23 final size:24
Alignment explanation
Indices: 65645776--65645831 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
65645766 AATTTCAAAT
*
65645776 TTTGAGTT-AATTGAATCAAGTTA
1 TTTGAGTTAAATTAAATCAAGTTA
*
65645799 TTTAAGTTAAATTAAAT-AAG-TA
1 TTTGAGTTAAATTAAATCAAGTTA
65645821 GTTTGAGTTAA
1 -TTTGAGTTAA
65645832 GCTGAATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 2 0.07
23 19 0.68
24 7 0.25
ACGTcount: A:0.39, C:0.02, G:0.16, T:0.43
Consensus pattern (24 bp):
TTTGAGTTAAATTAAATCAAGTTA
Found at i:65645964 original size:18 final size:19
Alignment explanation
Indices: 65645923--65645979 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
65645913 TGTCTCTAAA
65645923 AAAAATTCAAAATAATTT-T
1 AAAAATTCAAAAT-ATTTAT
*
65645942 CAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
*
65645961 AAAAATTCCAAA-ATTTAT
1 AAAAATTCAAAATATTTAT
65645979 A
1 A
65645980 TTTTTTTTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 11 0.32
19 23 0.68
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:65648595 original size:18 final size:18
Alignment explanation
Indices: 65648572--65648609 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
65648562 TCGAAATTTT
65648572 ATTTTAATATTT-TTATGC
1 ATTTTAAT-TTTATTATGC
65648590 ATTTTAATTTTATTATGC
1 ATTTTAATTTTATTATGC
65648608 AT
1 AT
65648610 AATTTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (18 bp):
ATTTTAATTTTATTATGC
Found at i:65648891 original size:18 final size:18
Alignment explanation
Indices: 65648845--65648904 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
65648835 CACCTCTATA
65648845 TTTTAAGTATAT-ATAA-T
1 TTTTAA-TATATAATAATT
*
65648862 TTTTACA-CTATAATAATT
1 TTTTA-ATATATAATAATT
*
65648880 TTTTAATATATAATTATT
1 TTTTAATATATAATAATT
65648898 ATTTTAA
1 -TTTTAA
65648905 AAGAATAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
16 3 0.09
17 10 0.29
18 16 0.46
19 6 0.17
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (18 bp):
TTTTAATATATAATAATT
Found at i:65656743 original size:39 final size:38
Alignment explanation
Indices: 65656676--65656749 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 38
65656666 CATATTAATT
*
65656676 TTTTATTTTTAATTTTTAAACTTATTTTGATAAAATAAG
1 TTTTATTTTTAACTTTTAAACTTATTTTGA-AAAATAAG
65656715 TTTTATTTTATAACTTTTAAA--TATTTTTGAAAAAT
1 TTTTATTTT-TAACTTTTAAACTTA-TTTTGAAAAAT
65656750 TTTCAAATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
38 7 0.22
39 15 0.47
40 10 0.31
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.57
Consensus pattern (38 bp):
TTTTATTTTTAACTTTTAAACTTATTTTGAAAAATAAG
Found at i:65670230 original size:17 final size:17
Alignment explanation
Indices: 65670208--65670241 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
65670198 ATCCACTAAT
*
65670208 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
65670225 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
65670242 AATCCACTAC
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:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:65674868 original size:17 final size:17
Alignment explanation
Indices: 65674846--65674879 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
65674836 ATCCACTAAT
*
65674846 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
65674863 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
65674880 AATCCACTAC
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:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:65678016 original size:21 final size:20
Alignment explanation
Indices: 65677991--65678032 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
65677981 ATTTAAAATT
65677991 TTAATTTTAATTAAATAATAG
1 TTAA-TTTAATTAAATAATAG
* *
65678012 TTAATTTCATTAAATTATAG
1 TTAATTTAATTAAATAATAG
65678032 T
1 T
65678033 ATTTCTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (20 bp):
TTAATTTAATTAAATAATAG
Found at i:65691965 original size:20 final size:20
Alignment explanation
Indices: 65691940--65691979 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
65691930 ACATGGCTGA
*
65691940 TTTGATGCTTATGTGATCCC
1 TTTGATGCTTATATGATCCC
65691960 TTTGATGCTTATATGATCCC
1 TTTGATGCTTATATGATCCC
65691980 CTGCAAGATC
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:0.17, C:0.20, G:0.17, T:0.45
Consensus pattern (20 bp):
TTTGATGCTTATATGATCCC
Found at i:65697716 original size:17 final size:17
Alignment explanation
Indices: 65697694--65697729 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
65697684 CACTTAATTT
*
65697694 ACATATATTACTGAAAC
1 ACATATATCACTGAAAC
*
65697711 ACATATATCACTGTAAC
1 ACATATATCACTGAAAC
65697728 AC
1 AC
65697730 TTTCATCACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.44, C:0.22, G:0.06, T:0.28
Consensus pattern (17 bp):
ACATATATCACTGAAAC
Found at i:65697737 original size:17 final size:17
Alignment explanation
Indices: 65697717--65697754 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
65697707 AAACACATAT
* *
65697717 ATCACTGTAACACTTTC
1 ATCACTATAACACTTGC
65697734 ATCACTATAACACTTGC
1 ATCACTATAACACTTGC
65697751 ATCA
1 ATCA
65697755 GTGAAGCACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (17 bp):
ATCACTATAACACTTGC
Found at i:65699413 original size:43 final size:43
Alignment explanation
Indices: 65699354--65699537 Score: 271
Period size: 43 Copynumber: 4.3 Consensus size: 43
65699344 AAAATGCCAC
*
65699354 AAAAGATCATGACTTTTAGCGGCGTTTGTGGGAAAAGCGCCGTT
1 AAAAG-TCATGACTTTTAGCGGCGTTTGTGGGAAAAGCGCCGCT
*
65699398 AAAAGTCATGACTTTTAGCGGCGTTTGTGGGAAAAGCGCCGTT
1 AAAAGTCATGACTTTTAGCGGCGTTTGTGGGAAAAGCGCCGCT
* *
65699441 AAAAGTCATGACTTTTAGCGGCGTTTGTGGGATAAGCACCGCT
1 AAAAGTCATGACTTTTAGCGGCGTTTGTGGGAAAAGCGCCGCT
* * * *
65699484 AAAAGTCCTGGCTTTTAACGGCATTTGTGGGATAAA-CGCCGCT
1 AAAAGTCATGACTTTTAGCGGCGTTTGTGGGA-AAAGCGCCGCT
65699527 AAAAGTCATGA
1 AAAAGTCATGA
65699538 GCGGCGCTTT
Statistics
Matches: 128, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
43 121 0.95
44 7 0.05
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (43 bp):
AAAAGTCATGACTTTTAGCGGCGTTTGTGGGAAAAGCGCCGCT
Found at i:65702341 original size:7 final size:7
Alignment explanation
Indices: 65702324--65702400 Score: 56
Period size: 7 Copynumber: 11.4 Consensus size: 7
65702314 TATTTTCAAG
65702324 TATAT-T
1 TATATAT
65702330 TATATAT
1 TATATAT
65702337 TATATTAT
1 TATA-TAT
*
65702345 T-TATTAA
1 TATA-TAT
65702352 TATATAT
1 TATATAT
65702359 TAT-T-T
1 TATATAT
*
65702364 TATATTT
1 TATATAT
*
65702371 TA-AAAT
1 TATATAT
*
65702377 TATACAT
1 TATATAT
65702384 TATATAT
1 TATATAT
*
65702391 TACATAT
1 TATATAT
65702398 TAT
1 TAT
65702401 CATGTATAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
5 4 0.07
6 11 0.19
7 36 0.63
8 6 0.11
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (7 bp):
TATATAT
Found at i:65702369 original size:20 final size:22
Alignment explanation
Indices: 65702330--65702397 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
65702320 CAAGTATATT
*
65702330 TATATATTATATTATTTATTAA
1 TATATATTATATTATATATTAA
* *
65702352 TATATATTATTTTATATTTTAA
1 TATATATTATATTATATATTAA
* *
65702374 AAT-TA-TACATTATATATTACA
1 TATATATTATATTATATATTA-A
65702395 TAT
1 TAT
65702398 TATCATGTAT
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
20 11 0.30
21 5 0.14
22 21 0.57
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (22 bp):
TATATATTATATTATATATTAA
Found at i:65702538 original size:19 final size:17
Alignment explanation
Indices: 65702516--65702555 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
65702506 TTTTATATTT
*
65702516 TATATGTTATTTTATTATA
1 TATAT-TTATATTATTA-A
65702535 TATATTTATATTATTAA
1 TATATTTATATTATTAA
65702552 TATA
1 TATA
65702556 GTATTACACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 10 0.50
19 5 0.25
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (17 bp):
TATATTTATATTATTAA
Found at i:65702612 original size:22 final size:23
Alignment explanation
Indices: 65702586--65702636 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
65702576 TTATAAATTA
* *
65702586 TTATTAAGCAT-TA-TATTTATG
1 TTATTAAACATGTAGTATGTATG
65702607 TGTATTAAACATGTAGTATGTATG
1 T-TATTAAACATGTAGTATGTATG
65702631 TTATTA
1 TTATTA
65702637 TAAAGTTCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 1 0.04
22 9 0.36
23 7 0.28
24 8 0.32
ACGTcount: A:0.33, C:0.04, G:0.14, T:0.49
Consensus pattern (23 bp):
TTATTAAACATGTAGTATGTATG
Found at i:65714701 original size:94 final size:94
Alignment explanation
Indices: 65714540--65714724 Score: 280
Period size: 94 Copynumber: 2.0 Consensus size: 94
65714530 TCGAAGAAAC
* * * * *
65714540 AGATTTGGCATCTCCGTATTCGAAAGAGAGCAGATCGGAGACATAGTAGATCTGACATTCGGATG
1 AGATTTGGCATCTCCATATTCGAAAGAGAGCAGATCGAAGACATAGCAGATCTAACATTCAGATG
65714605 TTTTCACATCGAAGCAGATCCAAGATAAT
66 TTTTCACATCGAAGCAGATCCAAGATAAT
* ** *
65714634 AGATTTGGCATCTCTATATTCGACGGAGAGCAGATCGAAGACATAGCAGATCTAACCTTCAGATG
1 AGATTTGGCATCTCCATATTCGAAAGAGAGCAGATCGAAGACATAGCAGATCTAACATTCAGATG
*
65714699 TTTTCACATCGAAGTAGATCCAAGAT
66 TTTTCACATCGAAGCAGATCCAAGAT
65714725 GATTTGGCAT
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
94 81 1.00
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (94 bp):
AGATTTGGCATCTCCATATTCGAAAGAGAGCAGATCGAAGACATAGCAGATCTAACATTCAGATG
TTTTCACATCGAAGCAGATCCAAGATAAT
Found at i:65714840 original size:86 final size:88
Alignment explanation
Indices: 65714541--65714849 Score: 261
Period size: 94 Copynumber: 3.4 Consensus size: 88
65714531 CGAAGAAACA
* ** * * * * **
65714541 GATTTGGCATCTCCGTATTCGAAAGAGAGCAGATCGGAGACATAGTAGATCTGACATTCGGATGT
1 GATTTGGCATCT-CTTATT-GTCAGAGAGCAGATCGAAGACATAGCAGATCTAACCTTCACATGT
*
65714606 TTTCACATCGAAGCAGATCCAAGATAAT
64 TTGCACATCGAAGCAGATCCAAG---AT
* * *
65714634 AGATTTGGCATCTCTATATTCGACGGAGAGCAGATCGAAGACATAGCAGATCTAACCTTCAGATG
1 -GATTTGGCATCTCT-TATT-GTCAGAGAGCAGATCGAAGACATAGCAGATCTAACCTTCACATG
* *
65714699 TTTTCACATCGAAGTAGATCCAAGAT
63 TTTGCACATCGAAGCAGATCCAAGAT
* ** * *
65714725 GATTTGGCATC-CTTACGTT-TACA-AGGAGCAGATCGAAGACATAGCAGGT-TGGCTTTCACTT
1 GATTTGGCATCTCTTA--TTGT-CAGA-GAGCAGATCGAAGACATAGCAGATCTAACCTTCACAT
*
65714786 GTTTGCGC-T-GAAGCAGATCCAAGAT
62 GTTTGCACATCGAAGCAGATCCAAGAT
*
65714811 GATTTGGCATCTCTGTATTGTCAGAGAGCAAATCGAAGA
1 GATTTGGCATCTCT-TATTGTCAGAGAGCAGATCGAAGA
65714850 AACCGATTTG
Statistics
Matches: 185, Mismatches: 21, Indels: 26
0.80 0.09 0.11
Matches are distributed among these distances:
86 43 0.23
87 5 0.03
88 18 0.10
89 26 0.14
90 13 0.07
91 2 0.01
93 1 0.01
94 77 0.42
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27
Consensus pattern (88 bp):
GATTTGGCATCTCTTATTGTCAGAGAGCAGATCGAAGACATAGCAGATCTAACCTTCACATGTTT
GCACATCGAAGCAGATCCAAGAT
Found at i:65714893 original size:44 final size:43
Alignment explanation
Indices: 65714811--65714893 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
65714801 GATCCAAGAT
** *
65714811 GATTTGGCATCTCTGTATTGTCAGAGAGCAAATCGAAGAAACC
1 GATTTGGCATCTCCATATTGACAGAGAGCAAATCGAAGAAACC
*
65714854 GATTTGGCATCTCCATATTCGACGGAGAG-AAGATCGAAGA
1 GATTTGGCATCTCCATATT-GACAGAGAGCAA-ATCGAAGA
65714894 CATAGCAGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
43 19 0.56
44 15 0.44
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (43 bp):
GATTTGGCATCTCCATATTGACAGAGAGCAAATCGAAGAAACC
Found at i:65715015 original size:133 final size:131
Alignment explanation
Indices: 65714795--65715034 Score: 308
Period size: 133 Copynumber: 1.8 Consensus size: 131
65714785 TGTTTGCGCT
*
65714795 GAAGCAGATCCAAGATGATTTGGCATCTCTGTATTGTCAGAGAGCAAATCGAAGAAACCGATTTG
1 GAAGCAGATCCAAGATGATTTGGCATCTCTGTATTGTCAGAGAGCAAATCGAAGAAACAGATTTG
*
65714860 GCATCTCCATATTCGACGGAGAGAAGATCGAAGACATAGCAGATCTAACTTTCAGATGTTTTTGC
66 GCATCTCCATATTCGACAGAGAGAAGATCGAAG--ATAGCAGATCTAACTTTCAGATGTTTTTGC
65714925 ATC
129 ATC
* * *
65714928 GAAGCAGATCCAAGATGATTTGGCATC-CTTGTGTT-TACA-AGGAGCAGATCGAAGATAGCAGA
1 GAAGCAGATCCAAGATGATTTGGCATCTC-TGTATTGT-CAGA-GAGCAAATCGAAGA-AACAGA
*** * *
65714990 TTTGGCATCTTTGTATT-GTCAGAGAGCAGATCGAAGATAGCAGAT
62 TTTGGCATCTCCATATTCGACAGAGAGAAGATCGAAGATAGCAGAT
65715035 TTGGCGTCTC
Statistics
Matches: 93, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
131 9 0.10
132 3 0.03
133 63 0.68
134 18 0.19
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (131 bp):
GAAGCAGATCCAAGATGATTTGGCATCTCTGTATTGTCAGAGAGCAAATCGAAGAAACAGATTTG
GCATCTCCATATTCGACAGAGAGAAGATCGAAGATAGCAGATCTAACTTTCAGATGTTTTTGCAT
C
Found at i:65715017 original size:44 final size:44
Alignment explanation
Indices: 65714944--65715064 Score: 174
Period size: 44 Copynumber: 2.8 Consensus size: 44
65714934 GATCCAAGAT
* *
65714944 GATTTGGCATCCTTGTGTT-TACA-AGGAGCAGATCGAAGATAGCA
1 GATTTGGCATCTTTGTATTGT-CAGA-GAGCAGATCGAAGATAGCA
65714988 GATTTGGCATCTTTGTATTGTCAGAGAGCAGATCGAAGATAGCA
1 GATTTGGCATCTTTGTATTGTCAGAGAGCAGATCGAAGATAGCA
* *
65715032 GATTTGGCGTCTCTGTATTGTCAGAGAGCAGAT
1 GATTTGGCATCTTTGTATTGTCAGAGAGCAGAT
65715065 TTGGCATCTC
Statistics
Matches: 71, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
44 69 0.97
45 2 0.03
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (44 bp):
GATTTGGCATCTTTGTATTGTCAGAGAGCAGATCGAAGATAGCA
Found at i:65715064 original size:30 final size:30
Alignment explanation
Indices: 65715028--65715091 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
65715018 GATCGAAGAT
*
65715028 AGCAGATTTGGCGTCTCTGTATTGTCAGAG
1 AGCAGATTTGGCATCTCTGTATTGTCAGAG
65715058 AGCAGATTTGGCATCTCTGTATTGTCAGAG
1 AGCAGATTTGGCATCTCTGTATTGTCAGAG
65715088 AGCA
1 AGCA
65715092 AATCGGAGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.31
Consensus pattern (30 bp):
AGCAGATTTGGCATCTCTGTATTGTCAGAG
Found at i:65716547 original size:15 final size:15
Alignment explanation
Indices: 65716523--65716556 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
65716513 AATTTTAATC
65716523 ATTTTTTTAAAT-TT
1 ATTTTTTTAAATATT
65716537 ATTTATTTTAAATATT
1 ATTT-TTTTAAATATT
65716553 ATTT
1 ATTT
65716557 GTTATTTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 8 0.44
16 6 0.33
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTTTTTTAAATATT
Found at i:65716676 original size:10 final size:10
Alignment explanation
Indices: 65716617--65716743 Score: 55
Period size: 9 Copynumber: 13.9 Consensus size: 10
65716607 TATTTTCAAG
*
65716617 TATATTTATA
1 TATATATATA
65716627 TAT-TATAT-
1 TATATATATA
*
65716635 TATTTAT-TA
1 TATATATATA
65716644 -ATATATATA
1 TATATATATA
* * *
65716653 TTTATTTTTA
1 TATATATATA
65716663 TATATATATA
1 TATATATATA
65716673 TATATAT-TA
1 TATATATATA
* * *
65716682 TTTATGT-TT
1 TATATATATA
*
65716691 TA-ATACAT-
1 TATATATATA
65716699 TATAT-TATA
1 TATATATATA
65716708 T-TATAT-TA
1 TATATATATA
*
65716716 TAT-TATTTA
1 TATATATATA
65716725 TAT-TATCATA
1 TATATAT-ATA
*
65716735 TATTTATAT
1 TATATATAT
65716744 CTTATTACAT
Statistics
Matches: 89, Mismatches: 16, Indels: 24
0.69 0.12 0.19
Matches are distributed among these distances:
8 24 0.27
9 32 0.36
10 30 0.34
11 3 0.03
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.60
Consensus pattern (10 bp):
TATATATATA
Found at i:65716736 original size:19 final size:18
Alignment explanation
Indices: 65716619--65716738 Score: 91
Period size: 19 Copynumber: 7.1 Consensus size: 18
65716609 TTTTCAAGTA
65716619 TATTTATA-TAT-TATAT
1 TATTTATATTATATATAT
*
65716635 TATTTAT-TAATATATA-
1 TATTTATATTATATATAT
65716651 TATTTAT-TT-T-TATA-
1 TATTTATATTATATATAT
65716665 TA--TATA-TATATATAT
1 TATTTATATTATATATAT
* * *
65716680 TATTTATGTTTTAATACAT
1 TATTTATATTAT-ATATAT
65716699 TATATTATATTATATTATAT
1 TAT-TTATATTATA-TATAT
65716719 TATTTATATTATCATATAT
1 TATTTATATTAT-ATATAT
65716738 T
1 T
65716739 TATATCTTAT
Statistics
Matches: 83, Mismatches: 8, Indels: 23
0.73 0.07 0.20
Matches are distributed among these distances:
12 4 0.05
13 1 0.01
14 10 0.12
15 3 0.04
16 17 0.20
17 7 0.08
18 2 0.02
19 24 0.29
20 15 0.18
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.60
Consensus pattern (18 bp):
TATTTATATTATATATAT
Found at i:65716892 original size:17 final size:17
Alignment explanation
Indices: 65716863--65716915 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
65716853 ATTTTATTCT
* *
65716863 TTTATATTTTATATGTTA
1 TTTATATTATATAT-ATA
65716881 TTT-TATTATATATATA
1 TTTATATTATATATATA
65716897 TTTATATTAT-TAATATA
1 TTTATATTATAT-ATATA
65716914 TT
1 TT
65716916 ATTACACTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 6 0.19
17 22 0.71
18 3 0.10
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (17 bp):
TTTATATTATATATATA
Found at i:65716900 original size:27 final size:27
Alignment explanation
Indices: 65716851--65716903 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
65716841 TATCATTACA
* *
65716851 TTATTTTATTCTTTTATATTTTATATG
1 TTATTTTATTATTATATATTTTATATG
65716878 TTATTTTATTA-TATATATATTTATAT
1 TTATTTTATTATTATATAT-TTTATAT
65716904 TATTAATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (27 bp):
TTATTTTATTATTATATATTTTATATG
Found at i:65716913 original size:11 final size:10
Alignment explanation
Indices: 65716865--65716919 Score: 50
Period size: 9 Copynumber: 6.0 Consensus size: 10
65716855 TTTATTCTTT
65716865 TATATT-TTA
1 TATATTATTA
*
65716874 TATGTTATT-
1 TATATTATTA
65716883 T-TATTA-TA
1 TATATTATTA
65716891 TATA-TATT-
1 TATATTATTA
65716899 TATATTATTAA
1 TATATTATT-A
65716910 TATATTATTA
1 TATATTATTA
65716920 CACTATTATG
Statistics
Matches: 37, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
7 1 0.03
8 11 0.30
9 13 0.35
10 3 0.08
11 9 0.24
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (10 bp):
TATATTATTA
Found at i:65716970 original size:22 final size:23
Alignment explanation
Indices: 65716944--65716994 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
65716934 TTATAAATTA
* *
65716944 TTATTAAGCAT-TA-TATTTATG
1 TTATTAAACATGTAGTATGTATG
65716965 TGTATTAAACATGTAGTATGTATG
1 T-TATTAAACATGTAGTATGTATG
65716989 TTATTA
1 TTATTA
65716995 TAAAGTTCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 1 0.04
22 9 0.36
23 7 0.28
24 8 0.32
ACGTcount: A:0.33, C:0.04, G:0.14, T:0.49
Consensus pattern (23 bp):
TTATTAAACATGTAGTATGTATG
Found at i:65718418 original size:8 final size:8
Alignment explanation
Indices: 65718389--65718445 Score: 53
Period size: 8 Copynumber: 6.9 Consensus size: 8
65718379 TAAATAAGAA
65718389 ATAATAACT
1 ATAATAA-T
65718398 ATAATAA-
1 ATAATAAT
65718405 ATTAATAAT
1 A-TAATAAT
65718414 ATAATAAT
1 ATAATAAT
**
65718422 ATATATGTT
1 ATA-ATAAT
65718431 ATAATAAT
1 ATAATAAT
*
65718439 AGAATAA
1 ATAATAA
65718446 AGAAAATAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
7 1 0.03
8 25 0.62
9 14 0.35
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.37
Consensus pattern (8 bp):
ATAATAAT
Found at i:65722986 original size:46 final size:46
Alignment explanation
Indices: 65722893--65723020 Score: 233
Period size: 46 Copynumber: 2.8 Consensus size: 46
65722883 CTTTTCTGAA
*
65722893 ATGAAATGTGTAAGACCAT-GTTGAAAG-TACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGACACCATGGCAACATGAT
65722937 ATGAAATGTGTAAGACCATGGTTGAAAGACACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGACACCATGGCAACATGAT
65722983 ATGAAATGTGTAAGACCATGGTTGAAAGACACCATGGC
1 ATGAAATGTGTAAGACCATGGTTGAAAGACACCATGGC
65723021 TGTAACGCCC
Statistics
Matches: 81, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
44 19 0.23
45 8 0.10
46 54 0.67
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGACACCATGGCAACATGAT
Found at i:65724379 original size:46 final size:46
Alignment explanation
Indices: 65724321--65724495 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
65724311 TGTAACCCGC
* *
65724321 CCATAAGCGAACTCGGACTCAACTCAACAAGCTCGGGCATTCGAAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCATTCGAAT
*
65724367 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT--ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG--G-C-A-TTCGA-AT
* * * *
65724417 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCATTCGAAT
*
65724460 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG
65724496 ATGCTCAACC
Statistics
Matches: 107, Mismatches: 11, Indels: 22
0.76 0.08 0.16
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 60 0.56
47 27 0.25
48 3 0.03
49 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCATTCGAAT
Found at i:65724441 original size:93 final size:93
Alignment explanation
Indices: 65724328--65724499 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
65724318 CGCCCATAAG
* *
65724328 CGAACTCGGACTCAACTCAACAAGCTCGGGCATTCGAATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACAAGCTCAGACATTCGAATCCATAAGTGAACTCGGACTCAACTCA
65724393 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* * *
65724421 CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACAAGCTCAGACATTCGAATCCATAAGTGAACTCGGACTCAACTCA
65724486 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
65724500 TCAACCATCC
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACAAGCTCAGACATTCGAATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:65724515 original size:46 final size:44
Alignment explanation
Indices: 65724329--65724515 Score: 139
Period size: 46 Copynumber: 4.0 Consensus size: 44
65724319 GCCCATAAGC
* * * * *
65724329 GAACTCGGACTCAACTCAACAAGCTCGGGCATTCGAATCCAT-AAGT
1 GAACTCGGACTCAACTCAACGAGTTC-GG-ATGCCAA-CCATCTAGT
*
65724375 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTA-CATCTCA-C
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATCT-AGT
* * * *
65724422 GAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCAT-AAGT
1 GAACTCGGACTCAACTCAACGAGTTC-G-GATGC-CAACCATCTAGT
65724468 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCAT-CTAGT
65724514 GA
1 GA
65724516 CATGTCACTT
Statistics
Matches: 112, Mismatches: 16, Indels: 26
0.73 0.10 0.17
Matches are distributed among these distances:
44 12 0.11
45 5 0.04
46 58 0.52
47 29 0.26
48 3 0.03
49 4 0.04
50 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.21
Consensus pattern (44 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATCTAGT
Found at i:65731884 original size:46 final size:46
Alignment explanation
Indices: 65731817--65731990 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
65731807 TGTAACCCGC
*
65731817 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
* * *
65731863 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCAT
* * *
65731913 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTC-GACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
*
65731955 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG
65731991 ATGCTCAACC
Statistics
Matches: 106, Mismatches: 12, Indels: 20
0.77 0.09 0.14
Matches are distributed among these distances:
41 2 0.02
42 3 0.03
43 2 0.02
44 2 0.02
45 26 0.25
46 35 0.33
47 25 0.24
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
Found at i:65731982 original size:92 final size:93
Alignment explanation
Indices: 65731824--65731994 Score: 299
Period size: 92 Copynumber: 1.8 Consensus size: 93
65731814 CGCCCATAAG
* *
65731824 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
65731889 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* *
65731917 CGAACTCGGACTCAACTCAACGAGTTC-GACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
65731981 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
65731995 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
92 48 0.65
93 26 0.35
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:65733365 original size:45 final size:45
Alignment explanation
Indices: 65733286--65733479 Score: 172
Period size: 46 Copynumber: 4.2 Consensus size: 45
65733276 GGATATTACA
** **
65733286 ATGGCAACATGATATGAAATGTGTAAGACCATGGTTGAAAGATACC
1 ATGGCAACATGA-CGGAAATGAATAAGACCATGGTTGAAAGATACC
* *
65733332 ATGGCAACATGACGGGAATGAATAAGACCATGGTTGAAAAATACC
1 ATGGCAACATGACGGAAATGAATAAGACCATGGTTGAAAGATACC
** * * * * *
65733377 ATGGCAATGTAACATGAAATGAACAAGACAATGGTTGACAGATACC
1 ATGGCAACATGAC-GGAAATGAATAAGACCATGGTTGAAAGATACC
* * * * * * *
65733423 ATGGCAACCTGATAGAAAATGAGTAAGACCATAGTTGAAAGACACT
1 ATGGCAACATGA-CGGAAATGAATAAGACCATGGTTGAAAGATACC
*
65733469 ATGGCATCATG
1 ATGGCAACATG
65733480 TCAAAGATAA
Statistics
Matches: 116, Mismatches: 30, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
45 37 0.32
46 79 0.68
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (45 bp):
ATGGCAACATGACGGAAATGAATAAGACCATGGTTGAAAGATACC
Found at i:65733496 original size:91 final size:90
Alignment explanation
Indices: 65733309--65733474 Score: 197
Period size: 91 Copynumber: 1.8 Consensus size: 90
65733299 ATGAAATGTG
* * ** * *
65733309 TAAGACCATGGTTGAAAGATACCATGGCAACATGACGGGAATGAATAAGACCATGGTTGAAAAAT
1 TAAGACAATGGTTGAAAGATACCATGGCAACATGAAGAAAATGAATAAGACCATAGTTGAAAAAC
*
65733374 ACCATGGCAATGTAACATGAAATGAA
66 ACCATGGCAATGTAACATG-AATAAA
* * * * *
65733400 CAAGACAATGGTTGACAGATACCATGGCAACCTGATAGAAAATGAGTAAGACCATAGTTGAAAGA
1 TAAGACAATGGTTGAAAGATACCATGGCAACATGA-AGAAAATGAATAAGACCATAGTTGAAAAA
*
65733465 CACTATGGCA
65 CACCATGGCA
65733475 TCATGTCAAA
Statistics
Matches: 62, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
91 31 0.50
92 31 0.50
ACGTcount: A:0.42, C:0.16, G:0.23, T:0.19
Consensus pattern (90 bp):
TAAGACAATGGTTGAAAGATACCATGGCAACATGAAGAAAATGAATAAGACCATAGTTGAAAAAC
ACCATGGCAATGTAACATGAATAAA
Found at i:65733781 original size:16 final size:17
Alignment explanation
Indices: 65733760--65733792 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
65733750 ATGATGGAGC
65733760 ATGAAAT-ATTGATATA
1 ATGAAATAATTGATATA
65733776 ATGAAATAATTGATATA
1 ATGAAATAATTGATATA
65733793 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (17 bp):
ATGAAATAATTGATATA
Found at i:65734370 original size:20 final size:20
Alignment explanation
Indices: 65734341--65734386 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
65734331 GGCCTGTGCC
*
65734341 CACGGCCATGTCCTAAGCAA
1 CACGGGCATGTCCTAAGCAA
* *
65734361 CACGGGCATGTCCTAGGCCA
1 CACGGGCATGTCCTAAGCAA
65734381 CACGGG
1 CACGGG
65734387 TGTGTGCTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.24, C:0.35, G:0.28, T:0.13
Consensus pattern (20 bp):
CACGGGCATGTCCTAAGCAA
Found at i:65735599 original size:18 final size:18
Alignment explanation
Indices: 65735561--65735600 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
65735551 TTGGTACAAG
*
65735561 TATTAAATAAATATTTGT
1 TATTAAATAAATATTTAT
* *
65735579 TATTAAATAGATTTTTAT
1 TATTAAATAAATATTTAT
65735597 TATT
1 TATT
65735601 GTCATTATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (18 bp):
TATTAAATAAATATTTAT
Found at i:65735634 original size:13 final size:13
Alignment explanation
Indices: 65735616--65735663 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
65735606 TATATATATA
65735616 AAAGAAACAAAAG
1 AAAGAAACAAAAG
*
65735629 AAAGAATCAAAAG
1 AAAGAAACAAAAG
* * * *
65735642 AAAAAAAGAGAGG
1 AAAGAAACAAAAG
65735655 AAAGAAACA
1 AAAGAAACA
65735664 TAATAGCAGG
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.73, C:0.06, G:0.19, T:0.02
Consensus pattern (13 bp):
AAAGAAACAAAAG
Found at i:65736391 original size:23 final size:23
Alignment explanation
Indices: 65736365--65736439 Score: 77
Period size: 21 Copynumber: 3.4 Consensus size: 23
65736355 AGGCACTTTA
65736365 TGTGTCGTATTTTAGGCACCTCG
1 TGTGTCGTATTTTAGGCACCTCG
*
65736388 TGTGTCGTA--TCAGGCACCTCG
1 TGTGTCGTATTTTAGGCACCTCG
* * **
65736409 TCTGTCG--TTTTAGGCACTTTA
1 TGTGTCGTATTTTAGGCACCTCG
65736430 TGTGTCGTAT
1 TGTGTCGTAT
65736440 ACTGATCAGG
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
21 31 0.76
23 10 0.24
ACGTcount: A:0.13, C:0.21, G:0.25, T:0.40
Consensus pattern (23 bp):
TGTGTCGTATTTTAGGCACCTCG
Found at i:65736456 original size:29 final size:29
Alignment explanation
Indices: 65736423--65736481 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
65736413 TCGTTTTAGG
65736423 CACTTTATGTGTCGTATACTGATCAGGTA
1 CACTTTATGTGTCGTATACTGATCAGGTA
65736452 CACTTTATGTGTCGTATACTGATCAGGTA
1 CACTTTATGTGTCGTATACTGATCAGGTA
65736481 C
1 C
65736482 CGTTTTAGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (29 bp):
CACTTTATGTGTCGTATACTGATCAGGTA
Found at i:65739121 original size:4 final size:4
Alignment explanation
Indices: 65739105--65739189 Score: 62
Period size: 4 Copynumber: 20.8 Consensus size: 4
65739095 CCCTTTTCTA
* ** * * * **
65739105 TTTC TTTC CTTC TTTC TTTC TTTC TTTC TCAC GTTTGC TCTC TGTA ACTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC -TTT-C TTTC TTTC TTTC
* *
65739155 TTTC TATC TTTC TATC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
65739190 TTTTTTAACT
Statistics
Matches: 61, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
4 57 0.93
5 3 0.05
6 1 0.02
ACGTcount: A:0.06, C:0.27, G:0.04, T:0.64
Consensus pattern (4 bp):
TTTC
Found at i:65739654 original size:25 final size:25
Alignment explanation
Indices: 65739626--65739676 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
65739616 TGACTGAGTA
65739626 TACCTATACTCAGCGTACGGTTTGT
1 TACCTATACTCAGCGTACGGTTTGT
*
65739651 TACCTATACTCAGCGTATGGTTTGT
1 TACCTATACTCAGCGTACGGTTTGT
65739676 T
1 T
65739677 TCCGTGCGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.39
Consensus pattern (25 bp):
TACCTATACTCAGCGTACGGTTTGT
Found at i:65742478 original size:4 final size:4
Alignment explanation
Indices: 65742469--65742505 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
65742459 AGCAAACGTG
65742469 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
65742506 TAGAAAAGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:65746213 original size:29 final size:29
Alignment explanation
Indices: 65746181--65746243 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 29
65746171 TTCCACTAGA
65746181 TATACACTATCCATAGAAAATCCATTTTT
1 TATACACTATCCATAGAAAATCCATTTTT
* *
65746210 TATACACTCTCCATAGAAAATTCATTTTT
1 TATACACTATCCATAGAAAATCCATTTTT
65746239 TATAC
1 TATAC
65746244 CCCCGAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.37, C:0.21, G:0.03, T:0.40
Consensus pattern (29 bp):
TATACACTATCCATAGAAAATCCATTTTT
Found at i:65746649 original size:9 final size:9
Alignment explanation
Indices: 65746614--65746767 Score: 74
Period size: 9 Copynumber: 17.6 Consensus size: 9
65746604 TATTTATGTA
65746614 TTATGTAAG
1 TTATGTAAG
*
65746623 TTAAGTAAG
1 TTATGTAAG
* *
65746632 TTCTCTAAG
1 TTATGTAAG
65746641 TTATGTAAG
1 TTATGTAAG
*
65746650 ATATG--A-
1 TTATGTAAG
65746656 -TATGATAA-
1 TTATG-TAAG
* *
65746664 ATATTTAAG
1 TTATGTAAG
65746673 TATTATGTAAG
1 --TTATGTAAG
*
65746684 TTATGATATG
1 TTATG-TAAG
* * *
65746694 ATATAT-AT
1 TTATGTAAG
65746702 TTATGTAAG
1 TTATGTAAG
65746711 TTATGTAAG
1 TTATGTAAG
65746720 TTATGTAAG
1 TTATGTAAG
*
65746729 TTATGGTATG
1 TTAT-GTAAG
* * *
65746739 ATATAT-AT
1 TTATGTAAG
65746747 TTATGT-A-
1 TTATGTAAG
65746754 TTATGTAAG
1 TTATGTAAG
65746763 TTATG
1 TTATG
65746768 ATATTATATA
Statistics
Matches: 108, Mismatches: 25, Indels: 24
0.69 0.16 0.15
Matches are distributed among these distances:
5 4 0.04
7 7 0.06
8 14 0.13
9 63 0.58
10 13 0.12
11 7 0.06
ACGTcount: A:0.36, C:0.01, G:0.18, T:0.45
Consensus pattern (9 bp):
TTATGTAAG
Found at i:65746679 original size:34 final size:34
Alignment explanation
Indices: 65746641--65746784 Score: 135
Period size: 34 Copynumber: 3.9 Consensus size: 34
65746631 GTTCTCTAAG
*
65746641 TTATGTAAGATATGATATGATAAATATTTAAGTA
1 TTATGTAAGTTATGATATGATAAATATTTAAGTA
* *
65746675 TTATGTAAGTTATGATATGATATATATTTATGTAA
1 TTATGTAAGTTATGATATGATAAATATTTAAGT-A
*
65746710 GTTATGTAAGTTATGTAAGTTATGGTATGATATATATTTATGTA
1 -TTATGTAAGTTATG--A--TAT-G-AT-A-A-ATATTTAAGTA
* *
65746754 TTATGTAAGTTATGATATTATATATATTTAA
1 TTATGTAAGTTATGATATGATAAATATTTAA
65746785 CATTAAGATA
Statistics
Matches: 92, Mismatches: 7, Indels: 22
0.76 0.06 0.18
Matches are distributed among these distances:
34 37 0.40
35 1 0.01
36 15 0.16
37 2 0.02
38 1 0.01
39 3 0.03
40 3 0.03
41 2 0.02
42 2 0.02
43 15 0.16
44 1 0.01
45 10 0.11
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (34 bp):
TTATGTAAGTTATGATATGATAAATATTTAAGTA
Found at i:65746721 original size:79 final size:79
Alignment explanation
Indices: 65746627--65746783 Score: 251
Period size: 79 Copynumber: 2.0 Consensus size: 79
65746617 TGTAAGTTAA
*
65746627 GTAAGTTCTCTAAGTTATGTAAGATATGATATGATAAATATTTAAGTATTATGTAAGTTATGATA
1 GTAAGTTATCTAAGTTATGTAAGATATGATATGATAAATATTTAAGTATTATGTAAGTTATGATA
65746692 TGATATATATTTAT
66 TGATATATATTTAT
* * * * *
65746706 GTAAGTTATGTAAGTTATGTAAGTTATGGTATGATATATATTTATGTATTATGTAAGTTATGATA
1 GTAAGTTATCTAAGTTATGTAAGATATGATATGATAAATATTTAAGTATTATGTAAGTTATGATA
*
65746771 TTATATATATTTA
66 TGATATATATTTA
65746784 ACATTAAGAT
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
79 71 1.00
ACGTcount: A:0.36, C:0.01, G:0.16, T:0.46
Consensus pattern (79 bp):
GTAAGTTATCTAAGTTATGTAAGATATGATATGATAAATATTTAAGTATTATGTAAGTTATGATA
TGATATATATTTAT
Found at i:65747128 original size:16 final size:16
Alignment explanation
Indices: 65747109--65747142 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
65747099 AAATATTAAA
*
65747109 TATTAAAATCAAACAT
1 TATTAAAATAAAACAT
*
65747125 TATTAATATAAAACAT
1 TATTAAAATAAAACAT
65747141 TA
1 TA
65747143 ATCAATATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (16 bp):
TATTAAAATAAAACAT
Found at i:65748074 original size:25 final size:25
Alignment explanation
Indices: 65748045--65748095 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
65748035 GCAGAAAATT
*
65748045 GGAGAAGCAGCAGAGGGATGCCGAC
1 GGAGAAGCAGCAGAAGGATGCCGAC
* * *
65748070 GGAGATGTAGCAGAAGGCTGCCGAC
1 GGAGAAGCAGCAGAAGGATGCCGAC
65748095 G
1 G
65748096 ACGATGCGGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.20, G:0.43, T:0.08
Consensus pattern (25 bp):
GGAGAAGCAGCAGAAGGATGCCGAC
Found at i:65748239 original size:24 final size:24
Alignment explanation
Indices: 65748209--65748255 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
65748199 AACCCAAGAA
*
65748209 ATATGCATATTGATATATGTATAT
1 ATATGCATATTGATATATATATAT
65748233 ATATGCATATTGATATATATATA
1 ATATGCATATTGATATATATATA
65748256 GACACACAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.40, C:0.04, G:0.11, T:0.45
Consensus pattern (24 bp):
ATATGCATATTGATATATATATAT
Found at i:65748248 original size:14 final size:14
Alignment explanation
Indices: 65748209--65748250 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
65748199 AACCCAAGAA
65748209 ATATGCATATTGAT
1 ATATGCATATTGAT
65748223 ATATG--TA-T-AT
1 ATATGCATATTGAT
65748233 ATATGCATATTGAT
1 ATATGCATATTGAT
65748247 ATAT
1 ATAT
65748251 ATATAGACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
10 7 0.29
11 1 0.04
12 4 0.17
13 1 0.04
14 11 0.46
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (14 bp):
ATATGCATATTGAT
Found at i:65749859 original size:40 final size:39
Alignment explanation
Indices: 65749782--65749864 Score: 96
Period size: 40 Copynumber: 2.1 Consensus size: 39
65749772 TTTTGCGGAA
*
65749782 AAAAGTGCCGCTAAAACTCGATCTTTTACAGCATTTTTAC
1 AAAAGCGCCGCTAAAACTCGATCTTTTACAGCATTTTT-C
** * *
65749822 AAAAGCGCCGCTAATTCTCGATC-TTTAGCGGCGTTTTTC
1 AAAAGCGCCGCTAAAACTCGATCTTTTA-CAGCATTTTTC
65749861 AAAA
1 AAAA
65749865 AAGTACCTCT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
39 9 0.24
40 28 0.76
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (39 bp):
AAAAGCGCCGCTAAAACTCGATCTTTTACAGCATTTTTC
Found at i:65750959 original size:34 final size:37
Alignment explanation
Indices: 65750915--65751002 Score: 119
Period size: 34 Copynumber: 2.4 Consensus size: 37
65750905 CAAAATAACA
*
65750915 AACCCCAAACCATAAACTT-A-ACATACTACCA-TTG
1 AACCCTAAACCATAAACTTAATACATACTACCATTTG
*
65750949 AACCCTAAACCATAAACTTAAAATATATACTACCATTTG
1 AACCCTAAACCATAAACTT--AATACATACTACCATTTG
65750988 AACCCTAAACCATAA
1 AACCCTAAACCATAA
65751003 GCCTTAAACC
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
34 18 0.38
37 1 0.02
38 10 0.21
39 18 0.38
ACGTcount: A:0.47, C:0.28, G:0.02, T:0.23
Consensus pattern (37 bp):
AACCCTAAACCATAAACTTAATACATACTACCATTTG
Found at i:65751556 original size:41 final size:41
Alignment explanation
Indices: 65751480--65751676 Score: 177
Period size: 41 Copynumber: 4.8 Consensus size: 41
65751470 ATTTTCGGCG
* *
65751480 TTTGGACAAAAAACGCCGCTATTGATCAG-TATTAGTGGCA
1 TTTGGACCAAAAACGCCGCTATTGATCAGTTTTTAGTGGCA
** * *
65751520 TTTGGACCAAAAACGCCGCTATTTCTTAGTTTTTAGTGGCGT
1 TTTGGACCAAAAACGCCGCTATTGATCAGTTTTTAGTGGC-A
* * * * * *
65751562 TTTAGA-TAAAAAAGCAGCTATTGATCAATTTTTAGTGGCG
1 TTTGGACCAAAAACGCCGCTATTGATCAGTTTTTAGTGGCA
* * *
65751602 TTT-TAGCTAAAAACGCCGCTATTGAACAGTTTTTAGTGGCA
1 TTTGGA-CCAAAAACGCCGCTATTGATCAGTTTTTAGTGGCA
* * *
65751643 TTTAGG-CCAAAAACGCTGTTATTGTTCAGTTTTT
1 TTT-GGACCAAAAACGCCGCTATTGATCAGTTTTT
65751677 TGCGGCGTTA
Statistics
Matches: 124, Mismatches: 27, Indels: 11
0.77 0.17 0.07
Matches are distributed among these distances:
39 1 0.01
40 28 0.23
41 90 0.73
42 5 0.04
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (41 bp):
TTTGGACCAAAAACGCCGCTATTGATCAGTTTTTAGTGGCA
Found at i:65752220 original size:31 final size:31
Alignment explanation
Indices: 65752185--65752267 Score: 80
Period size: 31 Copynumber: 2.6 Consensus size: 31
65752175 GTTTATTATG
*
65752185 AAAAATAATCTCAAAATAACAATATT-TAAAT
1 AAAAA-AATCTCAAAATAACAACATTATAAAT
* **
65752216 AAAAAAAAT-TGAGATTTAACAACATTATAAAT
1 -AAAAAAATCTCA-AAATAACAACATTATAAAT
*
65752248 AAAAAAAACTCAAAATAACA
1 AAAAAAATCTCAAAATAACA
65752268 TATCAAAATA
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
30 2 0.05
31 26 0.65
32 12 0.30
ACGTcount: A:0.64, C:0.10, G:0.02, T:0.24
Consensus pattern (31 bp):
AAAAAAATCTCAAAATAACAACATTATAAAT
Done.