Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold140
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: 3130556
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82166 characters in sequence are not A, C, G, or T
File 18 of 20
Found at i:2823274 original size:18 final size:17
Alignment explanation
Indices: 2823247--2823280 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2823237 AAAATTATGA
*
2823247 TAGTAAATATATATTAT
1 TAGTAAATATACATTAT
2823264 TAGTAAAATATACATTA
1 TAGT-AAATATACATTA
2823281 AAAATTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (17 bp):
TAGTAAATATACATTAT
Found at i:2828386 original size:14 final size:13
Alignment explanation
Indices: 2828351--2828391 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
2828341 TAGTATATTG
*
2828351 AAATTAACTTTAA
1 AAATTAAATTTAA
2828364 AAA-TAAATTTAA
1 AAATTAAATTTAA
2828376 AAATTTAAATTTAA
1 AAA-TTAAATTTAA
2828390 AA
1 AA
2828392 TTTTCAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 11 0.44
13 3 0.12
14 11 0.44
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (13 bp):
AAATTAAATTTAA
Found at i:2829246 original size:14 final size:15
Alignment explanation
Indices: 2829215--2829251 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
2829205 CATGGATAAA
2829215 AAAATAATATTATTTT
1 AAAA-AATATTATTTT
2829231 AAAAAATATT-TTTT
1 AAAAAATATTATTTT
2829245 AAAAAAT
1 AAAAAAT
2829252 TAATAGTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 11 0.52
15 6 0.29
16 4 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AAAAAATATTATTTT
Found at i:2830504 original size:17 final size:17
Alignment explanation
Indices: 2830464--2830498 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2830454 ATTTAAATAG
* *
2830464 AATTGATTTTTATTTTT
1 AATTAATTTTTAATTTT
2830481 AATTAATTTTTAATTTT
1 AATTAATTTTTAATTTT
2830498 A
1 A
2830499 TATAATATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (17 bp):
AATTAATTTTTAATTTT
Found at i:2831601 original size:14 final size:14
Alignment explanation
Indices: 2831582--2831608 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2831572 AATATGATAA
2831582 TAATTTATTATATT
1 TAATTTATTATATT
2831596 TAATTTATTATAT
1 TAATTTATTATAT
2831609 ATTTTTATGT
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:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TAATTTATTATATT
Found at i:2832032 original size:2 final size:2
Alignment explanation
Indices: 2832027--2832063 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2832017 TATATTTAAA
2832027 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2832064 CACTTTTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2832689 original size:15 final size:14
Alignment explanation
Indices: 2832663--2832711 Score: 50
Period size: 15 Copynumber: 3.6 Consensus size: 14
2832653 ATACAGTTAT
*
2832663 TATAATTTATTAAA
1 TATAAATTATTAAA
2832677 TATTAAATTATT--A
1 TA-TAAATTATTAAA
2832690 TATAAATTAATTAAA
1 TATAAATT-ATTAAA
2832705 T-TAAATT
1 TATAAATT
2832712 TAAAATTCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
12 6 0.20
13 6 0.20
14 8 0.27
15 10 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TATAAATTATTAAA
Found at i:2833522 original size:26 final size:26
Alignment explanation
Indices: 2833481--2833534 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
2833471 TGCAAATTAT
* *
2833481 ACTGGCAATTTTGTAGCCCATGATCA
1 ACTGGCAATGTAGTAGCCCATGATCA
2833507 ACTGGCAATGTAGTAGCCCATGATCA
1 ACTGGCAATGTAGTAGCCCATGATCA
2833533 AC
1 AC
2833535 ATTATTCTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (26 bp):
ACTGGCAATGTAGTAGCCCATGATCA
Found at i:2836078 original size:19 final size:19
Alignment explanation
Indices: 2836056--2836114 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 19
2836046 AAAAATAATT
2836056 AAAATATAATATAGTATTAA
1 AAAATATAATATAGTATT-A
*
2836076 AAAATATTAATATAATA-TA
1 AAAATA-TAATATAGTATTA
* *
2836095 AATATATGA-AT-GTATTA
1 AAAATATAATATAGTATTA
2836112 AAA
1 AAA
2836115 TTTATATAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
16 2 0.06
17 6 0.19
18 2 0.06
19 6 0.19
20 7 0.22
21 9 0.28
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (19 bp):
AAAATATAATATAGTATTA
Found at i:2837806 original size:24 final size:26
Alignment explanation
Indices: 2837765--2837817 Score: 74
Period size: 24 Copynumber: 2.1 Consensus size: 26
2837755 CTATATCATT
*
2837765 ATTATTTAATATAAATATAATTTTTA
1 ATTATTTAATATAAATATAAGTTTTA
*
2837791 ATTATTT-AT-TATATATAAGTTTTA
1 ATTATTTAATATAAATATAAGTTTTA
2837815 ATT
1 ATT
2837818 TAATATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 16 0.64
25 2 0.08
26 7 0.28
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (26 bp):
ATTATTTAATATAAATATAAGTTTTA
Found at i:2837824 original size:24 final size:24
Alignment explanation
Indices: 2837768--2837824 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
2837758 TATCATTATT
*
2837768 ATTTAATA-TAAATATAATTTTTA
1 ATTTAATATTAAATATAAGTTTTA
* *
2837791 A-TTATTTATTATATATAAGTTTTA
1 ATTTA-ATATTAAATATAAGTTTTA
2837815 ATTTAATATT
1 ATTTAATATT
2837825 TTAATAATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
22 3 0.11
23 3 0.11
24 18 0.67
25 3 0.11
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
ATTTAATATTAAATATAAGTTTTA
Found at i:2838494 original size:10 final size:10
Alignment explanation
Indices: 2838474--2838506 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
2838464 TTATAAATTT
2838474 TATTATATTTA
1 TATTAT-TTTA
2838485 TATTATTTTA
1 TATTATTTTA
2838495 TATTATTTTA
1 TATTATTTTA
2838505 TA
1 TA
2838507 AAAAAACTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 16 0.73
11 6 0.27
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TATTATTTTA
Found at i:2839549 original size:20 final size:20
Alignment explanation
Indices: 2839524--2839565 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
2839514 TAATCCTAAG
2839524 ACTTTTATATATAGTCAAAA
1 ACTTTTATATATAGTCAAAA
2839544 ACTTTTATATATAGTCAAAA
1 ACTTTTATATATAGTCAAAA
2839564 AC
1 AC
2839566 CAAGAAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (20 bp):
ACTTTTATATATAGTCAAAA
Found at i:2841928 original size:32 final size:33
Alignment explanation
Indices: 2841886--2841948 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
2841876 CAATTCACTA
* *
2841886 TGTATCGATACCAAG-ATCATGTATCGATACAG
1 TGTATCGATACAAAGCATCATGTATCAATACAG
* *
2841918 TGTATGGATACAAAGCATTATGTATCAATAC
1 TGTATCGATACAAAGCATCATGTATCAATAC
2841949 TTCTAGGTCG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 13 0.50
33 13 0.50
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (33 bp):
TGTATCGATACAAAGCATCATGTATCAATACAG
Found at i:2842830 original size:13 final size:13
Alignment explanation
Indices: 2842812--2842837 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2842802 CAATTTTTTG
2842812 TGTATCGATACAT
1 TGTATCGATACAT
2842825 TGTATCGATACAT
1 TGTATCGATACAT
2842838 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2842902 original size:21 final size:21
Alignment explanation
Indices: 2842876--2842951 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
2842866 CTGCCAAGAA
2842876 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
* ****
2842897 ATGTATTGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
2842917 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
2842938 ATGTATCGATACAT
1 ATGTATCGATACAT
2842952 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:2842921 original size:20 final size:20
Alignment explanation
Indices: 2842896--2842969 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
2842886 ACATCTTTTT
*
2842896 CATGTATTGATACATTGCAA
1 CATGTATCGATACATTGCAA
****
2842916 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGCAA
2842937 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
2842957 CATGTATCGATAC
1 CATGTATCGATAC
2842970 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Found at i:2842933 original size:41 final size:41
Alignment explanation
Indices: 2842876--2842969 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
2842866 CTGCCAAGAA
*
2842876 ATGTATCGATACATCTTTTTCATGTATTGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
2842917 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
2842958 ATGTATCGATAC
1 ATGTATCGATAC
2842970 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:2843748 original size:128 final size:128
Alignment explanation
Indices: 2843520--2843777 Score: 507
Period size: 128 Copynumber: 2.0 Consensus size: 128
2843510 AAAATAAATT
2843520 TTACGAATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTACCTCCCCCG
1 TTACGAATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTACCTCCCCCG
2843585 TTTATTAATAAATCTCCCCCTTAATCAAGTAATTCACATCAAAAATTTATTTGCACATGCCTA
66 TTTATTAATAAATCTCCCCCTTAATCAAGTAATTCACATCAAAAATTTATTTGCACATGCCTA
*
2843648 TTACGAATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTATCTCCCCCG
1 TTACGAATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTACCTCCCCCG
2843713 TTTATTAATAAATCTCCCCCTTAATCAAGTAATTCACATCAAAAATTTATTTGCACATGCCTA
66 TTTATTAATAAATCTCCCCCTTAATCAAGTAATTCACATCAAAAATTTATTTGCACATGCCTA
2843776 TT
1 TT
2843778 TTCTCTTCCC
Statistics
Matches: 129, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
128 129 1.00
ACGTcount: A:0.29, C:0.28, G:0.07, T:0.37
Consensus pattern (128 bp):
TTACGAATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCTTTACCTCCCCCG
TTTATTAATAAATCTCCCCCTTAATCAAGTAATTCACATCAAAAATTTATTTGCACATGCCTA
Found at i:2845566 original size:13 final size:13
Alignment explanation
Indices: 2845548--2845586 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
2845538 ATAATCACCC
*
2845548 TGTATCGATACAG
1 TGTATCGATACAA
2845561 TGTATCGATACAA
1 TGTATCGATACAA
2845574 TGTATCGATACAA
1 TGTATCGATACAA
2845587 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2845597 original size:20 final size:20
Alignment explanation
Indices: 2845572--2845650 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
2845562 GTATCGATAC
2845572 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
2845592 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
2845617 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
2845637 CATGTATCGATACA
1 AATGTATCGATACA
2845651 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:2849519 original size:21 final size:21
Alignment explanation
Indices: 2849490--2849534 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2849480 AAGTTTTCAT
*
2849490 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
2849510 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
2849532 TTT
1 TTT
2849535 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:2851767 original size:13 final size:13
Alignment explanation
Indices: 2851749--2851774 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2851739 CAATTTTTTG
2851749 TGTATCGATACAT
1 TGTATCGATACAT
2851762 TGTATCGATACAT
1 TGTATCGATACAT
2851775 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2851839 original size:21 final size:21
Alignment explanation
Indices: 2851813--2851888 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
2851803 CTGCCAAGAA
2851813 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
* ****
2851834 ATGTATTGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
2851854 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
2851875 ATGTATCGATACAT
1 ATGTATCGATACAT
2851889 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:2851858 original size:20 final size:20
Alignment explanation
Indices: 2851833--2851906 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
2851823 ACATCTTTTT
*
2851833 CATGTATTGATACATTGCAA
1 CATGTATCGATACATTGCAA
****
2851853 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGCAA
2851874 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
2851894 CATGTATCGATAC
1 CATGTATCGATAC
2851907 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Found at i:2851870 original size:41 final size:41
Alignment explanation
Indices: 2851813--2851906 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
2851803 CTGCCAAGAA
*
2851813 ATGTATCGATACATCTTTTTCATGTATTGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
2851854 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
2851895 ATGTATCGATAC
1 ATGTATCGATAC
2851907 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:2855205 original size:15 final size:16
Alignment explanation
Indices: 2855187--2855216 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2855177 CAACATTTCC
2855187 TCTATT-AAAATTTTT
1 TCTATTAAAAATTTTT
2855202 TCTATTAAAAATTTT
1 TCTATTAAAAATTTT
2855217 GAAAGCCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (16 bp):
TCTATTAAAAATTTTT
Found at i:2861848 original size:13 final size:13
Alignment explanation
Indices: 2861830--2861854 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2861820 CATGGGGATA
2861830 AAAAATAAAAAAT
1 AAAAATAAAAAAT
2861843 AAAAATAAAAAA
1 AAAAATAAAAAA
2861855 GAAATCACAA
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:2873858 original size:28 final size:28
Alignment explanation
Indices: 2873802--2873882 Score: 85
Period size: 28 Copynumber: 2.9 Consensus size: 28
2873792 ATATTTAATT
* *
2873802 ATTTAATATATTGTATTTTTAAATA-AAA
1 ATTTAATATATTATA-TTTAAAATATAAA
2873830 ATTTAATATATTATATTTAAAATATAAA
1 ATTTAATATATTATATTTAAAATATAAA
* * *
2873858 A-ATAATAATATAATAATTAAAATAT
1 ATTTAAT-ATATTATATTTAAAATAT
2873883 TTGTACCTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
27 12 0.26
28 34 0.74
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (28 bp):
ATTTAATATATTATATTTAAAATATAAA
Found at i:2873881 original size:14 final size:14
Alignment explanation
Indices: 2873832--2873882 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
2873822 AAATAAAAAT
* * *
2873832 TTAATATATTATAT
1 TTAAAATATAATAA
2873846 TTAAAATATAA-AA
1 TTAAAATATAATAA
*
2873859 ATAATAATATAATAA
1 TTAA-AATATAATAA
2873874 TTAAAATAT
1 TTAAAATAT
2873883 TTGTACCTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
13 4 0.13
14 21 0.70
15 5 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TTAAAATATAATAA
Found at i:2874228 original size:20 final size:20
Alignment explanation
Indices: 2874205--2874287 Score: 66
Period size: 20 Copynumber: 4.2 Consensus size: 20
2874195 AAAAAATAAT
*
2874205 TAAAATATGATATAAATATA
1 TAAAATATAATATAAATATA
**
2874225 TAAACATATCAA-A-ATTTATA
1 TAAA-ATAT-AATATAAATATA
2874245 TAAAATA-AATTATAAATATA
1 TAAAATATAA-TATAAATATA
*
2874265 TCAAAAT-TTATATAAATATA
1 T-AAAATATAATATAAATATA
2874285 TAA
1 TAA
2874288 TTTTTTAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 15
0.70 0.08 0.21
Matches are distributed among these distances:
17 2 0.04
19 6 0.12
20 30 0.60
21 11 0.22
22 1 0.02
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (20 bp):
TAAAATATAATATAAATATA
Found at i:2874244 original size:18 final size:17
Alignment explanation
Indices: 2874218--2874283 Score: 59
Period size: 18 Copynumber: 3.9 Consensus size: 17
2874208 AATATGATAT
*
2874218 AAATATATAAACATATCA
1 AAATTTATAAA-ATATCA
2874236 AAATTTATATAAA-AT--
1 AAATTTATA-AAATATCA
2874251 AAA-TTATAAATATATCA
1 AAATTTATAAA-ATATCA
2874268 AAATTTATATAAATAT
1 AAATTTATA-AAATAT
2874284 ATAATTTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
13 2 0.05
14 6 0.15
15 5 0.12
17 5 0.12
18 18 0.45
19 4 0.10
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATTTATAAAATATCA
Found at i:2874266 original size:32 final size:33
Alignment explanation
Indices: 2874214--2874289 Score: 118
Period size: 32 Copynumber: 2.3 Consensus size: 33
2874204 TTAAAATATG
2874214 ATATAAATATATAAACATATCAAAATTTATATAA
1 ATATAAAT-TATAAACATATCAAAATTTATATAA
*
2874248 A-ATAAATTATAAATATATCAAAATTTATATAA
1 ATATAAATTATAAACATATCAAAATTTATATAA
2874280 ATATATAATT
1 ATATA-AATT
2874290 TTTTAATACA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
32 25 0.64
33 9 0.23
34 5 0.13
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (33 bp):
ATATAAATTATAAACATATCAAAATTTATATAA
Found at i:2874281 original size:10 final size:10
Alignment explanation
Indices: 2874207--2874286 Score: 51
Period size: 10 Copynumber: 7.9 Consensus size: 10
2874197 AAAATAATTA
2874207 AAATATGATAT
1 AAATAT-ATAT
2874218 AAATATATA-
1 AAATATATAT
*
2874227 AACATAT-CA-
1 AA-ATATATAT
*
2874236 AAATTTATAT
1 AAATATATAT
*
2874246 AAAATAAATTAT
1 -AAATATA-TAT
2874258 AAATATATCA-
1 AAATATAT-AT
*
2874268 AAATTTATAT
1 AAATATATAT
2874278 AAATATATA
1 AAATATATA
2874287 ATTTTTTAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 15
0.70 0.10 0.19
Matches are distributed among these distances:
8 3 0.06
9 7 0.13
10 23 0.43
11 18 0.33
12 3 0.06
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (10 bp):
AAATATATAT
Found at i:2874610 original size:33 final size:34
Alignment explanation
Indices: 2874536--2874611 Score: 93
Period size: 34 Copynumber: 2.2 Consensus size: 34
2874526 CCTAATATAG
*
2874536 ATATATAAAATTATAAAATTATATTAATTTTATTA
1 ATATAT-AAATTATAAAATTATATTAATATTATTA
* *
2874571 AAATATAAATTATAAATTTA-ATATAATATT-TTA
1 ATATATAAATTATAAAATTATAT-TAATATTATTA
2874604 ATATATAA
1 ATATATAA
2874612 TTTCAAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
33 12 0.33
34 19 0.53
35 5 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (34 bp):
ATATATAAATTATAAAATTATATTAATATTATTA
Found at i:2875354 original size:30 final size:33
Alignment explanation
Indices: 2875302--2875370 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 33
2875292 TTTTAAAATA
*
2875302 TTTATATATTCATATAATATTTTTA-TTTATTT
1 TTTATATATTCATATAATATTTTAATTTTATTT
2875334 TTTA-ATATT-ATATTAA-ATTTTAATTTTA-TT
1 TTTATATATTCATA-TAATATTTTAATTTTATTT
2875364 TTTATAT
1 TTTATAT
2875371 CAAATAACCT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
30 15 0.45
31 14 0.42
32 4 0.12
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (33 bp):
TTTATATATTCATATAATATTTTAATTTTATTT
Found at i:2876704 original size:16 final size:14
Alignment explanation
Indices: 2876665--2876712 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
2876655 TATTAAATAA
2876665 TTAAAAATTAAATT
1 TTAAAAATTAAATT
2876679 TT-AAAA--AAATT
1 TTAAAAATTAAATT
2876690 GTATAAAAATTAAA-T
1 -T-TAAAAATTAAATT
2876705 TTAAAAAT
1 TTAAAAAT
2876713 ATAATATAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 11
0.73 0.00 0.28
Matches are distributed among these distances:
11 5 0.17
12 1 0.03
13 12 0.41
14 7 0.24
15 1 0.03
16 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (14 bp):
TTAAAAATTAAATT
Found at i:2876720 original size:26 final size:27
Alignment explanation
Indices: 2876659--2876721 Score: 85
Period size: 26 Copynumber: 2.4 Consensus size: 27
2876649 AAAGTTTATT
2876659 AAATAAT-TAAAAATTAAATTTTAAAA
1 AAATAATATAAAAATTAAATTTTAAAA
**
2876685 AAATTGTATAAAAATTAAA-TTTAAAA
1 AAATAATATAAAAATTAAATTTTAAAA
*
2876711 ATATAATATAA
1 AAATAATATAA
2876722 GTGAGTTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 20 0.65
27 11 0.35
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (27 bp):
AAATAATATAAAAATTAAATTTTAAAA
Found at i:2877113 original size:59 final size:59
Alignment explanation
Indices: 2876979--2877094 Score: 155
Period size: 60 Copynumber: 1.9 Consensus size: 59
2876969 TTTAATTGAG
* * *
2876979 GCCCAAAATAAAATTTAGAA-AAATAATTGAGTCCAATTCAAAATGTCCAAAATTATCGAT
1 GCCCAAAATAAAATTCA-AAGCAATAATTGAGTCCAATTCAAAATGTCCAAAATCATC-AT
*
2877039 GCCCAAAATAAAATTCAAAGCAATAATTGGGTCCAATTC-AAATGTCCAAACATCAT
1 GCCCAAAATAAAATTCAAAGCAATAATTGAGTCCAATTCAAAATGTCCAAA-ATCAT
2877095 AGTCCAAATT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
59 13 0.26
60 37 0.74
ACGTcount: A:0.47, C:0.18, G:0.10, T:0.25
Consensus pattern (59 bp):
GCCCAAAATAAAATTCAAAGCAATAATTGAGTCCAATTCAAAATGTCCAAAATCATCAT
Found at i:2878456 original size:12 final size:12
Alignment explanation
Indices: 2878439--2878496 Score: 80
Period size: 12 Copynumber: 4.8 Consensus size: 12
2878429 AGAAAACTTT
*
2878439 TATACATACATA
1 TATACATATATA
2878451 TATACATATATA
1 TATACATATATA
*
2878463 TATATATATATA
1 TATACATATATA
*
2878475 TATATATATATA
1 TATACATATATA
*
2878487 TATATATATA
1 TATACATATA
2878497 GAGAGAGAGA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 44 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (12 bp):
TATACATATATA
Found at i:2878461 original size:2 final size:2
Alignment explanation
Indices: 2878448--2878496 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
2878438 TTATACATAC
*
2878448 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2878490 AT AT AT A
1 AT AT AT A
2878497 GAGAGAGAGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2879756 original size:12 final size:12
Alignment explanation
Indices: 2879735--2879761 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2879725 AATATTTATT
2879735 TTAAAATTTTTA
1 TTAAAATTTTTA
2879747 TTAAAATTTTTA
1 TTAAAATTTTTA
2879759 TTA
1 TTA
2879762 TTTTTAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTAAAATTTTTA
Found at i:2880235 original size:28 final size:28
Alignment explanation
Indices: 2880204--2880257 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
2880194 ATTTAAAAAA
2880204 GATAAATAT-AAAATAATAAATATAATAT
1 GATAAATATAAAAATAATAAAT-TAATAT
* * *
2880232 GATATATTTAAAAATAATTAATTAAT
1 GATAAATATAAAAATAATAAATTAAT
2880258 TATTAACACG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 11 0.50
29 11 0.50
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (28 bp):
GATAAATATAAAAATAATAAATTAATAT
Found at i:2880307 original size:18 final size:19
Alignment explanation
Indices: 2880281--2880320 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
2880271 AAAATTTTTA
2880281 TTAAAAATTT-TAATATAT
1 TTAAAAATTTATAATATAT
* *
2880299 TTAATAATTTATATTATAT
1 TTAAAAATTTATAATATAT
2880318 TTA
1 TTA
2880321 TGTAAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTAAAAATTTATAATATAT
Found at i:2882863 original size:13 final size:13
Alignment explanation
Indices: 2882847--2882882 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 13
2882837 ATTAATATAA
2882847 TTTAAATTTTATT
1 TTTAAATTTTATT
2882860 TTTAAAAATTTTATT
1 TTT--AAATTTTATT
2882875 TTTAAATT
1 TTTAAATT
2882883 AATATTATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 8 0.38
15 13 0.62
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTAAATTTTATT
Found at i:2882870 original size:15 final size:15
Alignment explanation
Indices: 2882850--2882880 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2882840 AATATAATTT
2882850 AAATTTTATTTTTAA
1 AAATTTTATTTTTAA
2882865 AAATTTTATTTTTAA
1 AAATTTTATTTTTAA
2882880 A
1 A
2882881 TTAATATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
AAATTTTATTTTTAA
Found at i:2882995 original size:14 final size:14
Alignment explanation
Indices: 2882976--2883012 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2882966 TACATGTTTT
2882976 ATTTATATTTAATA
1 ATTTATATTTAATA
2882990 ATTTATATTTAATA
1 ATTTATATTTAATA
*
2883004 ATATATATT
1 ATTTATATT
2883013 AAAATATATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTATATTTAATA
Found at i:2883021 original size:14 final size:13
Alignment explanation
Indices: 2882979--2883021 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
2882969 ATGTTTTATT
*
2882979 TATATTTAATAATT
1 TATATTTAA-AATA
2882993 TATATTTAATAATA
1 TATATTTAA-AATA
2883007 TATA-TTAAAATA
1 TATATTTAAAATA
2883019 TAT
1 TAT
2883022 GATATTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
12 7 0.25
13 4 0.14
14 17 0.61
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TATATTTAAAATA
Found at i:2888170 original size:15 final size:17
Alignment explanation
Indices: 2888150--2888185 Score: 58
Period size: 15 Copynumber: 2.2 Consensus size: 17
2888140 TTAAATTTAA
2888150 ATATAAATAT-TA-AAT
1 ATATAAATATATATAAT
2888165 ATATAAATATATATAAT
1 ATATAAATATATATAAT
2888182 ATAT
1 ATAT
2888186 TTATTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.53
16 2 0.11
17 7 0.37
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATAAATATATATAAT
Found at i:2888227 original size:17 final size:17
Alignment explanation
Indices: 2888185--2888228 Score: 72
Period size: 18 Copynumber: 2.6 Consensus size: 17
2888175 ATATAATATA
2888185 TTTATT-TTTAAAAAAT
1 TTTATTATTTAAAAAAT
2888201 TTTATATATTTAAAAAAT
1 TTTAT-TATTTAAAAAAT
2888219 TTTATTATTT
1 TTTATTATTT
2888229 TTGTCAGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.19
17 6 0.23
18 15 0.58
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTATTATTTAAAAAAT
Found at i:2888839 original size:18 final size:18
Alignment explanation
Indices: 2888808--2888852 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
2888798 ATATCAAATA
2888808 TTAAAATA--TAAAATTT
1 TTAAAATATTTAAAATTT
2888824 TTAAAATATTTAAAATTT
1 TTAAAATATTTAAAATTT
*
2888842 TAAAAAATATT
1 T-TAAAATATT
2888853 ATTAGACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 8 0.32
18 9 0.36
19 8 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAAAATATTTAAAATTT
Found at i:2888844 original size:17 final size:16
Alignment explanation
Indices: 2888793--2888846 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
2888783 TTTTTAAATA
* *
2888793 AAAATATATCAAATATT
1 AAAATAT-TAAAATTTT
2888810 AAAATA-TAAAATTTTT
1 AAAATATTAAAA-TTTT
2888826 AAAATATTTAAAATTTT
1 AAAATA-TTAAAATTTT
2888843 AAAA
1 AAAA
2888847 AATATTATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 4 0.12
16 9 0.28
17 14 0.44
18 5 0.16
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (16 bp):
AAAATATTAAAATTTT
Found at i:2889294 original size:28 final size:28
Alignment explanation
Indices: 2889255--2889310 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
2889245 AATTCTTTAA
*
2889255 ATTATTTTTAAATAAAATTTTATATTTT
1 ATTATATTTAAATAAAATTTTATATTTT
* *
2889283 ATTATATTTAAATAAATTTTTATTTTTT
1 ATTATATTTAAATAAAATTTTATATTTT
2889311 GATTGGGATC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (28 bp):
ATTATATTTAAATAAAATTTTATATTTT
Found at i:2889407 original size:29 final size:28
Alignment explanation
Indices: 2889359--2889417 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
2889349 TTAATTTATT
*
2889359 TTAAAATTTATTTATATATAAATTAAAAG
1 TTAAAATTTATTCATATAT-AATTAAAAG
*
2889388 TTAAAATTTATTCA-AGTATAATTAAGAG
1 TTAAAATTTATTCATA-TATAATTAAAAG
2889416 TT
1 TT
2889418 TATTTGAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 11 0.41
29 16 0.59
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (28 bp):
TTAAAATTTATTCATATATAATTAAAAG
Found at i:2889453 original size:31 final size:29
Alignment explanation
Indices: 2889416--2889489 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
2889406 TAATTAAGAG
2889416 TTTATTTGAGTATAAATGAAAAAGT-TAAAAA
1 TTTATTTGAGTATAAA--AAAAA-TATAAAAA
* *
2889447 TTTATTTGAATGTAAAAAAAATATAAAAA
1 TTTATTTGAGTATAAAAAAAATATAAAAA
2889476 TTTATTT-AG-ATAAA
1 TTTATTTGAGTATAAA
2889490 GTTATAAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
27 4 0.11
28 2 0.05
29 18 0.47
31 14 0.37
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (29 bp):
TTTATTTGAGTATAAAAAAAATATAAAAA
Found at i:2889703 original size:21 final size:22
Alignment explanation
Indices: 2889657--2889708 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
2889647 GTGAATATTA
* *
2889657 AAATTTTAATTTCAAGTAAGTT
1 AAATTTTAAATTCAAGTAAATT
*
2889679 -AATTTTAAATT-AATTAAATT
1 AAATTTTAAATTCAAGTAAATT
2889699 AAATTTTAAA
1 AAATTTTAAA
2889709 ATTTTTTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 7 0.27
21 19 0.73
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (22 bp):
AAATTTTAAATTCAAGTAAATT
Found at i:2892277 original size:42 final size:42
Alignment explanation
Indices: 2892218--2892300 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
2892208 TTAATTTGAA
2892218 CTTGCGTGGCTAAATTCTTTATCTAGAATTCGATTGTTTTTG
1 CTTGCGTGGCTAAATTCTTTATCTAGAATTCGATTGTTTTTG
*
2892260 CTTGCGTGGCTAAATTCTTTATCTAGAATTCGATTTTTTTT
1 CTTGCGTGGCTAAATTCTTTATCTAGAATTCGATTGTTTTT
2892301 TTACCAATAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.19, C:0.14, G:0.17, T:0.49
Consensus pattern (42 bp):
CTTGCGTGGCTAAATTCTTTATCTAGAATTCGATTGTTTTTG
Found at i:2892823 original size:20 final size:23
Alignment explanation
Indices: 2892781--2892826 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 23
2892771 TTTAATACAT
*
2892781 TATTATTATTATTATAAATAATA
1 TATTATTATAATTATAAATAATA
2892804 TATTATT-TAATT-TAAA-AATA
1 TATTATTATAATTATAAATAATA
2892824 TAT
1 TAT
2892827 CCTAAAGACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 7 0.32
21 4 0.18
22 4 0.18
23 7 0.32
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TATTATTATAATTATAAATAATA
Found at i:2893586 original size:10 final size:10
Alignment explanation
Indices: 2893571--2893633 Score: 56
Period size: 10 Copynumber: 6.2 Consensus size: 10
2893561 CCATTATAGC
2893571 ATAAATATAT
1 ATAAATATAT
2893581 ATAAATATAT
1 ATAAATATAT
*
2893591 -TAAAATTTAT
1 AT-AAATATAT
**
2893601 ATATAACGTAT
1 ATA-AATATAT
*
2893612 CTAAATATAT
1 ATAAATATAT
*
2893622 ATATATATAT
1 ATAAATATAT
2893632 AT
1 AT
2893634 GTATTTATAA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
9 1 0.02
10 33 0.79
11 8 0.19
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (10 bp):
ATAAATATAT
Found at i:2908562 original size:12 final size:12
Alignment explanation
Indices: 2908545--2908573 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
2908535 ATAATTATTA
2908545 TTAAAAATAAAT
1 TTAAAAATAAAT
2908557 TT-AAAATAAAT
1 TTAAAAATAAAT
2908568 TTAAAA
1 TTAAAA
2908574 TTTTAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
TTAAAAATAAAT
Found at i:2908564 original size:11 final size:11
Alignment explanation
Indices: 2908548--2908574 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2908538 ATTATTATTA
2908548 AAAATAAATTT
1 AAAATAAATTT
2908559 AAAATAAATTT
1 AAAATAAATTT
2908570 AAAAT
1 AAAAT
2908575 TTTAAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AAAATAAATTT
Found at i:2908901 original size:17 final size:17
Alignment explanation
Indices: 2908872--2908907 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
2908862 ATTTTTTAAA
2908872 AAATAATTTATAAATTT
1 AAATAATTTATAAATTT
2908889 AAAT-ATTTAATAAATTT
1 AAATAATTT-ATAAATTT
2908906 AA
1 AA
2908908 CATCTTAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATAATTTATAAATTT
Found at i:2908954 original size:25 final size:25
Alignment explanation
Indices: 2908919--2909018 Score: 84
Period size: 25 Copynumber: 4.1 Consensus size: 25
2908909 ATCTTAACAT
*
2908919 ATAATACTATTTAATTTAAATTTAA
1 ATAATAATATTTAATTTAAATTTAA
* * *
2908944 ATACTAATATTTAAATT-AATATAA
1 ATAATAATATTTAATTTAAATTTAA
* *
2908968 ATAATAA-A--TAATATAAATTT-T
1 ATAATAATATTTAATTTAAATTTAA
*
2908989 ATAATAATTATATGAATTTAAATTTAA
1 ATAATAA-TAT-TTAATTTAAATTTAA
2909016 ATA
1 ATA
2909019 TTATAAAAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
21 11 0.20
22 4 0.07
23 2 0.04
24 12 0.21
25 14 0.25
26 10 0.18
27 3 0.05
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (25 bp):
ATAATAATATTTAATTTAAATTTAA
Found at i:2912557 original size:2 final size:2
Alignment explanation
Indices: 2912550--2912581 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2912540 TCCTTTTATT
2912550 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2912582 GTTGAATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2913368 original size:14 final size:15
Alignment explanation
Indices: 2913340--2913369 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2913330 TGCAATACAA
2913340 ATATAAAATATAAAT
1 ATATAAAATATAAAT
2913355 ATATAAAA-ATAAAT
1 ATATAAAATATAAAT
2913369 A
1 A
2913370 AATATTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
ATATAAAATATAAAT
Found at i:2914722 original size:17 final size:17
Alignment explanation
Indices: 2914686--2914718 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2914676 TAACCGTATC
2914686 TATAATGTAAATAATAA
1 TATAATGTAAATAATAA
*
2914703 TATAATTTAAA-AATAA
1 TATAATGTAAATAATAA
2914719 ATATGTACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (17 bp):
TATAATGTAAATAATAA
Found at i:2914745 original size:11 final size:11
Alignment explanation
Indices: 2914729--2914789 Score: 52
Period size: 11 Copynumber: 5.1 Consensus size: 11
2914719 ATATGTACTT
2914729 AAATTAATTAA
1 AAATTAATTAA
2914740 AAATTAATT-A
1 AAATTAATTAA
*
2914750 AATTATAATGTAAA
1 AAAT-TAAT-T-AA
2914764 AAAGTTAAATTTAA
1 AAA-TT-AA-TTAA
2914778 AAATTAATTAA
1 AAATTAATTAA
2914789 A
1 A
2914790 TTATTAATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
10 4 0.10
11 18 0.44
12 3 0.07
13 2 0.05
14 9 0.22
15 4 0.10
16 1 0.02
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (11 bp):
AAATTAATTAA
Found at i:2914764 original size:22 final size:18
Alignment explanation
Indices: 2914727--2914793 Score: 57
Period size: 20 Copynumber: 3.5 Consensus size: 18
2914717 AAATATGTAC
2914727 TTAAATTAATTAAAAATTAA
1 TTAAATT-A-TAAAAATTAA
*
2914747 TTAAATTATAATGTAAA-AAA
1 TTAAATTATAA---AAATTAA
2914767 GTTAAATT-TAAAAATTAA
1 -TTAAATTATAAAAATTAA
2914785 TTAAATTAT
1 TTAAATTAT
2914794 TAATATCTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
17 10 0.26
18 6 0.15
19 1 0.03
20 12 0.31
21 10 0.26
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
TTAAATTATAAAAATTAA
Found at i:2914918 original size:12 final size:13
Alignment explanation
Indices: 2914890--2914946 Score: 53
Period size: 13 Copynumber: 4.3 Consensus size: 13
2914880 ATCTATAACA
*
2914890 TAAATAAATTAAT
1 TAAAAAAATTAAT
2914903 TAAAAAAATT-AT
1 TAAAAAAATTAAT
*
2914915 TAAAAATTAATTAAA
1 TAAAAA--AATTAAT
* *
2914930 TATAAAAATTATT
1 TAAAAAAATTAAT
2914943 TAAA
1 TAAA
2914947 TTTATATAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
12 8 0.23
13 17 0.49
14 4 0.11
15 6 0.17
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
TAAAAAAATTAAT
Found at i:2914918 original size:82 final size:81
Alignment explanation
Indices: 2914770--2914922 Score: 209
Period size: 82 Copynumber: 1.9 Consensus size: 81
2914760 TAAAAAAGTT
* * * * **
2914770 AAATTTAAAAATTAATTAAATTATTAATATCTATAACGCAAACAAATTGATTAAAATTTTACTTA
1 AAATTTAAAAATTAATTAAATCATAAATATCTATAACACAAACAAATTAATTAAAAAATTACTTA
2914835 AAAATTTTTTAGTTAA
66 AAAATTTTTTAGTTAA
* *
2914851 AAATATTAAAAATTAATTAAATCATAAATATCTATAACATAAATAAATTAATTAAAAAAATTA-T
1 AAAT-TTAAAAATTAATTAAATCATAAATATCTATAACACAAACAAATTAATT-AAAAAATTACT
2914915 TAAAAATT
64 TAAAAATT
2914923 AATTAAATAT
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
81 4 0.06
82 51 0.82
83 7 0.11
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (81 bp):
AAATTTAAAAATTAATTAAATCATAAATATCTATAACACAAACAAATTAATTAAAAAATTACTTA
AAAATTTTTTAGTTAA
Found at i:2914937 original size:17 final size:17
Alignment explanation
Indices: 2914915--2914947 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2914905 AAAAAATTAT
2914915 TAAAAATTAATTAAATA
1 TAAAAATTAATTAAATA
*
2914932 TAAAAATTATTTAAAT
1 TAAAAATTAATTAAAT
2914948 TTATATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAAAATTAATTAAATA
Found at i:2914939 original size:27 final size:27
Alignment explanation
Indices: 2914848--2914942 Score: 102
Period size: 27 Copynumber: 3.4 Consensus size: 27
2914838 ATTTTTTAGT
2914848 TAAAAA-TATTAAAAATTAATTAAATCA
1 TAAAAATTATTAAAAATTAATTAAAT-A
* * * *
2914875 TAAATATCTATAACATAAATAAATTAATTA
1 TAAAAAT-TATTA-A-AAATTAATTAAATA
*
2914905 AAAAAATTATTAAAAATTAATTAAATA
1 TAAAAATTATTAAAAATTAATTAAATA
2914932 TAAAAATTATT
1 TAAAAATTATT
2914943 TAAATTTATA
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
27 27 0.50
28 1 0.02
29 8 0.15
30 7 0.13
31 11 0.20
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (27 bp):
TAAAAATTATTAAAAATTAATTAAATA
Found at i:2915758 original size:13 final size:14
Alignment explanation
Indices: 2915727--2915757 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2915717 AAAAAAGATT
2915727 AAAATCCGTTAGAA
1 AAAATCCGTTAGAA
*
2915741 AAAATCCTTTAGAA
1 AAAATCCGTTAGAA
2915755 AAA
1 AAA
2915758 TATGTGCCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.13, G:0.10, T:0.23
Consensus pattern (14 bp):
AAAATCCGTTAGAA
Found at i:2916108 original size:24 final size:24
Alignment explanation
Indices: 2916076--2916121 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
2916066 TTGTTGAGAA
2916076 ATTTTTTATACCAAGTTAAACTCT
1 ATTTTTTATACCAAGTTAAACTCT
*
2916100 ATTTTTTATATCAAGTTAAACT
1 ATTTTTTATACCAAGTTAAACT
2916122 TTGTCATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.35, C:0.13, G:0.04, T:0.48
Consensus pattern (24 bp):
ATTTTTTATACCAAGTTAAACTCT
Found at i:2916665 original size:19 final size:19
Alignment explanation
Indices: 2916633--2916669 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2916623 TATTTTTATT
2916633 TAAATTTAATTATAAATTA
1 TAAATTTAATTATAAATTA
2916652 TAAATATTAA-TATAAATT
1 TAAAT-TTAATTATAAATT
2916670 TTTTTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TAAATTTAATTATAAATTA
Found at i:2916762 original size:27 final size:28
Alignment explanation
Indices: 2916732--2916790 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
2916722 TTAATTAAAA
*
2916732 AAATGAATAA-ATAATT-TAAATTTTTTT
1 AAAT-AATAATATAATTATAAATATTTTT
* *
2916759 AAATTATAATTTAATTATAAATATTTTT
1 AAATAATAATATAATTATAAATATTTTT
2916787 AAAT
1 AAAT
2916791 TCAAGTAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 4 0.15
27 9 0.33
28 14 0.52
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (28 bp):
AAATAATAATATAATTATAAATATTTTT
Found at i:2917171 original size:20 final size:20
Alignment explanation
Indices: 2917113--2917172 Score: 52
Period size: 20 Copynumber: 3.0 Consensus size: 20
2917103 TGTAAAAATT
* *
2917113 TATATAATATTTTTTATTATAA
1 TATATAATA-TTTTAAATA-AA
* *
2917135 TA-ATAA-AATTTATATAAA
1 TATATAATATTTTAAATAAA
2917153 TATATAATATTTTAAATAAA
1 TATATAATATTTTAAATAAA
2917173 ATTATATCTT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
18 4 0.13
19 9 0.30
20 11 0.37
21 4 0.13
22 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TATATAATATTTTAAATAAA
Found at i:2918089 original size:30 final size:29
Alignment explanation
Indices: 2918055--2918122 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
2918045 CATATTATAT
*
2918055 ATTTTT-TATTTTAAAAATATTTTTAATTTA
1 ATTTTTATAATTT-AAAATATTTTTAA-TTA
* *
2918085 ATTTTTAATAATTTAATATATTTTTGATTA
1 ATTTTT-ATAATTTAAAATATTTTTAATTA
2918115 ATTTTTAT
1 ATTTTTAT
2918123 TAATATATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
29 2 0.06
30 15 0.45
31 11 0.33
32 5 0.15
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.63
Consensus pattern (29 bp):
ATTTTTATAATTTAAAATATTTTTAATTA
Found at i:2923177 original size:22 final size:21
Alignment explanation
Indices: 2923152--2923218 Score: 55
Period size: 21 Copynumber: 3.0 Consensus size: 21
2923142 GGTTAAATTT
2923152 AATAATATTAAATATGATTAAA
1 AATAATATTAAATAT-ATTAAA
* *
2923174 AATAAT-TAAAATATAATTTAA
1 AATAATATTAAATAT-ATTAAA
* *
2923195 TATGAAAATATAAATATATTAAA
1 AAT-AATAT-TAAATATATTAAA
2923218 A
1 A
2923219 TTTATATAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
21 14 0.41
22 8 0.24
23 6 0.18
24 6 0.18
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (21 bp):
AATAATATTAAATATATTAAA
Found at i:2923225 original size:14 final size:14
Alignment explanation
Indices: 2923208--2923258 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
2923198 GAAAATATAA
2923208 ATATATTAAAATTT
1 ATATATTAAAATTT
2923222 ATATAATATAAATTATTT
1 ATAT-AT-TAAA--ATTT
*
2923240 TTATATTAAAATTT
1 ATATATTAAAATTT
2923254 ATATA
1 ATATA
2923259 AATATAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
14 12 0.39
15 2 0.06
16 8 0.26
17 2 0.06
18 7 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATATATTAAAATTT
Found at i:2923233 original size:16 final size:16
Alignment explanation
Indices: 2923192--2923281 Score: 62
Period size: 16 Copynumber: 5.5 Consensus size: 16
2923182 AAATATAATT
* *
2923192 TAATATGAAAATATAAA
1 TAATAT-AAAATTTATA
2923209 T-ATATTAAAATTTATA
1 TAATA-TAAAATTTATA
*
2923225 TAATATAAATTATTTTTA
1 TAATATAAA--ATTTATA
2923243 T-AT-TAAAATTTATA
1 TAATATAAAATTTATA
*
2923257 TAAATATAAAATATTTTA
1 T-AATATAAAAT-TTATA
2923275 -AATATAA
1 TAATATAA
2923282 TTATAATAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
14 7 0.12
16 29 0.48
17 13 0.22
18 11 0.18
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (16 bp):
TAATATAAAATTTATA
Found at i:2923248 original size:32 final size:33
Alignment explanation
Indices: 2923209--2923273 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
2923199 AAAATATAAA
*
2923209 TATATTAAAATTTATAT-AATATAAATTATTTT
1 TATATTAAAATTTATATAAATATAAAATATTTT
2923241 TATATTAAAATTTATATAAATATAAAATATTTT
1 TATATTAAAATTTATATAAATATAAAATATTTT
2923274 AAATATAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 17 0.55
33 14 0.45
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (33 bp):
TATATTAAAATTTATATAAATATAAAATATTTT
Found at i:2923558 original size:2 final size:2
Alignment explanation
Indices: 2923551--2923589 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2923541 CAAATATTGC
2923551 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2923590 CATAACAGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2923908 original size:6 final size:6
Alignment explanation
Indices: 2923899--2923942 Score: 70
Period size: 6 Copynumber: 7.3 Consensus size: 6
2923889 CTTCCATTCC
**
2923899 TCCCAA TCCCAA TCCCAA TCCCAA TCCCAA TCCCGT TCCCAA TC
1 TCCCAA TCCCAA TCCCAA TCCCAA TCCCAA TCCCAA TCCCAA TC
2923943 TTATTAACAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.27, C:0.50, G:0.02, T:0.20
Consensus pattern (6 bp):
TCCCAA
Found at i:2924268 original size:2 final size:2
Alignment explanation
Indices: 2924261--2924288 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2924251 CAATTTTTAC
2924261 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2924289 ATGTCTGTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2924537 original size:2 final size:2
Alignment explanation
Indices: 2924525--2924598 Score: 60
Period size: 2 Copynumber: 37.5 Consensus size: 2
2924515 AGCTTGCTTT
* * * * *
2924525 TA TA TA CA TA TA TA T- TA TA CA TA TA TA TA TA TA TC TA CA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
2924566 CA AA TA TA TA TA TA TA TA TA TG TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2924599 CCCTTCTCAC
Statistics
Matches: 58, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
1 1 0.02
2 57 0.98
ACGTcount: A:0.47, C:0.09, G:0.01, T:0.42
Consensus pattern (2 bp):
TA
Found at i:2924545 original size:13 final size:14
Alignment explanation
Indices: 2924525--2924557 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
2924515 AGCTTGCTTT
2924525 TATATACATATATA
1 TATATACATATATA
2924539 T-TATACATATATA
1 TATATACATATATA
2924552 TATATA
1 TATATA
2924558 TCTACACACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATACATATATA
Found at i:2927095 original size:2 final size:2
Alignment explanation
Indices: 2927088--2927122 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2927078 CGGGAAAAGA
2927088 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2927123 ACGGCTTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2927708 original size:6 final size:6
Alignment explanation
Indices: 2927675--2927706 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
2927665 AGAACACTGC
*
2927675 TCCTGA TCCTGA TCCTGA TCCTGA TCTTGA TC
1 TCCTGA TCCTGA TCCTGA TCCTGA TCCTGA TC
2927707 TTCATCATCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.31, G:0.16, T:0.38
Consensus pattern (6 bp):
TCCTGA
Found at i:2927951 original size:3 final size:3
Alignment explanation
Indices: 2927945--2927975 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
2927935 TTGTCGTTGG
*
2927945 GGA GGA GGA GGA GGA GGA GGA GGA AGA GGA G
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA G
2927976 TGTTTGGAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:2928327 original size:15 final size:14
Alignment explanation
Indices: 2928309--2928346 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
2928299 TTTAATAAAA
2928309 AATATTATAATTTTT
1 AATATT-TAATTTTT
*
2928324 AATATTTAAATTTT
1 AATATTTAATTTTT
2928338 -ATATTTAAT
1 AATATTTAAT
2928347 AAATATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 8 0.38
14 7 0.33
15 6 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
AATATTTAATTTTT
Found at i:2929502 original size:32 final size:35
Alignment explanation
Indices: 2929438--2929509 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 35
2929428 TATTAAAAAT
2929438 TTTATAAAAATTATATTTAGATATATTATATTATA
1 TTTATAAAAATTATATTTAGATATATTATATTATA
* * *
2929473 TTTAT-AAAATTATTTTTATATTTATTAT-TATATA
1 TTTATAAAAATTATATTTAGATATATTATAT-TATA
2929507 TTT
1 TTT
2929510 TATATCACTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 1 0.03
34 27 0.82
35 5 0.15
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (35 bp):
TTTATAAAAATTATATTTAGATATATTATATTATA
Found at i:2930191 original size:15 final size:15
Alignment explanation
Indices: 2930171--2930226 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
2930161 GATATTTAAT
2930171 TTAAATTTAAATTTA
1 TTAAATTTAAATTTA
*
2930186 TTAAATATT-AATTAA
1 TTAAAT-TTAAATTTA
*
2930201 TT--ATATAAATTTA
1 TTAAATTTAAATTTA
2930214 TTAAA-TTAAATTT
1 TTAAATTTAAATTT
2930227 TAATTTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
12 1 0.03
13 9 0.27
14 7 0.21
15 14 0.42
16 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTAAATTTAAATTTA
Found at i:2930916 original size:12 final size:12
Alignment explanation
Indices: 2930899--2930950 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
2930889 ATTTTACATT
*
2930899 TTAAATTTAATA
1 TTAAATTTATTA
*
2930911 TTAAATTTTTTA
1 TTAAATTTATTA
*
2930923 TTTAATTTATTAA
1 TTAAATTTATT-A
2930936 TTTAAATTTATTA
1 -TTAAATTTATTA
2930949 TT
1 TT
2930951 TATAATATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
12 21 0.64
13 2 0.06
14 10 0.30
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTAAATTTATTA
Found at i:2930925 original size:26 final size:27
Alignment explanation
Indices: 2930887--2930964 Score: 72
Period size: 26 Copynumber: 2.9 Consensus size: 27
2930877 TTATATAAAA
**
2930887 AAATTTTACATTTTAAATTTAAT-A-TT
1 AAATTTTTTATTTT-AATTTAATAATTT
*
2930913 AAATTTTTTA-TTTAATTTATTAATTT
1 AAATTTTTTATTTTAATTTAATAATTT
* *
2930939 AAATTTATTATTTATAATATAATAAT
1 AAATTTTTTATTT-TAATTTAATAAT
2930965 ATATTTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
24 7 0.17
25 4 0.10
26 19 0.45
27 2 0.05
28 10 0.24
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (27 bp):
AAATTTTTTATTTTAATTTAATAATTT
Found at i:2930945 original size:14 final size:14
Alignment explanation
Indices: 2930905--2930952 Score: 57
Period size: 13 Copynumber: 3.6 Consensus size: 14
2930895 CATTTTAAAT
2930905 TTAATATTAAATTT-
1 TTAAT-TTAAATTTA
*
2930919 TTTATTT-AATTTA
1 TTAATTTAAATTTA
2930932 TTAATTTAAATTTA
1 TTAATTTAAATTTA
2930946 TT-ATTTA
1 TTAATTTA
2930953 TAATATAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
12 5 0.17
13 13 0.43
14 12 0.40
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTAATTTAAATTTA
Found at i:2931011 original size:33 final size:33
Alignment explanation
Indices: 2930935--2931003 Score: 79
Period size: 33 Copynumber: 2.1 Consensus size: 33
2930925 TAATTTATTA
* *
2930935 ATTT-AAATTTATTATTTATAATATAATAATAT
1 ATTTAAAAATTATTATTTATAATATAATAACAT
* *
2930967 ATTTAAAAATTATT-TTTATATTAATATTAACAT
1 ATTTAAAAATTATTATTTATAAT-ATAATAACAT
2931000 ATTT
1 ATTT
2931004 TATAATTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
32 11 0.35
33 20 0.65
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (33 bp):
ATTTAAAAATTATTATTTATAATATAATAACAT
Found at i:2934039 original size:3 final size:3
Alignment explanation
Indices: 2934021--2934058 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
2934011 AAATCTACAA
2934021 AAT ATAT AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2934059 AAGTATGATT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2935326 original size:16 final size:14
Alignment explanation
Indices: 2935299--2935356 Score: 59
Period size: 15 Copynumber: 4.1 Consensus size: 14
2935289 TTAATAAACG
2935299 TATAATATATTAAA
1 TATAATATATTAAA
2935313 TATAATTATAATTAAA
1 TATAA-TAT-ATTAAA
2935329 -A-AATA-ATATAAA
1 TATAATATAT-TAAA
2935341 TATAATATATATAAA
1 TATAATATAT-TAAA
2935356 T
1 T
2935357 TATTAAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
11 2 0.05
12 4 0.11
13 3 0.08
14 11 0.29
15 12 0.32
16 6 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TATAATATATTAAA
Found at i:2936273 original size:2 final size:2
Alignment explanation
Indices: 2936266--2936299 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2936256 TTTGTGGCTA
2936266 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2936300 AGTATATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2937558 original size:17 final size:17
Alignment explanation
Indices: 2937538--2937590 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
2937528 AATTTAAAAA
2937538 TATTTTTATATTTATAT
1 TATTTTTATATTTATAT
*
2937555 TATTTTT-TATAATATAT
1 TATTTTTATAT-TTATAT
*
2937572 TATTTTTA-ATTTTTAT
1 TATTTTTATATTTATAT
2937588 TAT
1 TAT
2937591 ATTTGCTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 10 0.32
17 21 0.68
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TATTTTTATATTTATAT
Found at i:2938005 original size:21 final size:20
Alignment explanation
Indices: 2937948--2938010 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
2937938 TTATATTAAC
* *
2937948 AAAATATAACTAATAAATAT
1 AAAAAATAAATAATAAATAT
*
2937968 GAAAAATAAATAATAAATAT
1 AAAAAATAAATAATAAATAT
* *
2937988 AAAAAATATATATTTAAATAT
1 AAAAAATAAATA-ATAAATAT
2938009 AA
1 AA
2938011 TTAATATAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
20 27 0.75
21 9 0.25
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (20 bp):
AAAAAATAAATAATAAATAT
Found at i:2939039 original size:12 final size:12
Alignment explanation
Indices: 2939022--2939081 Score: 51
Period size: 12 Copynumber: 5.4 Consensus size: 12
2939012 TAATTTAAAT
2939022 AAATAAATTATA
1 AAATAAATTATA
2939034 AAATAAA-TAT-
1 AAATAAATTATA
*
2939044 AAAT-TA-TAT-
1 AAATAAATTATA
2939053 AAA-AAATTATGA
1 AAATAAATTAT-A
*
2939065 AAATAGATTATA
1 AAATAAATTATA
2939077 AAATA
1 AAATA
2939082 TATATATATA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
9 8 0.20
10 7 0.17
11 3 0.08
12 16 0.40
13 6 0.15
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (12 bp):
AAATAAATTATA
Found at i:2939055 original size:31 final size:31
Alignment explanation
Indices: 2939004--2939085 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
2938994 ATAAATCTTT
* * *
2939004 AATAAATTTAATTTAAATAAATAAATTAT-AA
1 AATAAATATAAATTATATAAA-AAATTATGAA
2939035 AATAAATATAAATTATATAAAAAATTATGAA
1 AATAAATATAAATTATATAAAAAATTATGAA
* *
2939066 AATAGATTATAAAATATATA
1 AATA-AATATAAATTATATA
2939086 TATATATATA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
30 7 0.16
31 24 0.55
32 13 0.30
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (31 bp):
AATAAATATAAATTATATAAAAAATTATGAA
Found at i:2939104 original size:2 final size:2
Alignment explanation
Indices: 2939099--2939140 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2939089 ATATATATAT
2939099 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2939141 CTGTGAATGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2939635 original size:20 final size:21
Alignment explanation
Indices: 2939610--2939648 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2939600 AATATTTTAA
*
2939610 ATTTTTAATA-AAAAAATTAT
1 ATTTTTAAAATAAAAAATTAT
2939630 ATTTTTAAAATAAAAAATT
1 ATTTTTAAAATAAAAAATT
2939649 TATAAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTTTTAAAATAAAAAATTAT
Found at i:2939660 original size:23 final size:22
Alignment explanation
Indices: 2939620--2939684 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 22
2939610 ATTTTTAATA
* *
2939620 AAAAAATTAT-ATTTTTAAAAT
1 AAAAAATTATAAATATTAAAAT
2939641 AAAAAATTTATAAATATTAAAAT
1 AAAAAA-TTATAAATATTAAAAT
**
2939664 TTAAAATTAGTAAATATTAAA
1 AAAAAATTA-TAAATATTAAA
2939685 TAATTATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.16
22 7 0.19
23 24 0.65
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
AAAAAATTATAAATATTAAAAT
Found at i:2939701 original size:13 final size:13
Alignment explanation
Indices: 2939681--2939731 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
2939671 TAGTAAATAT
2939681 TAAA-TAATTATA
1 TAAATTAATTATA
2939693 TAAATTAATTAAATA
1 TAAATTAATT--ATA
* *
2939708 TTAATAAATTATA
1 TAAATTAATTATA
2939721 TAAATTAATTA
1 TAAATTAATTA
2939732 AATTAAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
12 4 0.12
13 17 0.53
15 11 0.34
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TAAATTAATTATA
Found at i:2939705 original size:28 final size:27
Alignment explanation
Indices: 2939651--2939734 Score: 113
Period size: 28 Copynumber: 3.2 Consensus size: 27
2939641 AAAAAATTTA
*
2939651 TAAATATTAA-AATT-TA-AAATT-AG
1 TAAATATTAATAATTATATAAATTAAT
2939674 TAAATATTAAATAATTATATAAATTAAT
1 TAAATATT-AATAATTATATAAATTAAT
2939702 TAAATATTAATAAATTATATAAATTAAT
1 TAAATATTAAT-AATTATATAAATTAAT
2939730 TAAAT
1 TAAAT
2939735 TAAATTTTAA
Statistics
Matches: 54, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
23 8 0.15
24 2 0.04
25 4 0.07
26 2 0.04
27 8 0.15
28 30 0.56
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (27 bp):
TAAATATTAATAATTATATAAATTAAT
Found at i:2939724 original size:19 final size:19
Alignment explanation
Indices: 2939665--2939725 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
2939655 TATTAAAATT
*
2939665 TAAA-ATTAGTAAA-TAT-
1 TAAATATTAATAAATTATA
2939681 TAAATAATTATATAAATTA-A
1 TAAAT-ATTA-ATAAATTATA
2939701 TTAAATATTAATAAATTATA
1 -TAAATATTAATAAATTATA
2939721 TAAAT
1 TAAAT
2939726 TAATTAAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
16 4 0.11
18 4 0.11
19 17 0.46
20 7 0.19
21 5 0.14
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
TAAATATTAATAAATTATA
Found at i:2940892 original size:13 final size:12
Alignment explanation
Indices: 2940858--2940955 Score: 69
Period size: 13 Copynumber: 8.2 Consensus size: 12
2940848 TAATTAAAAA
*
2940858 TATAATAAATAT
1 TATAATAATTAT
* *
2940870 TATCACAATTAAT
1 TATAATAATT-AT
2940883 TATAATAATTAT
1 TATAATAATTAT
*
2940895 TAATAATAAATAT
1 T-ATAATAATTAT
2940908 TAATAAT-ATTA-
1 T-ATAATAATTAT
* *
2940919 TAAAATAATAAT
1 TATAATAATTAT
*
2940931 TATAAT-GTTA-
1 TATAATAATTAT
*
2940941 TATTATAATTAT
1 TATAATAATTAT
2940953 TAT
1 TAT
2940956 TTAAATCTAA
Statistics
Matches: 66, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
10 9 0.14
11 9 0.14
12 21 0.32
13 27 0.41
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (12 bp):
TATAATAATTAT
Found at i:2940928 original size:22 final size:24
Alignment explanation
Indices: 2940900--2940942 Score: 56
Period size: 22 Copynumber: 1.9 Consensus size: 24
2940890 ATTATTAATA
2940900 ATAAAT-ATTAATAATATTATAAA
1 ATAAATAATTAATAATATTATAAA
*
2940923 AT-AATAATT-ATAATGTTATA
1 ATAAATAATTAATAATATTATA
2940943 TTATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (24 bp):
ATAAATAATTAATAATATTATAAA
Found at i:2941309 original size:7 final size:7
Alignment explanation
Indices: 2941297--2941337 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
2941287 AAAATAATTT
2941297 TATATTA
1 TATATTA
2941304 TATATTA
1 TATATTA
*
2941311 TATAATA
1 TATATTA
* *
2941318 TAAATGA
1 TATATTA
2941325 TATATTA
1 TATATTA
2941332 TATATT
1 TATATT
2941338 TTTAAATTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (7 bp):
TATATTA
Found at i:2941310 original size:28 final size:28
Alignment explanation
Indices: 2941278--2941337 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
2941268 AATTTAATTT
**
2941278 TATTATATAAAA-ATAATTTTATATTATA
1 TATTATATAAAATA-AATGATATATTATA
*
2941306 TATTATATAATATAAATGATATATTATA
1 TATTATATAAAATAAATGATATATTATA
2941334 TATT
1 TATT
2941338 TTTAAATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 27 0.96
29 1 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (28 bp):
TATTATATAAAATAAATGATATATTATA
Found at i:2945867 original size:20 final size:19
Alignment explanation
Indices: 2945826--2945875 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 19
2945816 GCTTAGTTTT
* *
2945826 ATATTGAAATTAATATTTA
1 ATATTAAAATTAATAGTTA
2945845 ATATTAAAATTACATAGTTA
1 ATATTAAAATTA-ATAGTTA
*
2945865 ATATTTAAATT
1 ATATTAAAATT
2945876 TTTATAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (19 bp):
ATATTAAAATTAATAGTTA
Found at i:2946099 original size:13 final size:13
Alignment explanation
Indices: 2946083--2946131 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 13
2946073 ATTAAAAAAT
2946083 AAAAATAAAATTAA
1 AAAAATAAAA-TAA
*
2946097 AAAAATAAAAGAA
1 AAAAATAAAATAA
* *
2946110 AAAAAGTAAAGTCA
1 AAAAA-TAAAATAA
2946124 AAAAATAA
1 AAAAATAA
2946132 GACTATTTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 10 0.33
14 20 0.67
ACGTcount: A:0.78, C:0.02, G:0.06, T:0.14
Consensus pattern (13 bp):
AAAAATAAAATAA
Found at i:2946362 original size:16 final size:16
Alignment explanation
Indices: 2946332--2946377 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
2946322 TAATATTATA
*
2946332 ATTATTATTTAATATT
1 ATTAATATTTAATATT
* *
2946348 TTTAATATTTTATATT
1 ATTAATATTTAATATT
2946364 ATTAATATTATAAT
1 ATTAATATT-TAAT
2946378 TAATTTTATA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
16 21 0.88
17 3 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTAATATTTAATATT
Found at i:2946363 original size:26 final size:28
Alignment explanation
Indices: 2946334--2946409 Score: 79
Period size: 26 Copynumber: 2.8 Consensus size: 28
2946324 ATATTATAAT
2946334 TATTATTTAATATTTTTAA-T-ATTTTA
1 TATTATTTAATATTTTTAATTAATTTTA
*
2946360 TATTA-TTAATA-TTATAATTAATTTTA
1 TATTATTTAATATTTTTAATTAATTTTA
* *
2946386 TAATATTTATTATATTTATAATTA
1 TATTATTTA--ATATTTTTAATTA
2946410 TAATTAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
24 5 0.12
25 7 0.17
26 15 0.36
27 3 0.07
29 3 0.07
30 9 0.21
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (28 bp):
TATTATTTAATATTTTTAATTAATTTTA
Found at i:2946363 original size:35 final size:37
Alignment explanation
Indices: 2946324--2946410 Score: 101
Period size: 35 Copynumber: 2.4 Consensus size: 37
2946314 TTAAATAATA
*
2946324 ATATTATAATTATTAT-TTAATATTTTTAATA-TT-TT
1 ATATTATAATTATTATATTAAT-TTTATAATATTTATT
2946359 ATATTATTAA-TATTATAATTAATTTTATAATATTTATT
1 ATATTA-TAATTATTAT-ATTAATTTTATAATATTTATT
2946397 ATATTTATAATTAT
1 ATA-TTATAATTAT
2946411 AATTAAAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
35 12 0.27
36 11 0.25
37 7 0.16
38 8 0.18
39 6 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (37 bp):
ATATTATAATTATTATATTAATTTTATAATATTTATT
Found at i:2946374 original size:44 final size:45
Alignment explanation
Indices: 2946322--2946410 Score: 123
Period size: 45 Copynumber: 2.0 Consensus size: 45
2946312 ATTTAAATAA
2946322 TAATATTATAATT-ATTATT-TAATATTT-TTAATATTT-TATATTAT
1 TAATATTATAATTAATT-TTATAATATTTATT-ATATTTATA-ATTAT
2946366 TAATATTATAATTAATTTTATAATATTTATTATATTTATAATTAT
1 TAATATTATAATTAATTTTATAATATTTATTATATTTATAATTAT
2946411 AATTAAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
44 15 0.37
45 22 0.54
46 4 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (45 bp):
TAATATTATAATTAATTTTATAATATTTATTATATTTATAATTAT
Done.