Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold54
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: 3629595
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 8670 characters in sequence are not A, C, G, or T
File 11 of 20
Found at i:1742490 original size:15 final size:16
Alignment explanation
Indices: 1742454--1742493 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
1742444 TCTAATTTTT
*
1742454 ATAAAATTTGTAATTAA
1 ATAAAA-TTATAATTAA
1742471 ATAAAATTATAATT-A
1 ATAAAATTATAATTAA
1742486 ATAAAATT
1 ATAAAATT
1742494 TATTTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
16 7 0.32
17 6 0.27
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (16 bp):
ATAAAATTATAATTAA
Found at i:1742496 original size:16 final size:17
Alignment explanation
Indices: 1742454--1742496 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
1742444 TCTAATTTTT
*
1742454 ATAAAATTTGTAATTAA
1 ATAAAATTTATAATTAA
1742471 ATAAAA-TTATAATT-A
1 ATAAAATTTATAATTAA
1742486 ATAAAATTTAT
1 ATAAAATTTAT
1742497 TTAAAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 7 0.29
16 11 0.46
17 6 0.25
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:1742922 original size:14 final size:16
Alignment explanation
Indices: 1742892--1742924 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
1742882 ATATGCACAT
1742892 CATATAAATACATATA
1 CATATAAATACATATA
1742908 CATATAAA-A-ATATA
1 CATATAAATACATATA
1742922 CAT
1 CAT
1742925 GAAATAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 1 0.06
16 8 0.47
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (16 bp):
CATATAAATACATATA
Found at i:1743723 original size:11 final size:11
Alignment explanation
Indices: 1743686--1743724 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1743676 AAATATTTAA
1743686 AATATAACATG
1 AATATAACATG
* *
1743697 AAAATAATATG
1 AATATAACATG
*
1743708 TATATAACATG
1 AATATAACATG
1743719 AATATA
1 AATATA
1743725 TATACATATA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.56, C:0.05, G:0.08, T:0.31
Consensus pattern (11 bp):
AATATAACATG
Found at i:1743741 original size:14 final size:14
Alignment explanation
Indices: 1743724--1743753 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1743714 ACATGAATAT
*
1743724 ATATACATATAAAA
1 ATATACATAAAAAA
1743738 ATATACATAAAAAA
1 ATATACATAAAAAA
1743752 AT
1 AT
1743754 TATCAATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (14 bp):
ATATACATAAAAAA
Found at i:1743785 original size:21 final size:19
Alignment explanation
Indices: 1743744--1743787 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
1743734 AAAAATATAC
*
1743744 ATAAAAAAATTATCAATAT
1 ATAAAAAAATTATCAAAAT
*
1743763 ATAAAAAATTTATACAAAAAT
1 ATAAAAAAATTAT-C-AAAAT
1743784 ATAA
1 ATAA
1743788 TATTTTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 12 0.57
20 1 0.05
21 8 0.38
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (19 bp):
ATAAAAAAATTATCAAAAT
Found at i:1743825 original size:29 final size:30
Alignment explanation
Indices: 1743748--1743826 Score: 74
Period size: 29 Copynumber: 2.7 Consensus size: 30
1743738 ATATACATAA
* **
1743748 AAAAATTATCAATATATAAA-AAATTTATAC
1 AAAAA-TATAAATATATAAATAAAAATATAC
*
1743778 AAAAATAT-AATATTTTAAATAAAAATA-AC
1 AAAAATATAAATA-TATAAATAAAAATATAC
*
1743807 ATAAATATAAATATATAAAT
1 AAAAATATAAATATATAAAT
1743827 TTTTTTCTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
28 4 0.10
29 23 0.56
30 14 0.34
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (30 bp):
AAAAATATAAATATATAAATAAAAATATAC
Found at i:1743839 original size:4 final size:4
Alignment explanation
Indices: 1743830--1743884 Score: 51
Period size: 4 Copynumber: 13.8 Consensus size: 4
1743820 TATAAATTTT
* * *
1743830 TTTC TTTC TTTC TTTTT TTTC TTT- TTT- TCTC TTTC TTTTT TTTC TTTC
1 TTTC TTTC TTTC -TTTC TTTC TTTC TTTC TTTC TTTC -TTTC TTTC TTTC
1743878 TTTC TTT
1 TTTC TTT
1743885 TTCGGCTGAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
3 5 0.12
4 31 0.74
5 6 0.14
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (4 bp):
TTTC
Found at i:1743848 original size:17 final size:17
Alignment explanation
Indices: 1743826--1743887 Score: 79
Period size: 17 Copynumber: 3.5 Consensus size: 17
1743816 AATATATAAA
1743826 TTTTTTTCTTTCTTTCT
1 TTTTTTTCTTTCTTTCT
*
1743843 TTTTTTTCTTTTTTTCT
1 TTTTTTTCTTTCTTTCT
*
1743860 CTTTCTTTTTTTTCTTTCT
1 -TTT-TTTTCTTTCTTTCT
1743879 TTCTTTTTC
1 TT-TTTTTC
1743888 GGCTGAACCC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
17 16 0.42
18 9 0.24
19 13 0.34
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTTTCTTTCTTTCT
Found at i:1743854 original size:23 final size:23
Alignment explanation
Indices: 1743828--1743884 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
1743818 TATATAAATT
1743828 TTTTTCTTTCTTTCTTTTTTTTC
1 TTTTTCTTTCTTTCTTTTTTTTC
1743851 TTTTT-TTCTCTTTCTTTTTTTTC
1 TTTTTCTT-TCTTTCTTTTTTTTC
1743874 --TTTCTTTCTTT
1 TTTTTCTTTCTTT
1743885 TTCGGCTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
21 8 0.25
22 4 0.12
23 20 0.62
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (23 bp):
TTTTTCTTTCTTTCTTTTTTTTC
Found at i:1748051 original size:13 final size:13
Alignment explanation
Indices: 1748035--1748060 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1748025 TTTTTATTTT
1748035 TTTAATATTTATA
1 TTTAATATTTATA
1748048 TTTAATATTTATA
1 TTTAATATTTATA
1748061 CTAATATTCA
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTAATATTTATA
Found at i:1748102 original size:22 final size:22
Alignment explanation
Indices: 1748077--1748139 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 22
1748067 TTCAGATATC
1748077 AATATAAAAATATAATTTTTTA
1 AATATAAAAATATAATTTTTTA
1748099 AATATATAAAA-AT-A-TTTTTA
1 AATATA-AAAATATAATTTTTTA
*
1748119 AA-AAAATTAAATATAATTTTT
1 AATATAA--AAATATAATTTTT
1748140 ATTAAAATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 11
0.74 0.02 0.24
Matches are distributed among these distances:
18 1 0.03
19 2 0.06
20 11 0.32
21 3 0.09
22 9 0.26
23 8 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
AATATAAAAATATAATTTTTTA
Found at i:1748140 original size:22 final size:23
Alignment explanation
Indices: 1748084--1748150 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 23
1748074 ATCAATATAA
* *
1748084 AAATATAATTTTT-TAAATATAT
1 AAATATAATTTTTAAAAAAATAT
*
1748106 AAAAAT-ATTTTTAAAAAAAT-T
1 AAATATAATTTTTAAAAAAATAT
**
1748127 AAATATAATTTTTATTAAAATAT
1 AAATATAATTTTTAAAAAAATAT
1748150 A
1 A
1748151 TACTTATATT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
21 12 0.33
22 22 0.61
23 2 0.06
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
AAATATAATTTTTAAAAAAATAT
Found at i:1748451 original size:14 final size:15
Alignment explanation
Indices: 1748432--1748460 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1748422 TATATAACAT
1748432 AAAAAAAT-AATATA
1 AAAAAAATAAATATA
1748446 AAAAAAATAAATATA
1 AAAAAAATAAATATA
1748461 TAAATTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAAAAATAAATATA
Found at i:1748489 original size:33 final size:32
Alignment explanation
Indices: 1748450--1748565 Score: 91
Period size: 32 Copynumber: 3.8 Consensus size: 32
1748440 AATATAAAAA
1748450 AAATAAATATATAAATTTATTAAAATTTTTAT
1 AAATAAATATATAAATTTATTAAAATTTTTAT
* ** *
1748482 AACATAAAT-TATTAATACATTAAAATTTATAT
1 AA-ATAAATATATAAATTTATTAAAATTTTTAT
* * **
1748514 AAAT--ATATAAAAATTTA--AATATAATTAT
1 AAATAAATATATAAATTTATTAAAATTTTTAT
*
1748542 AATATAAATATATGAA-TTATTAAA
1 AA-ATAAATATATAAATTTATTAAA
1748566 TATATTTTCA
Statistics
Matches: 62, Mismatches: 15, Indels: 14
0.68 0.16 0.15
Matches are distributed among these distances:
28 9 0.15
29 4 0.06
30 9 0.15
31 9 0.15
32 25 0.40
33 6 0.10
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (32 bp):
AAATAAATATATAAATTTATTAAAATTTTTAT
Found at i:1748526 original size:20 final size:20
Alignment explanation
Indices: 1748503--1748543 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1748493 TTAATACATT
*
1748503 AAAATTTATATA-AATATATA
1 AAAATTTAAATATAAT-TATA
1748523 AAAATTTAAATATAATTATA
1 AAAATTTAAATATAATTATA
1748543 A
1 A
1748544 TATAAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAATTTAAATATAATTATA
Found at i:1750074 original size:13 final size:13
Alignment explanation
Indices: 1750058--1750083 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1750048 GATTGTAAAT
1750058 GATGATTTGATAA
1 GATGATTTGATAA
1750071 GATGATTTGATAA
1 GATGATTTGATAA
1750084 AATAAGTAAA
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:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (13 bp):
GATGATTTGATAA
Found at i:1753450 original size:2 final size:2
Alignment explanation
Indices: 1753438--1753473 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
1753428 TTTCTATAAA
1753438 AT AT CAT 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
1753474 AGCATGCATA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1753616 original size:14 final size:13
Alignment explanation
Indices: 1753599--1753640 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 13
1753589 ATAAGAATTT
1753599 AATTCTATTAGATG
1 AATT-TATTAGATG
*
1753613 AATTTCATTAAATG
1 AATTT-ATTAGATG
1753627 AATTTATTAGATG
1 AATTTATTAGATG
1753640 A
1 A
1753641 CAAATAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.36
14 16 0.64
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.43
Consensus pattern (13 bp):
AATTTATTAGATG
Found at i:1758467 original size:24 final size:24
Alignment explanation
Indices: 1758386--1758468 Score: 62
Period size: 24 Copynumber: 3.3 Consensus size: 24
1758376 AGTCTCATCA
*
1758386 TATTTAAAATTATTATAA-TTTTATAT
1 TATTT-AATTTATT-TAATTTTTA-AT
* *
1758412 TATATTTATTTAATT-ATATTTTAAT
1 TAT-TTAATTTATTTAAT-TTTTAAT
* *
1758437 AAATTAATTTATTTAATTTTTAAT
1 TATTTAATTTATTTAATTTTTAAT
1758461 TATTTAAT
1 TATTTAAT
1758469 AAATTTGATT
Statistics
Matches: 44, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
24 23 0.52
25 6 0.14
26 13 0.30
27 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TATTTAATTTATTTAATTTTTAAT
Found at i:1759135 original size:16 final size:18
Alignment explanation
Indices: 1759116--1759150 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
1759106 AAATTTAAAA
1759116 ATATTAAA-A-ATATTTT
1 ATATTAAATATATATTTT
1759132 ATATTAAATATATATTTT
1 ATATTAAATATATATTTT
1759150 A
1 A
1759151 ATATAAGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 1 0.06
18 8 0.47
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATTAAATATATATTTT
Found at i:1761202 original size:23 final size:24
Alignment explanation
Indices: 1761146--1761202 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 24
1761136 TCATTATTTT
*
1761146 TTTAAAAAT-ATTCATATTTAATA
1 TTTAAAAATAATGCATATTTAATA
* *
1761169 TTTATATATAATGCATATTTAA-A
1 TTTAAAAATAATGCATATTTAATA
1761192 TTTAAAAATAA
1 TTTAAAAATAA
1761203 AAACATATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
23 17 0.61
24 11 0.39
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.46
Consensus pattern (24 bp):
TTTAAAAATAATGCATATTTAATA
Found at i:1763855 original size:22 final size:21
Alignment explanation
Indices: 1763830--1763873 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1763820 TACATATATG
1763830 AAAGAAAATGAAAAGAAAAAAA
1 AAAGAAAAT-AAAAGAAAAAAA
* *
1763852 AAAGAAAATTAAATAAAAAAA
1 AAAGAAAATAAAAGAAAAAAA
1763873 A
1 A
1763874 TTACAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (21 bp):
AAAGAAAATAAAAGAAAAAAA
Found at i:1765840 original size:19 final size:17
Alignment explanation
Indices: 1765805--1765840 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 17
1765795 TAAGATTAGT
1765805 TAATATATTATTTAAAG
1 TAATATATTATTTAAAG
1765822 TAATATCATTATGTTAAAG
1 TAATAT-ATTAT-TTAAAG
1765841 AATTTTGCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 5 0.29
19 6 0.35
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.44
Consensus pattern (17 bp):
TAATATATTATTTAAAG
Found at i:1771196 original size:2 final size:2
Alignment explanation
Indices: 1771183--1771241 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
1771173 TGAATCAAAC
*
1771183 TA TA TA TG TA 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 TA TA TA TA TA
1771225 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
1771242 GACAGGAAGC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1771594 original size:34 final size:34
Alignment explanation
Indices: 1771548--1771765 Score: 282
Period size: 34 Copynumber: 6.5 Consensus size: 34
1771538 GTAAAAACCA
*
1771548 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1771582 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
1771616 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
1771650 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
1771683 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
1771717 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
1771750 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
1771766 TCTCCCACTT
Statistics
Matches: 162, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
33 45 0.28
34 115 0.71
35 2 0.01
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:1771662 original size:68 final size:67
Alignment explanation
Indices: 1771546--1771765 Score: 323
Period size: 67 Copynumber: 3.3 Consensus size: 67
1771536 TGGTAAAAAC
* * *
1771546 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
1771611 AT
66 AT
* * *
1771613 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
1771678 AAT
65 AAT
* * * * * *
1771681 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
1771746 AT
66 AT
1771748 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
1771766 TCTCCCACTT
Statistics
Matches: 136, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
67 75 0.55
68 61 0.45
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:1776227 original size:34 final size:34
Alignment explanation
Indices: 1776181--1776396 Score: 287
Period size: 34 Copynumber: 6.4 Consensus size: 34
1776171 GTAAAAACCA
1776181 CCATTTAATCAACAATGGTAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1776215 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
1776249 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
1776283 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
1776316 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
1776350 CCATTTAATCAACAATGGTAAACTACTAAAT-TA
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
1776383 CCATTTAATCAACA
1 CCATTTAATCAACA
1776397 CTTCTGGTCT
Statistics
Matches: 160, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
33 43 0.27
34 115 0.72
35 2 0.01
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:1776295 original size:68 final size:67
Alignment explanation
Indices: 1776179--1776396 Score: 310
Period size: 67 Copynumber: 3.2 Consensus size: 67
1776169 TGGTAAAAAC
* * *
1776179 CACCATTTAATCAACAATGGTAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGTAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
1776244 AT
66 AT
* *
1776246 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGTAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
1776311 AAT
65 AAT
* * * * * * *
1776314 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGTAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
1776379 AT
66 AT
*
1776381 TACCATTTAATCAACA
1 CACCATTTAATCAACA
1776397 CTTCTGGTCT
Statistics
Matches: 134, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
67 72 0.54
68 62 0.46
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGTAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:1777026 original size:2 final size:2
Alignment explanation
Indices: 1777019--1777044 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1777009 TAAATATTAA
1777019 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
1777045 TTAATTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1781006 original size:3 final size:3
Alignment explanation
Indices: 1780998--1781028 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1780988 CGCCGGCAAC
*
1780998 AGA AGA AGA AGA AGA AGA AAA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1781029 AGAGAACAAC
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:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1781029 original size:12 final size:12
Alignment explanation
Indices: 1780998--1781034 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
1780988 CGCCGGCAAC
*
1780998 AGAAGAAGAAGA
1 AGAAGAAAAAGA
1781010 AGAAGAAAAAGA
1 AGAAGAAAAAGA
*
1781022 AGAAGAAAGAGA
1 AGAAGAAAAAGA
1781034 A
1 A
1781035 CAACTTTTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (12 bp):
AGAAGAAAAAGA
Found at i:1781579 original size:3 final size:3
Alignment explanation
Indices: 1781573--1781602 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1781563 TAATAATAAT
1781573 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1781603 CTAAGCTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1787990 original size:23 final size:23
Alignment explanation
Indices: 1787964--1788030 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
1787954 AATTATATTA
1787964 TTAAATTTTTATCATTAATAATT
1 TTAAATTTTTATCATTAATAATT
1787987 TT-AATTACTTTA-CA-T--T-A--
1 TTAAATT--TTTATCATTAATAATT
1788004 TTAAATTTTTATCATTAATAATT
1 TTAAATTTTTATCATTAATAATT
1788027 TTAA
1 TTAA
1788031 TCACTTTAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 20
0.63 0.00 0.37
Matches are distributed among these distances:
16 4 0.12
17 4 0.12
18 5 0.15
19 1 0.03
20 2 0.06
21 1 0.03
22 5 0.15
23 8 0.24
24 4 0.12
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (23 bp):
TTAAATTTTTATCATTAATAATT
Found at i:1787998 original size:24 final size:24
Alignment explanation
Indices: 1787971--1788038 Score: 62
Period size: 24 Copynumber: 3.2 Consensus size: 24
1787961 TTATTAAATT
1787971 TTTATCATTAATAATTTTAATTAC
1 TTTATCATTAATAATTTTAATTAC
*
1787995 TTTA-CA-T--T-A-TTAAATT--
1 TTTATCATTAATAATTTTAATTAC
*
1788011 TTTATCATTAATAATTTTAATCAC
1 TTTATCATTAATAATTTTAATTAC
1788035 TTTA
1 TTTA
1788039 ACTTATTATG
Statistics
Matches: 33, Mismatches: 3, Indels: 16
0.63 0.06 0.31
Matches are distributed among these distances:
16 4 0.12
17 2 0.06
18 7 0.21
19 1 0.03
20 2 0.06
21 1 0.03
22 6 0.18
23 2 0.06
24 8 0.24
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTATCATTAATAATTTTAATTAC
Found at i:1788009 original size:40 final size:39
Alignment explanation
Indices: 1787943--1788046 Score: 147
Period size: 40 Copynumber: 2.6 Consensus size: 39
1787933 CATAAACTTT
**
1787943 TAATTTT-ATCAAATTATATTATTAAATTTTTATCATTAA
1 TAATTTTAATCACTTTA-ATTATTAAATTTTTATCATTAA
*
1787982 TAATTTTAATTACTTTACATTATTAAATTTTTATCATTAA
1 TAATTTTAATCACTTTA-ATTATTAAATTTTTATCATTAA
1788022 TAATTTTAATCACTTTAACTTATTA
1 TAATTTTAATCACTTTAA-TTATTA
1788047 TGCATACGTT
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
39 8 0.14
40 50 0.86
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (39 bp):
TAATTTTAATCACTTTAATTATTAAATTTTTATCATTAA
Found at i:1794065 original size:2 final size:2
Alignment explanation
Indices: 1794021--1794046 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1794011 GATCCACTTT
1794021 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
1794047 ATTAAATTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1794099 original size:19 final size:19
Alignment explanation
Indices: 1794018--1794091 Score: 55
Period size: 18 Copynumber: 3.9 Consensus size: 19
1794008 AGAGATCCAC
*
1794018 TTTTATATATATATAT-AT
1 TTTTATATATATTTATAAT
* * *
1794036 ATATATATATAATTA-AATT
1 TTTTATATATATTTATAA-T
*
1794055 AGTTTTATATATTTTTATAAT
1 --TTTTATATATATTTATAAT
1794076 TTTTATATA-ATTTATA
1 TTTTATATATATTTATA
1794092 TTTGTTTAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
18 18 0.43
19 10 0.24
21 12 0.29
22 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (19 bp):
TTTTATATATATTTATAAT
Found at i:1794955 original size:14 final size:14
Alignment explanation
Indices: 1794936--1794964 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1794926 TACATTCTCC
1794936 AAATATATATATAT
1 AAATATATATATAT
1794950 AAATATATATATAT
1 AAATATATATATAT
1794964 A
1 A
1794965 TGCTACTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATATATATATAT
Found at i:1796496 original size:20 final size:22
Alignment explanation
Indices: 1796471--1796538 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
1796461 TTATACATTA
* *
1796471 TATTAATTA-TTTATTTTTATT
1 TATTAATAATTTTATATTTATT
1796492 T-TTAA-AATTTTATATTTATT
1 TATTAATAATTTTATATTTATT
**
1796512 TATTAATAAAATTATATTTATT
1 TATTAATAATTTTATATTTATT
*
1796534 GATTA
1 TATTA
1796539 TATATTAATG
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 16 0.41
21 5 0.13
22 17 0.44
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (22 bp):
TATTAATAATTTTATATTTATT
Found at i:1796504 original size:24 final size:24
Alignment explanation
Indices: 1796477--1796533 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
1796467 ATTATATTAA
**
1796477 TTATTTATTTTTATTTTTAAAATT
1 TTATTTATTTTTATTAATAAAATT
*
1796501 TTATATT-TATTTATTAATAAAATT
1 TTAT-TTATTTTTATTAATAAAATT
*
1796525 ATATTTATT
1 TTATTTATT
1796534 GATTATATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
23 2 0.08
24 22 0.85
25 2 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
TTATTTATTTTTATTAATAAAATT
Found at i:1798408 original size:14 final size:13
Alignment explanation
Indices: 1798389--1798418 Score: 51
Period size: 13 Copynumber: 2.2 Consensus size: 13
1798379 AAAAAATATT
1798389 AATATTAATATTTA
1 AATATTAA-ATTTA
1798403 AATATTAAATTTA
1 AATATTAAATTTA
1798416 AAT
1 AAT
1798419 TAAATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
AATATTAAATTTA
Found at i:1798429 original size:12 final size:13
Alignment explanation
Indices: 1798382--1798428 Score: 53
Period size: 14 Copynumber: 3.7 Consensus size: 13
1798372 TAAAAATAAA
*
1798382 AAATATTAATATT
1 AAATTTTAATATT
*
1798395 AATATTTAAATATT
1 AA-ATTTTAATATT
1798409 AAA-TTTAA-ATT
1 AAATTTTAATATT
1798420 AAATTTTAA
1 AAATTTTAA
1798429 AATTTTTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 6 0.21
12 9 0.31
13 3 0.10
14 11 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
AAATTTTAATATT
Found at i:1798431 original size:13 final size:12
Alignment explanation
Indices: 1798382--1798432 Score: 50
Period size: 13 Copynumber: 4.0 Consensus size: 12
1798372 TAAAAATAAA
*
1798382 AAATATTAATATT
1 AAAT-TTAAAATT
1798395 AATATTTAAATATT
1 AA-ATTTAAA-ATT
1798409 AAATTT-AAATT
1 AAATTTAAAATT
1798420 AAATTTTAAAATT
1 AAA-TTTAAAATT
1798433 TTTTATTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
11 6 0.18
12 5 0.15
13 15 0.45
14 7 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
AAATTTAAAATT
Found at i:1799176 original size:12 final size:12
Alignment explanation
Indices: 1799159--1799185 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1799149 TAATCGTAAA
1799159 AAAAAAAAAAAT
1 AAAAAAAAAAAT
1799171 AAAAAAAAAAAT
1 AAAAAAAAAAAT
1799183 AAA
1 AAA
1799186 GGATGAGCAT
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:0.93, C:0.00, G:0.00, T:0.07
Consensus pattern (12 bp):
AAAAAAAAAAAT
Found at i:1802030 original size:18 final size:19
Alignment explanation
Indices: 1802007--1802043 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
1801997 AATATTTAAT
1802007 AATATTTAT-TTTATTTTA
1 AATATTTATATTTATTTTA
1802025 AATATTTATAATTTATTTT
1 AATATTTAT-ATTTATTTT
1802044 TTTATTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
20 8 0.47
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
AATATTTATATTTATTTTA
Found at i:1802041 original size:29 final size:28
Alignment explanation
Indices: 1801997--1802057 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 28
1801987 TTTGAAATAT
1801997 AATATTTAATAATATTTATTTTA-TTTTA
1 AATATTTAATAATATTT-TTTTATTTTTA
1802025 AATATTT-ATAATTTATTTTTTTATTTTTA
1 AATATTTAATAA--TATTTTTTTATTTTTA
1802054 AATA
1 AATA
1802058 AAAATCTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
27 4 0.13
28 12 0.40
29 14 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (28 bp):
AATATTTAATAATATTTTTTTATTTTTA
Found at i:1806528 original size:2 final size:2
Alignment explanation
Indices: 1806521--1806605 Score: 65
Period size: 2 Copynumber: 44.5 Consensus size: 2
1806511 ATGTGCCTTG
* **
1806521 AT AT AT AT A- AT AT AT AT AT AT AT AT AT -T TT AT CAT AT -T CG
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
* *
1806561 AT -T GT -T A- AT ACT AT AT AT AA AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1806601 AT AT A
1 AT AT A
1806606 AATAATCCTT
Statistics
Matches: 69, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
1 6 0.09
2 59 0.86
3 4 0.06
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1809487 original size:22 final size:22
Alignment explanation
Indices: 1809457--1809513 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
1809447 AATTTAAAAT
1809457 TTTAA-AAATATATT-TAGTATA
1 TTTAATAAATATATTATA-TATA
* * *
1809478 TTTATTAAATAAATTATATATT
1 TTTAATAAATATATTATATATA
1809500 TTTAATAAATATAT
1 TTTAATAAATATAT
1809514 AATTAAAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 4 0.14
22 23 0.79
23 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TTTAATAAATATATTATATATA
Found at i:1809506 original size:18 final size:19
Alignment explanation
Indices: 1809474--1809514 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
1809464 ATATATTTAG
1809474 TATATTTATTAAATAAATTA
1 TATATTTATTAAATAAA-TA
1809494 TATATTT-TT-AATAAATA
1 TATATTTATTAAATAAATA
1809511 TATA
1 TATA
1809515 ATTAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.29
18 6 0.29
19 2 0.10
20 7 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATATTTATTAAATAAATA
Found at i:1809814 original size:14 final size:16
Alignment explanation
Indices: 1809795--1809831 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
1809785 TATATAAAAT
1809795 AATTTTAA-ATTT-TA
1 AATTTTAATATTTATA
1809809 AATTTTAATATTTATA
1 AATTTTAATATTTATA
1809825 ATATTTT
1 A-ATTTT
1809832 TTTTAGATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 8 0.40
15 4 0.20
16 3 0.15
17 5 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
AATTTTAATATTTATA
Found at i:1810274 original size:27 final size:27
Alignment explanation
Indices: 1810236--1810292 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
1810226 AAAAAAAATA
1810236 ATACAAAGCTACAAAAACCCTAATGTC
1 ATACAAAGCTACAAAAACCCTAATGTC
1810263 ATACAAAGCTACAAAAACCCTAATGTC
1 ATACAAAGCTACAAAAACCCTAATGTC
1810290 ATA
1 ATA
1810293 AAACAAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.49, C:0.25, G:0.07, T:0.19
Consensus pattern (27 bp):
ATACAAAGCTACAAAAACCCTAATGTC
Found at i:1810722 original size:12 final size:12
Alignment explanation
Indices: 1810705--1810734 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1810695 CACCTACTAC
*
1810705 TATATATAATTA
1 TATATATAAATA
1810717 TATATATAAATA
1 TATATATAAATA
1810729 TATATA
1 TATATA
1810735 ATCATCCTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TATATATAAATA
Found at i:1811298 original size:2 final size:2
Alignment explanation
Indices: 1811291--1811318 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1811281 CATTAGACAA
1811291 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
1811319 GTAGCTTAAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1812199 original size:8 final size:8
Alignment explanation
Indices: 1812186--1812238 Score: 51
Period size: 8 Copynumber: 6.8 Consensus size: 8
1812176 TAAATTTAAT
1812186 TATAAATA
1 TATAAATA
1812194 TATAAATA
1 TATAAATA
1812202 T-T-AATA
1 TATAAATA
1812208 TA-AAATA
1 TATAAATA
1812215 TTATAATATTA
1 -TATAA-A-TA
1812226 TATAAATA
1 TATAAATA
1812234 -ATAAA
1 TATAAA
1812239 ATTGATTGTC
Statistics
Matches: 39, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
6 5 0.13
7 10 0.26
8 13 0.33
9 3 0.08
10 6 0.15
11 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TATAAATA
Found at i:1812213 original size:21 final size:21
Alignment explanation
Indices: 1812176--1812238 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
1812166 AATTTTTATC
1812176 TAAAT-TTAAT-TATAAATATA
1 TAAATATTAATATA-AAATATA
1812196 TAAATATTAATATAAAATAT-
1 TAAATATTAATATAAAATATA
1812216 TATAATATT-ATAT-AAATA-A
1 TA-AATATTAATATAAAATATA
1812235 TAAA
1 TAAA
1812239 ATTGATTGTC
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
18 2 0.05
19 7 0.18
20 11 0.28
21 17 0.44
22 2 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAATATTAATATAAAATATA
Found at i:1832505 original size:13 final size:14
Alignment explanation
Indices: 1832478--1832514 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
1832468 AATAAATATT
1832478 AATATCAAA--ATA
1 AATATCAAATTATA
1832490 AATAT-AAATTATA
1 AATATCAAATTATA
1832503 AATATCAAATTA
1 AATATCAAATTA
1832515 AAAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 3 0.14
12 5 0.23
13 8 0.36
14 6 0.27
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (14 bp):
AATATCAAATTATA
Found at i:1832511 original size:25 final size:24
Alignment explanation
Indices: 1832469--1832516 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
1832459 CTTTAAAAAA
*
1832469 ATAAATATTAATATCAAAATAAAT
1 ATAAATATAAATATCAAAATAAAT
*
1832493 ATAAATTATAAATATCAAATTAAA
1 ATAAA-TATAAATATCAAAATAAA
1832517 AAAAAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (24 bp):
ATAAATATAAATATCAAAATAAAT
Found at i:1833208 original size:20 final size:20
Alignment explanation
Indices: 1833170--1833220 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1833160 AATAATTTTT
1833170 TTTAATTAAATAAACATTAA
1 TTTAATTAAATAAACATTAA
* *
1833190 TTTAAGTTAAATTAA-ATTAG
1 TTTAA-TTAAATAAACATTAA
1833210 TTTAAATTAAA
1 TTT-AATTAAA
1833221 AGAAACTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (20 bp):
TTTAATTAAATAAACATTAA
Found at i:1835488 original size:2 final size:2
Alignment explanation
Indices: 1835481--1835522 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1835471 TCTACTTGTA
1835481 AT AT AT AT 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
1835523 TTACCAGATA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1838704 original size:22 final size:21
Alignment explanation
Indices: 1838657--1838704 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
1838647 TATATGTATA
*
1838657 TAAAATTTATTTATGAATTAT
1 TAAAATTTATTTATGAATAAT
*
1838678 GAAAATTATATTTAATGAA-AAT
1 TAAAATT-TATTT-ATGAATAAT
1838700 TAAAA
1 TAAAA
1838705 ATAAATTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 6 0.27
22 11 0.50
23 5 0.23
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (21 bp):
TAAAATTTATTTATGAATAAT
Found at i:1840146 original size:22 final size:22
Alignment explanation
Indices: 1840111--1840155 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1840101 ACATGTTCGG
*
1840111 TTTAATTAATTTAAA-TAATTT
1 TTTAATTAAATTAAATTAATTT
1840132 TTTAATTTAAATTAAATTAATTT
1 TTTAA-TTAAATTAAATTAATTT
1840155 T
1 T
1840156 ATTTAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.24
22 9 0.43
23 7 0.33
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTAATTAAATTAAATTAATTT
Found at i:1841118 original size:2 final size:2
Alignment explanation
Indices: 1841111--1841142 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1841101 CTAGACCAAT
*
1841111 TC TC TC TC TC TC TC TC GC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1841143 CTAAATACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.03, T:0.47
Consensus pattern (2 bp):
TC
Found at i:1844599 original size:14 final size:14
Alignment explanation
Indices: 1844580--1844613 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
1844570 ATCAAAATAA
1844580 TTGAGATTTTTTTT
1 TTGAGATTTTTTTT
1844594 TTGAGATTTTTTTT
1 TTGAGATTTTTTTT
1844608 TTGAGA
1 TTGAGA
1844614 ATTTATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.65
Consensus pattern (14 bp):
TTGAGATTTTTTTT
Found at i:1844696 original size:25 final size:26
Alignment explanation
Indices: 1844642--1844697 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
1844632 GATAAAATTA
1844642 ATTTTAAAATAAATAAAAATAATAAT
1 ATTTTAAAATAAATAAAAATAATAAT
*
1844668 -TTTTAAAA-AAATTAAAAT-ATCAAT
1 ATTTTAAAATAAATAAAAATAAT-AAT
1844692 ATTTTA
1 ATTTTA
1844698 TATTTAATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 2 0.07
24 12 0.44
25 13 0.48
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (26 bp):
ATTTTAAAATAAATAAAAATAATAAT
Found at i:1845060 original size:12 final size:12
Alignment explanation
Indices: 1845043--1845092 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 12
1845033 ATAATAATTT
1845043 ATTTAAATATAA
1 ATTTAAATATAA
1845055 ATTTAAATAT-A
1 ATTTAAATATAA
**
1845066 ATAAAAATATAGAA
1 ATTTAAATAT--AA
1845080 ATTTAAATA-AA
1 ATTTAAATATAA
1845091 AT
1 AT
1845093 GATAAAAGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
11 13 0.42
12 10 0.32
14 8 0.26
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (12 bp):
ATTTAAATATAA
Found at i:1845090 original size:20 final size:21
Alignment explanation
Indices: 1845065--1845108 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
1845055 ATTTAAATAT
1845065 AATAAAAAT-ATAGAAA-TTTA
1 AATAAAAATGATA-AAAGTTTA
1845085 AAT-AAAATGATAAAAGTTTA
1 AATAAAAATGATAAAAGTTTA
1845105 AATA
1 AATA
1845109 TTTTTATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.30
Consensus pattern (21 bp):
AATAAAAATGATAAAAGTTTA
Found at i:1845550 original size:3 final size:3
Alignment explanation
Indices: 1845542--1845578 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1845532 CACCATACTT
1845542 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1845579 AAATAAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1847190 original size:2 final size:2
Alignment explanation
Indices: 1847183--1847209 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1847173 AAATAAATAA
1847183 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1847210 CATGACATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1847706 original size:2 final size:2
Alignment explanation
Indices: 1847699--1847729 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1847689 TTCTTTTATG
*
1847699 TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1847730 TGTGACTAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1852211 original size:22 final size:23
Alignment explanation
Indices: 1852180--1852222 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
1852170 AATAATAATT
*
1852180 AAATATTTATTTTTTTATTTAAA
1 AAATATTTATTTTTTAATTTAAA
1852203 AAAT-TTTATTTTTTAATTTA
1 AAATATTTATTTTTTAATTTA
1852223 TTATTTATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
AAATATTTATTTTTTAATTTAAA
Found at i:1853379 original size:6 final size:6
Alignment explanation
Indices: 1853364--1853448 Score: 71
Period size: 6 Copynumber: 14.0 Consensus size: 6
1853354 GTTATCCTCC
* * * * * * * *
1853364 TCATCA TCATCT TCATCT TCATCC TCCTCC TCATCG TCATCC TCCTCA
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* *
1853412 TCAACT TCATCT TCATCT TCATCG TCATCT TCTATCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TC-ATCT
1853449 GGAGCTCATC
Statistics
Matches: 64, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
6 60 0.94
7 4 0.06
ACGTcount: A:0.18, C:0.39, G:0.02, T:0.41
Consensus pattern (6 bp):
TCATCT
Found at i:1857227 original size:39 final size:39
Alignment explanation
Indices: 1857184--1857259 Score: 152
Period size: 39 Copynumber: 1.9 Consensus size: 39
1857174 GCCCCAACAG
1857184 ATAACCAGTACCTGCAGAAAACAGTCACAATAGAAGTGT
1 ATAACCAGTACCTGCAGAAAACAGTCACAATAGAAGTGT
1857223 ATAACCAGTACCTGCAGAAAACAGTCACAATAGAAGT
1 ATAACCAGTACCTGCAGAAAACAGTCACAATAGAAGT
1857260 ATATCCATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.45, C:0.21, G:0.17, T:0.17
Consensus pattern (39 bp):
ATAACCAGTACCTGCAGAAAACAGTCACAATAGAAGTGT
Found at i:1859156 original size:5 final size:5
Alignment explanation
Indices: 1859146--1859170 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1859136 TGAATTTGAG
1859146 GAAAA GAAAA GAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA
1859171 ATGGTTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:1859931 original size:102 final size:102
Alignment explanation
Indices: 1859755--1859957 Score: 372
Period size: 102 Copynumber: 2.0 Consensus size: 102
1859745 CTGGCGAGTC
*
1859755 TATTGTCTCAGATAGTAGGGAGCCTGCTAAAATGGTGGCTTTGGAAGGAAAGGTGGTTGATGGAG
1 TATTGTCTCAGATAGTAGGAAGCCTGCTAAAATGGTGGCTTTGGAAGGAAAGGTGGTTGATGGAG
1859820 GTTCTGAAAGTGCTGTTAT-CCGAGACAAGGGATTGAA
66 GTTCTGAAAGTGCTGTTATCCCG-GACAAGGGATTGAA
1859857 TATTGTCTCAGATAGTAGGAAGCCTGCTAAAATGGTGGCTTTGGAAGGAAAGGTGGTTGATGGAG
1 TATTGTCTCAGATAGTAGGAAGCCTGCTAAAATGGTGGCTTTGGAAGGAAAGGTGGTTGATGGAG
*
1859922 GTTCTGAAAGTGCTGTTTTCCCGGACAAGGGATTGA
66 GTTCTGAAAGTGCTGTTATCCCGGACAAGGGATTGA
1859958 GTGAGACGCA
Statistics
Matches: 98, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
102 95 0.97
103 3 0.03
ACGTcount: A:0.27, C:0.11, G:0.34, T:0.28
Consensus pattern (102 bp):
TATTGTCTCAGATAGTAGGAAGCCTGCTAAAATGGTGGCTTTGGAAGGAAAGGTGGTTGATGGAG
GTTCTGAAAGTGCTGTTATCCCGGACAAGGGATTGAA
Found at i:1861219 original size:5 final size:5
Alignment explanation
Indices: 1861209--1861240 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
1861199 TTATACCCAA
*
1861209 AAAAG AAAAG AAAAG AAAGG AAAAG AAAAG AA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AA
1861241 TATGACATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:1863041 original size:2 final size:2
Alignment explanation
Indices: 1863036--1863114 Score: 77
Period size: 2 Copynumber: 39.5 Consensus size: 2
1863026 TCTCTCTCTC
* * * * *
1863036 TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA CA TA CA TA CA TC
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
1863078 TA TA TA TA TA TA CA AA CA TA CA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1863115 GTATCTTTCA
Statistics
Matches: 61, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.48, C:0.09, G:0.01, T:0.42
Consensus pattern (2 bp):
TA
Found at i:1863085 original size:24 final size:24
Alignment explanation
Indices: 1863051--1863113 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
1863041 ATATATATAT
* *
1863051 ATATATGTATATATACATACATAC
1 ATATATATATATATACAAACATAC
*
1863075 ATCTATATATATATACAAACATAC
1 ATATATATATATATACAAACATAC
1863099 ATATATATATATATA
1 ATATATATATATATA
1863114 TGTATCTTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (24 bp):
ATATATATATATATACAAACATAC
Found at i:1865396 original size:26 final size:26
Alignment explanation
Indices: 1865360--1865418 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
1865350 TACACTCGAG
1865360 CTTTGCATTTTTCTGAATTCAAACAT
1 CTTTGCATTTTTCTGAATTCAAACAT
1865386 CTTTGCATTTTTCTGAATTCAAACAT
1 CTTTGCATTTTTCTGAATTCAAACAT
*
1865412 GTTTGCA
1 CTTTGCA
1865419 GCAGGAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.25, C:0.19, G:0.10, T:0.46
Consensus pattern (26 bp):
CTTTGCATTTTTCTGAATTCAAACAT
Found at i:1872380 original size:13 final size:14
Alignment explanation
Indices: 1872353--1872381 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1872343 TTATAGTAGA
1872353 TTAAATTTATTAAG
1 TTAAATTTATTAAG
1872367 TTAAATTT-TTAAG
1 TTAAATTTATTAAG
1872380 TT
1 TT
1872382 TGTCTATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (14 bp):
TTAAATTTATTAAG
Found at i:1872815 original size:13 final size:13
Alignment explanation
Indices: 1872797--1872821 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1872787 AAAATTAATA
1872797 TAAAATTATTTTT
1 TAAAATTATTTTT
1872810 TAAAATTATTTT
1 TAAAATTATTTT
1872822 AAATAATAAT
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAAATTATTTTT
Found at i:1876786 original size:23 final size:23
Alignment explanation
Indices: 1876721--1876786 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 23
1876711 TATTGTATTT
* * *
1876721 ATTATAATTATATATGTATATAA
1 ATTATAATTATAAATATTTATAA
*
1876744 ATT-TAATATATCAATATTTATAA
1 ATTATAAT-TATAAATATTTATAA
1876767 ATTATAAATTATAAAT-TTTA
1 ATTAT-AATTATAAATATTTA
1876787 ATGAGTTTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
22 4 0.11
23 21 0.60
24 7 0.20
25 3 0.09
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
ATTATAATTATAAATATTTATAA
Found at i:1880248 original size:32 final size:32
Alignment explanation
Indices: 1880212--1880275 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
1880202 ACGGACCCGC
1880212 CCTAATGGACGCAAAAAATTCAAATTATTTGT
1 CCTAATGGACGCAAAAAATTCAAATTATTTGT
*
1880244 CCTAATGGATGCAAAAAATTCAAATTATTTGT
1 CCTAATGGACGCAAAAAATTCAAATTATTTGT
1880276 TAAAATATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (32 bp):
CCTAATGGACGCAAAAAATTCAAATTATTTGT
Found at i:1881003 original size:20 final size:20
Alignment explanation
Indices: 1880980--1881017 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1880970 TTAATAAATT
1880980 TTATAATTTATA-TATTTATA
1 TTAT-ATTTATATTATTTATA
1881000 TTATATTTATATTATTTA
1 TTATATTTATATTATTTA
1881018 CTTAAATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTATATTTATATTATTTATA
Found at i:1881006 original size:11 final size:11
Alignment explanation
Indices: 1880990--1881014 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1880980 TTATAATTTA
1880990 TATATTTATAT
1 TATATTTATAT
1881001 TATATTTATAT
1 TATATTTATAT
1881012 TAT
1 TAT
1881015 TTACTTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1882673 original size:23 final size:24
Alignment explanation
Indices: 1882647--1882700 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
1882637 TTAATTTTTT
* *
1882647 TATCAATTTACTTGTTGA-ATTAA
1 TATCAATTTAATTCTTGAGATTAA
1882670 TATCCAA-TTAATTCTTGAGATTAA
1 TAT-CAATTTAATTCTTGAGATTAA
1882694 T-TCAATT
1 TATCAATT
1882701 AGAAATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
22 3 0.12
23 14 0.54
24 9 0.35
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.46
Consensus pattern (24 bp):
TATCAATTTAATTCTTGAGATTAA
Found at i:1883485 original size:28 final size:26
Alignment explanation
Indices: 1883430--1883485 Score: 67
Period size: 28 Copynumber: 2.1 Consensus size: 26
1883420 TTATTTATTA
**
1883430 TTTTATATTTATTAAAAGTATTTTAT
1 TTTTATATTTATTAAAAGTATTAAAT
*
1883456 TTTTATATTGTATTTAAAATTATTAAAT
1 TTTTATATT-TA-TTAAAAGTATTAAAT
1883484 TT
1 TT
1883486 AATTATTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 9 0.36
27 2 0.08
28 14 0.56
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.61
Consensus pattern (26 bp):
TTTTATATTTATTAAAAGTATTAAAT
Found at i:1884424 original size:11 final size:11
Alignment explanation
Indices: 1884408--1884432 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1884398 TTGGTATTTT
1884408 TAATTTTTAAA
1 TAATTTTTAAA
1884419 TAATTTTTAAA
1 TAATTTTTAAA
1884430 TAA
1 TAA
1884433 AAAATAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TAATTTTTAAA
Found at i:1884750 original size:2 final size:2
Alignment explanation
Indices: 1884729--1884769 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
1884719 CCAATCTCAG
* * *
1884729 CT CT CC CT CC CT CC CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1884770 CTTCCGTGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (2 bp):
CT
Found at i:1884931 original size:14 final size:14
Alignment explanation
Indices: 1884912--1884967 Score: 51
Period size: 14 Copynumber: 3.6 Consensus size: 14
1884902 ATATTAAAAT
1884912 TTATTAAATATAAA
1 TTATTAAATATAAA
1884926 TTATTAATATATAAAAA
1 TTATTAA-ATAT--AAA
1884943 TTTATATAAATATATAA
1 -TTAT-TAAATATA-AA
1884960 -TATTAAAT
1 TTATTAAAT
1884968 TATTATTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
14 12 0.33
15 7 0.19
16 1 0.03
17 5 0.14
18 8 0.22
19 3 0.08
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTATTAAATATAAA
Found at i:1884935 original size:32 final size:33
Alignment explanation
Indices: 1884894--1884965 Score: 103
Period size: 32 Copynumber: 2.2 Consensus size: 33
1884884 AAATGTTAAT
* *
1884894 ATATAAATATATTAAAATTTAT-TAAATATA-A
1 ATATTAATATATAAAAATTTATATAAATATATA
1884925 ATTATTAATATATAAAAATTTATATAAATATATA
1 A-TATTAATATATAAAAATTTATATAAATATATA
1884959 ATATTAA
1 ATATTAA
1884966 ATTATTATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
31 1 0.03
32 19 0.53
33 14 0.39
34 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (33 bp):
ATATTAATATATAAAAATTTATATAAATATATA
Found at i:1891133 original size:40 final size:39
Alignment explanation
Indices: 1891089--1891249 Score: 132
Period size: 39 Copynumber: 4.1 Consensus size: 39
1891079 AGATCAACTG
*
1891089 AAATTTAAAAGATACGACTAATGCATGAATTTTTTTATTA
1 AAATTTAAAAGATATGACTAATGCAT-AATTTTTTTATTA
* * * *
1891129 AAATTTAAAAGATATTAGTAATGTATAGA-TTATTTATTA
1 AAATTTAAAAGATATGACTAATGCATA-ATTTTTTTATTA
* * * * *
1891168 GAATCTAAAAGATGTGACTAATACATAATTTTTTTATTG
1 AAATTTAAAAGATATGACTAATGCATAATTTTTTTATTA
* * *
1891207 AAA-TTCAAA-ATATGAAACTAATGCATGTATTTTGTT-TTA
1 AAATTTAAAAGATATG--ACTAATGCAT-AATTTTTTTATTA
1891246 AAAT
1 AAAT
1891250 AAATGTGATT
Statistics
Matches: 93, Mismatches: 22, Indels: 12
0.73 0.17 0.09
Matches are distributed among these distances:
37 4 0.04
38 5 0.05
39 54 0.58
40 30 0.32
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.41
Consensus pattern (39 bp):
AAATTTAAAAGATATGACTAATGCATAATTTTTTTATTA
Found at i:1891729 original size:87 final size:85
Alignment explanation
Indices: 1891622--1891789 Score: 212
Period size: 87 Copynumber: 1.9 Consensus size: 85
1891612 AGACTAATAT
* * **
1891622 ATTGATTGTAAACATTAGACTACAAAAATTAGACTAAT-ATATGAATTTTATTTAAGAATCAGAT
1 ATTGATTGTAAACATAAGACTACAAAAATTAAACTAATCATA-G-ATGATATTTAAGAATCAGAT
1891686 TCCTTTTGGTAGAAAAAAAATTG
64 TCCTTTTGGTA-AAAAAAAATTG
** * *
1891709 ATTGATTGTAAATGTAAGACTACAAAGATTAAACTAATGCATAGATGATATTTAAGAATTAGATT
1 ATTGATTGTAAACATAAGACTACAAAAATTAAACTAAT-CATAGATGATATTTAAGAATCAGATT
*
1891774 TCTTTTGGTAAAAAAA
65 CCTTTTGGTAAAAAAA
1891790 GAGAAAACTT
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
86 6 0.09
87 60 0.86
88 1 0.01
89 3 0.04
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.35
Consensus pattern (85 bp):
ATTGATTGTAAACATAAGACTACAAAAATTAAACTAATCATAGATGATATTTAAGAATCAGATTC
CTTTTGGTAAAAAAAAATTG
Found at i:1894060 original size:12 final size:12
Alignment explanation
Indices: 1894043--1894070 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1894033 TAGGCAGAAG
1894043 TTAAAGTTAAGT
1 TTAAAGTTAAGT
1894055 TTAAAGTTAAGT
1 TTAAAGTTAAGT
1894067 TTAA
1 TTAA
1894071 TAGGTCAGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (12 bp):
TTAAAGTTAAGT
Found at i:1894215 original size:33 final size:34
Alignment explanation
Indices: 1894165--1894279 Score: 89
Period size: 33 Copynumber: 3.4 Consensus size: 34
1894155 TTAGCTTAAA
1894165 AAATTTAAAC-TCATATAATCATATCAAAAAAAT
1 AAATTTAAACTTCATATAATCATATCAAAAAAAT
* *
1894198 AAATTTAAACTTC-TATAAATAAATAT-AAATAAACTTT
1 AAATTTAAACTTCATAT-AAT-CATATCAAA-AAA--AT
* *
1894235 AAAATTTTAAA-TTCGTATAATCA-AAC-AAAAAAT
1 -AAA-TTTAAACTTCATATAATCATATCAAAAAAAT
1894268 AAATTTAAACTT
1 AAATTTAAACTT
1894280 TTACAAATAA
Statistics
Matches: 66, Mismatches: 5, Indels: 23
0.70 0.05 0.24
Matches are distributed among these distances:
31 6 0.09
32 5 0.08
33 14 0.21
34 8 0.12
35 10 0.15
36 3 0.05
37 2 0.03
38 9 0.14
39 9 0.14
ACGTcount: A:0.56, C:0.10, G:0.01, T:0.34
Consensus pattern (34 bp):
AAATTTAAACTTCATATAATCATATCAAAAAAAT
Found at i:1894312 original size:72 final size:70
Alignment explanation
Indices: 1894163--1894379 Score: 256
Period size: 72 Copynumber: 3.0 Consensus size: 70
1894153 TATTAGCTTA
* *
1894163 AAAAATTTAAACTCATATAATCATATCAAAAAAATAAATTTAAACTTCTATAAATAAATATAAAT
1 AAAAATTTAAACTCATATAATCA-AAC-AAAAAATAAATTTAAACTTCTACAAATAAA-ATAAAT
* *
1894228 -AAACTTT
63 CATACCTT
* * * *
1894235 AAAATTTTAAATTCGTATAATCAAACAAAAAATAAATTTAAACTTTTACAAATAAAAGTAAATCA
1 AAAAATTTAAACTCATATAATCAAACAAAAAATAAATTTAAACTTCTACAAATAAAA-TAAATCA
1894300 TACCTT
65 TACCTT
* * ** *
1894306 AAAAATTTAAACTCATATAATCGTACCTCATAATAAATTTAAACTTCTACAAATAAAAATAAATC
1 AAAAATTTAAACTCATATAATC-AAACAAAAAATAAATTTAAACTTCTACAAAT-AAAATAAATC
1894371 ATACCTT
64 ATACCTT
1894378 AA
1 AA
1894380 CATAAAATAA
Statistics
Matches: 124, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
69 1 0.01
70 33 0.27
71 26 0.21
72 60 0.48
73 4 0.03
ACGTcount: A:0.54, C:0.12, G:0.01, T:0.32
Consensus pattern (70 bp):
AAAAATTTAAACTCATATAATCAAACAAAAAATAAATTTAAACTTCTACAAATAAAATAAATCAT
ACCTT
Found at i:1894366 original size:26 final size:25
Alignment explanation
Indices: 1894337--1894420 Score: 93
Period size: 26 Copynumber: 3.4 Consensus size: 25
1894327 CGTACCTCAT
1894337 AATAAATTTAAACTTCTACAAATAAA
1 AATAAATTTAAACTT-TACAAATAAA
* * * *
1894363 AATAAA-TCATACCTTA-ACAT-AA
1 AATAAATTTAAACTTTACAAATAAA
1894385 AATAAATTTAAACTTTTACAAATAAA
1 AATAAATTTAAAC-TTTACAAATAAA
1894411 AATAAATTTA
1 AATAAATTTA
1894421 TACTCGTATA
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
22 8 0.17
23 7 0.15
24 5 0.11
25 8 0.17
26 18 0.39
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (25 bp):
AATAAATTTAAACTTTACAAATAAA
Found at i:1895904 original size:30 final size:30
Alignment explanation
Indices: 1895870--1895933 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
1895860 TAAATATAAA
*
1895870 ATAATTTTATAATTTAATGATAAT-TATTTT
1 ATAATTTT-TAATTTAATGAGAATATATTTT
* * *
1895900 ATAATTTTTTATTTTATGAGAATATTTTTT
1 ATAATTTTTAATTTAATGAGAATATATTTT
1895930 ATAA
1 ATAA
1895934 ATAATTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 12 0.41
30 17 0.59
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.58
Consensus pattern (30 bp):
ATAATTTTTAATTTAATGAGAATATATTTT
Found at i:1896823 original size:11 final size:13
Alignment explanation
Indices: 1896814--1896904 Score: 59
Period size: 13 Copynumber: 6.9 Consensus size: 13
1896804 GGAATTAAAA
1896814 ATAATATAAATAT
1 ATAATATAAATAT
1896827 ATAATATTTTAAAT-T
1 ATAATA---TAAATAT
1896842 -TAAT-TATAATAT
1 ATAATATA-AATAT
*
1896854 AAAATAATATAA-AT
1 ATAAT-ATA-AATAT
*
1896868 ATGATATAAATAT
1 ATAATATAAATAT
1896881 ATAA-A-AAATAT
1 ATAATATAAATAT
1896892 ATCAATATAAATA
1 AT-AATATAAATA
1896905 AAATTAAATT
Statistics
Matches: 62, Mismatches: 4, Indels: 23
0.70 0.04 0.26
Matches are distributed among these distances:
10 2 0.03
11 11 0.18
12 6 0.10
13 18 0.29
14 14 0.23
15 6 0.10
16 5 0.08
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (13 bp):
ATAATATAAATAT
Found at i:1896879 original size:27 final size:27
Alignment explanation
Indices: 1896809--1896906 Score: 83
Period size: 27 Copynumber: 3.6 Consensus size: 27
1896799 ATTAAGGAAT
* * * *
1896809 TAAAAATAATATAAATATATAATATTT
1 TAAATATAATATAAATATAAAATAATA
*
1896836 TAAATTTAAT-TATAATATAAAATAATA
1 TAAATATAATATA-AATATAAAATAATA
* *
1896863 TAAATATGATATAAATATATAAAAAATA
1 TAAATATAATATAAATATA-AAATAATA
1896891 TATCAATATAA-ATAAA
1 TA--AATATAATATAAA
1896907 ATTAAATTAG
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
26 2 0.04
27 33 0.58
28 11 0.19
29 5 0.09
30 6 0.11
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (27 bp):
TAAATATAATATAAATATAAAATAATA
Found at i:1896891 original size:17 final size:17
Alignment explanation
Indices: 1896859--1896913 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
1896849 AATATAAAAT
**
1896859 AATATAAATATGATATA
1 AATATAAATAAAATATA
1896876 AATATATAA-AAAATATA
1 AATATA-AATAAAATATA
1896893 TCAATATAAATAAAAT-TA
1 --AATATAAATAAAATATA
1896911 AAT
1 AAT
1896914 TAGAAAAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
16 3 0.09
17 12 0.38
18 6 0.19
19 11 0.34
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (17 bp):
AATATAAATAAAATATA
Found at i:1896908 original size:19 final size:20
Alignment explanation
Indices: 1896850--1896908 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
1896840 TTTAATTATA
1896850 ATATAAA-ATAATATAAATATG
1 ATATAAATATAA-ATAAA-ATG
1896871 ATATAAATATATAA-AAAAT-
1 ATATAAATATA-AATAAAATG
*
1896890 ATATCAATATAAATAAAAT
1 ATATAAATATAAATAAAAT
1896909 TAAATTAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 2 0.06
19 15 0.44
20 2 0.06
21 10 0.29
22 4 0.12
23 1 0.03
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (20 bp):
ATATAAATATAAATAAAATG
Found at i:1897160 original size:18 final size:18
Alignment explanation
Indices: 1897137--1897182 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1897127 TGTTTAATAT
1897137 AAATAAATAATTCATTTA
1 AAATAAATAATTCATTTA
* *
1897155 AAATAAA-ATTTTATTTA
1 AAATAAATAATTCATTTA
1897172 AATATAAATAA
1 AA-ATAAATAA
1897183 AATATAAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 10 0.43
18 12 0.52
19 1 0.04
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
AAATAAATAATTCATTTA
Found at i:1901346 original size:3 final size:3
Alignment explanation
Indices: 1901338--1901372 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1901328 TTTTCATCTT
1901338 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1901373 CAAATGATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1901855 original size:3 final size:3
Alignment explanation
Indices: 1901849--1901896 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
1901839 TATACTACTG
1901849 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1901897 GTACTAATTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1902293 original size:27 final size:27
Alignment explanation
Indices: 1902251--1902320 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 27
1902241 AAAAATTTAT
1902251 TATAAAAAATATTTTTCAGTCTTAAAAA
1 TATAAAAAATATTTTTCAGTC-TAAAAA
* *
1902279 TATAAAAAATATTTTTCATTCTCAAAA
1 TATAAAAAATATTTTTCAGTCTAAAAA
1902306 TATAAATAAATATTT
1 TATAAA-AAATATTT
1902321 ATTAATATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
27 11 0.28
28 28 0.72
ACGTcount: A:0.50, C:0.07, G:0.01, T:0.41
Consensus pattern (27 bp):
TATAAAAAATATTTTTCAGTCTAAAAA
Found at i:1914248 original size:9 final size:9
Alignment explanation
Indices: 1914231--1914264 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1914221 GCATTGGAAG
*
1914231 AAAGGAAAA
1 AAAGAAAAA
1914240 AAAGAAAAA
1 AAAGAAAAA
*
1914249 AAAAAAAAA
1 AAAGAAAAA
1914258 AAAGAAA
1 AAAGAAA
1914265 CATGTTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAGAAAAA
Found at i:1924443 original size:2 final size:2
Alignment explanation
Indices: 1924432--1924460 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1924422 CATGAGCATC
1924432 AT AT -T 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
1924461 TGAAAGATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1925621 original size:21 final size:21
Alignment explanation
Indices: 1925592--1925631 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1925582 AAATTTTAAG
1925592 AATAAATAATT-TTAGTTAATT
1 AATAAATAATTATT-GTTAATT
*
1925613 AATATATAATTATTGTTAA
1 AATAAATAATTATTGTTAA
1925632 AACAATAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (21 bp):
AATAAATAATTATTGTTAATT
Found at i:1929665 original size:22 final size:22
Alignment explanation
Indices: 1929634--1929687 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
1929624 AAATGAAATT
** *
1929634 TTTATATTTAAAAGTTATTTAGA
1 TTTA-ATTTAAAAAATATTTAAA
1929657 TTTAATTTAAAAAATATTTAAA
1 TTTAATTTAAAAAATATTTAAA
1929679 TTTAATTTA
1 TTTAATTTA
1929688 TTATTAAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 24 0.86
23 4 0.14
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (22 bp):
TTTAATTTAAAAAATATTTAAA
Found at i:1929720 original size:31 final size:32
Alignment explanation
Indices: 1929677--1929747 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
1929667 AAAATATTTA
* * *
1929677 AATTTAATTTATT-ATTAAGTTAAATTTAAAT
1 AATTTAAATTATTGAATAAATTAAATTTAAAT
*
1929708 AATTTAAATTATTGAATAAATTAAATTTAAGT
1 AATTTAAATTATTGAATAAATTAAATTTAAAT
*
1929740 ATTTTAAA
1 AATTTAAA
1929748 AATTAATTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 12 0.35
32 22 0.65
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (32 bp):
AATTTAAATTATTGAATAAATTAAATTTAAAT
Found at i:1929750 original size:22 final size:22
Alignment explanation
Indices: 1929725--1929775 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
1929715 ATTATTGAAT
*
1929725 AAATTAAATTT-AAGTATTTTAA
1 AAATTAAATTTGAA-TAGTTTAA
1929747 AAATT-AATTTGAATAGTTTAA
1 AAATTAAATTTGAATAGTTTAA
*
1929768 AATTTAAA
1 AAATTAAA
1929776 ATTATTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (22 bp):
AAATTAAATTTGAATAGTTTAA
Found at i:1929846 original size:12 final size:12
Alignment explanation
Indices: 1929829--1929867 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1929819 AAAAAACTTT
*
1929829 AATTTGAGTTTA
1 AATTTGAATTTA
1929841 AATTTGAATTTA
1 AATTTGAATTTA
* *
1929853 AATTTAAATATA
1 AATTTGAATTTA
1929865 AAT
1 AAT
1929868 AATCGATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (12 bp):
AATTTGAATTTA
Found at i:1929929 original size:14 final size:14
Alignment explanation
Indices: 1929912--1929951 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1929902 ATTTTTTATA
1929912 AATTAAATAAATTT
1 AATTAAATAAATTT
1929926 AA-T---TAAATTT
1 AATTAAATAAATTT
1929936 AATTAAATAAATTT
1 AATTAAATAAATTT
1929950 AA
1 AA
1929952 ATAATTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 8
0.73 0.00 0.27
Matches are distributed among these distances:
10 9 0.41
11 1 0.05
13 1 0.05
14 11 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AATTAAATAAATTT
Found at i:1929932 original size:10 final size:10
Alignment explanation
Indices: 1929910--1929943 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
1929900 TTATTTTTTA
*
1929910 TAAA-TTAAA
1 TAAATTTAAT
1929919 TAAATTTAAT
1 TAAATTTAAT
1929929 TAAATTTAAT
1 TAAATTTAAT
1929939 TAAAT
1 TAAAT
1929944 AAATTTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 4 0.17
10 19 0.83
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
TAAATTTAAT
Found at i:1929969 original size:23 final size:24
Alignment explanation
Indices: 1929912--1929996 Score: 91
Period size: 24 Copynumber: 3.5 Consensus size: 24
1929902 ATTTTTTATA
* *
1929912 AATTAAATAAATTTAATTAAATTT
1 AATTAATTAAATTTAAATAAATTT
*
1929936 AATTAAATAAATTTAAAT-AATTT
1 AATTAATTAAATTTAAATAAATTT
* * *
1929959 AATTATTTAAAATCAAATAAATTAT
1 AATTAATTAAATTTAAATAAATT-T
*
1929984 TATTAATTAAATT
1 AATTAATTAAATT
1929997 AAAAATTTAT
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
23 19 0.37
24 21 0.41
25 11 0.22
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (24 bp):
AATTAATTAAATTTAAATAAATTT
Found at i:1929977 original size:33 final size:33
Alignment explanation
Indices: 1929909--1929981 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 33
1929899 ATTATTTTTT
*
1929909 ATAAA-TTAAATAAATTTAATTAAATTTAATTAA
1 ATAAATTTAAATAAATTTAATT-AATTTAATCAA
1929942 ATAAATTTAAAT-AATTTAATT-ATTTAAAATCAA
1 ATAAATTTAAATAAATTTAATTAATTT--AATCAA
1929975 ATAAATT
1 ATAAATT
1929982 ATTATTAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
31 4 0.11
33 26 0.72
34 6 0.17
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (33 bp):
ATAAATTTAAATAAATTTAATTAATTTAATCAA
Found at i:1930011 original size:23 final size:23
Alignment explanation
Indices: 1929907--1930011 Score: 72
Period size: 24 Copynumber: 4.4 Consensus size: 23
1929897 AAATTATTTT
* *
1929907 TTATAAATTAAATAAATTTAATTAAA
1 TTAT-AATTAATTAAA-TTAAAT-AA
*
1929933 TT-TAATTAAATAAATTTAAATAA
1 TTATAATTAATTAAA-TTAAATAA
* *
1929956 TT-TAATTATTTAAAATCAAATAAA
1 TTATAATTAATT-AAATTAAAT-AA
*
1929980 TTATTATTAATTAAATTAAA-AA
1 TTATAATTAATTAAATTAAATAA
1930002 TTTATAATTA
1 -TTATAATTA
1930012 TATACCAATC
Statistics
Matches: 67, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
22 2 0.03
23 24 0.36
24 31 0.46
25 8 0.12
26 2 0.03
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (23 bp):
TTATAATTAATTAAATTAAATAA
Found at i:1932802 original size:27 final size:28
Alignment explanation
Indices: 1932772--1932835 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 28
1932762 AGGACATATA
1932772 AAATTATAATTTAAATTAAA-TTAATT-T
1 AAATTATAATTT-AATTAAATTTAATTAT
* *
1932799 AAATTATTATTTATTTAAATTTAATTAT
1 AAATTATAATTTAATTAAATTTAATTAT
*
1932827 AAAATATAA
1 AAATTATAA
1932836 ATATTAATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 6 0.19
27 17 0.55
28 8 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
AAATTATAATTTAATTAAATTTAATTAT
Found at i:1932816 original size:16 final size:15
Alignment explanation
Indices: 1932778--1932825 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
1932768 TATAAAATTA
1932778 TAATTTAAATTAAAT
1 TAATTTAAATTAAAT
*
1932793 TAATTTAAATTATTAT
1 TAATTTAAATTA-AAT
* *
1932809 TTATTTAAATTTAAT
1 TAATTTAAATTAAAT
1932824 TA
1 TA
1932826 TAAAATATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 15 0.56
16 12 0.44
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TAATTTAAATTAAAT
Done.