Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014939.1 Kokia drynarioides strain JFW-HI SEQ_129982, whole genome shotgun sequence
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: 76750
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Warning! 44 characters in sequence are not A, C, G, or T
Found at i:798 original size:11 final size:11
Alignment explanation
Indices: 779--862 Score: 51
Period size: 11 Copynumber: 7.2 Consensus size: 11
769 TGGACCTTTT
779 AATTAAATTTA
1 AATTAAATTTA
*
790 AATTCAATTTA
1 AATTAAATTTA
* *
801 AATTTAAACTTG
1 AA-TTAAATTTA
*
813 ATTTAAATTTA
1 AATTAAATTTA
***
824 AACTTTAAAAGAA
1 AA--TTAAATTTA
*
837 AAGTTTAAACTTA
1 AA--TTAAATTTA
850 AATTAAATTTA
1 AATTAAATTTA
861 AA
1 AA
863 CCCAAAATGA
Statistics
Matches: 54, Mismatches: 16, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
11 30 0.56
12 7 0.13
13 17 0.31
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (11 bp):
AATTAAATTTA
Found at i:803 original size:17 final size:17
Alignment explanation
Indices: 777--863 Score: 79
Period size: 17 Copynumber: 5.0 Consensus size: 17
767 ATTGGACCTT
777 TTAA-TTAAATTTAAA-
1 TTAATTTAAATTTAAAC
792 TTCAATTTAAATTTAAAC
1 TT-AATTTAAATTTAAAC
*
810 TTGATTTAAATTTAAAC
1 TTAATTTAAATTTAAAC
***
827 TTTAAAAGAAAAGTTTAAAC
1 -TT-AATTTAAA-TTTAAAC
*
847 TTAAATTAAATTTAAAC
1 TTAATTTAAATTTAAAC
864 CCAAAATGAA
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
15 2 0.03
16 2 0.03
17 32 0.54
18 10 0.17
19 6 0.10
20 7 0.12
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.41
Consensus pattern (17 bp):
TTAATTTAAATTTAAAC
Found at i:832 original size:7 final size:6
Alignment explanation
Indices: 781--862 Score: 62
Period size: 6 Copynumber: 13.8 Consensus size: 6
771 GACCTTTTAA
* * *
781 TTAAAT TTAAA- TTCAAT TTAAAT TTAAAC TT-GAT TTAAAT TTAAACT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA-T
* ** *
828 TTAAAA GAAAAGT TTAAAC TTAAA- TTAAAT TTAAA
1 TTAAAT TTAAA-T TTAAAT TTAAAT TTAAAT TTAAA
863 CCCAAAATGA
Statistics
Matches: 58, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
5 12 0.21
6 37 0.64
7 9 0.16
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (6 bp):
TTAAAT
Found at i:2371 original size:20 final size:22
Alignment explanation
Indices: 2332--2373 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2322 AAGTATATTT
2332 GTTTTTTTATTTTGATATTTAA
1 GTTTTTTTATTTTGATATTTAA
*
2354 GTTTTTTTGTTTT-A-ATTTAA
1 GTTTTTTTATTTTGATATTTAA
2374 TATTTAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 1 0.05
22 12 0.63
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (22 bp):
GTTTTTTTATTTTGATATTTAA
Found at i:2705 original size:13 final size:13
Alignment explanation
Indices: 2687--2746 Score: 63
Period size: 13 Copynumber: 4.7 Consensus size: 13
2677 TTTAAAAATA
2687 TAAAAAATTATAT
1 TAAAAAATTATAT
2700 TAAAAAATT-TA-
1 TAAAAAATTATAT
*
2711 -AAAATATATAATAT
1 TAAAA-A-ATTATAT
2725 TAAAAAATTATAT
1 TAAAAAATTATAT
*
2738 AAAAAAATT
1 TAAAAAATT
2747 CATTAAGTCC
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
10 4 0.10
11 1 0.03
12 4 0.10
13 25 0.64
14 1 0.03
15 4 0.10
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
TAAAAAATTATAT
Found at i:3443 original size:17 final size:18
Alignment explanation
Indices: 3402--3448 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
3392 TGTTTGTTTT
3402 GAGAAGAAAGATGGAGTG
1 GAGAAGAAAGATGGAGTG
* *
3420 GATAAGAAA-ATGGATTG
1 GAGAAGAAAGATGGAGTG
*
3437 GGGAAG-AAGATG
1 GAGAAGAAAGATG
3449 AAGGAGAGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 2 0.08
17 14 0.58
18 8 0.33
ACGTcount: A:0.45, C:0.00, G:0.40, T:0.15
Consensus pattern (18 bp):
GAGAAGAAAGATGGAGTG
Found at i:4420 original size:16 final size:16
Alignment explanation
Indices: 4360--4422 Score: 58
Period size: 16 Copynumber: 3.8 Consensus size: 16
4350 AAAATTTTAG
4360 AAAGTATAAAAATAAA
1 AAAGTATAAAAATAAA
4376 AAA-TCACTTAAAAAT-AA
1 AAAGT-A--TAAAAATAAA
* *
4393 CAAGTTACAAAAATAAA
1 AAAG-TATAAAAATAAA
4410 AAAGTATAAAAAT
1 AAAGTATAAAAAT
4423 TTTAAAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
15 1 0.03
16 18 0.49
17 9 0.24
18 8 0.22
19 1 0.03
ACGTcount: A:0.68, C:0.06, G:0.05, T:0.21
Consensus pattern (16 bp):
AAAGTATAAAAATAAA
Found at i:4667 original size:16 final size:17
Alignment explanation
Indices: 4630--4671 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
4620 TTTTATTTTA
4630 ATTTTTAGAACTTTAGAT
1 ATTTTTA-AACTTTAGAT
*
4648 -TTTTTAAA-TTTATAT
1 ATTTTTAAACTTTAGAT
4663 ATTTTTAAA
1 ATTTTTAAA
4672 ATTCATGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 6 0.27
16 10 0.45
17 6 0.27
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (17 bp):
ATTTTTAAACTTTAGAT
Found at i:10889 original size:17 final size:16
Alignment explanation
Indices: 10863--10899 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 16
10853 TTTCCATCAT
10863 TGGGGACTCTAATTAA
1 TGGGGACTCTAATTAA
10879 TGGGTGACTCTAATTAA
1 TGGG-GACTCTAATTAA
10896 TGGG
1 TGGG
10900 CTTGAGTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.27, C:0.11, G:0.30, T:0.32
Consensus pattern (16 bp):
TGGGGACTCTAATTAA
Found at i:12527 original size:2 final size:2
Alignment explanation
Indices: 12520--12547 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12510 CCCCTTTTTA
12520 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
12548 TAAAACAGTG
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:12677 original size:21 final size:21
Alignment explanation
Indices: 12653--12706 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
12643 GTCATGAATG
*
12653 ATCTACCGATACAACTCTAT-T
1 ATCTACCGATACAACT-TATCC
* *
12674 ATCTACCGAAACATCTTATCC
1 ATCTACCGATACAACTTATCC
12695 ATCTACCGATAC
1 ATCTACCGATAC
12707 TATAAGTTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 3 0.11
21 25 0.89
ACGTcount: A:0.33, C:0.31, G:0.06, T:0.30
Consensus pattern (21 bp):
ATCTACCGATACAACTTATCC
Found at i:17541 original size:109 final size:109
Alignment explanation
Indices: 17350--17556 Score: 387
Period size: 109 Copynumber: 1.9 Consensus size: 109
17340 GAATGATCGG
*
17350 TTAAGAACTTTTGAAGCCATTGATCGCCTCCGAACGTACTCCCGTTTGGTGTATTCCGCAAGTAT
1 TTAAGAACTTTTGAAGCCATTGACCGCCTCCGAACGTACTCCCGTTTGGTGTATTCCGCAAGTAT
*
17415 ACGGGTTGAGTTGTAATATAGTTACTACAAAGTTTCAAGATCAA
66 ACGGGTTAAGTTGTAATATAGTTACTACAAAGTTTCAAGATCAA
*
17459 TTAAGAACTTTTGAAGCCATTGACCGCCTCCGAATGTACTCCCGTTTGGTGTATTCCGCAAGTAT
1 TTAAGAACTTTTGAAGCCATTGACCGCCTCCGAACGTACTCCCGTTTGGTGTATTCCGCAAGTAT
17524 ACGGGTTAAGTTGTAATATAGTTACTACAAAGT
66 ACGGGTTAAGTTGTAATATAGTTACTACAAAGT
17557 AGCAAGTACT
Statistics
Matches: 95, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
109 95 1.00
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.32
Consensus pattern (109 bp):
TTAAGAACTTTTGAAGCCATTGACCGCCTCCGAACGTACTCCCGTTTGGTGTATTCCGCAAGTAT
ACGGGTTAAGTTGTAATATAGTTACTACAAAGTTTCAAGATCAA
Found at i:19962 original size:16 final size:16
Alignment explanation
Indices: 19941--19976 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
19931 AAATAATCCC
*
19941 AAAATTACAAGTCTCA
1 AAAATTAAAAGTCTCA
19957 AAAATTAAAAGTCTCA
1 AAAATTAAAAGTCTCA
19973 AAAA
1 AAAA
19977 CACTTTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.58, C:0.14, G:0.06, T:0.22
Consensus pattern (16 bp):
AAAATTAAAAGTCTCA
Found at i:26888 original size:6 final size:6
Alignment explanation
Indices: 26847--26902 Score: 53
Period size: 6 Copynumber: 9.5 Consensus size: 6
26837 TTAATAGGAT
* * * *
26847 TTTCAA TTTACAA -TTC-A TATCAC TTTCAA TTCCAA TTTCAA TTTCAC
1 TTTCAA TTT-CAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
26894 TTTCAA TTT
1 TTTCAA TTT
26903 TGATCACAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
4 1 0.03
5 3 0.08
6 32 0.82
7 3 0.08
ACGTcount: A:0.30, C:0.21, G:0.00, T:0.48
Consensus pattern (6 bp):
TTTCAA
Found at i:30116 original size:16 final size:17
Alignment explanation
Indices: 30095--30126 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
30085 ATATTTTTTT
30095 ATTAAAAT-TATAAATA
1 ATTAAAATATATAAATA
30111 ATTAAAATATATAAAT
1 ATTAAAATATATAAAT
30127 TATCCATCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATTAAAATATATAAATA
Found at i:31683 original size:22 final size:22
Alignment explanation
Indices: 31655--31734 Score: 97
Period size: 22 Copynumber: 3.5 Consensus size: 22
31645 GAATTGTATC
31655 TAAATTTATTTTAGGTAATCAA
1 TAAATTTATTTTAGGTAATCAA
* * *
31677 TAAATTTATTTTATGTGAATTGTATC
1 TAAATTTATTTTAGGT-AA-T-CA-A
31703 TAAATTTATTTTAGGTAATCAA
1 TAAATTTATTTTAGGTAATCAA
31725 TAAATTTATT
1 TAAATTTATT
31735 AAAAAAAATT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
22 25 0.52
23 3 0.06
24 2 0.04
25 3 0.06
26 15 0.31
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.50
Consensus pattern (22 bp):
TAAATTTATTTTAGGTAATCAA
Found at i:31693 original size:48 final size:48
Alignment explanation
Indices: 31640--31734 Score: 190
Period size: 48 Copynumber: 2.0 Consensus size: 48
31630 AATATCGTAA
31640 TATGTGAATTGTATCTAAATTTATTTTAGGTAATCAATAAATTTATTT
1 TATGTGAATTGTATCTAAATTTATTTTAGGTAATCAATAAATTTATTT
31688 TATGTGAATTGTATCTAAATTTATTTTAGGTAATCAATAAATTTATT
1 TATGTGAATTGTATCTAAATTTATTTTAGGTAATCAATAAATTTATT
31735 AAAAAAAATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (48 bp):
TATGTGAATTGTATCTAAATTTATTTTAGGTAATCAATAAATTTATTT
Found at i:31706 original size:26 final size:26
Alignment explanation
Indices: 31640--31715 Score: 97
Period size: 26 Copynumber: 3.1 Consensus size: 26
31630 AATATCGTAA
31640 TATGTGAATTGTATCTAAATTTATTT
1 TATGTGAATTGTATCTAAATTTATTT
* * *
31666 TAGGT-AA-T-CA-ATAAATTTATTT
1 TATGTGAATTGTATCTAAATTTATTT
31688 TATGTGAATTGTATCTAAATTTATTT
1 TATGTGAATTGTATCTAAATTTATTT
31714 TA
1 TA
31716 GGTAATCAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
22 15 0.38
23 3 0.08
24 2 0.05
25 3 0.08
26 17 0.43
ACGTcount: A:0.34, C:0.04, G:0.11, T:0.51
Consensus pattern (26 bp):
TATGTGAATTGTATCTAAATTTATTT
Found at i:34377 original size:103 final size:105
Alignment explanation
Indices: 34256--34466 Score: 390
Period size: 105 Copynumber: 2.0 Consensus size: 105
34246 TCTTCTTCCG
* *
34256 ATATAATTTTTATATTTTTTAAATAGTTTTTA-TTTAAAAAAATATAT-TTTTTAAAATTTTTTA
1 ATATAATTTTTATATTTTTTAAATAGTTTTTATTTTAAAAAAATATATATTTTAAAAAATTTTTA
34319 AATACTAAAAAAGTGAACCACCTTAATTGGAATGAAATTC
66 AATACTAAAAAAGTGAACCACCTTAATTGGAATGAAATTC
34359 ATATAATTTTTATATTTTTTAAATAGTTTTTATTTTAAAAAAATATATATTTTAAAAAATTTTTA
1 ATATAATTTTTATATTTTTTAAATAGTTTTTATTTTAAAAAAATATATATTTTAAAAAATTTTTA
34424 AATACTAAAAAAGTGAACCACCTTAATTGGAATGAAATTC
66 AATACTAAAAAAGTGAACCACCTTAATTGGAATGAAATTC
34464 ATA
1 ATA
34467 ATATAAAAAT
Statistics
Matches: 104, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
103 32 0.31
104 15 0.14
105 57 0.55
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.45
Consensus pattern (105 bp):
ATATAATTTTTATATTTTTTAAATAGTTTTTATTTTAAAAAAATATATATTTTAAAAAATTTTTA
AATACTAAAAAAGTGAACCACCTTAATTGGAATGAAATTC
Found at i:37569 original size:46 final size:46
Alignment explanation
Indices: 37437--37571 Score: 137
Period size: 46 Copynumber: 2.9 Consensus size: 46
37427 TAAATAATAT
** * *
37437 GTCACCTATGAAATTGTCGTTCAATGAGAGTTGAAGCCAAAGCCAC
1 GTCACCTATGAAATTGTCACTCAATGAGAGTTGAAGCCAGAGTCAC
* * * * * * * *
37483 GCCACGTATGAAACTATCACTTAGTGAGAATCGACA-CCAGAGTCAC
1 GTCACCTATGAAATTGTCACTCAATGAGAGTTGA-AGCCAGAGTCAC
*
37529 GTCACTTATGAAATTGTCACTCAATGAGAGTTGAAGCCAGAGT
1 GTCACCTATGAAATTGTCACTCAATGAGAGTTGAAGCCAGAGT
37572 GAGATATGTT
Statistics
Matches: 67, Mismatches: 20, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
45 1 0.01
46 65 0.97
47 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.24
Consensus pattern (46 bp):
GTCACCTATGAAATTGTCACTCAATGAGAGTTGAAGCCAGAGTCAC
Found at i:38166 original size:49 final size:48
Alignment explanation
Indices: 38106--38205 Score: 128
Period size: 49 Copynumber: 2.1 Consensus size: 48
38096 TCACATATGG
* * *
38106 AACCGTTACTCAGTGAAAGTTGAAATTAGAGCCATGCGCCCACCTATAA
1 AACCGTCACTCAGTGAAAGTCGAAATTAGAGCCACGCG-CCACCTATAA
* * * *
38155 AACCGTCACTCAGTTAACGTCGAAATTAGAGCCACGCGTCACTTATAA
1 AACCGTCACTCAGTGAAAGTCGAAATTAGAGCCACGCGCCACCTATAA
38203 AAC
1 AAC
38206 TATGATTCAG
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
48 11 0.25
49 33 0.75
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (48 bp):
AACCGTCACTCAGTGAAAGTCGAAATTAGAGCCACGCGCCACCTATAA
Found at i:38774 original size:27 final size:27
Alignment explanation
Indices: 38744--38799 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
38734 TGTCTTCTCT
38744 CGATATATTTTGTTCACTTTTTAGCAA
1 CGATATATTTTGTTCACTTTTTAGCAA
*
38771 CGATATATTTTGTTCACTTTTTTGCAA
1 CGATATATTTTGTTCACTTTTTAGCAA
38798 CG
1 CG
38800 TCTTTTCTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.23, C:0.16, G:0.12, T:0.48
Consensus pattern (27 bp):
CGATATATTTTGTTCACTTTTTAGCAA
Found at i:40124 original size:46 final size:46
Alignment explanation
Indices: 39988--40124 Score: 184
Period size: 46 Copynumber: 3.0 Consensus size: 46
39978 CCTAAATAAT
* * *
39988 ACATCACTTATGAAACCGTCACTCAATGAGAGTCGAAGCCAGAGCC
1 ACATCACTTATGAAACTGTCACTCAATGAGAGTCGAAGCCAAAGTC
* * * *
40034 ACACCACTTATGAAACTGTCACTCAGTGAAAGTCGAAACCAAAGTC
1 ACATCACTTATGAAACTGTCACTCAATGAGAGTCGAAGCCAAAGTC
* * *
40080 ACGTCACTTATGAAATTGTCACTCAATGAGAGTTGAAGCCAAAGT
1 ACATCACTTATGAAACTGTCACTCAATGAGAGTCGAAGCCAAAGT
40125 GAGATATATT
Statistics
Matches: 77, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.21
Consensus pattern (46 bp):
ACATCACTTATGAAACTGTCACTCAATGAGAGTCGAAGCCAAAGTC
Found at i:40729 original size:48 final size:47
Alignment explanation
Indices: 40657--40754 Score: 117
Period size: 48 Copynumber: 2.1 Consensus size: 47
40647 GTCACGTATG
* * * *
40657 AAACTGTCACTCAGTAAAATTTGAAATC-AGAGCCAAACGTTACCTATA
1 AAACCGTCACTCAATAAAAATTGAAATCAAGA-CCAAACGTCACCTA-A
* *
40705 AAACCGTCGCTCAATAAAAATTGAAATCAAGACCACACGTCACCTAA
1 AAACCGTCACTCAATAAAAATTGAAATCAAGACCAAACGTCACCTAA
40752 AAA
1 AAA
40755 TCTGTGATTC
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
47 4 0.09
48 36 0.84
49 3 0.07
ACGTcount: A:0.45, C:0.23, G:0.11, T:0.20
Consensus pattern (47 bp):
AAACCGTCACTCAATAAAAATTGAAATCAAGACCAAACGTCACCTAA
Found at i:42974 original size:214 final size:214
Alignment explanation
Indices: 42593--43440 Score: 1218
Period size: 214 Copynumber: 4.0 Consensus size: 214
42583 ATAATGCTTA
*
42593 GTGCAGTGCAATTATGAATGAAGATTTTCATTGAA-ATTTCACATTACACATTGAATTCACACCT
1 GTGCAGTGCAATTATGAATGAAGATTTTCACT-AAGATTTCACATTACACATTGAATTCACACCT
** * * * * * *
42657 AATTGATATATCATGTACGAAA-TCGTCACTCTGTGAAAATCGAAGCCAGATTCTCAAAACCACA
65 AATTGATACGTCACGTATGAAACT-GTCGCTCTGTGAAAATCAAAGCCAGATTCCCAAAACCACG
* * ** *
42721 CGTCACCTATGAAACAATCATTCAATGAA-AATAGAAGCCAAATCCACATCATTTATGCAACTGT
129 CGTCACCTATGAAACAATCATTCAAT-AAGAATCGAAGCCAAATCCACGTCACATATGCAACCGT
42785 CATTCAATGAGAATAACGCTCG
193 CATTCAATGAGAATAACGCTCG
* ** **
42807 GTGCAATGCAATTATGAATGAAGATTTTCACTGGGATTTCACATTACACATTGAATTCACATTTA
1 GTGCAGTGCAATTATGAATGAAGATTTTCACTAAGATTTCACATTACACATTGAATTCACACCTA
* * *
42872 ATTGATACGTCATGTATGAAACTGTCCCTCTGTGAAAATCAAAGCCAGATTCCCAAAACCACGTG
66 ATTGATACGTCACGTATGAAACTGTCGCTCTGTGAAAATCAAAGCCAGATTCCCAAAACCACGCG
* *
42937 TCACCTATGAAACAATCATTCAATAAGAATCGAAGCCAAATCCACGTTACATATGTAACCGTCAT
131 TCACCTATGAAACAATCATTCAATAAGAATCGAAGCCAAATCCACGTCACATATGCAACCGTCAT
43002 TCAATGAGAATAACGCTCG
196 TCAATGAGAATAACGCTCG
43021 GTGCAGTGCAATTATGAATGAAGATTTTCACTAAGATTTCACATTACACATTGAATTCACACCTA
1 GTGCAGTGCAATTATGAATGAAGATTTTCACTAAGATTTCACATTACACATTGAATTCACACCTA
* * *
43086 ATTGATACGTCGCGTATGAAACTGTTGCTCTGTGAAAATCAAAACCAGATTCCCAAAACCACGCG
66 ATTGATACGTCACGTATGAAACTGTCGCTCTGTGAAAATCAAAGCCAGATTCCCAAAACCACGCG
* * *
43151 TCACCTATGAAACAATCATTCAATAAGAATCGAAACCAAATCCACGTTACATATGTAACCGTCAT
131 TCACCTATGAAACAATCATTCAATAAGAATCGAAGCCAAATCCACGTCACATATGCAACCGTCAT
*
43216 TCAATAAGAATAACGCTCG
196 TCAATGAGAATAACGCTCG
43235 GTGCAGTGCAATTATGAATGAAGATTTTCACTAAGATTTCACATTACACATTGAATTCACACCTA
1 GTGCAGTGCAATTATGAATGAAGATTTTCACTAAGATTTCACATTACACATTGAATTCACACCTA
* * * * *** * *
43300 ATTGATACGTCACATATGAAACCGTCGCTTTGTGAAAATCGAAGCCAGATTATTAGAACCACGCA
66 ATTGATACGTCACGTATGAAACTGTCGCTCTGTGAAAATCAAAGCCAGATTCCCAAAACCACGCG
** * * * *
43365 TCACCTATGAAACCGTCATTCAATGAGAATCGAAGCCAAAGT-CATGTCACTTGTGCAACCGTCA
131 TCACCTATGAAACAATCATTCAATAAGAATCGAAGCCAAA-TCCACGTCACATATGCAACCGTCA
43429 TTCAATGAGAAT
195 TTCAATGAGAAT
43441 CGAAGTTGGA
Statistics
Matches: 574, Mismatches: 56, Indels: 8
0.90 0.09 0.01
Matches are distributed among these distances:
213 2 0.00
214 570 0.99
215 2 0.00
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.27
Consensus pattern (214 bp):
GTGCAGTGCAATTATGAATGAAGATTTTCACTAAGATTTCACATTACACATTGAATTCACACCTA
ATTGATACGTCACGTATGAAACTGTCGCTCTGTGAAAATCAAAGCCAGATTCCCAAAACCACGCG
TCACCTATGAAACAATCATTCAATAAGAATCGAAGCCAAATCCACGTCACATATGCAACCGTCAT
TCAATGAGAATAACGCTCG
Found at i:43818 original size:206 final size:204
Alignment explanation
Indices: 43464--44521 Score: 1329
Period size: 206 Copynumber: 5.2 Consensus size: 204
43454 AGGTACATTG
* * * ** * *
43464 AAACTAATGTCCTCTTTCCCTTTGATATTGAACAAAAA-ATTATTTTTTGAAATTTAAATTACAA
1 AAACTAGTCTCCTATTTCCCTCCGATATTGAACAAAAACA-TA-ATTTTGAAATTTGAATTACAA
* * *
43528 TATAATAATGCTTGGTGCAATATAATTAATGAATGTAGATTCTCACTGAAAATTTTGATTACACA
64 TATAATAATGCTTGGTGCAATGTAATTAATGAATGGAGATTCTCAGTGAAAATTTTGATTACACA
* * * * * *
43593 TTCCATTCATACACAAATGATATATCATTTATGAAACTATCACTCAGTGAGAGTCAAAGCCAGAG
129 TTTCATTCACAC-CAAATGATACATCACTTATGAAACTGTCACTCAGTGAGAGTCGAAGCCAGAG
* *
43658 CCAGGTACATCG
193 CCAAGTACATCA
* *
43670 AAACTAGTCTCTTATTTCCCTCCGATATTGAACAAAAACATAATTTTTGATATTTGAATTACAAT
1 AAACTAGTCTCCTATTTCCCTCCGATATTGAACAAAAACATAA-TTTTGAAATTTGAATTACAAT
* *
43735 ATAATAATGCTTGGTACAATGTAAATAATGAATGGAGATTCTCAGTGAAAATTTTGATTACACAT
65 ATAATAATGCTTGGTGCAATGTAATTAATGAATGGAGATTCTCAGTGAAAATTTTGATTACACAT
* * * *
43800 TTAATTCACACGCAAATGATACATCACATATGAAACTGTCACTCAGTGAAAGTTGAAGCCAGAGC
130 TTCATTCACAC-CAAATGATACATCACTTATGAAACTGTCACTCAGTGAGAGTCGAAGCCAGAGC
* *
43865 TAGGTACATCA
194 CAAGTACATCA
* *
43876 AAACTAGTCTCCTATTTCCCTCCGATATTGAACAAAAACATAATTTTAAAAGTTGAATTACAATA
1 AAACTAGTCTCCTATTTCCCTCCGATATTGAACAAAAACATAATTTTGAAATTTGAATTACAATA
* * * *
43941 TAATAAAGCTTGGTGCAGA-GTAATTAATAAATGGAGATTTTCAGTGAAAATTTTGATTACACGT
66 TAATAATGCTTGGTGCA-ATGTAATTAATGAATGGAGATTCTCAGTGAAAATTTTGATTACACAT
* * * * * *
44005 TTCATTTACA-CAAATGATAAATCACTTATAAAACTATCACTCAGTGAGAGTTGAAGCCAGAGTC
130 TTCATTCACACCAAATGATACATCACTTATGAAACTGTCACTCAGTGAGAGTCGAAGCCAGAGCC
44069 AAGTACATCA
195 AAGTACATCA
* **
44079 AAACTAGTCTCTTATTTCCCTATGATATTGAACAAAAACATAATTTTGAAATTTGAATTACAATA
1 AAACTAGTCTCCTATTTCCCTCCGATATTGAACAAAAACATAATTTTGAAATTTGAATTACAATA
* * * * * *
44144 TAATAATGTTTGGTGCAGTGTAATTAATGAAT-GAGATTCTCAATAAAAATTTTGATTGCACGTT
66 TAATAATGCTTGGTGCAATGTAATTAATGAATGGAGATTCTCAGTGAAAATTTTGATTACACATT
* * * * * *
44208 TCATTTACA-CAAATGATACCTCACTTATGAAATTGTCACTTAGTGAGAGTCGAAGTCAAAGCCA
131 TCATTCACACCAAATGATACATCACTTATGAAACTGTCACTCAGTGAGAGTCGAAGCCAGAGCCA
**
44272 AGTACATTG
196 AGTACATCA
* * * * *
44281 AAATTAGTCTCCTATTTCCCTCCTATATTGAACAAAAAAAATAAATTTGAAATTTAAATTACAAT
1 AAACTAGTCTCCTATTTCCCTCCGATATTGAAC-AAAAACATAATTTTGAAATTTGAATTACAAT
* * *
44346 ATAATAATGCTTGGTGCATTGTAATTAATGAATGGATATTC-CTTGTGAAAATTTTGATTACAC-
65 ATAATAATGCTTGGTGCAATGTAATTAATGAATGGAGATTCTC-AGTGAAAATTTTGATTACACA
* * * * **
44409 GTTCATTCACACACAAATGATATATCACTTATGAAATTGTCACTCAGTGAAAGTCGAAATCAGAG
129 TTTCATTCACAC-CAAATGATACATCACTTATGAAACTGTCACTCAGTGAGAGTCGAAGCCAGAG
44474 CCAAGTACATCA
193 CCAAGTACATCA
**
44486 AAACTAGTCTCCTATTTCCCTCATATATTGAACAAA
1 AAACTAGTCTCCTATTTCCCTCCGATATTGAACAAA
44522 GACCCAAGTT
Statistics
Matches: 744, Mismatches: 99, Indels: 20
0.86 0.11 0.02
Matches are distributed among these distances:
202 117 0.16
203 212 0.28
204 25 0.03
205 170 0.23
206 219 0.29
207 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (204 bp):
AAACTAGTCTCCTATTTCCCTCCGATATTGAACAAAAACATAATTTTGAAATTTGAATTACAATA
TAATAATGCTTGGTGCAATGTAATTAATGAATGGAGATTCTCAGTGAAAATTTTGATTACACATT
TCATTCACACCAAATGATACATCACTTATGAAACTGTCACTCAGTGAGAGTCGAAGCCAGAGCCA
AGTACATCA
Found at i:44483 original size:205 final size:204
Alignment explanation
Indices: 43488--44521 Score: 1321
Period size: 203 Copynumber: 5.1 Consensus size: 204
43478 TTTCCCTTTG
* * *
43488 ATATTGAACAAAAA-ATTATTTTTTGAAATTTAAATTACAATATAATAATGCTTGGTGCAATATA
1 ATATTGAACAAAAACA-TA-ATTTTGAAATTTGAATTACAATATAATAATGCTTGGTGCAATGTA
* * * *
43552 ATTAATGAATGTAGATTCTCACTGAAAATTTTGATTACACATTCCATTCATACACAAATGATATA
64 ATTAATGAATGGAGATTCTCAGTGAAAATTTTGATTACACGTT-CATTCATACACAAATGATACA
* * * * * *
43617 TCATTTATGAAACTATCACTCAGTGAGAGTCAAAGCCAGAGCCAGGTACATCGAAACTAGTCTCT
128 TCACTTATGAAACTGTCACTCAGTGAGAGTCGAAGCCAGAGCCAAGTACATCAAAACTAGTCTCC
*
43682 TATTTCCCTCCG
193 TATTTCCCTCCT
* *
43694 ATATTGAACAAAAACATAATTTTTGATATTTGAATTACAATATAATAATGCTTGGTACAATGTAA
1 ATATTGAACAAAAACATAA-TTTTGAAATTTGAATTACAATATAATAATGCTTGGTGCAATGTAA
* * * * *
43759 ATAATGAATGGAGATTCTCAGTGAAAATTTTGATTACACATTTAATTCACACGCAAATGATACAT
65 TTAATGAATGGAGATTCTCAGTGAAAATTTTGATTACAC-GTTCATTCATACACAAATGATACAT
* * * * *
43824 CACATATGAAACTGTCACTCAGTGAAAGTTGAAGCCAGAGCTAGGTACATCAAAACTAGTCTCCT
129 CACTTATGAAACTGTCACTCAGTGAGAGTCGAAGCCAGAGCCAAGTACATCAAAACTAGTCTCCT
*
43889 ATTTCCCTCCG
194 ATTTCCCTCCT
* * *
43900 ATATTGAACAAAAACATAATTTTAAAAGTTGAATTACAATATAATAAAGCTTGGTGCAGA-GTAA
1 ATATTGAACAAAAACATAATTTTGAAATTTGAATTACAATATAATAATGCTTGGTGCA-ATGTAA
* * *
43964 TTAATAAATGGAGATTTTCAGTGAAAATTTTGATTACACGTTTCATT--TACACAAATGATAAAT
65 TTAATGAATGGAGATTCTCAGTGAAAATTTTGATTACACG-TTCATTCATACACAAATGATACAT
* * * * *
44027 CACTTATAAAACTATCACTCAGTGAGAGTTGAAGCCAGAGTCAAGTACATCAAAACTAGTCTCTT
129 CACTTATGAAACTGTCACTCAGTGAGAGTCGAAGCCAGAGCCAAGTACATCAAAACTAGTCTCCT
*
44092 ATTTCCCT-AT
194 ATTTCCCTCCT
* *
44102 GATATTGAACAAAAACATAATTTTGAAATTTGAATTACAATATAATAATGTTTGGTGCAGTGTAA
1 -ATATTGAACAAAAACATAATTTTGAAATTTGAATTACAATATAATAATGCTTGGTGCAATGTAA
* * * *
44167 TTAATGAAT-GAGATTCTCAATAAAAATTTTGATTGCACGTTTCATT--TACACAAATGATACCT
65 TTAATGAATGGAGATTCTCAGTGAAAATTTTGATTACACG-TTCATTCATACACAAATGATACAT
* * * * ** *
44229 CACTTATGAAATTGTCACTTAGTGAGAGTCGAAGTCAAAGCCAAGTACATTGAAATTAGTCTCCT
129 CACTTATGAAACTGTCACTCAGTGAGAGTCGAAGCCAGAGCCAAGTACATCAAAACTAGTCTCCT
44294 ATTTCCCTCCT
194 ATTTCCCTCCT
* * * *
44305 ATATTGAACAAAAAAAATAAATTTGAAATTTAAATTACAATATAATAATGCTTGGTGCATTGTAA
1 ATATTGAAC-AAAAACATAATTTTGAAATTTGAATTACAATATAATAATGCTTGGTGCAATGTAA
* * * *
44370 TTAATGAATGGATATTC-CTTGTGAAAATTTTGATTACACGTTCATTCACACACAAATGATATAT
65 TTAATGAATGGAGATTCTC-AGTGAAAATTTTGATTACACGTTCATTCATACACAAATGATACAT
* * **
44434 CACTTATGAAATTGTCACTCAGTGAAAGTCGAAATCAGAGCCAAGTACATCAAAACTAGTCTCCT
129 CACTTATGAAACTGTCACTCAGTGAGAGTCGAAGCCAGAGCCAAGTACATCAAAACTAGTCTCCT
*
44499 ATTTCCCTCAT
194 ATTTCCCTCCT
44510 ATATTGAACAAA
1 ATATTGAACAAA
44522 GACCCAAGTT
Statistics
Matches: 724, Mismatches: 91, Indels: 28
0.86 0.11 0.03
Matches are distributed among these distances:
202 117 0.16
203 211 0.29
204 26 0.04
205 169 0.23
206 198 0.27
207 3 0.00
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (204 bp):
ATATTGAACAAAAACATAATTTTGAAATTTGAATTACAATATAATAATGCTTGGTGCAATGTAAT
TAATGAATGGAGATTCTCAGTGAAAATTTTGATTACACGTTCATTCATACACAAATGATACATCA
CTTATGAAACTGTCACTCAGTGAGAGTCGAAGCCAGAGCCAAGTACATCAAAACTAGTCTCCTAT
TTCCCTCCT
Found at i:44865 original size:28 final size:28
Alignment explanation
Indices: 44807--44867 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
44797 TGAAATACAT
* **
44807 AATTTAAAAATTAATTAAAACATTTTAA
1 AATTTAAAAATCAATTAAAACATAATAA
*
44835 AATTTAAAAATCAACTTAAAAC-TAATGA
1 AATTTAAAAATCAA-TTAAAACATAATAA
44863 AATTT
1 AATTT
44868 GGCCTTTGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 21 0.75
29 7 0.25
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.36
Consensus pattern (28 bp):
AATTTAAAAATCAATTAAAACATAATAA
Found at i:46030 original size:59 final size:59
Alignment explanation
Indices: 45960--46076 Score: 225
Period size: 59 Copynumber: 2.0 Consensus size: 59
45950 CTTAAACCAA
45960 CACAACGACACTTTTCTTTCAATCATTTGATTTGAGTTTGAAATCTTTAAAACATAGAG
1 CACAACGACACTTTTCTTTCAATCATTTGATTTGAGTTTGAAATCTTTAAAACATAGAG
*
46019 CACAACTACACTTTTCTTTCAATCATTTGATTTGAGTTTGAAATCTTTAAAACATAGA
1 CACAACGACACTTTTCTTTCAATCATTTGATTTGAGTTTGAAATCTTTAAAACATAGA
46077 ATGCTTTACT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.38
Consensus pattern (59 bp):
CACAACGACACTTTTCTTTCAATCATTTGATTTGAGTTTGAAATCTTTAAAACATAGAG
Found at i:47134 original size:3 final size:3
Alignment explanation
Indices: 47126--47150 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
47116 CAGAATAAAC
47126 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
47151 CGTTCTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:49561 original size:96 final size:96
Alignment explanation
Indices: 49397--49589 Score: 368
Period size: 96 Copynumber: 2.0 Consensus size: 96
49387 CTTATGTAAA
*
49397 TCTTAAATAAAAGCTCTAAACAAATACCTCCAATTTATTTGTGACTTGACTAAAACATGTTCCAA
1 TCTTAAATAAAAGCTCTAAACAAATACCTCCAATTTATTTGTAACTTGACTAAAACATGTTCCAA
*
49462 ACTTATCTAATTTAAAACTTAAATTAGAATT
66 ACTTATCTAATTTAAAACTTAAATTAAAATT
49493 TCTTAAATAAAAGCTCTAAACAAATACCTCCAATTTATTTGTAACTTGACTAAAACATGTTCCAA
1 TCTTAAATAAAAGCTCTAAACAAATACCTCCAATTTATTTGTAACTTGACTAAAACATGTTCCAA
49558 ACTTATCTAATTTAAAACTTAAATTAAAATT
66 ACTTATCTAATTTAAAACTTAAATTAAAATT
49589 T
1 T
49590 TTTTACTCCT
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 95 1.00
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.36
Consensus pattern (96 bp):
TCTTAAATAAAAGCTCTAAACAAATACCTCCAATTTATTTGTAACTTGACTAAAACATGTTCCAA
ACTTATCTAATTTAAAACTTAAATTAAAATT
Found at i:50414 original size:26 final size:25
Alignment explanation
Indices: 50383--50432 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 25
50373 AAAAATTCAT
50383 AAATAT-AAATAAAAATGAAAGTAAAC
1 AAATATGAAATAAAAAT-AAA-TAAAC
50409 AAATATGAAATAAAAATAAATAAA
1 AAATATGAAATAAAAATAAATAAA
50433 AATTATGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 4 0.17
26 9 0.39
27 10 0.43
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.20
Consensus pattern (25 bp):
AAATATGAAATAAAAATAAATAAAC
Found at i:51374 original size:154 final size:155
Alignment explanation
Indices: 51026--51382 Score: 455
Period size: 155 Copynumber: 2.3 Consensus size: 155
51016 AAAATAATAT
* * * *
51026 TTTACTTAAAAATCTAAA-CTTTTATTTCGAAATAATT----AAAAAATCGAAACTTTGTTAAAA
1 TTTACTTAAAAATCCAAAGTTTTTATTTCGAAATAGTTAGAAAAAAAATCAAAACTTTGTTAAAA
* * *
51086 ATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTTAAAAAATCTAAACTTTC
66 ATTTAAACTTTTTCTTTAAAATAACTAAAAAACAAAATTTTATTTTTTAAAAAATATAAACTTTC
* *
51151 TCCTTTTTTTTAAAAAAATCACTAT
131 TCCTTTTTTTCAAAAAAATCACTAG
*
51176 TTTACTTAAAAATCCAAATTTTTTATTTCGAAATAGTTAGAAAAAAAATCAAAACTTTGTTAAAA
1 TTTACTTAAAAATCCAAAGTTTTTATTTCGAAATAGTTAGAAAAAAAATCAAAACTTTGTTAAAA
* *
51241 TTTTAAATTTTTTCTTTAAAATAACTAAAAAAACAAAATTTTA-TTTTT-AAAAATATAAACTTT
66 ATTTAAACTTTTTCTTTAAAATAACT-AAAAAACAAAATTTTATTTTTTAAAAAATATAAACTTT
*
51304 CT-C-TTTTTTCAAGAAAATCACTAG
130 CTCCTTTTTTTCAAAAAAATCACTAG
* * ** *
51328 TTTGCTTAAAAAAAT-CAAAGTTTTTATTTCGAAATTGTTTTAAAAAAAACCAAAA
1 TTTACTT--AAAAATCCAAAGTTTTTATTTCGAAATAGTTAGAAAAAAAATCAAAA
51383 TATTTCCCAA
Statistics
Matches: 181, Mismatches: 18, Indels: 13
0.85 0.08 0.06
Matches are distributed among these distances:
150 17 0.09
151 17 0.09
152 24 0.13
153 36 0.20
154 22 0.12
155 51 0.28
156 14 0.08
ACGTcount: A:0.45, C:0.10, G:0.04, T:0.41
Consensus pattern (155 bp):
TTTACTTAAAAATCCAAAGTTTTTATTTCGAAATAGTTAGAAAAAAAATCAAAACTTTGTTAAAA
ATTTAAACTTTTTCTTTAAAATAACTAAAAAACAAAATTTTATTTTTTAAAAAATATAAACTTTC
TCCTTTTTTTCAAAAAAATCACTAG
Found at i:51395 original size:154 final size:155
Alignment explanation
Indices: 51082--51395 Score: 395
Period size: 153 Copynumber: 2.0 Consensus size: 155
51072 AAACTTTGTT
* * * *
51082 AAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTTAAAAAATCTAAAC
1 AAAATTTTAAACTTTTTCTTTAAAATAACTAAAAAACAAAATTTTATTTTTTAAAAAATATAAAC
* * *
51147 TTTCTCCTTTTTTTTAAAAAAATCACTATTTTACTTAAAAATCCAAATTTTTTATTTCGAAATAG
66 TTTCTCCTTTTTTTCAAAAAAATCACTAGTTTACTTAAAAATCCAAAGTTTTTATTTCGAAATAG
* * ***
51212 TTAGAAAAAAAATCAAAACTTTGTT
131 TTAGAAAAAAAACCAAAAATTTCCC
*
51237 AAAATTTTAAATTTTTTCTTTAAAATAACTAAAAAAACAAAATTTTA-TTTTT-AAAAATATAAA
1 AAAATTTTAAACTTTTTCTTTAAAATAACT-AAAAAACAAAATTTTATTTTTTAAAAAATATAAA
* *
51300 CTTTCT-C-TTTTTTCAAGAAAATCACTAGTTTGCTTAAAAAAAT-CAAAGTTTTTATTTCGAAA
65 CTTTCTCCTTTTTTTCAAAAAAATCACTAGTTTACTT--AAAAATCCAAAGTTTTTATTTCGAAA
* **
51362 TTGTTTTAAAAAAAACCAAAATATTTCCC
128 TAGTTAGAAAAAAAACCAAAA-ATTTCCC
51391 AAAAT
1 AAAAT
51396 CAAGTTATTT
Statistics
Matches: 137, Mismatches: 18, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
152 24 0.18
153 36 0.26
154 30 0.22
155 33 0.24
156 14 0.10
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.41
Consensus pattern (155 bp):
AAAATTTTAAACTTTTTCTTTAAAATAACTAAAAAACAAAATTTTATTTTTTAAAAAATATAAAC
TTTCTCCTTTTTTTCAAAAAAATCACTAGTTTACTTAAAAATCCAAAGTTTTTATTTCGAAATAG
TTAGAAAAAAAACCAAAAATTTCCC
Found at i:51875 original size:11 final size:11
Alignment explanation
Indices: 51861--51885 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
51851 CTCAAAAAAG
51861 AAAGAAAAATA
1 AAAGAAAAATA
51872 AAAGAAAAATA
1 AAAGAAAAATA
51883 AAA
1 AAA
51886 ACCTCTATTT
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:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAGAAAAATA
Found at i:62788 original size:28 final size:28
Alignment explanation
Indices: 62748--62805 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
62738 CATTTCGCAG
62748 TTAGGAAAATTTTGAAAATAATTACGGA
1 TTAGGAAAATTTTGAAAATAATTACGGA
* *
62776 TTAGGAAAATTTTGAAATTAATTGCGGA
1 TTAGGAAAATTTTGAAAATAATTACGGA
62804 TT
1 TT
62806 CAATTTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.41, C:0.03, G:0.19, T:0.36
Consensus pattern (28 bp):
TTAGGAAAATTTTGAAAATAATTACGGA
Found at i:63197 original size:21 final size:20
Alignment explanation
Indices: 63173--63213 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
63163 TAATATTTTT
63173 TATTTAATTAATTTTTGTAAA
1 TATTTAATTAATTTTT-TAAA
**
63194 TATTTCGTTAATTTTTTAAA
1 TATTTAATTAATTTTTTAAA
63214 CAATATACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (20 bp):
TATTTAATTAATTTTTTAAA
Found at i:70550 original size:28 final size:28
Alignment explanation
Indices: 70514--70576 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
70504 AAAATGAGAC
* *
70514 ATTTCGGATACCCGGGGGTAAAATGGTA
1 ATTTTGGATACCCGAGGGTAAAATGGTA
* * *
70542 ATTTTGGATTCTCGAGGGTGAAATGGTA
1 ATTTTGGATACCCGAGGGTAAAATGGTA
70570 ATTTTGG
1 ATTTTGG
70577 GAAAATTCGG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.25, C:0.10, G:0.32, T:0.33
Consensus pattern (28 bp):
ATTTTGGATACCCGAGGGTAAAATGGTA
Found at i:70720 original size:30 final size:29
Alignment explanation
Indices: 70678--71050 Score: 225
Period size: 30 Copynumber: 12.9 Consensus size: 29
70668 ATCCGGGGGC
*
70678 AAAATGGTAATTTTTGGAAGTTTTAGGGTTT
1 AAAAT-GTAATTTTTGGAAGTTTTAGGG-TA
** *
70709 AAAATGTAATTTTTAAAAGTTTGAGGGTA
1 AAAATGTAATTTTTGGAAGTTTTAGGGTA
* *
70738 AAAATGGAAATTTTGGAAGTTTTAGGGTTA
1 AAAATGTAATTTTTGGAAGTTTTAGGG-TA
** *
70768 AAAATGGGATTTTTGGAAGTTTTGGGGTTA
1 AAAATGTAATTTTTGGAAGTTTTAGGG-TA
* * * *
70798 AAATTGGAGTTTTT-G--G-----GGTTA
1 AAAATGTAATTTTTGGAAGTTTTAGGGTA
* *
70819 AAATTG-AGATTTTTAGAAG-TTTAGGGGTA
1 AAAATGTA-ATTTTTGGAAGTTTTA-GGGTA
* *
70848 AAAATGTAATTTTTGGAAGCTTTGGGGTTA
1 AAAATGTAATTTTTGGAAGTTTTAGGG-TA
** * * *
70878 AAAATGGGATTTTTAGAAGCTTAAGGGTTA
1 AAAATGTAATTTTTGGAAGTTTTAGGG-TA
* * * *
70908 AAAATAG-AATTTTCGGAAGTTTGAAGGTT
1 AAAAT-GTAATTTTTGGAAGTTTTAGGGTA
* **
70937 AAAATGTGATTTTTGGAAGTTCGAGGGTA
1 AAAATGTAATTTTTGGAAGTTTTAGGGTA
** *
70966 AAAATAAAATTTTTGGAAGTTTTGGGGTA
1 AAAATGTAATTTTTGGAAGTTTTAGGGTA
* *
70995 AAAATTGTGATTTTTAGAAG-TTTAGGGGT-
1 AAAA-TGTAATTTTTGGAAGTTTTA-GGGTA
*
71024 AAAATGGAATTTTTGGGAAG-TTTAGGG
1 AAAATGTAATTTTT-GGAAGTTTTAGGG
71051 ACCTCCAGGG
Statistics
Matches: 272, Mismatches: 52, Indels: 39
0.75 0.14 0.11
Matches are distributed among these distances:
20 1 0.00
21 13 0.05
22 3 0.01
24 1 0.00
27 1 0.00
28 12 0.04
29 111 0.41
30 124 0.46
31 6 0.02
ACGTcount: A:0.33, C:0.01, G:0.28, T:0.38
Consensus pattern (29 bp):
AAAATGTAATTTTTGGAAGTTTTAGGGTA
Found at i:70752 original size:59 final size:59
Alignment explanation
Indices: 70678--71050 Score: 305
Period size: 59 Copynumber: 6.5 Consensus size: 59
70668 ATCCGGGGGC
* * * *
70678 AAAATGGTAATTTTTGGAAGTTTTAGGGTTTAAAATGTAATTTTTAAAAGTTTGAGGGTA
1 AAAATGG-AAATTTTGGAAGTTTTAGGGTTAAAAATGTGATTTTTAGAAGTTTGAGGGTA
* *
70738 AAAATGGAAATTTTGGAAGTTTTAGGGTTAAAAATGGGATTTTTGGAAGTTTTG-GGGT-
1 AAAATGGAAATTTTGGAAGTTTTAGGGTTAAAAATGTGATTTTTAGAAG-TTTGAGGGTA
* * * *
70796 ----T--AAA-ATTGG-AGTTTTTGGGGTTAAAATTGAGATTTTTAGAAGTTT-AGGGGTA
1 AAAATGGAAATTTTGGAAG-TTTTAGGGTTAAAAATGTGATTTTTAGAAGTTTGA-GGGTA
* * * * * * *
70848 AAAATGTAATTTTTGGAAGCTTTGGGGTTAAAAATGGGATTTTTAGAAGCTTAAGGGTTA
1 AAAATGGAAATTTTGGAAGTTTTAGGGTTAAAAATGTGATTTTTAGAAGTTTGAGGG-TA
* * * * *
70908 AAAATAG-AATTTTCGGAAGTTTGAAGGTT-AAAATGTGATTTTTGGAAGTTCGAGGGTA
1 AAAATGGAAATTTT-GGAAGTTTTAGGGTTAAAAATGTGATTTTTAGAAGTTTGAGGGTA
* *
70966 AAAAT-AAAATTTTTGGAAGTTTT-GGGGTAAAAATTGTGATTTTTAGAAGTTT-AGGGGT-
1 AAAATGGAAA-TTTTGGAAGTTTTAGGGTTAAAAA-TGTGATTTTTAGAAGTTTGA-GGGTA
*
71024 AAAATGGAATTTTTGGGAAG-TTTAGGG
1 AAAATGGAAATTTT-GGAAGTTTTAGGG
71051 ACCTCCAGGG
Statistics
Matches: 252, Mismatches: 37, Indels: 49
0.75 0.11 0.14
Matches are distributed among these distances:
50 5 0.02
51 34 0.13
52 3 0.01
54 1 0.00
56 1 0.00
57 3 0.01
58 36 0.14
59 137 0.54
60 32 0.13
ACGTcount: A:0.33, C:0.01, G:0.28, T:0.38
Consensus pattern (59 bp):
AAAATGGAAATTTTGGAAGTTTTAGGGTTAAAAATGTGATTTTTAGAAGTTTGAGGGTA
Found at i:70804 original size:21 final size:21
Alignment explanation
Indices: 70787--70832 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
70777 TTTTTGGAAG
70787 TTTTGGGGTTAAAATTGGAGT
1 TTTTGGGGTTAAAATTGGAGT
70808 TTTTGGGGTTAAAATT-GAGAT
1 TTTTGGGGTTAAAATTGGAG-T
70829 TTTT
1 TTTT
70833 AGAAGTTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (21 bp):
TTTTGGGGTTAAAATTGGAGT
Found at i:70810 original size:20 final size:22
Alignment explanation
Indices: 70780--70824 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
70770 AATGGGATTT
70780 TTGGAAG-TTTTGGGGTTAAAA
1 TTGGAAGTTTTTGGGGTTAAAA
70801 TTGG-AGTTTTTGGGGTTAAAA
1 TTGGAAGTTTTTGGGGTTAAAA
70822 TTG
1 TTG
70825 AGATTTTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.24, C:0.00, G:0.33, T:0.42
Consensus pattern (22 bp):
TTGGAAGTTTTTGGGGTTAAAA
Found at i:72031 original size:31 final size:32
Alignment explanation
Indices: 71955--72035 Score: 94
Period size: 34 Copynumber: 2.5 Consensus size: 32
71945 ACCTTTCGTT
* *
71955 TTTTTATTATTTAATAATTATTAATATCAAAACA
1 TTTTTATTA-TTAATGATTATTAAGA-CAAAACA
71989 TTTATTATTATTAATGATTATTAAGA-AAAAC-
1 TTT-TTATTATTAATGATTATTAAGACAAAACA
72020 TTATTTATTATTAATG
1 TT-TTTATTATTAATG
72036 GGGTCATTAG
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
31 14 0.33
32 6 0.14
34 17 0.40
35 6 0.14
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (32 bp):
TTTTTATTATTAATGATTATTAAGACAAAACA
Found at i:72668 original size:40 final size:38
Alignment explanation
Indices: 72599--72678 Score: 99
Period size: 39 Copynumber: 2.1 Consensus size: 38
72589 TTTAGGCTAG
** *
72599 TTTGGGTCATTTAGTTTGGGCTTATTTGGGCCTTTGTAA
1 TTTGGGTCATTTAGTTTGGGCCCAATTGGG-CTTTGTAA
72638 TTTGGGTCATCTTTA-TTTGGGCCCAATTGGGCTTTGTAA
1 TTTGGGTCA--TTTAGTTTGGGCCCAATTGGGCTTTGTAA
72677 TT
1 TT
72679 GGACATTTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
39 19 0.53
40 13 0.36
41 4 0.11
ACGTcount: A:0.14, C:0.12, G:0.26, T:0.47
Consensus pattern (38 bp):
TTTGGGTCATTTAGTTTGGGCCCAATTGGGCTTTGTAA
Found at i:72723 original size:17 final size:17
Alignment explanation
Indices: 72703--72778 Score: 80
Period size: 18 Copynumber: 4.4 Consensus size: 17
72693 TGAACTTCAT
* *
72703 TTTAAATTTATAATAAT
1 TTTAAATTTAAAATAAA
*
72720 TTTAATTTTGAAAATAAA
1 TTTAAATTT-AAAATAAA
*
72738 TTTAAACTTAAAATAAA
1 TTTAAATTTAAAATAAA
* *
72755 TTTAAATTTTTAAACAAA
1 TTTAAA-TTTAAAATAAA
72773 TTTAAA
1 TTTAAA
72779 CCTAAAAATA
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
17 22 0.45
18 27 0.55
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:72764 original size:36 final size:35
Alignment explanation
Indices: 72703--72796 Score: 100
Period size: 36 Copynumber: 2.7 Consensus size: 35
72693 TGAACTTCAT
* * * *
72703 TTTAAATTTATAAT-AATTTTAATTTTGAAAATAAA
1 TTTAAACTTAAAATAAATTTAAATTTT-AAAACAAA
*
72738 TTTAAACTTAAAATAAATTTAAATTTTTAAACAAA
1 TTTAAACTTAAAATAAATTTAAATTTTAAAACAAA
* *
72773 TTTAAACCTAAAAATATATTTAAA
1 TTTAAA-CTTAAAATAAATTTAAA
72797 ATGAGTTTGG
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
35 24 0.48
36 26 0.52
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (35 bp):
TTTAAACTTAAAATAAATTTAAATTTTAAAACAAA
Found at i:73637 original size:206 final size:206
Alignment explanation
Indices: 73268--74023 Score: 1103
Period size: 206 Copynumber: 3.7 Consensus size: 206
73258 TTACTTCCCT
* *
73268 GTATTTCATCAGGACGCTAACCATTTTATTACTTCGA-CTCGCTTCTCAGTATCTCATCAGGAAG
1 GTATCTCATCAGGAAGCTAACC-TTTTATTACTTCGACCT-GCTTCTCAGTATCTCATCAGGAAG
* * * * * **
73332 CTGTGGTTCGAAGA-TTTGCTCACATCGAACGTGAATTTGGTTTGGTCTTCTTCTCAGTATCTCA
64 CTGGGGTTCGAAGATTTTGCTCGCTTTGAGCGTGGGTTTGGTTTGGTCTTCTTCTCAGTATCTCA
** * * * *
73396 TCAGGAAGATGGTCGCATCATTTGTTTCAATTCGCTTGTCTGTAACTCATCCGAAAGACGAATTT
129 TCAGGAAGATGACCGCGTCATTAGTTTCAATTCGCTTGTCTGTAACTCATCAGGAAGACGAATTT
73461 GGTCCACTTCTCA
194 GGTCCACTTCTCA
* * *
73474 GTATCTCATCGGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCT
1 GTATCTCATCAGGAAGCTAACCTTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT
* *
73539 GAGGTTCGAAGATTTTGCTCGTTTTGAGCGTGGGTTTGGTTTGGTCTTCTTCTCAGTATCTCATC
66 GGGGTTCGAAGATTTTGCTCGCTTTGAGCGTGGGTTTGGTTTGGTCTTCTTCTCAGTATCTCATC
73604 AGGAAGATGACCGCGTCATTAGTTTCAATTCGCTTGTCTGTAACTCATCAGGAAGACGAATTTGG
131 AGGAAGATGACCGCGTCATTAGTTTCAATTCGCTTGTCTGTAACTCATCAGGAAGACGAATTTGG
73669 TCCACTTCTCA
196 TCCACTTCTCA
* * * * * ** *
73680 ATATCTCATTAGGAAACTAACCTTTTATTACTTCGACCTGCTTTTCAGTGTCTCATCAATAAGTT
1 GTATCTCATCAGGAAGCTAACCTTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT
* *
73745 GGGGTTCGAAGATTTTGCTCGTTTTGAGCATGGGTTTGGTTTGGTCTTCTTCTCAGTATCTCATC
66 GGGGTTCGAAGATTTTGCTCGCTTTGAGCGTGGGTTTGGTTTGGTCTTCTTCTCAGTATCTCATC
*
73810 AAGAAGATGACCGCGTCATTAGTTTCAATTCGCTTGTCTGTAACTCATCAGGAAGACGAATTTGG
131 AGGAAGATGACCGCGTCATTAGTTTCAATTCGCTTGTCTGTAACTCATCAGGAAGACGAATTTGG
* *
73875 TTCACTTCTCT
196 TCCACTTCTCA
* *
73886 GTATCTCATCAGGAAGCTAACCTTTTATTGCTTTGACCTGCTTCTCAGTATCTCATCAGGAAGCT
1 GTATCTCATCAGGAAGCTAACCTTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT
* * *
73951 GGGGTTCAAAGATTTTGCTCGCTTTGAGCCT-CGTTT-G---GGTCTTCTTCTCAGTATCTCATC
66 GGGGTTCGAAGATTTTGCTCGCTTTGAGCGTGGGTTTGGTTTGGTCTTCTTCTCAGTATCTCATC
74011 AGGAAGATGACCG
131 AGGAAGATGACCG
74024 TATCGCTGTT
Statistics
Matches: 500, Mismatches: 48, Indels: 9
0.90 0.09 0.02
Matches are distributed among these distances:
201 35 0.07
204 1 0.00
205 53 0.11
206 411 0.82
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (206 bp):
GTATCTCATCAGGAAGCTAACCTTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT
GGGGTTCGAAGATTTTGCTCGCTTTGAGCGTGGGTTTGGTTTGGTCTTCTTCTCAGTATCTCATC
AGGAAGATGACCGCGTCATTAGTTTCAATTCGCTTGTCTGTAACTCATCAGGAAGACGAATTTGG
TCCACTTCTCA
Done.