Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010872.1 Kokia drynarioides strain JFW-HI SEQ_125840, 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: 137820
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 36 characters in sequence are not A, C, G, or T
Found at i:8687 original size:28 final size:28
Alignment explanation
Indices: 8616--8672 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
8606 TTCATACTTC
8616 ATTCAATAATTAATCATAAAAATAACAT
1 ATTCAATAATTAATCATAAAAATAACAT
8644 ATTCAATAATTAATCATAAAAATAACAT
1 ATTCAATAATTAATCATAAAAATAACAT
8672 A
1 A
8673 CTTTATATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.32
Consensus pattern (28 bp):
ATTCAATAATTAATCATAAAAATAACAT
Found at i:15973 original size:42 final size:42
Alignment explanation
Indices: 15871--16101 Score: 327
Period size: 42 Copynumber: 5.5 Consensus size: 42
15861 TTGATGTATA
* * * * * *
15871 AAAGGAAGACTCGTGTCTCGGGTTGAGGATGAGAATTTGTATA
1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATG-ATT
* *
15914 AAAGGAAGACTCATGTCTCGAGATAAGAATGAGATTATGATT
1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATT
* *
15956 AAAGGAAGACTCGTGTCTCGAGATGAGAATGAGAATATGATC
1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATT
*
15998 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGTTT
1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATT
*
16040 AAAGGAAGACTCATGTCTCGGGATGAGAATGAGAATATGATT
1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATT
* *
16082 AAAGGAAGACTTATGACTCG
1 AAAGGAAGACTCATGTCTCG
16102 TTAGAGCATA
Statistics
Matches: 169, Mismatches: 19, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
42 137 0.81
43 32 0.19
ACGTcount: A:0.37, C:0.10, G:0.28, T:0.25
Consensus pattern (42 bp):
AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGATT
Found at i:17572 original size:43 final size:43
Alignment explanation
Indices: 17502--17599 Score: 126
Period size: 43 Copynumber: 2.3 Consensus size: 43
17492 AACATGGGGA
* *
17502 AGACACA-GAGGCGTGTTCCAAACCGTGTGTGTATACTGTTTTG
1 AGACACACG-GGCGTGTGCCAAACCGTGTGTGTATACTATTTTG
* * *
17545 AGGCACACGGGCGTGTGCCAGACCGTGTGTGTATCCTATTTTG
1 AGACACACGGGCGTGTGCCAAACCGTGTGTGTATACTATTTTG
*
17588 AGACACATGGGC
1 AGACACACGGGC
17600 CAGGCACACG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 46 0.98
44 1 0.02
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.27
Consensus pattern (43 bp):
AGACACACGGGCGTGTGCCAAACCGTGTGTGTATACTATTTTG
Found at i:18283 original size:15 final size:16
Alignment explanation
Indices: 18263--18293 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
18253 CATCTGAATC
18263 TATTTT-TGTATCTGA
1 TATTTTGTGTATCTGA
18278 TATTTTGTGTATCTGA
1 TATTTTGTGTATCTGA
18294 GTGGCACTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.19, C:0.06, G:0.16, T:0.58
Consensus pattern (16 bp):
TATTTTGTGTATCTGA
Found at i:23557 original size:37 final size:37
Alignment explanation
Indices: 23498--23638 Score: 165
Period size: 37 Copynumber: 3.8 Consensus size: 37
23488 GTTCTTGGAT
* * ** * *
23498 CACCGGCATAAAGCCTGTTAGGCACATAGCCCGAATA
1 CACCGACACAAAGCCTACTAGGCACAAAGCCTGAATA
*
23535 CACCAACACAAAGCCTACTAGGCACAAAGCCTGAATA
1 CACCGACACAAAGCCTACTAGGCACAAAGCCTGAATA
* * *
23572 CACCGGCACAAAGCCTACTAGGCACACAGCTTGAATA
1 CACCGACACAAAGCCTACTAGGCACAAAGCCTGAATA
** *
23609 CACCGACATGAAGCCTACTCGGCACAAAGC
1 CACCGACACAAAGCCTACTAGGCACAAAGC
23639 TTAAAAACAT
Statistics
Matches: 88, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 88 1.00
ACGTcount: A:0.36, C:0.33, G:0.18, T:0.13
Consensus pattern (37 bp):
CACCGACACAAAGCCTACTAGGCACAAAGCCTGAATA
Found at i:23562 original size:16 final size:16
Alignment explanation
Indices: 23541--23597 Score: 60
Period size: 16 Copynumber: 3.2 Consensus size: 16
23531 AATACACCAA
23541 CACAAAGCCTACTAGG
1 CACAAAGCCTACTAGG
*
23557 CACAAAGCCTGAATACACCGG
1 CACAAAGCCT-ACT--A--GG
23578 CACAAAGCCTACTAGG
1 CACAAAGCCTACTAGG
23594 CACA
1 CACA
23598 CAGCTTGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
16 16 0.47
17 2 0.06
18 1 0.03
19 1 0.03
20 2 0.06
21 12 0.35
ACGTcount: A:0.39, C:0.33, G:0.18, T:0.11
Consensus pattern (16 bp):
CACAAAGCCTACTAGG
Found at i:23623 original size:74 final size:74
Alignment explanation
Indices: 23498--23638 Score: 192
Period size: 74 Copynumber: 1.9 Consensus size: 74
23488 GTTCTTGGAT
* ** *
23498 CACCGGCATAAAGCCTGTTAGGCACATAGCCCGAATACACCAACACAAAGCCTACTAGGCACAAA
1 CACCGGCACAAAGCCTACTAGGCACACAGCCCGAATACACCAACACAAAGCCTACTAGGCACAAA
23563 GCCTGAATA
66 GCCTGAATA
** * ** *
23572 CACCGGCACAAAGCCTACTAGGCACACAGCTTGAATACACCGACATGAAGCCTACTCGGCACAAA
1 CACCGGCACAAAGCCTACTAGGCACACAGCCCGAATACACCAACACAAAGCCTACTAGGCACAAA
23637 GC
66 GC
23639 TTAAAAACAT
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
74 57 1.00
ACGTcount: A:0.36, C:0.33, G:0.18, T:0.13
Consensus pattern (74 bp):
CACCGGCACAAAGCCTACTAGGCACACAGCCCGAATACACCAACACAAAGCCTACTAGGCACAAA
GCCTGAATA
Found at i:23679 original size:21 final size:21
Alignment explanation
Indices: 23628--23682 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
23618 GAAGCCTACT
* *
23628 CGGCACAAAGCTTAAAAACAT
1 CGGCACAAAGCCTAAAAACAC
*
23649 TGGC-CAAAGCCTAAAAACAC
1 CGGCACAAAGCCTAAAAACAC
*
23669 CGGCACGAAGCCTA
1 CGGCACAAAGCCTA
23683 CTAGGCACAC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.42, C:0.29, G:0.18, T:0.11
Consensus pattern (21 bp):
CGGCACAAAGCCTAAAAACAC
Found at i:23707 original size:37 final size:37
Alignment explanation
Indices: 23653--23811 Score: 237
Period size: 37 Copynumber: 4.3 Consensus size: 37
23643 AAACATTGGC
*
23653 CAAAGCCTAAAAACACCGGCACGAAGCCTACTAGGCA
1 CAAAGCCTGAAAACACCGGCACGAAGCCTACTAGGCA
* ** * *
23690 CACAGTTTGAATACACCGGCACGAAGCCTACTCGGCA
1 CAAAGCCTGAAAACACCGGCACGAAGCCTACTAGGCA
* *
23727 CAAAGCCTAAAAACACCGGCATGAAGCCTACTAGGCA
1 CAAAGCCTGAAAACACCGGCACGAAGCCTACTAGGCA
23764 CAAAGCCTGAAAACACCGGCACGAAGCCTACTAGGCA
1 CAAAGCCTGAAAACACCGGCACGAAGCCTACTAGGCA
*
23801 CAATGCCTGAA
1 CAAAGCCTGAA
23812 TTTTAAATGT
Statistics
Matches: 106, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 106 1.00
ACGTcount: A:0.37, C:0.31, G:0.20, T:0.11
Consensus pattern (37 bp):
CAAAGCCTGAAAACACCGGCACGAAGCCTACTAGGCA
Found at i:23720 original size:94 final size:94
Alignment explanation
Indices: 23559--23741 Score: 303
Period size: 94 Copynumber: 1.9 Consensus size: 94
23549 CTACTAGGCA
* * *
23559 CAAAGCCTGAATACACCGGCACAAAGCCTACTAGGCACACAGCTTGAATACACCGACATGAAGCC
1 CAAAGCCTAAAAACACCGGCACAAAGCCTACTAGGCACACAGCTTGAATACACCGACACGAAGCC
*
23624 TACTCGGCACAAAGCTTAAAAACATTGGC
66 TACTCGGCACAAAGCCTAAAAACATTGGC
* * *
23653 CAAAGCCTAAAAACACCGGCACGAAGCCTACTAGGCACACAGTTTGAATACACCGGCACGAAGCC
1 CAAAGCCTAAAAACACCGGCACAAAGCCTACTAGGCACACAGCTTGAATACACCGACACGAAGCC
23718 TACTCGGCACAAAGCCTAAAAACA
66 TACTCGGCACAAAGCCTAAAAACA
23742 CCGGCATGAA
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
94 82 1.00
ACGTcount: A:0.38, C:0.31, G:0.18, T:0.13
Consensus pattern (94 bp):
CAAAGCCTAAAAACACCGGCACAAAGCCTACTAGGCACACAGCTTGAATACACCGACACGAAGCC
TACTCGGCACAAAGCCTAAAAACATTGGC
Found at i:27086 original size:34 final size:35
Alignment explanation
Indices: 27028--27104 Score: 129
Period size: 34 Copynumber: 2.2 Consensus size: 35
27018 AAAATCAGAT
*
27028 CTTATTAGATTACATATATATTCTAAGATTACTTTC
1 CTTATTTGATTACA-ATATATTCTAAGATTACTTTC
27064 CTTATTTGATTAC-ATATATTCTAAGATTACTTTC
1 CTTATTTGATTACAATATATTCTAAGATTACTTTC
27098 CTTATTT
1 CTTATTT
27105 ACCAAGGTAG
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
34 28 0.70
36 12 0.30
ACGTcount: A:0.30, C:0.14, G:0.05, T:0.51
Consensus pattern (35 bp):
CTTATTTGATTACAATATATTCTAAGATTACTTTC
Found at i:27514 original size:34 final size:35
Alignment explanation
Indices: 27452--27523 Score: 110
Period size: 34 Copynumber: 2.0 Consensus size: 35
27442 TAAATATTAG
27452 GTAGTTAATAGTTAGTAACTGTTAGTAGCAGTTATGA
1 GTAGTTAATAGTTAGT-A-TGTTAGTAGCAGTTATGA
*
27489 GTAGTTAGTAGTTAGT-TGTTAGTAGCAGTTATGA
1 GTAGTTAATAGTTAGTATGTTAGTAGCAGTTATGA
27523 G
1 G
27524 CAGTAGAGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
34 19 0.56
37 15 0.44
ACGTcount: A:0.29, C:0.04, G:0.28, T:0.39
Consensus pattern (35 bp):
GTAGTTAATAGTTAGTATGTTAGTAGCAGTTATGA
Found at i:30969 original size:9 final size:9
Alignment explanation
Indices: 30955--31024 Score: 52
Period size: 9 Copynumber: 7.3 Consensus size: 9
30945 AAAATTCTTT
30955 AAAATTTAA
1 AAAATTTAA
30964 AAAATTTAA
1 AAAATTTAA
30973 AATAATTTTGAA
1 AA-AA-TTT-AA
*
30985 TAAATTT-A
1 AAAATTTAA
*
30993 AAAATAATAA
1 AAAAT-TTAA
*
31003 AAAATATAA
1 AAAATTTAA
*
31012 AAATTTCTAA
1 AAAATT-TAA
31022 AAA
1 AAA
31025 TTCAAATAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
8 5 0.10
9 20 0.40
10 17 0.34
11 5 0.10
12 3 0.06
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (9 bp):
AAAATTTAA
Found at i:31596 original size:45 final size:45
Alignment explanation
Indices: 31530--31620 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
31520 ATGTTACAAT
* *
31530 ATAATGGTTAATTAGGGAACTTTAAGGCAAATTATTTATGGGTAA
1 ATAATGGTTAACTAGGAAACTTTAAGGCAAATTATTTATGGGTAA
*
31575 ATAATGGTTAACTAGGAAACTTTGAGGCAAATTATTTATGGGTAA
1 ATAATGGTTAACTAGGAAACTTTAAGGCAAATTATTTATGGGTAA
31620 A
1 A
31621 ATTAAAGTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.38, C:0.05, G:0.22, T:0.34
Consensus pattern (45 bp):
ATAATGGTTAACTAGGAAACTTTAAGGCAAATTATTTATGGGTAA
Found at i:32551 original size:17 final size:19
Alignment explanation
Indices: 32521--32562 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
32511 TATTTTTATT
32521 AATTTACAATTTATAATTA
1 AATTTACAATTTATAATTA
*
32540 AATTTA-AA-TTATATTTA
1 AATTTACAATTTATAATTA
*
32557 TATTTA
1 AATTTA
32563 TTTTATACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 13 0.62
18 2 0.10
19 6 0.29
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
AATTTACAATTTATAATTA
Found at i:32788 original size:16 final size:17
Alignment explanation
Indices: 32751--32792 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
32741 TTAAAAAAAT
*
32751 AATAAATTTATTTTATA
1 AATAAATTTATATTATA
*
32768 TATAAATTTA-ATTATA
1 AATAAATTTATATTATA
32784 AATAAATTT
1 AATAAATTT
32793 TTATATTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AATAAATTTATATTATA
Found at i:37128 original size:29 final size:30
Alignment explanation
Indices: 37067--37128 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
37057 AAAATATTCA
* * *
37067 TTAATGACTATTTTGTTATTTTTGTAAAAT
1 TTAATGACTAATTTATTATTTTTGCAAAAT
*
37097 TTAATGATTAATTTATTATTTTT-CAAAAT
1 TTAATGACTAATTTATTATTTTTGCAAAAT
37126 TTA
1 TTA
37129 GTCACTGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 8 0.29
30 20 0.71
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.56
Consensus pattern (30 bp):
TTAATGACTAATTTATTATTTTTGCAAAAT
Found at i:41544 original size:21 final size:21
Alignment explanation
Indices: 41505--41544 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
41495 TATAAATTTT
*
41505 ATTAATTTTTACTATTTAAAA
1 ATTAATTTTTACTAATTAAAA
41526 ATTAATTTTTA-TAGATTAA
1 ATTAATTTTTACTA-ATTAA
41545 CTTAAGGTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (21 bp):
ATTAATTTTTACTAATTAAAA
Found at i:41799 original size:59 final size:60
Alignment explanation
Indices: 41736--41871 Score: 161
Period size: 58 Copynumber: 2.3 Consensus size: 60
41726 TTCTTGATTT
*
41736 GGTACTTAAACTTTTTTTTATCC-AATTTAATATCTGAACTTG-ATATTTTTTCCTAATTA
1 GGTACATAAACTTTTTTTTA-CCTAATTTAATATCTGAACTTGAATATTTTTTCCTAATTA
* * * * *
41795 GGTACATAAAC-TTGTTTTACCTAATTTGATATTTGAACTTGACATTTTTTTTCCTAATTT
1 GGTACATAAACTTTTTTTTACCTAATTTAATATCTGAACTTGA-ATATTTTTTCCTAATTA
* *
41855 GTTACCTAAACTTTTTT
1 GGTACATAAACTTTTTT
41872 AAAATTCAAT
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
57 2 0.03
58 24 0.38
59 10 0.16
60 24 0.38
61 4 0.06
ACGTcount: A:0.27, C:0.14, G:0.08, T:0.51
Consensus pattern (60 bp):
GGTACATAAACTTTTTTTTACCTAATTTAATATCTGAACTTGAATATTTTTTCCTAATTA
Found at i:41834 original size:58 final size:58
Alignment explanation
Indices: 41749--41872 Score: 153
Period size: 60 Copynumber: 2.1 Consensus size: 58
41739 ACTTAAACTT
41749 TTTTTTATCCAATTTAATATCTGAACTTG-ATATTTTTTCCTAATTAGGTACATAAAC
1 TTTTTTATCCAATTTAATATCTGAACTTGAATATTTTTTCCTAATTAGGTACATAAAC
* * * * * *
41806 TTGTTTTA-CCTAATTTGATATTTGAACTTGACATTTTTTTTCCTAATTTGTTACCTAAAC
1 TT-TTTTATCC-AATTTAATATCTGAACTTGA-ATATTTTTTCCTAATTAGGTACATAAAC
41866 TTTTTTA
1 TTTTTTA
41873 AAATTCAATT
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
57 4 0.07
58 22 0.39
59 5 0.09
60 26 0.46
ACGTcount: A:0.27, C:0.14, G:0.07, T:0.52
Consensus pattern (58 bp):
TTTTTTATCCAATTTAATATCTGAACTTGAATATTTTTTCCTAATTAGGTACATAAAC
Found at i:42156 original size:30 final size:31
Alignment explanation
Indices: 42101--42162 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
42091 AAGTATCAAC
* * * *
42101 TTAAAAAAAAGTGTCAAGTTTAAATACTAAA
1 TTAAAAAAAAGTATCAAATTCAAATACCAAA
42132 TTAAAAAAAA-TATCAAATTCAAATACCAAA
1 TTAAAAAAAAGTATCAAATTCAAATACCAAA
42162 T
1 T
42163 ATTATATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 17 0.63
31 10 0.37
ACGTcount: A:0.58, C:0.10, G:0.05, T:0.27
Consensus pattern (31 bp):
TTAAAAAAAAGTATCAAATTCAAATACCAAA
Found at i:44773 original size:22 final size:22
Alignment explanation
Indices: 44748--44793 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
44738 TATTGCCTAG
44748 TTAGGGTTCTTAAATTTGAGTT
1 TTAGGGTTCTTAAATTTGAGTT
44770 TTAGGGTTCTTAAATTTGAGTT
1 TTAGGGTTCTTAAATTTGAGTT
44792 TT
1 TT
44794 TAAAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.04, G:0.22, T:0.52
Consensus pattern (22 bp):
TTAGGGTTCTTAAATTTGAGTT
Found at i:50457 original size:26 final size:26
Alignment explanation
Indices: 50427--50486 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
50417 ATTTCAAAAA
*
50427 TAATATTATTTAATATTTTATTAATT
1 TAATATTATTTAATATTATATTAATT
** *
50453 TAATAAGATTTAATATTATGTTAATT
1 TAATATTATTTAATATTATATTAATT
*
50479 TCATATTA
1 TAATATTA
50487 AAATGATCAA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (26 bp):
TAATATTATTTAATATTATATTAATT
Found at i:56899 original size:18 final size:18
Alignment explanation
Indices: 56864--56917 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
56854 AAGTAATTGC
*
56864 AAATATCAAATAATAAAAT
1 AAATATAAAAT-ATAAAAT
56883 AAATATAAAATATAAAAT
1 AAATATAAAATATAAAAT
**
56901 ATTTATAAAATATAAAA
1 AAATATAAAATATAAAA
56918 CTTTAATTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
18 22 0.69
19 10 0.31
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
AAATATAAAATATAAAAT
Found at i:57364 original size:22 final size:21
Alignment explanation
Indices: 57336--57405 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 21
57326 TTGGTGCTAT
57336 TTTTTTTACTGTTTTGATGTTG
1 TTTTTTTACTGTTTTG-TGTTG
* *
57358 TTTTTTTATTGTTTTGGTGTTTTT
1 TTTTTTTACTGTTTT-GTG--TTG
57382 TTTTTTTACTGTTTTG-GTTG
1 TTTTTTTACTGTTTTGTGTTG
57402 TTTT
1 TTTT
57406 GATGTTATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
20 6 0.15
22 17 0.41
23 2 0.05
24 16 0.39
ACGTcount: A:0.06, C:0.03, G:0.17, T:0.74
Consensus pattern (21 bp):
TTTTTTTACTGTTTTGTGTTG
Found at i:57385 original size:24 final size:23
Alignment explanation
Indices: 57322--57405 Score: 98
Period size: 24 Copynumber: 3.6 Consensus size: 23
57312 ATTATATTGT
* *
57322 TGTTTTGGTGCTATTTTTTTTAC
1 TGTTTTGGTGTTTTTTTTTTTAC
* * *
57345 TGTTTTGATG-TTGTTTTTTTAT
1 TGTTTTGGTGTTTTTTTTTTTAC
57367 TGTTTTGGTGTTTTTTTTTTTTAC
1 TGTTTTGGTG-TTTTTTTTTTTAC
57391 TGTTTTGGTTGTTTT
1 TGTTTTGG-TGTTTT
57406 GATGTTATTT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
22 18 0.35
23 9 0.18
24 22 0.43
25 2 0.04
ACGTcount: A:0.06, C:0.04, G:0.19, T:0.71
Consensus pattern (23 bp):
TGTTTTGGTGTTTTTTTTTTTAC
Found at i:57429 original size:45 final size:45
Alignment explanation
Indices: 57321--57405 Score: 129
Period size: 46 Copynumber: 1.9 Consensus size: 45
57311 AATTATATTG
57321 TTGTTTTGGTGCTA-TTTTTTTTACTGTTTTGATGTTGTTTTTTTA
1 TTGTTTTGGTGCTATTTTTTTTTACTGTTTTGA-GTTGTTTTTTTA
* *
57366 TTGTTTTGGTGTTTTTTTTTTTTACTGTTTTG-GTTGTTTT
1 TTGTTTTGGTGCTATTTTTTTTTACTGTTTTGAGTTGTTTT
57406 GATGTTATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
44 8 0.22
45 12 0.32
46 17 0.46
ACGTcount: A:0.06, C:0.04, G:0.19, T:0.72
Consensus pattern (45 bp):
TTGTTTTGGTGCTATTTTTTTTTACTGTTTTGAGTTGTTTTTTTA
Found at i:57524 original size:12 final size:12
Alignment explanation
Indices: 57402--57520 Score: 102
Period size: 12 Copynumber: 10.2 Consensus size: 12
57392 GTTTTGGTTG
*
57402 TTTTGATGTTAT
1 TTTTGTTGTTAT
*
57414 TTTTGTTGCTAT
1 TTTTGTTGTTAT
57426 TTTTGTTGTTAT
1 TTTTGTTGTTAT
* *
57438 TTCTGTTGCTAT
1 TTTTGTTGTTAT
*
57450 TTTTGTTGCTAT
1 TTTTGTTGTTAT
*
57462 TTTTATTG---T
1 TTTTGTTGTTAT
* *
57471 TTTTGTTATT-G
1 TTTTGTTGTTAT
*
57482 TTTTGCTGTTAT
1 TTTTGTTGTTAT
* *
57494 TTGTGTTGCTAT
1 TTTTGTTGTTAT
*
57506 TTTGGTTGTTAT
1 TTTTGTTGTTAT
57518 TTT
1 TTT
57521 GGTTATTTGG
Statistics
Matches: 85, Mismatches: 19, Indels: 6
0.77 0.17 0.05
Matches are distributed among these distances:
9 7 0.08
11 8 0.09
12 70 0.82
ACGTcount: A:0.09, C:0.05, G:0.18, T:0.68
Consensus pattern (12 bp):
TTTTGTTGTTAT
Found at i:58932 original size:20 final size:20
Alignment explanation
Indices: 58907--58976 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 20
58897 AACTTTCACA
58907 ATAATAATTATATTGTTTTT
1 ATAATAATTATATTGTTTTT
*
58927 ATAATAA-TATATTAAGCACTTTT
1 ATAATAATTATATT--G--TTTTT
* * *
58950 ATAACATTTAAATTGTTTTT
1 ATAATAATTATATTGTTTTT
58970 ATAATAA
1 ATAATAA
58977 ACTTTTTTGT
Statistics
Matches: 38, Mismatches: 7, Indels: 10
0.69 0.13 0.18
Matches are distributed among these distances:
19 6 0.16
20 16 0.42
21 1 0.03
22 1 0.03
23 9 0.24
24 5 0.13
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.50
Consensus pattern (20 bp):
ATAATAATTATATTGTTTTT
Found at i:59367 original size:6 final size:6
Alignment explanation
Indices: 59356--59395 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
59346 TAAATAATAA
59356 AAAATT AAAATT -AAATT AAAATT AAAATT AAAATT AAAAT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAAT
59396 ATATTTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.15
6 28 0.85
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
AAAATT
Found at i:59373 original size:11 final size:11
Alignment explanation
Indices: 59357--59393 Score: 65
Period size: 11 Copynumber: 3.3 Consensus size: 11
59347 AAATAATAAA
59357 AAATTAAAATT
1 AAATTAAAATT
59368 AAATTAAAATT
1 AAATTAAAATT
59379 AAAATTAAAATT
1 -AAATTAAAATT
59391 AAA
1 AAA
59394 ATATATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATTAAAATT
Found at i:59378 original size:17 final size:18
Alignment explanation
Indices: 59356--59395 Score: 73
Period size: 17 Copynumber: 2.3 Consensus size: 18
59346 TAAATAATAA
59356 AAAATTAAAATT-AAATT
1 AAAATTAAAATTAAAATT
59373 AAAATTAAAATTAAAATT
1 AAAATTAAAATTAAAATT
59391 AAAAT
1 AAAAT
59396 ATATTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAATTAAAATTAAAATT
Found at i:62046 original size:17 final size:18
Alignment explanation
Indices: 62012--62048 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
62002 GCTTTCCATA
62012 TTAAATGTGGAAATTTTT
1 TTAAATGTGGAAATTTTT
*
62030 TTAAATGTGG-CATTTTT
1 TTAAATGTGGAAATTTTT
62047 TT
1 TT
62049 GATCTAGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.27, C:0.03, G:0.16, T:0.54
Consensus pattern (18 bp):
TTAAATGTGGAAATTTTT
Found at i:89278 original size:21 final size:21
Alignment explanation
Indices: 89239--89297 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
89229 ACAATGCAGA
**
89239 CTTCTACCGATACCTGTGACAG
1 CTTCTACCGATACAAGTGA-AG
89261 -TTCTACCGATACAAGTGAAG
1 CTTCTACCGATACAAGTGAAG
* *
89281 CTTCTATCGAAACAAGT
1 CTTCTACCGATACAAGT
89298 CATGCTTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 2 0.06
21 30 0.94
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (21 bp):
CTTCTACCGATACAAGTGAAG
Found at i:89304 original size:21 final size:21
Alignment explanation
Indices: 89261--89309 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
89251 CCTGTGACAG
* *
89261 TTCTACCGATACAAGTGAAGC
1 TTCTACCGAAACAAGTCAAGC
* *
89282 TTCTATCGAAACAAGTCATGC
1 TTCTACCGAAACAAGTCAAGC
*
89303 TTTTACC
1 TTCTACC
89310 AGTACTAAAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (21 bp):
TTCTACCGAAACAAGTCAAGC
Found at i:102679 original size:17 final size:18
Alignment explanation
Indices: 102645--102683 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
102635 TTTTATTTAG
*
102645 TTGTCATTGCATTTTCAT
1 TTGTCACTGCATTTTCAT
102663 TTGTCACTGCA-TTTCAT
1 TTGTCACTGCATTTTCAT
102680 TTGT
1 TTGT
102684 TAGTACATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.15, C:0.18, G:0.13, T:0.54
Consensus pattern (18 bp):
TTGTCACTGCATTTTCAT
Found at i:103292 original size:10 final size:10
Alignment explanation
Indices: 103279--103312 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
103269 AAAAATTCAC
103279 AAAAAGAAAG
1 AAAAAGAAAG
103289 AAAAAGAAAG
1 AAAAAGAAAG
*
103299 AACAAGAAAAG
1 AAAAAG-AAAG
103310 AAA
1 AAA
103313 TATATTGCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 15 0.71
11 6 0.29
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:111198 original size:21 final size:21
Alignment explanation
Indices: 111159--111206 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
111149 ATAGTGCAGA
**
111159 CTTCTACCGATACCTGTGACAG
1 CTTCTACCGATACAAGTGA-AG
*
111181 -TTCTATCGATACAAGTGAAG
1 CTTCTACCGATACAAGTGAAG
111201 CTTCTA
1 CTTCTA
111207 AGTGATTGGC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (21 bp):
CTTCTACCGATACAAGTGAAG
Found at i:111812 original size:45 final size:45
Alignment explanation
Indices: 111761--111850 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
111751 TAGAAGCAAG
*
111761 GTTGAATAAAATCTTATTTAGTCTAGAAATCAAGTGTACTTCCAT
1 GTTGAATAAAATCTCATTTAGTCTAGAAATCAAGTGTACTTCCAT
111806 GTTGAATAAAATCTCATTTAGTCTAGAAATCAAGTGTACTTCCAT
1 GTTGAATAAAATCTCATTTAGTCTAGAAATCAAGTGTACTTCCAT
111851 ACAAAAATGA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (45 bp):
GTTGAATAAAATCTCATTTAGTCTAGAAATCAAGTGTACTTCCAT
Found at i:120722 original size:17 final size:18
Alignment explanation
Indices: 120702--120743 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
120692 AATACAATGC
120702 AAATGTACTAACAAAT-A
1 AAATGTACTAACAAATAA
* * *
120719 AAATGCAGTGACAAATAA
1 AAATGTACTAACAAATAA
120737 AAATGTA
1 AAATGTA
120744 ATGACAACTA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.57, C:0.10, G:0.12, T:0.21
Consensus pattern (18 bp):
AAATGTACTAACAAATAA
Found at i:120741 original size:18 final size:18
Alignment explanation
Indices: 120712--120755 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
120702 AAATGTACTA
*
120712 ACAAAT-AAAATGCAGTG
1 ACAAATAAAAATGCAATG
*
120729 ACAAATAAAAATGTAATG
1 ACAAATAAAAATGCAATG
*
120747 ACAACTAAA
1 ACAAATAAA
120756 TACTATGCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.59, C:0.11, G:0.11, T:0.18
Consensus pattern (18 bp):
ACAAATAAAAATGCAATG
Found at i:120863 original size:20 final size:19
Alignment explanation
Indices: 120835--120883 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
120825 TTGGCTTTCT
*
120835 TCTTCTTCTTCTTTGGGCGC
1 TCTTATTCTTCTTTGGGC-C
*
120855 TCTTATTCTTCTTTGTGCC
1 TCTTATTCTTCTTTGGGCC
*
120874 TCTTTTTCTT
1 TCTTATTCTT
120884 GTCCTTGTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.02, C:0.27, G:0.12, T:0.59
Consensus pattern (19 bp):
TCTTATTCTTCTTTGGGCC
Found at i:131735 original size:25 final size:26
Alignment explanation
Indices: 131707--131760 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
131697 ATTAAAAGAC
*
131707 TAAAGAATAAAATTAACCC-AATTAT
1 TAAAGAATAAAATAAACCCAAATTAT
* *
131732 TAAATAATTAAATAAACCCAAATTAT
1 TAAAGAATAAAATAAACCCAAATTAT
131758 TAA
1 TAA
131761 TGAAATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 16 0.64
26 9 0.36
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (26 bp):
TAAAGAATAAAATAAACCCAAATTAT
Found at i:133499 original size:4 final size:4
Alignment explanation
Indices: 133490--133516 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
133480 AAGAACCTCA
133490 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
133517 CAAGACAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Done.