Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024869.1 Corchorus olitorius cultivar O-4 contig24902, 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: 43853
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:8685 original size:26 final size:26
Alignment explanation
Indices: 8649--8719 Score: 142
Period size: 26 Copynumber: 2.7 Consensus size: 26
8639 ATGTTAATTG
8649 GATAATAATAGACGCATTGAAGAAAT
1 GATAATAATAGACGCATTGAAGAAAT
8675 GATAATAATAGACGCATTGAAGAAAT
1 GATAATAATAGACGCATTGAAGAAAT
8701 GATAATAATAGACGCATTG
1 GATAATAATAGACGCATTG
8720 GATAATAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.48, C:0.08, G:0.20, T:0.24
Consensus pattern (26 bp):
GATAATAATAGACGCATTGAAGAAAT
Found at i:15555 original size:16 final size:16
Alignment explanation
Indices: 15527--15560 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
15517 GACATGTCTA
15527 ATAATACAACAATAAT
1 ATAATACAACAATAAT
15543 ATAAT-CAATCAATAAT
1 ATAATACAA-CAATAAT
15559 AT
1 AT
15561 GCTTCCATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.18
16 14 0.82
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (16 bp):
ATAATACAACAATAAT
Found at i:16767 original size:12 final size:11
Alignment explanation
Indices: 16750--16782 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
16740 AGCACATCTC
16750 TAATTTTTCAT
1 TAATTTTTCAT
16761 GTAATTTTTCA-
1 -TAATTTTTCAT
16772 TAATTTTTCAT
1 TAATTTTTCAT
16783 CAAAATAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
12 10 0.50
ACGTcount: A:0.27, C:0.09, G:0.03, T:0.61
Consensus pattern (11 bp):
TAATTTTTCAT
Found at i:18327 original size:14 final size:14
Alignment explanation
Indices: 18288--18327 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
18278 AAAAAAAACT
*
18288 AAAATTAAATTATA
1 AAAATTACATTATA
*
18302 AAAAATATCATTATA
1 AAAATTA-CATTATA
18317 AAAATTACATT
1 AAAATTACATT
18328 GATATCTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (14 bp):
AAAATTACATTATA
Found at i:19302 original size:21 final size:21
Alignment explanation
Indices: 19276--19316 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
19266 ACGTAATTTG
*
19276 ACTATCAAACTTTGGGGTTTA
1 ACTATCAAAATTTGGGGTTTA
19297 ACTATCAAAATTTGGGGTTT
1 ACTATCAAAATTTGGGGTTT
19317 GACCATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (21 bp):
ACTATCAAAATTTGGGGTTTA
Found at i:19438 original size:55 final size:55
Alignment explanation
Indices: 19286--19490 Score: 170
Period size: 55 Copynumber: 3.7 Consensus size: 55
19276 ACTATCAAAC
* * * * *
19286 TTTGGGGTTTAACTATCAAAATTTGGGGTTTGACCAT-ATATATAATAAATTTTTT
1 TTTGTGGTTTAACTATCAAACTTTGGGGTTTGACTATCATGTATAATAAA-TGTTT
* * *
19341 TTTGTGGTTTCACTA-CTAAACTTT-GGATTTGA-TCATGCATGTACAAT-AATGTTT
1 TTTGTGGTTTAACTATC-AAACTTTGGGGTTTGACT-AT-CATGTATAATAAATGTTT
* ** *
19395 TTTGTGGTTTAACTATCAAACTTTGCGGTTTGACTATACATGTATAATGGA-GTGGT
1 TTTGTGGTTTAACTATCAAACTTTGGGGTTTGACTAT-CATGTATAATAAATGT-TT
* ** *
19451 TTTGTGGTTTGACTATTGAACTTTGGGGTTTGACCATCAT
1 TTTGTGGTTTAACTATCAAACTTTGGGGTTTGACTATCAT
19491 CCTCTGGGGT
Statistics
Matches: 121, Mismatches: 20, Indels: 18
0.76 0.13 0.11
Matches are distributed among these distances:
54 35 0.29
55 44 0.36
56 42 0.35
ACGTcount: A:0.25, C:0.11, G:0.20, T:0.44
Consensus pattern (55 bp):
TTTGTGGTTTAACTATCAAACTTTGGGGTTTGACTATCATGTATAATAAATGTTT
Found at i:19537 original size:74 final size:73
Alignment explanation
Indices: 19421--19791 Score: 379
Period size: 76 Copynumber: 4.9 Consensus size: 73
19411 CAAACTTTGC
* * *
19421 GGTTTGACTATACATGTATAATGGAGTGGTTTTGTGGTTTGACTATTGAACTTTGGGGTTTGACC
1 GGTTTGACCATACATGTACAAT-GA-T-GTTTTGTGGTTTGACTATTAAACTTTGGGGTTTGACC
*
19486 ATCATCCTCTGG
63 ATCATCCT-TGA
* * * *
19498 GGTTTGCCCATGCATATACAATGATGTTTTGTGGTTTGACTATTGAACTTTGGGGTTTGACCATC
1 GGTTTGACCATACATGTACAATGATGTTTTGTGGTTTGACTATTAAACTTTGGGGTTTGACCATC
19563 ATCCTTTG-
66 ATCC-TTGA
* * * *
19571 GGTTTGACCGTGA-ATGTACAATGAATTAATGCTTTTTGTGGTTTGAATATCAAACTTCGGGGTT
1 GGTTTGACCAT-ACATGTACAATG-----ATG--TTTTGTGGTTTGACTATTAAACTTTGGGGTT
19635 TGACCATCATCCTTTGA
58 TGACCATCATCC-TTGA
* * * *
19652 GGTTTGATCATACATGTACAATGATGATTTTTGTGGTTTGACTATCAAACTTTGGGATTTAACCA
1 GGTTTGACCATACATGTACAATGATG--TTTTGTGGTTTGACTATTAAACTTTGGGGTTTGACCA
19717 TCATCCTGTGA
64 TCATCCT-TGA
* * * *
19728 GCTTTGACCATACATGTGCAATGATATTTTTGTGGTTTGACTATCAAA-TTTGGGGTTTGACCAT
1 GGTTTGACCATACATGTACAATGAT-GTTTTGTGGTTTGACTATTAAACTTTGGGGTTTGACCAT
19792 ACATATACAA
Statistics
Matches: 255, Mismatches: 26, Indels: 29
0.82 0.08 0.09
Matches are distributed among these distances:
73 18 0.07
74 60 0.24
75 24 0.09
76 70 0.27
77 17 0.07
78 3 0.01
80 44 0.17
81 19 0.07
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.40
Consensus pattern (73 bp):
GGTTTGACCATACATGTACAATGATGTTTTGTGGTTTGACTATTAAACTTTGGGGTTTGACCATC
ATCCTTGA
Found at i:19883 original size:56 final size:56
Alignment explanation
Indices: 19754--19952 Score: 314
Period size: 56 Copynumber: 3.6 Consensus size: 56
19744 TGCAATGATA
* * * *
19754 TTTTTGTGGTTTGACTATCAAATTTGGGGTTTGACCATACATATACAAT--GAT-T
1 TTTTTGTGGTTTGACTATCAACTTTGGGGTTTGACCATGCATATAGAATAAAATGT
19807 TTTTTGTGGTTTGACTATCAACTTTGGGGTTTGACCATGCATATAGAATAAAATGT
1 TTTTTGTGGTTTGACTATCAACTTTGGGGTTTGACCATGCATATAGAATAAAATGT
*
19863 TTTTTGTGGTTTGACTATCAACTTTGGGGTTTAACCATGCATATAGAATAAAATGT
1 TTTTTGTGGTTTGACTATCAACTTTGGGGTTTGACCATGCATATAGAATAAAATGT
*
19919 TTTTTGTGGTTTGACTATCAAATTTTGGGGTTTG
1 TTTTTGTGGTTTGACTATC-AACTTTGGGGTTTG
19953 CTTATCAAAA
Statistics
Matches: 135, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
53 46 0.34
55 2 0.01
56 75 0.56
57 12 0.09
ACGTcount: A:0.25, C:0.10, G:0.21, T:0.44
Consensus pattern (56 bp):
TTTTTGTGGTTTGACTATCAACTTTGGGGTTTGACCATGCATATAGAATAAAATGT
Found at i:19950 original size:21 final size:22
Alignment explanation
Indices: 19920--19974 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
19910 ATAAAATGTT
*
19920 TTTTGTGGTTTGAC-TATCAAA
1 TTTTGGGGTTTGACTTATCAAA
19941 TTTTGGGGTTTG-CTTATCAAA
1 TTTTGGGGTTTGACTTATCAAA
* *
19962 ATTCGGGGTTTGA
1 TTTTGGGGTTTGA
19975 TCATGTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 1 0.03
21 28 0.97
ACGTcount: A:0.20, C:0.09, G:0.25, T:0.45
Consensus pattern (22 bp):
TTTTGGGGTTTGACTTATCAAA
Found at i:20025 original size:55 final size:55
Alignment explanation
Indices: 19966--20088 Score: 158
Period size: 55 Copynumber: 2.2 Consensus size: 55
19956 ATCAAAATTC
* *
19966 GGGGTTTGATCATGTATATAAAATGAAATTTTTTGTGATTTGTCTATCGAACTTT
1 GGGGTTTGATCATGCATATAAAATGAAATTTTTTGTGATTTGACTATCGAACTTT
* * * * **
20021 GGGGTTTGA-CTATGCATGTATAATGATATTTTTTGTGGTTTGACTATTTAACTTT
1 GGGGTTTGATC-ATGCATATAAAATGAAATTTTTTGTGATTTGACTATCGAACTTT
20076 GGGGTTTGATCAT
1 GGGGTTTGATCAT
20089 CATCCTTTTG
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
54 1 0.02
55 56 0.97
56 1 0.02
ACGTcount: A:0.24, C:0.07, G:0.23, T:0.46
Consensus pattern (55 bp):
GGGGTTTGATCATGCATATAAAATGAAATTTTTTGTGATTTGACTATCGAACTTT
Found at i:20304 original size:111 final size:108
Alignment explanation
Indices: 20138--20354 Score: 285
Period size: 111 Copynumber: 2.0 Consensus size: 108
20128 CCCCATCCTC
* * *
20138 TGGGGTTGACCATGCATGTACAATGATGTTTTTTGTAGTTTGACTATTAACCTTTGGAGTTTGAC
1 TGGGGTTGACCATGCATATACAATGATGTTTTTTGTAGCTTGACTATGAACCTTTGGAGTTTGAC
* *
20203 CATCAT-TATTTGGGGTTTGACTATGCATGTATAATGATTTTTT
66 CATCATCCA-TTGGGGTTTGACCATGCATGTATAATGATTTTTT
* * *
20246 TGGGGTTTGACCATGCATATTCAATGAAATGTTTTTTGTGGCTTGACTATCGAA-CTTTGGGGTT
1 TGGGG-TTGACCATGCATATACAATG--ATGTTTTTTGTAGCTTGACTAT-GAACCTTTGGAGTT
* *
20310 TGATCATTATCCATTGGGGTTTGACCATGCATGTATAATGATTTT
62 TGACCATCATCCATTGGGGTTTGACCATGCATGTATAATGATTTT
20355 AACTTTAAGT
Statistics
Matches: 94, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
108 5 0.05
109 18 0.19
111 68 0.72
112 3 0.03
ACGTcount: A:0.22, C:0.12, G:0.23, T:0.43
Consensus pattern (108 bp):
TGGGGTTGACCATGCATATACAATGATGTTTTTTGTAGCTTGACTATGAACCTTTGGAGTTTGAC
CATCATCCATTGGGGTTTGACCATGCATGTATAATGATTTTTT
Found at i:21902 original size:26 final size:27
Alignment explanation
Indices: 21873--21936 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 27
21863 TTTGAATGTA
* *
21873 AAATAAATATATTTTTTCGAT-CCCAT
1 AAATAAATATATTTTTTCGATAACAAT
*
21899 AAAT--ATATATTTTTTTGATAACAAT
1 AAATAAATATATTTTTTCGATAACAAT
21924 AAGATAAATATAT
1 AA-ATAAATATAT
21937 GTTAAACTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 14 0.45
25 5 0.16
26 6 0.19
28 6 0.19
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (27 bp):
AAATAAATATATTTTTTCGATAACAAT
Found at i:22482 original size:94 final size:93
Alignment explanation
Indices: 22356--22542 Score: 320
Period size: 94 Copynumber: 2.0 Consensus size: 93
22346 CCTTTCTTCT
* * * * *
22356 AAAAAAACGAACTTTAACTGAAAATTCGAACTTTAGCCAAATTTTTCCTTTTTCTCCAGAAAAAG
1 AAAAAAACGAACTTTAACTGAAAATTCAAACTTTAGACAAAATTTTCCTTTTCCTCAAGAAAAAG
22421 GTACAAACTTTAACTGAAAAAACGCAAAA
66 GTACAAACTTTAACTGAAAAAACG-AAAA
22450 AAAAAAACGAACTTTAACTGAAAATTCAAACTTTAGACAAAATTTTCCTTTTCCTCAAGAAAAAG
1 AAAAAAACGAACTTTAACTGAAAATTCAAACTTTAGACAAAATTTTCCTTTTCCTCAAGAAAAAG
22515 GTACAAACTTTAACTGAAAAAACGAAAA
66 GTACAAACTTTAACTGAAAAAACGAAAA
22543 CTTTTCTTTT
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
93 4 0.05
94 84 0.95
ACGTcount: A:0.48, C:0.17, G:0.09, T:0.26
Consensus pattern (93 bp):
AAAAAAACGAACTTTAACTGAAAATTCAAACTTTAGACAAAATTTTCCTTTTCCTCAAGAAAAAG
GTACAAACTTTAACTGAAAAAACGAAAA
Found at i:23026 original size:16 final size:16
Alignment explanation
Indices: 23005--23069 Score: 67
Period size: 16 Copynumber: 3.8 Consensus size: 16
22995 CTGACTATGT
23005 AATTTATAAATAAGGA
1 AATTTATAAATAAGGA
*
23021 AATTTATAACATACAGTAA
1 AATTTATAA-ATA-AG-GA
23040 TATATTTATAAATAAGGA
1 -A-ATTTATAAATAAGGA
*
23058 AATTTTTAAATA
1 AATTTATAAATA
23070 GTAATTAGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
16 19 0.46
17 4 0.10
18 3 0.07
19 3 0.07
20 4 0.10
21 8 0.20
ACGTcount: A:0.52, C:0.03, G:0.08, T:0.37
Consensus pattern (16 bp):
AATTTATAAATAAGGA
Found at i:28568 original size:30 final size:30
Alignment explanation
Indices: 28532--28597 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
28522 CCATGTGGGC
28532 ATACACGTGTCATCCACATCAGCGCCTGTT
1 ATACACGTGTCATCCACATCAGCGCCTGTT
* *
28562 ATACACGTGTCATCCACGTCAGCGCGTGTT
1 ATACACGTGTCATCCACATCAGCGCCTGTT
28592 ATACAC
1 ATACAC
28598 ACACCCCAGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.26
Consensus pattern (30 bp):
ATACACGTGTCATCCACATCAGCGCCTGTT
Found at i:28647 original size:36 final size:36
Alignment explanation
Indices: 28607--28678 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
28597 CACACCCCAG
28607 CCATTTTCAATTTATCCTGAATTGACACAACCCGAT
1 CCATTTTCAATTTATCCTGAATTGACACAACCCGAT
28643 CCATTTTCAATTTATCCTGAATTGACACAACCCGAT
1 CCATTTTCAATTTATCCTGAATTGACACAACCCGAT
28679 AACGTTTGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.31, C:0.28, G:0.08, T:0.33
Consensus pattern (36 bp):
CCATTTTCAATTTATCCTGAATTGACACAACCCGAT
Found at i:30814 original size:17 final size:16
Alignment explanation
Indices: 30792--30844 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
30782 CCATGAAAAA
30792 TTATTAATTTAGAGAGG
1 TTATTAATTTAG-GAGG
*
30809 TTATTAATTTATCGA-G
1 TTATTAATTTA-GGAGG
30825 -TATTAATTTATGGAGG
1 TTATTAATTTA-GGAGG
30841 TTAT
1 TTAT
30845 ATTGTAATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
15 13 0.42
16 2 0.06
17 16 0.52
ACGTcount: A:0.32, C:0.02, G:0.19, T:0.47
Consensus pattern (16 bp):
TTATTAATTTAGGAGG
Found at i:30814 original size:76 final size:76
Alignment explanation
Indices: 30688--30835 Score: 278
Period size: 76 Copynumber: 1.9 Consensus size: 76
30678 AAACCTCTAT
*
30688 AAATTAATAATGTTGGGACAATGAAAAATTATTAATTTAGAGAGGTTATTAATTTATCGAGTGTT
1 AAATTAATAATGTTGGGACAATGAAAAATTATTAATTTAGAGAGGTTATTAATTTATCGAGTATT
30753 AATTTATATGG
66 AATTTATATGG
*
30764 AAATTAATAATGTTGGGACCATGAAAAATTATTAATTTAGAGAGGTTATTAATTTATCGAGTATT
1 AAATTAATAATGTTGGGACAATGAAAAATTATTAATTTAGAGAGGTTATTAATTTATCGAGTATT
30829 AATTTAT
66 AATTTAT
30836 GGAGGTTATA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 70 1.00
ACGTcount: A:0.40, C:0.03, G:0.17, T:0.40
Consensus pattern (76 bp):
AAATTAATAATGTTGGGACAATGAAAAATTATTAATTTAGAGAGGTTATTAATTTATCGAGTATT
AATTTATATGG
Found at i:32482 original size:56 final size:56
Alignment explanation
Indices: 32394--32504 Score: 195
Period size: 56 Copynumber: 2.0 Consensus size: 56
32384 ATTAATCCTC
* **
32394 AATTTGGCCTTTTAGTAATTTCTCTGGTAACTAAAAATAATATATAGTATATATAA
1 AATTTGGCCTTTTAGTAATTTCCCTGAAAACTAAAAATAATATATAGTATATATAA
32450 AATTTGGCCTTTTAGTAATTTCCCTGAAAACTAAAAATAATATATAGTATATATA
1 AATTTGGCCTTTTAGTAATTTCCCTGAAAACTAAAAATAATATATAGTATATATA
32505 TATATATAAC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.40
Consensus pattern (56 bp):
AATTTGGCCTTTTAGTAATTTCCCTGAAAACTAAAAATAATATATAGTATATATAA
Found at i:32638 original size:18 final size:17
Alignment explanation
Indices: 32597--32631 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
32587 AATTAATATT
*
32597 AAATATTTTTATTTATA
1 AAATATTTTTATTTAGA
32614 AACATATTTTTATTTAGA
1 AA-ATATTTTTATTTAGA
32632 TTAATATGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (17 bp):
AAATATTTTTATTTAGA
Found at i:34858 original size:7 final size:7
Alignment explanation
Indices: 34846--34924 Score: 63
Period size: 7 Copynumber: 10.9 Consensus size: 7
34836 TTTTCAGTAG
34846 AATAAAA
1 AATAAAA
34853 AATAAAAA
1 AAT-AAAA
34861 AATAAAA
1 AATAAAA
34868 AATAAAA
1 AATAAAA
34875 AATAAATA
1 AATAAA-A
34883 TAA-AAATA
1 -AATAAA-A
*
34891 AATAGAA
1 AATAAAA
* *
34898 AATTAGA
1 AATAAAA
*
34905 AAT-AGA
1 AATAAAA
34911 AATATAAA
1 AATA-AAA
34919 AATAAA
1 AATAAA
34925 TATAAATATA
Statistics
Matches: 61, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
6 6 0.10
7 32 0.52
8 21 0.34
9 2 0.03
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (7 bp):
AATAAAA
Found at i:34887 original size:12 final size:12
Alignment explanation
Indices: 34846--34952 Score: 86
Period size: 12 Copynumber: 9.5 Consensus size: 12
34836 TTTTCAGTAG
34846 AATA-AAAAATA
1 AATATAAAAATA
*
34857 AA-A-AAATAAAA
1 AATATAAA-AATA
34868 AATA-AAAAATA
1 AATATAAAAATA
34879 AATATAAAAATA
1 AATATAAAAATA
*
34891 AATA-GAAAAT-
1 AATATAAAAATA
* * *
34901 --TAGAAATAGA
1 AATATAAAAATA
34911 AATATAAAAATA
1 AATATAAAAATA
*
34923 AATATAAATATA
1 AATATAAAAATA
*
34935 AATATAAATATA
1 AATATAAAAATA
34947 AATATA
1 AATATA
34953 TTTCCTCTTC
Statistics
Matches: 79, Mismatches: 10, Indels: 13
0.77 0.10 0.13
Matches are distributed among these distances:
8 2 0.03
9 3 0.04
10 4 0.05
11 19 0.24
12 51 0.65
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (12 bp):
AATATAAAAATA
Found at i:34949 original size:6 final size:6
Alignment explanation
Indices: 34867--34952 Score: 93
Period size: 6 Copynumber: 14.2 Consensus size: 6
34857 AAAAAATAAA
* * * * *
34867 AAATA- AAAAAT AAATAT AAAAAT AAATAGA AAATTAG AAATAG AAATAT
1 AAATAT AAATAT AAATAT AAATAT AAATA-T AAA-TAT AAATAT AAATAT
*
34916 AAAAAT AAATAT AAATAT AAATAT AAATAT AAATAT A
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT A
34953 TTTCCTCTTC
Statistics
Matches: 69, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
5 4 0.06
6 57 0.83
7 6 0.09
8 2 0.03
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (6 bp):
AAATAT
Found at i:35629 original size:46 final size:47
Alignment explanation
Indices: 35541--35629 Score: 135
Period size: 46 Copynumber: 1.9 Consensus size: 47
35531 TTAAAAAGCT
*
35541 AAAAAAAATCTTCTTTTTACTAAGTGGCATCTTGTGTAACTAAACTA
1 AAAAAAAATCTTCTTTTTACTAAGTGGCATCTTGTATAACTAAACTA
* * *
35588 AAAAAAAATCTTC-TTTTACTAAGTGGCGTTTTGTATGACTAA
1 AAAAAAAATCTTCTTTTTACTAAGTGGCATCTTGTATAACTAA
35630 GTTGCATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
46 25 0.66
47 13 0.34
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.37
Consensus pattern (47 bp):
AAAAAAAATCTTCTTTTTACTAAGTGGCATCTTGTATAACTAAACTA
Found at i:38754 original size:2 final size:2
Alignment explanation
Indices: 38747--38789 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
38737 TCTTGTGGAT
38747 TA TA TA TA 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
38789 T
1 T
38790 GTATGCTATC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.