Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010056.1 Kokia drynarioides strain JFW-HI SEQ_124830, 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: 65979
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:714 original size:164 final size:164
Alignment explanation
Indices: 525--857 Score: 614
Period size: 167 Copynumber: 2.0 Consensus size: 164
515 AATAAAAATG
525 AAATAATAAAATATAAAACAAGAAAAAAAATATCAAAACTTGA-TTTTTTTTTTTAAAAAGGTTT
1 AAATAATAAAATATAAAACAAGAAAAAAAATATCAAAACTTGATTTTTTTTTTTTAAAAAGGTTT
589 CCAATCCAGATTTTAGGTTTTCTAAAAAACAAAAAGACAAAACTTTCCTTTTGGTTCGAATTCGG
66 CCAATCCAGATTTTAGGTTTTCTAAAAAACAAAAAGACAAAACTTTCCTTTTGGTTCGAATTCGG
*
654 GGTTTTCAAACCCGAATTTGAATTTTTTTTTAAA
131 GGTTTTCAAACCCGAATTTGAATTTATTTTTAAA
688 AAANTAATAAAATATAAAACAAGAAAAAAAATATCAAAACTTGATTTTTTTTTTTTTTAAAAAGG
1 AAA-TAATAAAATATAAAACAAGAAAAAAAATATCAAAACTTGA--TTTTTTTTTTTTAAAAAGG
753 TTTCCAATCCAGATTTTAGGTTTTCTAAAAAACAAAAAGACAAAACTTTCCTTTTGGTTCGAATT
63 TTTCCAATCCAGATTTTAGGTTTTCTAAAAAACAAAAAGACAAAACTTTCCTTTTGGTTCGAATT
*
818 TGGGGTTTTCAAACCCGAATTTGAATTTATTTTTAAA
128 CGGGGTTTTCAAACCCGAATTTGAATTTATTTTTAAA
855 AAA
1 AAA
858 AGAGAGAGAA
Statistics
Matches: 164, Mismatches: 2, Indels: 4
0.96 0.01 0.02
Matches are distributed among these distances:
163 3 0.02
164 40 0.24
167 121 0.74
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.36
Consensus pattern (164 bp):
AAATAATAAAATATAAAACAAGAAAAAAAATATCAAAACTTGATTTTTTTTTTTTAAAAAGGTTT
CCAATCCAGATTTTAGGTTTTCTAAAAAACAAAAAGACAAAACTTTCCTTTTGGTTCGAATTCGG
GGTTTTCAAACCCGAATTTGAATTTATTTTTAAA
Found at i:2222 original size:106 final size:106
Alignment explanation
Indices: 2089--2301 Score: 399
Period size: 106 Copynumber: 2.0 Consensus size: 106
2079 AATGTTTAAG
*
2089 TGCTATTAGCTTAAATAATTTAAAATGTAATTGTTAACCGGTCTCAATTATTAATAATGCTAATA
1 TGCTATTAGCTTAAATAATATAAAATGTAATTGTTAACCGGTCTCAATTATTAATAATGCTAATA
*
2154 GTGGATACAGGAAAGAGTAATCCATATTGAAATTGAAATCT
66 GTGGATACAGGAAAAAGTAATCCATATTGAAATTGAAATCT
2195 TGCTATTAGCTTAAATAATATAAAATGTAATTGTTAACCGGTCTCAATTATTAATAATGCTAATA
1 TGCTATTAGCTTAAATAATATAAAATGTAATTGTTAACCGGTCTCAATTATTAATAATGCTAATA
*
2260 GTGGATACAGGAAAAAGTAATCCATATTGAAATTGGAATCT
66 GTGGATACAGGAAAAAGTAATCCATATTGAAATTGAAATCT
2301 T
1 T
2302 AAATTGATGA
Statistics
Matches: 104, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
106 104 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (106 bp):
TGCTATTAGCTTAAATAATATAAAATGTAATTGTTAACCGGTCTCAATTATTAATAATGCTAATA
GTGGATACAGGAAAAAGTAATCCATATTGAAATTGAAATCT
Found at i:4523 original size:7 final size:6
Alignment explanation
Indices: 4509--4544 Score: 63
Period size: 6 Copynumber: 5.8 Consensus size: 6
4499 AAGTCTCTCA
4509 AAGGGG AAGGGGG AAGGGG AAGGGG AAGGGG AAGGG
1 AAGGGG AA-GGGG AAGGGG AAGGGG AAGGGG AAGGG
4545 AAAAAGGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (6 bp):
AAGGGG
Found at i:5893 original size:24 final size:24
Alignment explanation
Indices: 5866--5948 Score: 67
Period size: 24 Copynumber: 3.2 Consensus size: 24
5856 ATTATTTTCA
*
5866 TTTAAAATTAAATTATTTAAGTAT
1 TTTAAAATTAAACTATTTAAGTAT
* * *
5890 TTTAATATTTAGCAAAAACTATTCAAGTCT
1 TTTAA-AATT-----AAACTATTTAAGTAT
*
5920 TTTAATATTAAACTATTTAAGTAT
1 TTTAAAATTAAACTATTTAAGTAT
5944 TTTAA
1 TTTAA
5949 TATTTAAGTA
Statistics
Matches: 45, Mismatches: 8, Indels: 12
0.69 0.12 0.18
Matches are distributed among these distances:
24 23 0.51
25 3 0.07
29 2 0.04
30 17 0.38
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.47
Consensus pattern (24 bp):
TTTAAAATTAAACTATTTAAGTAT
Found at i:5949 original size:24 final size:24
Alignment explanation
Indices: 5905--5961 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
5895 TATTTAGCAA
* *
5905 AAACTATTCAAGTCTTTTAATATT
1 AAACTATTTAAGTATTTTAATATT
5929 AAACTATTTAAGTATTTTAATATT
1 AAACTATTTAAGTATTTTAATATT
* *
5953 TAAGTATTT
1 AAACTATTT
5962 CCAAATGCTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.49
Consensus pattern (24 bp):
AAACTATTTAAGTATTTTAATATT
Found at i:10072 original size:29 final size:31
Alignment explanation
Indices: 10039--10115 Score: 92
Period size: 29 Copynumber: 2.6 Consensus size: 31
10029 ATTCAAAATA
*
10039 TTTTTTA-AAACTTTTAA-AG-GTCAAATTT
1 TTTTTTACAAACTTTTAAGAGCCTCAAATTT
* *
10067 TTTTTTACCAACTTTTAAGAGCCTTAAATTT
1 TTTTTTACAAACTTTTAAGAGCCTCAAATTT
10098 TTTTTT-C-AACTTTTAAGA
1 TTTTTTACAAACTTTTAAGA
10116 AACTTAAAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
28 7 0.16
29 20 0.47
30 3 0.07
31 13 0.30
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.51
Consensus pattern (31 bp):
TTTTTTACAAACTTTTAAGAGCCTCAAATTT
Found at i:10121 original size:29 final size:30
Alignment explanation
Indices: 10061--10123 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 30
10051 TTTAAAGGTC
**
10061 AAATTTTTTTTTACCAACTTTTAAGAGCCTT
1 AAATTTTTTTTTA-CAACTTTTAAGAAACTT
10092 AAATTTTTTTTT-CAACTTTTAAGAAACTT
1 AAATTTTTTTTTACAACTTTTAAGAAACTT
10121 AAA
1 AAA
10124 ACATTATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 18 0.60
31 12 0.40
ACGTcount: A:0.35, C:0.13, G:0.05, T:0.48
Consensus pattern (30 bp):
AAATTTTTTTTTACAACTTTTAAGAAACTT
Found at i:10273 original size:26 final size:25
Alignment explanation
Indices: 10230--10291 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 25
10220 AATAATATTG
*
10230 TTAATAATTTTTATAAA-TTCAATTTT
1 TTAA-AATTTTCATAAATTTCAA-TTT
*
10256 TTAAAATTTTCATAAAATTTTAATTT
1 TTAAAATTTTCAT-AAATTTCAATTT
*
10282 TTAAGATTTT
1 TTAAAATTTT
10292 TTAATGATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
25 8 0.26
26 19 0.61
27 4 0.13
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (25 bp):
TTAAAATTTTCATAAATTTCAATTT
Found at i:11561 original size:22 final size:22
Alignment explanation
Indices: 11533--11577 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
11523 CATATGTATG
11533 TCATGTTAACATTTAATTAATT
1 TCATGTTAACATTTAATTAATT
11555 TCATGTTAACATTTAATTAATT
1 TCATGTTAACATTTAATTAATT
11577 T
1 T
11578 TAAAAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.51
Consensus pattern (22 bp):
TCATGTTAACATTTAATTAATT
Found at i:20938 original size:3 final size:3
Alignment explanation
Indices: 20932--20984 Score: 54
Period size: 3 Copynumber: 17.7 Consensus size: 3
20922 CTCGAGCTCT
* * * *
20932 TCA TCA TCA ACT TCA T-A TACA TCA TCA TCA TCA TCA TCA TAA TCT
1 TCA TCA TCA TCA TCA TCA T-CA TCA TCA TCA TCA TCA TCA TCA TCA
20977 TCA TCA TC
1 TCA TCA TC
20985 TTCAACTTCA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
2 2 0.05
3 36 0.90
4 2 0.05
ACGTcount: A:0.34, C:0.30, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:30556 original size:18 final size:18
Alignment explanation
Indices: 30533--30575 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
30523 GTTCAATGTA
30533 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
30551 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
30569 TAATTAA
1 TAATTAA
30576 AAATCTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:30947 original size:14 final size:15
Alignment explanation
Indices: 30928--30956 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
30918 GTATTATTTA
30928 TTAATTA-AAATATT
1 TTAATTATAAATATT
30942 TTAATTATAAATATT
1 TTAATTATAAATATT
30957 AAGGAGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTAATTATAAATATT
Found at i:32256 original size:10 final size:10
Alignment explanation
Indices: 32243--32334 Score: 56
Period size: 10 Copynumber: 9.5 Consensus size: 10
32233 AGAAATCATC
32243 AAAAATTATT
1 AAAAATTATT
32253 AAAAATTA-T
1 AAAAATTATT
*
32262 AAATAGTTATT
1 AAA-AATTATT
32273 ---AATT-TT
1 AAAAATTATT
32279 AAAAAATTATT
1 -AAAAATTATT
* *
32290 AGAAAGTATT
1 AAAAATTATT
32300 AAAACATTA-T
1 AAAA-ATTATT
32310 AAAAA--ATGT
1 AAAAATTAT-T
32319 AGAAAATTATT
1 A-AAAATTATT
32330 AAAAA
1 AAAAA
32335 AGAAATTAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 26
0.66 0.06 0.27
Matches are distributed among these distances:
6 2 0.03
7 4 0.06
9 7 0.11
10 40 0.63
11 8 0.13
12 2 0.03
ACGTcount: A:0.59, C:0.01, G:0.05, T:0.35
Consensus pattern (10 bp):
AAAAATTATT
Found at i:32724 original size:2 final size:2
Alignment explanation
Indices: 32719--32746 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
32709 TTTTTTTTGA
32719 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
32747 TTTAGATTTA
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:36518 original size:55 final size:55
Alignment explanation
Indices: 36452--36564 Score: 217
Period size: 55 Copynumber: 2.1 Consensus size: 55
36442 TTAATAGAAT
*
36452 GTATGTCAGAATGAGGGCTGAGATCAGGATCATTCAACAAATAAGAGACAGAGAG
1 GTATGTCAGAATGAGGGCTGAGATCAGGATCATTCAACAAACAAGAGACAGAGAG
36507 GTATGTCAGAATGAGGGCTGAGATCAGGATCATTCAACAAACAAGAGACAGAGAG
1 GTATGTCAGAATGAGGGCTGAGATCAGGATCATTCAACAAACAAGAGACAGAGAG
36562 GTA
1 GTA
36565 ACACTAAGGA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.40, C:0.13, G:0.29, T:0.18
Consensus pattern (55 bp):
GTATGTCAGAATGAGGGCTGAGATCAGGATCATTCAACAAACAAGAGACAGAGAG
Found at i:38367 original size:17 final size:17
Alignment explanation
Indices: 38347--38380 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
38337 AAAAAAAATT
*
38347 ATTTAAATGTTATTTAA
1 ATTTAAATATTATTTAA
38364 ATTTAAATATTATTTAA
1 ATTTAAATATTATTTAA
38381 TCATGTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTAAATATTATTTAA
Found at i:38855 original size:31 final size:33
Alignment explanation
Indices: 38820--38880 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
38810 GTTTCTACTG
38820 TATT-AAAATTT-AAAAAAAAAATATTTTTTAA
1 TATTAAAAATTTGAAAAAAAAAATATTTTTTAA
*
38851 TATTAAAAATTTGAAATAAAAAATATTTTT
1 TATTAAAAATTTGAAAAAAAAAATATTTTT
38881 AAAATTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 4 0.15
32 7 0.26
33 16 0.59
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (33 bp):
TATTAAAAATTTGAAAAAAAAAATATTTTTTAA
Found at i:38893 original size:33 final size:32
Alignment explanation
Indices: 38822--38893 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 32
38812 TTCTACTGTA
*
38822 TTAAAATTTAAAAAAAAAATATTTTTTAATAT
1 TTAAAATTTAAAAAAAAAATATTTTTAAATAT
* *
38854 TAAAAATTTGAAATAAAAAATATTTTTAAA-ATT
1 TTAAAATTT-AAAAAAAAAATATTTTTAAATA-T
38887 TTAAAAT
1 TTAAAAT
38894 GAAAAATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 9 0.26
33 25 0.74
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (32 bp):
TTAAAATTTAAAAAAAAAATATTTTTAAATAT
Found at i:44806 original size:32 final size:31
Alignment explanation
Indices: 44770--44833 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
44760 ATATTTATAT
*
44770 TATTTAAGT-TATTAATTTTATTTTTTGTATTA
1 TATTTAAGTGTA-TAATTAT-TTTTTTGTATTA
**
44802 TATTTTGGTGTATAATTATTTTTTTGTATTA
1 TATTTAAGTGTATAATTATTTTTTTGTATTA
44833 T
1 T
44834 TTATGTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 13 0.46
32 13 0.46
33 2 0.07
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (31 bp):
TATTTAAGTGTATAATTATTTTTTTGTATTA
Found at i:44918 original size:27 final size:27
Alignment explanation
Indices: 44888--44986 Score: 117
Period size: 27 Copynumber: 3.7 Consensus size: 27
44878 GGTTGGTGGA
* *
44888 GCTTGCCAGGTAGGCACCTTTGGTGCC
1 GCTTGTCAGATAGGCACCTTTGGTGCC
* * * *
44915 GCTTGACAGATAGACACCTCTAGTGCC
1 GCTTGTCAGATAGGCACCTTTGGTGCC
*
44942 GCTTGTCAGGTAGGCACCTTTGGTGCC
1 GCTTGTCAGATAGGCACCTTTGGTGCC
* *
44969 ACCTGTCAGATAGGCACC
1 GCTTGTCAGATAGGCACC
44987 ACCCCCTGTA
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 59 1.00
ACGTcount: A:0.18, C:0.29, G:0.28, T:0.24
Consensus pattern (27 bp):
GCTTGTCAGATAGGCACCTTTGGTGCC
Found at i:47457 original size:16 final size:18
Alignment explanation
Indices: 47419--47457 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
47409 TATCTGAACT
*
47419 TTTATCCAACACTTATAA
1 TTTATCCAACACTAATAA
47437 TTTATCCAAC-CTAAT-A
1 TTTATCCAACACTAATAA
47453 TTTAT
1 TTTAT
47458 TTGCTATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 4 0.20
18 10 0.50
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTATCCAACACTAATAA
Found at i:47604 original size:48 final size:48
Alignment explanation
Indices: 47552--47649 Score: 178
Period size: 48 Copynumber: 2.0 Consensus size: 48
47542 AGTGACTATA
*
47552 TTTAATTGCCTTATTCAACAATTTCATGATGAATAATTAATTTAATTC
1 TTTAATTGCCTTATTCAACAAATTCATGATGAATAATTAATTTAATTC
*
47600 TTTAATTTCCTTATTCAACAAATTCATGATGAATAATTAATTTAATTC
1 TTTAATTGCCTTATTCAACAAATTCATGATGAATAATTAATTTAATTC
47648 TT
1 TT
47650 ACTTCGGGCT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.47
Consensus pattern (48 bp):
TTTAATTGCCTTATTCAACAAATTCATGATGAATAATTAATTTAATTC
Found at i:55772 original size:241 final size:241
Alignment explanation
Indices: 55349--55827 Score: 922
Period size: 241 Copynumber: 2.0 Consensus size: 241
55339 ATACCACTTT
55349 TGGCGGATCCTTATATTGGCTATGGCGGGCCGTCAGTACTCCAGTCACGCTGCATCTTCAAATTG
1 TGGCGGATCCTTATATTGGCTATGGCGGGCCGTCAGTACTCCAGTCACGCTGCATCTTCAAATTG
55414 ATCAGACAACGAACTTGGTTTGATCCATGGTCTTTCCACATATCTACCACACTAGCCTTTTCTCG
66 ATCAGACAACGAACTTGGTTTGATCCATGGTCTTTCCACATATCTACCACACTAGCCTTTTCTCG
* *
55479 TGTTTACTATCCCTGCAGACCTCATGTTTAAGTCTCGACGAACTATAGTTTTGCCAATTTGTCCT
131 TGTTTACTATCCCTGCAGACCTCATGTTTAAGTCCCGACAAACTATAGTTTTGCCAATTTGTCCT
55544 TCGTGTTTACTATCCCGACGGACGTCATCAAAGCACCACCACAGAG
196 TCGTGTTTACTATCCCGACGGACGTCATCAAAGCACCACCACAGAG
*
55590 TGGCGGATCCTTATATTGGCTATGGCGGGCCGTCAGTACTCCAGTCACGTTGCATCTTCAAATTG
1 TGGCGGATCCTTATATTGGCTATGGCGGGCCGTCAGTACTCCAGTCACGCTGCATCTTCAAATTG
*
55655 ATCAGACAACGAACTTGGTTTGATCCATGGTCTTTCCACATATCTACCGCACTAGCCTTTTCTCG
66 ATCAGACAACGAACTTGGTTTGATCCATGGTCTTTCCACATATCTACCACACTAGCCTTTTCTCG
55720 TGTTTACTATCCCTGCAGACCTCATGTTTAAGTCCCGACAAACTATAGTTTTGCCAATTTGTCCT
131 TGTTTACTATCCCTGCAGACCTCATGTTTAAGTCCCGACAAACTATAGTTTTGCCAATTTGTCCT
55785 TCGTGTTTACTATCCCGACGGACGTCATCAAAGCACCACCACA
196 TCGTGTTTACTATCCCGACGGACGTCATCAAAGCACCACCACA
55828 AAGTCCATTA
Statistics
Matches: 234, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
241 234 1.00
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.31
Consensus pattern (241 bp):
TGGCGGATCCTTATATTGGCTATGGCGGGCCGTCAGTACTCCAGTCACGCTGCATCTTCAAATTG
ATCAGACAACGAACTTGGTTTGATCCATGGTCTTTCCACATATCTACCACACTAGCCTTTTCTCG
TGTTTACTATCCCTGCAGACCTCATGTTTAAGTCCCGACAAACTATAGTTTTGCCAATTTGTCCT
TCGTGTTTACTATCCCGACGGACGTCATCAAAGCACCACCACAGAG
Found at i:56626 original size:26 final size:25
Alignment explanation
Indices: 56597--56650 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
56587 AACATATTAT
56597 TAATAC-AAATACAAAAAATATAAATA
1 TAATACTAAA-ACAAAAAAT-TAAATA
**
56623 TAATACTAAAACATTAAATTAAATA
1 TAATACTAAAACAAAAAATTAAATA
56648 TAA
1 TAA
56651 AATAAATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 9 0.36
26 13 0.52
27 3 0.12
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (25 bp):
TAATACTAAAACAAAAAATTAAATA
Found at i:56647 original size:20 final size:20
Alignment explanation
Indices: 56603--56652 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
56593 TTATTAATAC
56603 AAATAC-AAAAAATATAAAT
1 AAATACTAAAAAATATAAAT
*
56622 ATAATACTAAAACAT-TAAATT
1 A-AATACTAAAAAATATAAA-T
56643 AAATA-TAAAA
1 AAATACTAAAA
56653 TAAATTTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 6 0.22
20 13 0.48
21 8 0.30
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (20 bp):
AAATACTAAAAAATATAAAT
Found at i:60135 original size:2 final size:2
Alignment explanation
Indices: 60128--60154 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
60118 TCTTTAATGC
60128 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
60155 AACTATTAAT
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:62791 original size:26 final size:26
Alignment explanation
Indices: 62713--62799 Score: 68
Period size: 26 Copynumber: 3.1 Consensus size: 26
62703 CTGCACATAT
* *
62713 TATTTTTAATTTTTTAAAATATTTATA
1 TATTTTTTATTTATTAAAAT-TTTATA
*
62740 TTATATTATTT-TAGTATTTAATAATTTTATA
1 -TAT-TT-TTTAT-TTA-TTAA-AATTTTATA
*
62771 TATTTTTTATTTATTAAAATTTTTTA
1 TATTTTTTATTTATTAAAATTTTATA
62797 TAT
1 TAT
62800 AGTCATGTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
26 11 0.23
27 4 0.08
28 8 0.17
29 6 0.12
30 6 0.12
31 10 0.21
32 3 0.06
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (26 bp):
TATTTTTTATTTATTAAAATTTTATA
Found at i:62800 original size:28 final size:28
Alignment explanation
Indices: 62713--62800 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 28
62703 CTGCACATAT
* * *
62713 TATTTTTAATTTTTTAAAATATTTATATTA
1 TATTTTTTATTTATTAAAAT-TTTTTA-TA
*
62743 TATTATTTTA-GTATTTAATAA--TTTTATA
1 TATT-TTTTATTTA-TTAA-AATTTTTTATA
62771 TATTTTTTATTTATTAAAATTTTTTATA
1 TATTTTTTATTTATTAAAATTTTTTATA
62799 TA
1 TA
62801 GTCATGTTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
26 2 0.04
27 9 0.19
28 17 0.36
29 4 0.09
30 5 0.11
31 8 0.17
32 2 0.04
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (28 bp):
TATTTTTTATTTATTAAAATTTTTTATA
Found at i:63762 original size:30 final size:30
Alignment explanation
Indices: 63691--63763 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 30
63681 TATTTTTAAA
*
63691 AAAATATTTATATTATATTATTTTAATATTT
1 AAAAT-TTTATATTATATTATTTTAATATTG
*
63722 AATAATTTTATA-TATATT-TTTTATTTATTG
1 AA-AATTTTATATTATATTATTTTA-ATATTG
63752 AAAATCTTTATA
1 AAAAT-TTTATA
63764 CAGCCATGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
29 8 0.22
30 18 0.49
31 8 0.22
32 3 0.08
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (30 bp):
AAAATTTTATATTATATTATTTTAATATTG
Done.