Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009742.1 Kokia drynarioides strain JFW-HI SEQ_124461, 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: 42653
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:797 original size:23 final size:23
Alignment explanation
Indices: 767--816 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
757 TAGCGCGCTC
*
767 ACTGTTTCGCACTTCGTGTGCTT
1 ACTGTTTCGCACTTCGTGTGCCT
*
790 ACTGTTTCGCACTTTGTGTGCCT
1 ACTGTTTCGCACTTCGTGTGCCT
813 ACTG
1 ACTG
817 ATTTGTGCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.42
Consensus pattern (23 bp):
ACTGTTTCGCACTTCGTGTGCCT
Found at i:830 original size:23 final size:22
Alignment explanation
Indices: 782--884 Score: 89
Period size: 23 Copynumber: 4.5 Consensus size: 22
772 TTCGCACTTC
* * *
782 GTGTGCTTACTGTTTCGCACTTT
1 GTGTGCCTACTGATT-GCACTAT
**
805 GTGTGCCTACTGATTTGTGCTAT
1 GTGTGCCTACTGA-TTGCACTAT
* * *
828 GTGCGCCTAATGATTGCACTGT
1 GTGTGCCTACTGATTGCACTAT
*
850 GTGTGCCTACTGGATTGCACTGT
1 GTGTGCCTACT-GATTGCACTAT
*
873 GTGTGCTTACTG
1 GTGTGCCTACTG
885 TTTCCCCAGC
Statistics
Matches: 65, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
22 16 0.25
23 47 0.72
24 2 0.03
ACGTcount: A:0.13, C:0.20, G:0.27, T:0.40
Consensus pattern (22 bp):
GTGTGCCTACTGATTGCACTAT
Found at i:1525 original size:16 final size:17
Alignment explanation
Indices: 1494--1528 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1484 TTAAAAAATG
1494 TTAATTAATTAAATTTAT
1 TTAATTAA-TAAATTTAT
1512 TTAATTAA-AAATTTAT
1 TTAATTAATAAATTTAT
1528 T
1 T
1529 CTCATTCCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
18 8 0.47
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTAATTAATAAATTTAT
Found at i:5381 original size:19 final size:18
Alignment explanation
Indices: 5357--5392 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
5347 ATTAATTTTT
5357 AAAATTCAAAATATTTATA
1 AAAATTCAAAA-ATTTATA
*
5376 AAAATTCCAAAATTTAT
1 AAAATTCAAAAATTTAT
5393 GTTTTTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAATTCAAAAATTTATA
Found at i:14106 original size:17 final size:17
Alignment explanation
Indices: 14084--14128 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
14074 TTTAACCAAA
14084 TTTTTTTATTTTAAAT-T
1 TTTTTTTATTTT-AATGT
14101 TTTTTTTACTTTTAATGT
1 TTTTTTTA-TTTTAATGT
*
14119 TTATTTTATT
1 TTTTTTTATT
14129 GAATTGGATC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (17 bp):
TTTTTTTATTTTAATGT
Found at i:14471 original size:8 final size:8
Alignment explanation
Indices: 14458--14511 Score: 56
Period size: 8 Copynumber: 6.5 Consensus size: 8
14448 TGACACGTTC
14458 TTTATAAT
1 TTTATAAT
14466 TTTATAA-
1 TTTATAAT
14473 TTTATTATAT
1 TTTA-TA-AT
*
14483 TTATTTAAT
1 TT-TATAAT
14492 TTTATAAT
1 TTTATAAT
*
14500 TTTATAGT
1 TTTATAAT
14508 TTTA
1 TTTA
14512 ACAAGTTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
7 4 0.10
8 25 0.64
9 5 0.13
10 4 0.10
11 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (8 bp):
TTTATAAT
Found at i:14794 original size:22 final size:20
Alignment explanation
Indices: 14744--14801 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
14734 CATATAAACC
14744 AAATAAAAATAACGAAAATA
1 AAATAAAAATAACGAAAATA
*
14764 AAATGAAAATAACAGTAAAAT-
1 AAATAAAAATAAC-G-AAAATA
*
14785 AAACAAAAA-AACGAAAA
1 AAATAAAAATAACGAAAA
14802 AAGATTGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 4 0.12
19 1 0.03
20 15 0.45
21 8 0.24
22 5 0.15
ACGTcount: A:0.74, C:0.07, G:0.07, T:0.12
Consensus pattern (20 bp):
AAATAAAAATAACGAAAATA
Found at i:16755 original size:20 final size:21
Alignment explanation
Indices: 16727--16769 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
16717 TTTAATTTTT
16727 AATTAATATTTTT-ACAAAATA
1 AATTAATATTTTTCA-AAAATA
16748 AATT-ATATTTTTCAAAAATA
1 AATTAATATTTTTCAAAAATA
16768 AA
1 AA
16770 CAAAATTCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (21 bp):
AATTAATATTTTTCAAAAATA
Found at i:21183 original size:27 final size:28
Alignment explanation
Indices: 21135--21190 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
21125 TTTTGTTGAT
*
21135 ATTTTATATATTTTTATAATTTAATTTA
1 ATTTTATATATTTTTATAATTTAAATTA
*
21163 ATTTTA-ATTTTTTTACT-ATTTAAATTA
1 ATTTTATATATTTTTA-TAATTTAAATTA
21190 A
1 A
21191 ATTTGAGTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 18 0.72
28 7 0.28
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (28 bp):
ATTTTATATATTTTTATAATTTAAATTA
Found at i:21193 original size:28 final size:28
Alignment explanation
Indices: 21135--21194 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
21125 TTTTGTTGAT
*
21135 ATTTTATATATTTTTATAATTTAATTTA
1 ATTTTATATATTTTTATAATTTAATTAA
*
21163 ATTTTA-ATTTTTTTACT-ATTTAAATTAA
1 ATTTTATATATTTTTA-TAATTT-AATTAA
21191 ATTT
1 ATTT
21195 GAGTCGGGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 12 0.43
28 16 0.57
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (28 bp):
ATTTTATATATTTTTATAATTTAATTAA
Found at i:25855 original size:9 final size:9
Alignment explanation
Indices: 25841--25871 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
25831 CGAGTTGATC
25841 CGAATAACT
1 CGAATAACT
25850 CGAATAACT
1 CGAATAACT
*
25859 CAAATAACT
1 CGAATAACT
25868 CGAA
1 CGAA
25872 CTATTTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.48, C:0.23, G:0.10, T:0.19
Consensus pattern (9 bp):
CGAATAACT
Found at i:27131 original size:52 final size:51
Alignment explanation
Indices: 26979--27210 Score: 286
Period size: 51 Copynumber: 4.5 Consensus size: 51
26969 TTTCATTTAA
* * *
26979 TACTCACGATGACA-TATAGTCATCGGACCTTTTATTCCATATAGGAATTCATA
1 TACTCACGATGACACT-TAGTCATCGGACC-TTTAATCCATAAAGG-ATTCATT
** * * *
27032 TACTCACGAATGACACAAAGTCATCGGACCCTTAATCCATCATGGATTCATT
1 TACTCACG-ATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
* *
27084 TACTCACGATGACACTTAGTCCTCGGACCTTTAATCCTGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCC-ATAAAGGATTCATT
* * *
27136 TACTCACGATGACACTTAGTCATTGAACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
*
27187 TACTTACGATGACACTTAGTCATC
1 TACTCACGATGACACTTAGTCATC
27211 AGAGCTTTTC
Statistics
Matches: 156, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
51 61 0.39
52 59 0.38
53 18 0.12
54 18 0.12
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.32
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
Found at i:27186 original size:103 final size:105
Alignment explanation
Indices: 26979--27219 Score: 292
Period size: 103 Copynumber: 2.3 Consensus size: 105
26969 TTTCATTTAA
* *
26979 TACTCACGATGACA-TATAGTCATCGGACCTTTTATTCCATATAGGAATTCATATACTCACGAAT
1 TACTCACGATGACACT-TAGTCATCGGACCTTTTAATCCATAAAGGAATTCATATACTCACGAAT
* * *
27043 GACACAAAGTCATCGGACCCTTAATCCATCATGGATTCATT
65 GACACAAAGTCATCGAACCCTTAATCCATAAAGGATTCATT
* * *
27084 TACTCACGATGACACTTAGTCCTCGGACC-TTTAATCCTGTAAAGG-ATTCATTTACTCACG-AT
1 TACTCACGATGACACTTAGTCATCGGACCTTTTAATCC-ATAAAGGAATTCATATACTCACGAAT
** * * *
27146 GACACTTAGTCATTGAACCTTTAATCCGTAAAGGATTCATT
65 GACACAAAGTCATCGAACCCTTAATCCATAAAGGATTCATT
* * *
27187 TACTTACGATGACACTTAGTCATCAGAGCTTTT
1 TACTCACGATGACACTTAGTCATCGGACCTTTT
27220 CGTTTATAGC
Statistics
Matches: 116, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
103 60 0.52
104 24 0.21
105 31 0.27
106 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.32
Consensus pattern (105 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTTAATCCATAAAGGAATTCATATACTCACGAATG
ACACAAAGTCATCGAACCCTTAATCCATAAAGGATTCATT
Found at i:28682 original size:42 final size:42
Alignment explanation
Indices: 28622--28712 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
28612 TTTTCGAATA
* *
28622 TTTTTTTTTGTTCATATATTAGTTGTCTACAATGT-TAGTATT
1 TTTTTTTTTGTTCATATATCAGTTGTCTACAATGTGTA-TAAT
* * *
28664 TTTTTTTTTGTTCGTATATCATTTGTCTACCATGTGTATAAT
1 TTTTTTTTTGTTCATATATCAGTTGTCTACAATGTGTATAAT
28706 TTTTTTT
1 TTTTTTT
28713 ATGGTTATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 41 0.95
43 2 0.05
ACGTcount: A:0.19, C:0.09, G:0.11, T:0.62
Consensus pattern (42 bp):
TTTTTTTTTGTTCATATATCAGTTGTCTACAATGTGTATAAT
Found at i:31426 original size:13 final size:13
Alignment explanation
Indices: 31408--31432 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31398 AACTGTTGAG
31408 TGTTTTTTTTTTT
1 TGTTTTTTTTTTT
31421 TGTTTTTTTTTT
1 TGTTTTTTTTTT
31433 AAATAATAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (13 bp):
TGTTTTTTTTTTT
Found at i:34275 original size:54 final size:54
Alignment explanation
Indices: 33968--34255 Score: 542
Period size: 54 Copynumber: 5.3 Consensus size: 54
33958 CCAACCACCA
33968 TGGTCCAGTTGCAAAGCCACCCACAGGATCATCTCCAGTTCCTGCTCTGGCTCC
1 TGGTCCAGTTGCAAAGCCACCCACAGGATCATCTCCAGTTCCTGCTCTGGCTCC
*
34022 TGGTCCAGTTACAAAGCCACCCACAGGATCATCTCCAGTTCCTGCTCTGGCTCC
1 TGGTCCAGTTGCAAAGCCACCCACAGGATCATCTCCAGTTCCTGCTCTGGCTCC
34076 TGGTCCAGTTGCAAAGCCACCCACAGGATCATCTCCAGTTCCTGCTCTGGCTCC
1 TGGTCCAGTTGCAAAGCCACCCACAGGATCATCTCCAGTTCCTGCTCTGGCTCC
*
34130 TGGTCCAGTTACAAAGCCACCCACAGGATCATCTCCAGTTCCTGCTCTGGCTCC
1 TGGTCCAGTTGCAAAGCCACCCACAGGATCATCTCCAGTTCCTGCTCTGGCTCC
34184 TGGTCCAGTTGCAAAGCCACCCACAGGATCATCTCCAGTTCCTGCTCTGGCTCC
1 TGGTCCAGTTGCAAAGCCACCCACAGGATCATCTCCAGTTCCTGCTCTGGCTCC
34238 TGGTCCTA-TTGCAAAGCC
1 TGGTCC-AGTTGCAAAGCC
34256 TCCTACAGCA
Statistics
Matches: 229, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
54 228 1.00
55 1 0.00
ACGTcount: A:0.19, C:0.36, G:0.20, T:0.24
Consensus pattern (54 bp):
TGGTCCAGTTGCAAAGCCACCCACAGGATCATCTCCAGTTCCTGCTCTGGCTCC
Found at i:34292 original size:54 final size:54
Alignment explanation
Indices: 33968--34292 Score: 310
Period size: 54 Copynumber: 6.0 Consensus size: 54
33958 CCAACCACCA
* * * * * *
33968 TGGTCCAGTTGCAAAGCCACCCACAGGATCATCTCCAGTTCCTGCTCTGGCTCC
1 TGGTCCAGTTGCAAAGCCACCCACAGCATCAACTCCAGGTCCAGCACAGGCTCC
* * * * * * *
34022 TGGTCCAGTTACAAAGCCACCCACAGGATCATCTCCAGTTCCTGCTCTGGCTCC
1 TGGTCCAGTTGCAAAGCCACCCACAGCATCAACTCCAGGTCCAGCACAGGCTCC
* * * * * *
34076 TGGTCCAGTTGCAAAGCCACCCACAGGATCATCTCCAGTTCCTGCTCTGGCTCC
1 TGGTCCAGTTGCAAAGCCACCCACAGCATCAACTCCAGGTCCAGCACAGGCTCC
* * * * * * *
34130 TGGTCCAGTTACAAAGCCACCCACAGGATCATCTCCAGTTCCTGCTCTGGCTCC
1 TGGTCCAGTTGCAAAGCCACCCACAGCATCAACTCCAGGTCCAGCACAGGCTCC
* * * * * *
34184 TGGTCCAGTTGCAAAGCCACCCACAGGATCATCTCCAGTTCCTGCTCTGGCTCC
1 TGGTCCAGTTGCAAAGCCACCCACAGCATCAACTCCAGGTCCAGCACAGGCTCC
* * * *
34238 TGGTCCTA-TTGCAAAGCCTCCTACAGCATTAACTCCAGGTCCAGCACAGTCTCC
1 TGGTCC-AGTTGCAAAGCCACCCACAGCATCAACTCCAGGTCCAGCACAGGCTCC
34292 T
1 T
34293 TATCACCATG
Statistics
Matches: 256, Mismatches: 14, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
54 255 1.00
55 1 0.00
ACGTcount: A:0.20, C:0.37, G:0.19, T:0.24
Consensus pattern (54 bp):
TGGTCCAGTTGCAAAGCCACCCACAGCATCAACTCCAGGTCCAGCACAGGCTCC
Found at i:36138 original size:22 final size:22
Alignment explanation
Indices: 36113--36156 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
36103 TTCATAAAAA
*
36113 AAAAAAATTATTA-ATTTAAATT
1 AAAAAAA-TAATACATTTAAATT
*
36135 AAAAAGATAATACATTTAAATT
1 AAAAAAATAATACATTTAAATT
36157 TACTATCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (22 bp):
AAAAAAATAATACATTTAAATT
Found at i:37090 original size:13 final size:13
Alignment explanation
Indices: 37072--37097 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
37062 ATCTCAAATC
37072 TTTAAACTTTAAA
1 TTTAAACTTTAAA
37085 TTTAAACTTTAAA
1 TTTAAACTTTAAA
37098 CCTCAAATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
TTTAAACTTTAAA
Found at i:37096 original size:20 final size:20
Alignment explanation
Indices: 37065--37127 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
37055 CCCTTTAATC
37065 TCAAATCTTTAAACTTTAAAT
1 TCAAA-CTTTAAACTTTAAAT
* * *
37086 TTAAACTTTAAACCTCAAAT
1 TCAAACTTTAAACTTTAAAT
* * *
37106 TCGAACCTTAAATTTTAAAT
1 TCAAACTTTAAACTTTAAAT
37126 TC
1 TC
37128 CAAATTCAAA
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
20 29 0.88
21 4 0.12
ACGTcount: A:0.41, C:0.17, G:0.02, T:0.40
Consensus pattern (20 bp):
TCAAACTTTAAACTTTAAAT
Found at i:37131 original size:27 final size:28
Alignment explanation
Indices: 37101--37154 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
37091 CTTTAAACCT
*
37101 CAAATTCGAACCTTAAATTTTA-AATTC
1 CAAATTCAAACCTTAAATTTTAGAATTC
* *
37128 CAAATTCAAATCTTGAATTTTAGAATT
1 CAAATTCAAACCTTAAATTTTAGAATT
37155 TGGGGTTCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.39
Consensus pattern (28 bp):
CAAATTCAAACCTTAAATTTTAGAATTC
Found at i:40016 original size:6 final size:6
Alignment explanation
Indices: 40005--40030 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
39995 CGATAAATAA
40005 TTTCAT TTTCAT TTTCAT TTTCAT TT
1 TTTCAT TTTCAT TTTCAT TTTCAT TT
40031 GATATGTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTCAT
Found at i:40094 original size:17 final size:17
Alignment explanation
Indices: 40072--40159 Score: 95
Period size: 17 Copynumber: 5.1 Consensus size: 17
40062 CCCATTCCTT
40072 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
* *
40089 TTAAATTTGTTTAAAAA
1 TTAAATTTATTTTAAAA
*
40106 TTTAAATTTATTTTAAAT
1 -TTAAATTTATTTTAAAA
* **
40124 TTAAATTTAATTTAAGT
1 TTAAATTTATTTTAAAA
* *
40141 TTAAAATTATTTTTAAA
1 TTAAATTTATTTTAAAA
40158 TT
1 TT
40160 TAAAGTTTAA
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
17 44 0.76
18 14 0.24
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:40122 original size:11 final size:11
Alignment explanation
Indices: 40106--40161 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
40096 TGTTTAAAAA
40106 TTTAAATTTAT
1 TTTAAATTTAT
*
40117 TTTAAATTTAAA
1 TTTAAATTT-AT
*
40129 TTT-AATTTAAG
1 TTTAAATTT-AT
*
40140 TTTAAAATTATT
1 TTTAAATTTA-T
40152 TTTAAATTTA
1 TTTAAATTTA
40162 AAGTTTAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
11 20 0.54
12 17 0.46
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:40148 original size:35 final size:35
Alignment explanation
Indices: 40071--40169 Score: 121
Period size: 35 Copynumber: 2.8 Consensus size: 35
40061 GCCCATTCCT
* *
40071 TTTAAATTTATTTTAAAATTAAATTT-GTTTAAAAA
1 TTTAAATTTATTTTAAATTTAAATTTAATTT-AAAA
*
40106 TTTAAATTTATTTTAAATTTAAATTTAATTT-AAG
1 TTTAAATTTATTTTAAATTTAAATTTAATTTAAAA
*
40140 TTTAAAATTATTTTTAAATTTAAAGTTTAA
1 TTTAAATTTA-TTTTAAATTTAAA-TTTAA
40170 AATAAATAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
34 11 0.19
35 38 0.67
36 8 0.14
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (35 bp):
TTTAAATTTATTTTAAATTTAAATTTAATTTAAAA
Found at i:40170 original size:7 final size:6
Alignment explanation
Indices: 40103--40170 Score: 68
Period size: 6 Copynumber: 11.5 Consensus size: 6
40093 ATTTGTTTAA
* * *
40103 AAATTT AAATTT -ATTTT AAATTT AAATTT -AATTT AAGTTT AAAATT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
**
40149 ATTTTT AAATTT AAAGTTT AAA
1 AAATTT AAATTT AAA-TTT AAA
40171 ATAAATAAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 5
0.77 0.16 0.08
Matches are distributed among these distances:
5 9 0.18
6 34 0.69
7 6 0.12
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (6 bp):
AAATTT
Found at i:40876 original size:21 final size:21
Alignment explanation
Indices: 40851--40894 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
40841 TATTAATCGG
*
40851 TATTAATAATAATAATATTAA
1 TATTAATAATAATAACATTAA
* *
40872 TATTAATATTAATGACATTAA
1 TATTAATAATAATAACATTAA
40893 TA
1 TA
40895 AAGACGGGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
TATTAATAATAATAACATTAA
Found at i:41329 original size:78 final size:78
Alignment explanation
Indices: 41176--41320 Score: 211
Period size: 78 Copynumber: 1.9 Consensus size: 78
41166 TTTTGAACTT
* * *
41176 ACCGGTGATCGGAGATGTGGGACGCGTGGACGGTCGGAAGTTGTCTTGGCGGAAGCGCACAACGG
1 ACCGGTGACCGGAGATGAGGGACGCGTGGACGGTCGGAAGTTGCCTTGGCGGAAGCGCACAACGG
41241 CGCATAGCTACGG
66 CGCATAGCTACGG
* * * *
41254 ACCGGTGACCGGAGATGCAGGG-CGCGTGGGCTGTCGGACGTTGCCTTGGCGGAGGCGCACAACG
1 ACCGGTGACCGGAGATG-AGGGACGCGTGGACGGTCGGAAGTTGCCTTGGCGGAAGCGCACAACG
41318 GCG
65 GCG
41321 TGTGGCTACA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
78 56 0.95
79 3 0.05
ACGTcount: A:0.18, C:0.24, G:0.43, T:0.15
Consensus pattern (78 bp):
ACCGGTGACCGGAGATGAGGGACGCGTGGACGGTCGGAAGTTGCCTTGGCGGAAGCGCACAACGG
CGCATAGCTACGG
Found at i:41985 original size:29 final size:29
Alignment explanation
Indices: 41951--42441 Score: 385
Period size: 29 Copynumber: 16.8 Consensus size: 29
41941 CCCTAAGCTA
41951 TCCAAAAATTACCATTTTACCCCCGAACT
1 TCCAAAAATTACCATTTTACCCCCGAACT
*
41980 TCCAAAAA-TCCCATTTTGA-CCCCGAAACT
1 TCCAAAAATTACCATTTT-ACCCCCG-AACT
* *
42009 TCCAAAAATTACCATTTTACCCTCGAACA
1 TCCAAAAATTACCATTTTACCCCCGAACT
42038 TCCAAAAA-T-CTCATTTTTA-CCCCGAAACT
1 TCCAAAAATTAC-CA-TTTTACCCCCG-AACT
* * * *
42067 TCCAAAAATTACAATTTTACCCTCAAAAT
1 TCCAAAAATTACCATTTTACCCCCGAACT
*
42096 TCCAAAAA-TCCCATTTTTGA-CCCCGAAACT
1 TCCAAAAATTACCA-TTTT-ACCCCCG-AACT
* * * *
42126 TCCAAAAATTACAATTTCACCCTCGAGCT
1 TCCAAAAATTACCATTTTACCCCCGAACT
* *
42155 T-CAAAAAAT-CTCATTTTTTA-CCTCGAAACT
1 TCCAAAAATTAC-CA--TTTTACCCCCG-AACT
42185 TCC-AAAATTACCATTTTACCCCCGAACT
1 TCCAAAAATTACCATTTTACCCCCGAACT
*
42213 TCCAAAAA-T-CTCATTTTGA-CTCCGAAACCT
1 TCCAAAAATTAC-CATTTT-ACCCCCG-AA-CT
*
42243 TCCAAAAATTACCATTTTACCCCTGAACT
1 TCCAAAAATTACCATTTTACCCCCGAACT
**
42272 TCCAAAAATT-CCATTTTTGACCCCAAAACT
1 TCCAAAAATTACCA-TTTT-ACCCCCGAACT
*
42302 TCCAAAAATTACCATTTTACCCTCGAACT
1 TCCAAAAATTACCATTTTACCCCCGAACT
* * *
42331 TCCAAAAA-TCCCATTTTTGA-CTCCAAACCT
1 TCCAAAAATTACCA-TTTT-ACCCCCGAA-CT
*
42361 TCCAAAAATTACCATTTTACCCCCGGACT
1 TCCAAAAATTACCATTTTACCCCCGAACT
*
42390 TCCAAAAA-T-CTCATTTTTGA-CCCTGAATCT
1 TCCAAAAATTAC-CA-TTTT-ACCCCCGAA-CT
*
42420 ACC-AAAATTACCATTTTACCCC
1 TCCAAAAATTACCATTTTACCCC
42442 GTATGTTTGA
Statistics
Matches: 372, Mismatches: 45, Indels: 90
0.73 0.09 0.18
Matches are distributed among these distances:
27 4 0.01
28 65 0.17
29 164 0.44
30 114 0.31
31 24 0.06
32 1 0.00
ACGTcount: A:0.35, C:0.31, G:0.04, T:0.30
Consensus pattern (29 bp):
TCCAAAAATTACCATTTTACCCCCGAACT
Found at i:42142 original size:59 final size:59
Alignment explanation
Indices: 41951--42440 Score: 679
Period size: 59 Copynumber: 8.4 Consensus size: 59
41941 CCCTAAGCTA
*
41951 TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCA-TTTTGACCCCGAAACT
1 TCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAAACT
* *
42009 TCCAAAAATTACCATTTTACCCTCGAACATCCAAAAATCTCATTTTT-ACCCCGAAACT
1 TCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAAACT
* * *
42067 TCCAAAAATTACAATTTTACCCTCAAAATTCCAAAAATCCCATTTTTGACCCCGAAACT
1 TCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAAACT
* * * * * * *
42126 TCCAAAAATTACAATTTCACCCTCGAGCTTCAAAAAATCTCATTTTTTACCTCGAAACT
1 TCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAAACT
* * *
42185 TCC-AAAATTACCATTTTACCCCCGAACTTCCAAAAATCTCA-TTTTGACTCCGAAACCT
1 TCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAAA-CT
* *
42243 TCCAAAAATTACCATTTTACCC-CTGAACTTCCAAAAATTCCATTTTTGACCCCAAAACT
1 TCCAAAAATTACCATTTTACCCTC-GAACTTCCAAAAATCCCATTTTTGACCCCGAAACT
*
42302 TCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACTCC-AAACCT
1 TCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAAA-CT
* * * * *
42361 TCCAAAAATTACCATTTTACCCCCGGACTTCCAAAAATCTCATTTTTGACCCTGAATCT
1 TCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAAACT
*
42420 ACC-AAAATTACCATTTTACCC
1 TCCAAAAATTACCATTTTACCC
42441 CGTATGTTTG
Statistics
Matches: 386, Mismatches: 37, Indels: 18
0.88 0.08 0.04
Matches are distributed among these distances:
57 11 0.03
58 152 0.39
59 208 0.54
60 15 0.04
ACGTcount: A:0.35, C:0.31, G:0.04, T:0.30
Consensus pattern (59 bp):
TCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAAACT
Done.