Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002304.1 Kokia drynarioides strain JFW-HI SEQ_114342, 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: 115981
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 24 characters in sequence are not A, C, G, or T
Found at i:1852 original size:2 final size:2
Alignment explanation
Indices: 1845--1870 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1835 AAGTCACTGC
1845 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
1871 CATTTTGGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11672 original size:19 final size:19
Alignment explanation
Indices: 11649--11699 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
11639 GCTAAAGTAC
11649 AAAATTCAAATGAACG-AAA
1 AAAATTCAAATGAA-GTAAA
*
11668 GAAA-TCGAAACTGAAGTAAA
1 AAAATTC-AAA-TGAAGTAAA
11688 AAAATTCAAATG
1 AAAATTCAAATG
11700 TGGAGATCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
18 2 0.08
19 9 0.35
20 13 0.50
21 2 0.08
ACGTcount: A:0.59, C:0.10, G:0.14, T:0.18
Consensus pattern (19 bp):
AAAATTCAAATGAAGTAAA
Found at i:11685 original size:38 final size:39
Alignment explanation
Indices: 11622--11699 Score: 113
Period size: 38 Copynumber: 2.0 Consensus size: 39
11612 AAGATATTAA
* *
11622 GAACAAAAGAAATCGAAGCTAAAGT-ACAAAATTCAAAT
1 GAACAAAAGAAATCGAAACTAAAGTAAAAAAATTCAAAT
* *
11660 GAACGAAAGAAATCGAAACTGAAGTAAAAAAATTCAAAT
1 GAACAAAAGAAATCGAAACTAAAGTAAAAAAATTCAAAT
11699 G
1 G
11700 TGGAGATCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
38 22 0.63
39 13 0.37
ACGTcount: A:0.58, C:0.12, G:0.15, T:0.15
Consensus pattern (39 bp):
GAACAAAAGAAATCGAAACTAAAGTAAAAAAATTCAAAT
Found at i:11692 original size:20 final size:20
Alignment explanation
Indices: 11626--11692 Score: 50
Period size: 20 Copynumber: 3.4 Consensus size: 20
11616 TATTAAGAAC
* *
11626 AAAAGAAATCGAAGCTAAAGT
1 AAAA-AAATCGAAACTGAAGT
* *
11647 ACAAAATTC-AAA-TGAACG-
1 AAAAAAATCGAAACTGAA-GT
*
11665 AAAGAAATCGAAACTGAAGT
1 AAAAAAATCGAAACTGAAGT
11685 AAAAAAAT
1 AAAAAAAT
11693 TCAAATGTGG
Statistics
Matches: 34, Mismatches: 8, Indels: 9
0.67 0.16 0.18
Matches are distributed among these distances:
18 9 0.26
19 7 0.21
20 15 0.44
21 3 0.09
ACGTcount: A:0.60, C:0.10, G:0.15, T:0.15
Consensus pattern (20 bp):
AAAAAAATCGAAACTGAAGT
Found at i:22955 original size:17 final size:17
Alignment explanation
Indices: 22933--22970 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
22923 TTGAACCGGA
*
22933 TTTTTAT-TTTATTATAT
1 TTTTTATGTTTAATA-AT
22950 TTTTTATGTTTAATAAT
1 TTTTTATGTTTAATAAT
22967 TTTT
1 TTTT
22971 AATCGGACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTTTATGTTTAATAAT
Found at i:34005 original size:2 final size:2
Alignment explanation
Indices: 33998--34023 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
33988 TGATTTGATA
33998 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
34024 CTAGCTTACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35423 original size:95 final size:95
Alignment explanation
Indices: 35260--35446 Score: 356
Period size: 95 Copynumber: 2.0 Consensus size: 95
35250 AGTAGCACCT
**
35260 AATCTTTCCAATCATAAAAGTTAAACCAAATCCCTGCCCAAGTGACCTTCAGGAAGATAAAAAGC
1 AATCTTTCCAATCATAAAAGTTAAACCAAATCCCTGCCCAAAAGACCTTCAGGAAGATAAAAAGC
35325 TAGCTAACTATGAAAACATAAATCCTCGTG
66 TAGCTAACTATGAAAACATAAATCCTCGTG
35355 AATCTTTCCAATCATAAAAGTTAAACCAAATCCCTGCCCAAAAGACCTTCAGGAAGATAAAAAGC
1 AATCTTTCCAATCATAAAAGTTAAACCAAATCCCTGCCCAAAAGACCTTCAGGAAGATAAAAAGC
35420 TAGCTAACTATGAAAACATAAATCCTC
66 TAGCTAACTATGAAAACATAAATCCTC
35447 ATTTTACAAA
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
95 90 1.00
ACGTcount: A:0.43, C:0.24, G:0.11, T:0.22
Consensus pattern (95 bp):
AATCTTTCCAATCATAAAAGTTAAACCAAATCCCTGCCCAAAAGACCTTCAGGAAGATAAAAAGC
TAGCTAACTATGAAAACATAAATCCTCGTG
Found at i:44263 original size:27 final size:28
Alignment explanation
Indices: 44225--44285 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
44215 ATATGTGATT
*
44225 TTTTGGATACTCG-GGGCAAAATAATAA
1 TTTTGGACACTCGAGGGCAAAATAATAA
**
44252 TTTTGGACACTCGAGGGCAAAATGGTAA
1 TTTTGGACACTCGAGGGCAAAATAATAA
44280 TTTTGG
1 TTTTGG
44286 GAAAGTTCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 12 0.40
28 18 0.60
ACGTcount: A:0.31, C:0.11, G:0.26, T:0.31
Consensus pattern (28 bp):
TTTTGGACACTCGAGGGCAAAATAATAA
Found at i:44313 original size:58 final size:57
Alignment explanation
Indices: 44250--44622 Score: 218
Period size: 58 Copynumber: 6.6 Consensus size: 57
44240 GCAAAATAAT
* * * * *
44250 AATTTT-GGACACTCGAGGGCAAAATGGTAATTTTGGGAAAGTTCAAGGTTAAAAATGG
1 AATTTTAGGACATTCGGGGGTAAAATGGTAATTTTGGGAAA-ATC-AGGTAAAAAATGG
* * *
44308 AATTTTAGG-CATTCGGGGGTAAAATAGTAATTTTTGGAAAATCTGGTAAAAAATGG
1 AATTTTAGGACATTCGGGGGTAAAATGGTAATTTTGGGAAAATCAGGTAAAAAATGG
* * * * * **
44364 AATTTTGGGA-AGTTCGGGGGTAAAATGGTAATTTTTGGAGAAATCGGGGTTAAATATAA
1 AATTTTAGGACA-TTCGGGGGTAAAATGGTAATTTTGGGA-AAATC-AGGTAAAAAATGG
* **
44423 AATTTTAGG-CATTCGGGGGTAAAA--G-----TTGGAAAAATC-GAGT-TCAAATGG
1 AATTTTAGGACATTCGGGGGTAAAATGGTAATTTTGGGAAAATCAG-GTAAAAAATGG
* * * * * *
44471 AATTTT-TGAAAGTCTGGGGGTAAAATGGTAATTTTTGGAAAAATAAGGTTAAAAATGG
1 AATTTTAGGACATTC-GGGGGTAAAATGGTAA-TTTTGGGAAAATCAGGTAAAAAATGG
* * ** * * * *
44529 AATTTTGGGAAATTTAGGGGTAAAATGATAATTTTTTGAAAAATCGAGGTCAAAAATGG
1 AATTTTAGGACATTCGGGGGTAAAATGGTAA-TTTTGGGAAAATC-AGGTAAAAAATGG
* * * *
44588 AATTTTTGGACTTTTGAGGGTAAAAATGG-AATTTT
1 AATTTTAGGACATTCGGGGGT-AAAATGGTAATTTT
44623 TAGAAAGTTC
Statistics
Matches: 250, Mismatches: 43, Indels: 44
0.74 0.13 0.13
Matches are distributed among these distances:
47 1 0.00
48 13 0.05
49 12 0.05
50 5 0.02
51 5 0.02
56 21 0.08
57 40 0.16
58 93 0.37
59 54 0.22
60 6 0.02
ACGTcount: A:0.37, C:0.05, G:0.27, T:0.32
Consensus pattern (57 bp):
AATTTTAGGACATTCGGGGGTAAAATGGTAATTTTGGGAAAATCAGGTAAAAAATGG
Found at i:44339 original size:28 final size:28
Alignment explanation
Indices: 44308--44446 Score: 86
Period size: 28 Copynumber: 4.9 Consensus size: 28
44298 TTAAAAATGG
*
44308 AATTTTAGGCATTCGGGGGTAAAATAGT
1 AATTTTAGGAATTCGGGGGTAAAATAGT
* * * * *
44336 AATTTTTGGAAAATC--TGGTAAAAAATGG
1 AATTTTAGG-AATTCGGGGGTAAAATA-GT
* *
44364 AATTTTGGGAAGTTCGGGGGTAAAATGGT
1 AATTTTAGGAA-TTCGGGGGTAAAATAGT
* * * *
44393 AATTTTTGGAGAAATCGGGGTTAAATATA-A
1 AA-TTTTAG-GAATTCGGGGGTAAA-ATAGT
*
44423 AATTTTAGGCATTCGGGGGTAAAA
1 AATTTTAGGAATTCGGGGGTAAAA
44447 GTTGGAAAAA
Statistics
Matches: 83, Mismatches: 20, Indels: 17
0.69 0.17 0.14
Matches are distributed among these distances:
27 11 0.13
28 31 0.37
29 11 0.13
30 25 0.30
31 5 0.06
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.32
Consensus pattern (28 bp):
AATTTTAGGAATTCGGGGGTAAAATAGT
Found at i:44523 original size:29 final size:28
Alignment explanation
Indices: 44491--44597 Score: 88
Period size: 29 Copynumber: 3.6 Consensus size: 28
44481 AGTCTGGGGG
44491 TAAAATGGTAATTTTTGGAAAAATAAGGT
1 TAAAATGG-AATTTTTGGAAAAATAAGGT
* ** * *
44520 TAAAAATGGAATTTTGGGAAATTTAGGGG
1 T-AAAATGGAATTTTTGGAAAAATAAGGT
* * *
44549 TAAAATGATAATTTTTTGAAAAATCGAGGT
1 TAAAATG-GAATTTTTGGAAAAAT-AAGGT
*
44579 CAAAAATGGAATTTTTGGA
1 -TAAAATGGAATTTTTGGA
44598 CTTTTGAGGG
Statistics
Matches: 58, Mismatches: 16, Indels: 7
0.72 0.20 0.09
Matches are distributed among these distances:
28 6 0.10
29 28 0.48
30 18 0.31
31 6 0.10
ACGTcount: A:0.42, C:0.02, G:0.22, T:0.34
Consensus pattern (28 bp):
TAAAATGGAATTTTTGGAAAAATAAGGT
Found at i:44549 original size:107 final size:107
Alignment explanation
Indices: 44358--44553 Score: 252
Period size: 107 Copynumber: 1.8 Consensus size: 107
44348 ATCTGGTAAA
* * ** *
44358 AAATGGAATTTTGGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAGAAATCGGGGTTAAATATAA
1 AAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGGAAAAATCAAGGTTAAAAATAA
* *
44423 AATTTTAGGCATTCGGGGGTAAAAGTTGGAAAAATCGAGTTC
66 AATTTTAGGAATTCAGGGGTAAAAGTTGGAAAAATCGAGTTC
* *
44465 AAATGGAATTTTTGAAAG-TCTGGGGGTAAAATGGTAATTTTTGGAAAAAT-AAGGTTAAAAATG
1 AAATGGAATTTTGGAAAGTTC-GGGGGTAAAATGGTAATTTTTGGAAAAATCAAGGTTAAAAATA
* * *
44528 GAATTTTGGGAAATTTAGGGGTAAAA
65 AAATTTTAGG-AATTCAGGGGTAAAA
44554 TGATAATTTT
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
106 19 0.25
107 56 0.75
ACGTcount: A:0.37, C:0.04, G:0.29, T:0.31
Consensus pattern (107 bp):
AAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGGAAAAATCAAGGTTAAAAATAA
AATTTTAGGAATTCAGGGGTAAAAGTTGGAAAAATCGAGTTC
Found at i:44553 original size:28 final size:27
Alignment explanation
Indices: 44465--44555 Score: 74
Period size: 29 Copynumber: 3.2 Consensus size: 27
44455 AATCGAGTTC
* * *
44465 AAATGGAATTTTTGAAAGTCTGGGGGTA
1 AAATGGAATTTTGGAAA-TATAGGGGTA
* * *
44493 AAATGGTAATTTTTGGAAAAATAAGGTTAA
1 AAATGG-AA-TTTTGGAAATATAGGGGT-A
*
44523 AAATGGAATTTTGGGAAATTTAGGGGTA
1 AAATGGAATTTT-GGAAATATAGGGGTA
44551 AAATG
1 AAATG
44556 ATAATTTTTT
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
28 16 0.33
29 18 0.37
30 15 0.31
ACGTcount: A:0.40, C:0.01, G:0.27, T:0.32
Consensus pattern (27 bp):
AAATGGAATTTTGGAAATATAGGGGTA
Found at i:44609 original size:59 final size:58
Alignment explanation
Indices: 44451--44643 Score: 180
Period size: 59 Copynumber: 3.3 Consensus size: 58
44441 GTAAAAGTTG
* * * *
44451 GAAAAATCGAGTTC--AAATGGAATTTTT-GAAAGTCTGGGGGTAAAATGGTAATTTTTG
1 GAAAAATCGAGGTCAAAAATGGAATTTTTGGAAA-TTTGAGGGTAAAAT-GTAATTTTTA
* * * *
44508 GAAAAAT-AAGGTTAAAAATGGAATTTTGGGAAATTT-AGGGGTAAAATGATAATTTTTT
1 GAAAAATCGAGGTCAAAAATGGAATTTTTGGAAATTTGA-GGGTAAAATG-TAATTTTTA
** *
44566 GAAAAATCGAGGTCAAAAATGGAATTTTTGGACTTTTGAGGGTAAAAATGGAATTTTTA
1 GAAAAATCGAGGTCAAAAATGGAATTTTTGGAAATTTGAGGGT-AAAATGTAATTTTTA
**
44625 GAAAGTTCGAGGGTCAAAA
1 GAAAAATCGA-GGTCAAAA
44644 TATAGTTTTG
Statistics
Matches: 111, Mismatches: 16, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
56 3 0.03
57 8 0.07
58 38 0.34
59 47 0.42
60 15 0.14
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.32
Consensus pattern (58 bp):
GAAAAATCGAGGTCAAAAATGGAATTTTTGGAAATTTGAGGGTAAAATGTAATTTTTA
Found at i:44644 original size:59 final size:59
Alignment explanation
Indices: 44451--44643 Score: 166
Period size: 58 Copynumber: 3.3 Consensus size: 59
44441 GTAAAAGTTG
* * * * *
44451 GAAAAATCGAGTTC--AAATGGAATTTT-TGAAAGTCTGGGGGTAAAATG-GTAATTTTTG
1 GAAAAATCGAGGTCAAAAATGGAATTTTGGGAAA-TTTAGGGGTAAAATGAG-AATTTTTA
* * * *
44508 GAAAAAT-AAGGTTAAAAATGGAATTTTGGGAAATTTAGGGGTAAAATGATAATTTTTT
1 GAAAAATCGAGGTCAAAAATGGAATTTTGGGAAATTTAGGGGTAAAATGAGAATTTTTA
* * *
44566 GAAAAATCGAGGTCAAAAATGGAATTTTTGG-ACTTTTGAGGGTAAAAATG-GAATTTTTA
1 GAAAAATCGAGGTCAAAAATGGAATTTTGGGAAATTTAG-GGGT-AAAATGAGAATTTTTA
**
44625 GAAAGTTCGAGGGTCAAAA
1 GAAAAATCGA-GGTCAAAA
44644 TATAGTTTTG
Statistics
Matches: 111, Mismatches: 17, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
56 3 0.03
57 7 0.06
58 44 0.40
59 43 0.39
60 14 0.13
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.32
Consensus pattern (59 bp):
GAAAAATCGAGGTCAAAAATGGAATTTTGGGAAATTTAGGGGTAAAATGAGAATTTTTA
Found at i:44692 original size:30 final size:30
Alignment explanation
Indices: 44529--44696 Score: 100
Period size: 30 Copynumber: 5.7 Consensus size: 30
44519 TTAAAAATGG
*
44529 AATTTTGGGAAA-TTT-AGGGGT-AAAATGAT
1 AATTTTTGGAAAGTTTGA-GGGTCAAAAT-AT
* ** *
44558 AATTTTTTGAAAAATCGA-GGTCAAAA-AT
1 AATTTTTGGAAAGTTTGAGGGTCAAAATAT
** * **
44586 GGAATTTTTGG-ACTTTTGAGGGTAAAAATGG
1 --AATTTTTGGAAAGTTTGAGGGTCAAAATAT
* *
44617 AATTTTTAGAAAGTTCGAGGGTCAAAATAT
1 AATTTTTGGAAAGTTTGAGGGTCAAAATAT
* *
44647 -AGTTTTGGAGAAGTTTGACGGTCAAAATAT
1 AATTTTTGGA-AAGTTTGAGGGTCAAAATAT
*
44677 AATTTTTGGACAGTTT-AGGG
1 AATTTTTGGAAAGTTTGAGGG
44697 ACCTCTAAGG
Statistics
Matches: 103, Mismatches: 26, Indels: 20
0.69 0.17 0.13
Matches are distributed among these distances:
28 2 0.02
29 35 0.34
30 57 0.55
31 9 0.09
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.35
Consensus pattern (30 bp):
AATTTTTGGAAAGTTTGAGGGTCAAAATAT
Found at i:45788 original size:3 final size:3
Alignment explanation
Indices: 45727--45773 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
45717 TTTCCCCTTT
*
45727 TTA TT- TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
45774 ACACATTTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:46497 original size:6 final size:6
Alignment explanation
Indices: 46486--46523 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
46476 TTTTTAATTC
*
46486 AATTTA AATTTA AACTT- AATTTA AATTTA AACTTTA AA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AA-TTTA AA
46524 AGAAAAGTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
5 4 0.14
6 18 0.64
7 6 0.21
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (6 bp):
AATTTA
Found at i:46508 original size:17 final size:17
Alignment explanation
Indices: 46486--46519 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
46476 TTTTTAATTC
46486 AATTTAAATTTAAACTT
1 AATTTAAATTTAAACTT
46503 AATTTAAATTTAAACTT
1 AATTTAAATTTAAACTT
46520 TAAAAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTTAAATTTAAACTT
Found at i:49429 original size:18 final size:18
Alignment explanation
Indices: 49406--49448 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
49396 GGATAGGTTT
49406 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
49424 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
49442 TTAATTA
1 TTAATTA
49449 CACTTTGAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:56691 original size:10 final size:10
Alignment explanation
Indices: 56673--56726 Score: 56
Period size: 10 Copynumber: 5.4 Consensus size: 10
56663 AGTGATTTTT
*
56673 TAAATAATTA
1 TAAAAAATTA
*
56683 TAAAGAATTA
1 TAAAAAATTA
56693 -AAAAAATTA
1 TAAAAAATTA
56702 TTAAAAAATTA
1 -TAAAAAATTA
* *
56713 TAATAAATTG
1 TAAAAAATTA
56723 TAAA
1 TAAA
56727 CGGTGATTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
9 8 0.22
10 20 0.54
11 9 0.24
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:57014 original size:20 final size:21
Alignment explanation
Indices: 56981--57038 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
56971 TAAAAAATTA
* *
56981 ATAATTATTCATAAATTCT-T
1 ATAATTTTTAATAAATTCTAT
*
57001 ATAATTTTTAAT-AATTTTAT
1 ATAATTTTTAATAAATTCTAT
57021 ATAATTTTTTAATAAATT
1 ATAA-TTTTTAATAAATT
57039 AATTCAGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 5 0.16
20 15 0.47
21 8 0.25
22 4 0.12
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
ATAATTTTTAATAAATTCTAT
Found at i:57146 original size:21 final size:19
Alignment explanation
Indices: 57121--57192 Score: 63
Period size: 21 Copynumber: 3.5 Consensus size: 19
57111 TTCGACATGA
57121 TTTTTAATCATTTTTATACTT
1 TTTTTAAT-ATTTTTATA-TT
* *
57142 TTTTTTATGATTTCTTATAAT
1 TTTTTAAT-ATTT-TTATATT
*
57163 TTTTAAATATTTTTCTATATT
1 TTTTTAATA-TTTT-TATATT
57184 TTTTTAATA
1 TTTTTAATA
57193 ATGATAGAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
20 2 0.05
21 34 0.83
22 5 0.12
ACGTcount: A:0.26, C:0.06, G:0.01, T:0.67
Consensus pattern (19 bp):
TTTTTAATATTTTTATATT
Found at i:65619 original size:14 final size:14
Alignment explanation
Indices: 65600--65626 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
65590 AAAAGGAAAG
65600 TCAATGGTTGCCAA
1 TCAATGGTTGCCAA
65614 TCAATGGTTGCCA
1 TCAATGGTTGCCA
65627 GTGCGTAGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (14 bp):
TCAATGGTTGCCAA
Found at i:68210 original size:32 final size:32
Alignment explanation
Indices: 68173--68239 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
68163 TATATATATA
*
68173 TATATATGTATATATTATTGTCAAGAAAAGGC
1 TATATATATATATATTATTGTCAAGAAAAGGC
68205 TATATATATATATATTATTGTCAAGAAAAGGC
1 TATATATATATATATTATTGTCAAGAAAAGGC
68237 TAT
1 TAT
68240 TTTGGATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (32 bp):
TATATATATATATATTATTGTCAAGAAAAGGC
Found at i:83580 original size:51 final size:51
Alignment explanation
Indices: 83499--83602 Score: 145
Period size: 51 Copynumber: 2.0 Consensus size: 51
83489 TGATATGAGG
* ** *
83499 TTGGAGCAGGCTGTTGAATCAAGAAAAGAAGTTGGAATATCAGGGAGAAGT
1 TTGGAACAGGCTGCCGAATCAAGAAAAGAAGTTGGAATAGCAGGGAGAAGT
* * *
83550 TTGGAACAGGCTGCCGAATCTAGAAGAGAAGTTGGAATAGCTGGGAGAAGT
1 TTGGAACAGGCTGCCGAATCAAGAAAAGAAGTTGGAATAGCAGGGAGAAGT
83601 TT
1 TT
83603 AGAGCCGAGC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.35, C:0.10, G:0.34, T:0.22
Consensus pattern (51 bp):
TTGGAACAGGCTGCCGAATCAAGAAAAGAAGTTGGAATAGCAGGGAGAAGT
Found at i:88187 original size:23 final size:23
Alignment explanation
Indices: 88153--88235 Score: 85
Period size: 23 Copynumber: 3.5 Consensus size: 23
88143 ATAACATCCA
* **
88153 AACAACCAAAACAGCAGTAAAAAT
1 AACAA-CAAAACAACAACAAAAAT
88177 AACAACAAAACAACAACAAAAAT
1 AACAACAAAACAACAACAAAAAT
* *
88200 AACAATAAAAATAACAACAAAAAT
1 AACAA-CAAAACAACAACAAAAAT
* *
88224 AATACCAAAACA
1 AACAACAAAACA
88236 GTAAAAAGAT
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
23 25 0.51
24 24 0.49
ACGTcount: A:0.70, C:0.19, G:0.02, T:0.08
Consensus pattern (23 bp):
AACAACAAAACAACAACAAAAAT
Found at i:88209 original size:35 final size:32
Alignment explanation
Indices: 88132--88221 Score: 99
Period size: 35 Copynumber: 2.7 Consensus size: 32
88122 CAATAGTAAA
* *
88132 AACACATAAAAATAACATCCAAACAACCAAAAC
1 AACA-ATAAAAATAACAACAAAACAACCAAAAC
* * *
88165 AGCAGTAAAAATAACAACAAAACAACAACAAAAAT
1 AACAATAAAAATAACAACAAAACAAC--C-AAAAC
88200 AACAATAAAAATAACAACAAAA
1 AACAATAAAAATAACAACAAAA
88222 ATAATACCAA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
32 19 0.40
33 3 0.06
34 1 0.02
35 24 0.51
ACGTcount: A:0.69, C:0.20, G:0.02, T:0.09
Consensus pattern (32 bp):
AACAATAAAAATAACAACAAAACAACCAAAAC
Found at i:88233 original size:12 final size:12
Alignment explanation
Indices: 88171--88225 Score: 85
Period size: 12 Copynumber: 4.7 Consensus size: 12
88161 AAACAGCAGT
88171 AAAAATAACAAC
1 AAAAATAACAAC
*
88183 -AAAACAACAAC
1 AAAAATAACAAC
*
88194 AAAAATAACAAT
1 AAAAATAACAAC
88206 AAAAATAACAAC
1 AAAAATAACAAC
88218 AAAAATAA
1 AAAAATAA
88226 TACCAAAACA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
11 10 0.26
12 28 0.74
ACGTcount: A:0.76, C:0.15, G:0.00, T:0.09
Consensus pattern (12 bp):
AAAAATAACAAC
Found at i:88233 original size:24 final size:24
Alignment explanation
Indices: 88153--88225 Score: 85
Period size: 24 Copynumber: 3.1 Consensus size: 24
88143 ATAACATCCA
* * **
88153 AACAACCAAAACAGCAGTAAAAAT
1 AACAACAAAAACAACAACAAAAAT
88177 AACAAC-AAAACAACAACAAAAAT
1 AACAACAAAAACAACAACAAAAAT
* *
88200 AACAATAAAAATAACAACAAAAAT
1 AACAACAAAAACAACAACAAAAAT
88224 AA
1 AA
88226 TACCAAAACA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 19 0.44
24 24 0.56
ACGTcount: A:0.71, C:0.18, G:0.03, T:0.08
Consensus pattern (24 bp):
AACAACAAAAACAACAACAAAAAT
Found at i:88285 original size:21 final size:22
Alignment explanation
Indices: 88252--88325 Score: 78
Period size: 22 Copynumber: 3.3 Consensus size: 22
88242 AGATAACACT
*
88252 AAAACAGCAATCAAAACAATAA
1 AAAAAAGCAATCAAAACAATAA
* *
88274 AAAAAAGC-ATCAAAATAGTAAAAA
1 AAAAAAGCAATC-AAA-A-CAATAA
*
88298 AAAAAAGCAATCAAAACAGTAA
1 AAAAAAGCAATCAAAACAATAA
88320 AAAAAA
1 AAAAAA
88326 AACAACACCA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
21 3 0.07
22 19 0.45
23 2 0.05
24 15 0.36
25 3 0.07
ACGTcount: A:0.72, C:0.12, G:0.07, T:0.09
Consensus pattern (22 bp):
AAAAAAGCAATCAAAACAATAA
Found at i:88299 original size:24 final size:25
Alignment explanation
Indices: 88252--88327 Score: 97
Period size: 25 Copynumber: 3.2 Consensus size: 25
88242 AGATAACACT
* *
88252 AAAACAGCAATCAAAAC---AATAA
1 AAAAAAGCAATCAAAACAGTAAAAA
*
88274 AAAAAAGC-ATCAAAATAGTAAAAA
1 AAAAAAGCAATCAAAACAGTAAAAA
88298 AAAAAAGCAATCAAAACAGTAAAAA
1 AAAAAAGCAATCAAAACAGTAAAAA
88323 AAAAA
1 AAAAA
88328 CAACACCAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
21 7 0.15
22 7 0.15
24 12 0.26
25 20 0.43
ACGTcount: A:0.72, C:0.12, G:0.07, T:0.09
Consensus pattern (25 bp):
AAAAAAGCAATCAAAACAGTAAAAA
Found at i:88337 original size:25 final size:25
Alignment explanation
Indices: 88284--88338 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
88274 AAAAAAGCAT
* * *
88284 CAAAATAGTAAAAAAAAAAAGCAAT
1 CAAAACAGTAAAAAAAAAAAACAAC
88309 CAAAACAGTAAAAAAAAAACAAC-AC
1 CAAAACAGTAAAAAAAAAA-AACAAC
88334 CAAAA
1 CAAAA
88339 TAACATTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 24 0.92
26 2 0.08
ACGTcount: A:0.73, C:0.15, G:0.05, T:0.07
Consensus pattern (25 bp):
CAAAACAGTAAAAAAAAAAAACAAC
Found at i:93729 original size:2 final size:2
Alignment explanation
Indices: 93678--93712 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
93668 TATTCATTGA
* *
93678 AT AT AA AT AT AA 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 AT AT AT AT A
93713 ATTTTAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:93772 original size:6 final size:6
Alignment explanation
Indices: 93761--93788 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
93751 GATTTCAATC
93761 ACTTTT ACTTTT ACTTTT ACTTTT ACTT
1 ACTTTT ACTTTT ACTTTT ACTTTT ACTT
93789 AAATGTAGCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (6 bp):
ACTTTT
Found at i:94092 original size:29 final size:30
Alignment explanation
Indices: 94060--94120 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
94050 ATCAGTCTTA
*
94060 AAAT-AAGCTTTAATTTTTAATTTATATTC
1 AAATAAAGCTTTAATTTCTAATTTATATTC
* * *
94089 AAATAAATCTTTAATTTCTATTTTTTATTC
1 AAATAAAGCTTTAATTTCTAATTTATATTC
94119 AA
1 AA
94121 GATATCTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.52
Consensus pattern (30 bp):
AAATAAAGCTTTAATTTCTAATTTATATTC
Found at i:102726 original size:11 final size:11
Alignment explanation
Indices: 102710--102738 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
102700 TAATTACATT
102710 TAAAATAAAAA
1 TAAAATAAAAA
102721 TAAAAT-AAAA
1 TAAAATAAAAA
102731 TAAAATAA
1 TAAAATAA
102739 TAGTGTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (11 bp):
TAAAATAAAAA
Done.