Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004933.1 Kokia drynarioides strain JFW-HI SEQ_118636, 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: 39425
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Warning! 21 characters in sequence are not A, C, G, or T
Found at i:502 original size:3 final size:3
Alignment explanation
Indices: 494--589 Score: 84
Period size: 3 Copynumber: 30.7 Consensus size: 3
484 CTTCGATTTT
* ** **
494 TTA TTA TTAA TTA TTA TTA ATA TTTA AAA TTTA TTA TTA AAA TTA TTA
1 TTA TTA TT-A TTA TTA TTA TTA -TTA TTA -TTA TTA TTA TTA TTA TTA
* * *
542 TTA ATA TTG TTA TTA ATA TTA CTTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
588 TT
1 TT
590 GACGTTTTAA
Statistics
Matches: 73, Mismatches: 16, Indels: 8
0.75 0.16 0.08
Matches are distributed among these distances:
3 64 0.88
4 9 0.12
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:541 original size:12 final size:12
Alignment explanation
Indices: 494--589 Score: 96
Period size: 12 Copynumber: 8.4 Consensus size: 12
484 CTTCGATTTT
494 TTATTATT-A-A
1 TTATTATTAATA
504 TTATTATTAATA
1 TTATTATTAATA
*
516 -T-TTA-AAAT-
1 TTATTATTAATA
*
524 TTATTATTAAAA
1 TTATTATTAATA
536 TTATTATTAATA
1 TTATTATTAATA
*
548 TTGTTATTAATA
1 TTATTATTAATA
*
560 TTACTTATTATTA
1 TTA-TTATTAATA
*
573 TTATTATTATTA
1 TTATTATTAATA
585 TTATT
1 TTATT
590 GACGTTTTAA
Statistics
Matches: 72, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
9 4 0.06
10 14 0.19
11 4 0.06
12 39 0.54
13 11 0.15
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (12 bp):
TTATTATTAATA
Found at i:1276 original size:17 final size:17
Alignment explanation
Indices: 1246--1315 Score: 77
Period size: 17 Copynumber: 4.1 Consensus size: 17
1236 TTTTAATATT
* *
1246 AATAATTTTTAATTCAA
1 AATAAATTTAAATTCAA
1263 AATAAATTTAAATTCAA
1 AATAAATTTAAATTCAA
* * *
1280 CATGAATTTAAATTTAA
1 AATAAATTTAAATTCAA
* *
1297 AATAAATTCAAATTTAA
1 AATAAATTTAAATTCAA
1314 AA
1 AA
1316 ATTAAAAGTT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 45 1.00
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.39
Consensus pattern (17 bp):
AATAAATTTAAATTCAA
Found at i:2383 original size:23 final size:23
Alignment explanation
Indices: 2357--2638 Score: 290
Period size: 23 Copynumber: 12.2 Consensus size: 23
2347 TAGCGCGCTT
*
2357 TCTGATTAGCACTGTGTGTGCTC
1 TCTGATTAGCACTGTGTGTGCCC
* * *
2380 TCTGATTAGCATTATGTGTGCTC
1 TCTGATTAGCACTGTGTGTGCCC
2403 TCTG-TTCAGCACTGTGTGTGCCC
1 TCTGATT-AGCACTGTGTGTGCCC
* *
2426 TCTGTTTAGCAC-GTTTCGTGCCC
1 TCTGATTAGCACTGTGT-GTGCCC
*
2449 TCTG-TTCAGCACTGTGTGTGCTC
1 TCTGATT-AGCACTGTGTGTGCCC
* *
2472 ACTGATTAGCACTGTGTGTGCTC
1 TCTGATTAGCACTGTGTGTGCCC
* * * *
2495 TTTGATCAGCACTATGTGTGCTC
1 TCTGATTAGCACTGTGTGTGCCC
2518 TCTG-TTCAGCACTGTGTGTGCCC
1 TCTGATT-AGCACTGTGTGTGCCC
* *
2541 TCTGTTTAGCAC-GTTTCGTGCCC
1 TCTGATTAGCACTGTGT-GTGCCC
2564 TCTG-TTCAGCACTGTGTGTGCCC
1 TCTGATT-AGCACTGTGTGTGCCC
2587 TCTGTTATTAGCACT-TCGTGTGCCC
1 TCTG--ATTAGCACTGT-GTGTGCCC
*
2612 TCTGATTAGCACTTTGTGTGCCC
1 TCTGATTAGCACTGTGTGTGCCC
2635 TCTG
1 TCTG
2639 TTACCCAACA
Statistics
Matches: 224, Mismatches: 19, Indels: 32
0.81 0.07 0.12
Matches are distributed among these distances:
22 13 0.06
23 177 0.79
24 14 0.06
25 18 0.08
26 2 0.01
ACGTcount: A:0.12, C:0.26, G:0.24, T:0.38
Consensus pattern (23 bp):
TCTGATTAGCACTGTGTGTGCCC
Found at i:2560 original size:115 final size:115
Alignment explanation
Indices: 2358--2640 Score: 460
Period size: 115 Copynumber: 2.4 Consensus size: 115
2348 AGCGCGCTTT
*
2358 CTGATTAGCACTGTGTGTGCTCTCTGATTAGCATTATGTGTGCTCTCTGTTCAGCACTGTGTGTG
1 CTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTATGTGTGCTCTCTGTTCAGCACTGTGTGTG
*
2423 CCCTCTGTTTAGCACGTTTCGTGCCCTCTGTTCAGCACTGTGTGTGCTCA
66 CCCTCTGTTTAGCACGTTTCGTGCCCTCTGTTCAGCACTGTGTGTGCCCA
* *
2473 CTGATTAGCACTGTGTGTGCTCTTTGATCAGCACTATGTGTGCTCTCTGTTCAGCACTGTGTGTG
1 CTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTATGTGTGCTCTCTGTTCAGCACTGTGTGTG
*
2538 CCCTCTGTTTAGCACGTTTCGTGCCCTCTGTTCAGCACTGTGTGTGCCCT
66 CCCTCTGTTTAGCACGTTTCGTGCCCTCTGTTCAGCACTGTGTGTGCCCA
* * *
2588 CTGTTATTAGCACT-TCGTGTGCCCTCTGATTAGCACTTTGTGTGCCCTCTGTT
1 CTG--ATTAGCACTGT-GTGTGCTCTCTGATTAGCACTATGTGTGCTCTCTGTT
2641 ACCCAACACT
Statistics
Matches: 155, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
115 113 0.73
116 1 0.01
117 41 0.26
ACGTcount: A:0.12, C:0.26, G:0.24, T:0.39
Consensus pattern (115 bp):
CTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTATGTGTGCTCTCTGTTCAGCACTGTGTGTG
CCCTCTGTTTAGCACGTTTCGTGCCCTCTGTTCAGCACTGTGTGTGCCCA
Found at i:6094 original size:19 final size:19
Alignment explanation
Indices: 6056--6094 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
6046 GAAGGAAAGA
*
6056 ATGAGAGATGAATGAGATG
1 ATGAGAGATGAATGAAATG
* *
6075 ATGAGCGATGATTGAAATG
1 ATGAGAGATGAATGAAATG
6094 A
1 A
6095 GAAATTGTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.03, G:0.33, T:0.23
Consensus pattern (19 bp):
ATGAGAGATGAATGAAATG
Found at i:9369 original size:22 final size:22
Alignment explanation
Indices: 9344--9388 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
9334 AGTTCTGTTG
*
9344 CTATTGGTTATTGTTGTAACTC
1 CTATTGGCTATTGTTGTAACTC
9366 CTATTGGCTATTGTTGTAACTC
1 CTATTGGCTATTGTTGTAACTC
9388 C
1 C
9389 CTTGTCTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.47
Consensus pattern (22 bp):
CTATTGGCTATTGTTGTAACTC
Found at i:15383 original size:36 final size:36
Alignment explanation
Indices: 15307--15383 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
15297 ATATAATCAA
* **
15307 TCACATGGCATGAAGAACATACCCACATATTTTCTG
1 TCACATGACATGAAGAACATACCCACATATTCACTG
* *
15343 TCACATGACATGAATAACATACCCACATATTCACTT
1 TCACATGACATGAAGAACATACCCACATATTCACTG
15379 TCACA
1 TCACA
15384 GCAGTCATCA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.27, G:0.09, T:0.27
Consensus pattern (36 bp):
TCACATGACATGAAGAACATACCCACATATTCACTG
Found at i:19421 original size:3 final size:3
Alignment explanation
Indices: 19413--19444 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
19403 TTTTATTTTT
*
19413 TAA TAA TAA TAA TCA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
19445 TACGTTTTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:20115 original size:17 final size:17
Alignment explanation
Indices: 20093--20152 Score: 75
Period size: 17 Copynumber: 3.5 Consensus size: 17
20083 GGACAATATT
20093 AATTTAAATTTAGAATA
1 AATTTAAATTTAGAATA
*
20110 AATTTAAATTTAAGAATT
1 AATTTAAATTT-AGAATA
* *
20128 AATTTAAACTTAAAATA
1 AATTTAAATTTAGAATA
*
20145 AATCTAAA
1 AATTTAAA
20153 AAATGGGGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
17 22 0.59
18 15 0.41
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (17 bp):
AATTTAAATTTAGAATA
Found at i:20131 original size:18 final size:18
Alignment explanation
Indices: 20090--20140 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
20080 TTTGGACAAT
20090 ATTAATTTAAATTT-AGA
1 ATTAATTTAAATTTAAGA
*
20107 ATAAATTTAAATTTAAGA
1 ATTAATTTAAATTTAAGA
*
20125 ATTAATTTAAACTTAA
1 ATTAATTTAAATTTAA
20141 AATAAATCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 13 0.43
18 17 0.57
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (18 bp):
ATTAATTTAAATTTAAGA
Found at i:20656 original size:39 final size:39
Alignment explanation
Indices: 20602--20703 Score: 177
Period size: 39 Copynumber: 2.6 Consensus size: 39
20592 GACTGTAATC
*
20602 TACCCCAGGCTCGGGGTAATAGATTTGCTGATGATGATT
1 TACCCCAGGCTCGGGGTAAAAGATTTGCTGATGATGATT
*
20641 TACCCCAGGCTCGGGGTAAGAGATTTGCTGATGATGATT
1 TACCCCAGGCTCGGGGTAAAAGATTTGCTGATGATGATT
*
20680 TACCCCAGGTTCGGGGTAAAAGAT
1 TACCCCAGGCTCGGGGTAAAAGAT
20704 CGGATGGCTG
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 60 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (39 bp):
TACCCCAGGCTCGGGGTAAAAGATTTGCTGATGATGATT
Found at i:20731 original size:78 final size:78
Alignment explanation
Indices: 20651--20939 Score: 384
Period size: 78 Copynumber: 3.7 Consensus size: 78
20641 TACCCCAGGC
* * * *
20651 TCGGGGTAAGAGATTTGCTGATGATGATTTACCCCAGGTTCGGGGTAAAAGATCGGATGGCTGCA
1 TCGGGGTAAGAGATTTGCTGATGATGATCTACCCCAGGCTCGGGGTAAGAGATCGGATGGTTGCA
*
20716 ATCTGCCCC-TGGC
66 ATCTGCCCCAT-GA
* * * * * *
20729 TCGAGGTAGGAGATTGGCTGATGGTGATCTACCCCAAGCTTGGGGTAAGAGATCGGATGGTTGCA
1 TCGGGGTAAGAGATTTGCTGATGATGATCTACCCCAGGCTCGGGGTAAGAGATCGGATGGTTGCA
*
20794 ATCTACCCCATGA
66 ATCTGCCCCATGA
* *
20807 TCGGGGTAAGAGA-TTGACTGATGATGATCTGCCCCAGGCTCGGGGTAAGAGATCGGATGGTTAC
1 TCGGGGTAAGAGATTTG-CTGATGATGATCTACCCCAGGCTCGGGGTAAGAGATCGGATGGTTGC
20871 AATCTGCCCCATGA
65 AATCTGCCCCATGA
* * * *
20885 TTGGGGTAAGAGATTTGCTGATGATAATCTGCCCCAAGCTCGGGGTAAGAGATCG
1 TCGGGGTAAGAGATTTGCTGATGATGATCTACCCCAGGCTCGGGGTAAGAGATCG
20940 AATCTTCAAT
Statistics
Matches: 184, Mismatches: 24, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
77 2 0.01
78 178 0.97
79 4 0.02
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (78 bp):
TCGGGGTAAGAGATTTGCTGATGATGATCTACCCCAGGCTCGGGGTAAGAGATCGGATGGTTGCA
ATCTGCCCCATGA
Found at i:20798 original size:39 final size:39
Alignment explanation
Indices: 20690--20939 Score: 175
Period size: 39 Copynumber: 6.4 Consensus size: 39
20680 TACCCCAGGT
* * **
20690 TCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCCTGGC
1 TCGGGGTAAGAGATCGGATGGTTGCAATCTGCCCCAAGC
* * * * * * ** *
20729 TCGAGGTAGGAGATTGGCTGATGGTGATCTACCCCAAGC
1 TCGGGGTAAGAGATCGGATGGTTGCAATCTGCCCCAAGC
* * * *
20768 TTGGGGTAAGAGATCGGATGGTTGCAATCTACCCCATGA
1 TCGGGGTAAGAGATCGGATGGTTGCAATCTGCCCCAAGC
* * *
20807 TCGGGGTAAGAGAT-TGACT-GATG-ATGATCTGCCCCAGGC
1 TCGGGGTAAGAGATCGGA-TGGTTGCA--ATCTGCCCCAAGC
* * *
20846 TCGGGGTAAGAGATCGGATGGTTACAATCTGCCCCATGA
1 TCGGGGTAAGAGATCGGATGGTTGCAATCTGCCCCAAGC
* ** * * *
20885 TTGGGGTAAGAGATTTGCT-GATGATAATCTGCCCCAAGC
1 TCGGGGTAAGAGATCGGATGGTTG-CAATCTGCCCCAAGC
20924 TCGGGGTAAGAGATCG
1 TCGGGGTAAGAGATCG
20940 AATCTTCAAT
Statistics
Matches: 157, Mismatches: 47, Indels: 14
0.72 0.22 0.06
Matches are distributed among these distances:
37 1 0.01
38 7 0.04
39 144 0.92
40 4 0.03
41 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.24
Consensus pattern (39 bp):
TCGGGGTAAGAGATCGGATGGTTGCAATCTGCCCCAAGC
Found at i:33313 original size:29 final size:29
Alignment explanation
Indices: 33281--33345 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
33271 GAAGTAGAAC
* *
33281 TTTTGGAAAATTGATGGTAAAATGGTAAT
1 TTTTGGAAAATCGAGGGTAAAATGGTAAT
*** *
33310 TTTTGGATGCTCGGGGGTAAAATGGTAAT
1 TTTTGGAAAATCGAGGGTAAAATGGTAAT
33339 TTTTGGA
1 TTTTGGA
33346 TGCTCGGGGG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.29, C:0.03, G:0.29, T:0.38
Consensus pattern (29 bp):
TTTTGGAAAATCGAGGGTAAAATGGTAAT
Found at i:33391 original size:30 final size:30
Alignment explanation
Indices: 33299--33580 Score: 215
Period size: 29 Copynumber: 9.5 Consensus size: 30
33289 AATTGATGGT
* * *
33299 AAAATGGTAATTTTTG-GATGCTCGGGGGT-
1 AAAAT-GTAATTTTTGAGAAGTTCGAGGGTA
* * * *
33328 AAAATGGTAATTTTTG-GATGCTCGGGGGCA
1 AAAAT-GTAATTTTTGAGAAGTTCGAGGGTA
* **
33358 AAAATGTAATTTTTGAGAAGTTCAAATGTA
1 AAAATGTAATTTTTGAGAAGTTCGAGGGTA
* *
33388 AAAATGTAATTTTTG-GAAGTACGGGGGTA
1 AAAATGTAATTTTTGAGAAGTTCGAGGGTA
* * ** *
33417 AAAATATAATTTTTGATAA-TTTTAGGGAA
1 AAAATGTAATTTTTGAGAAGTTCGAGGGTA
*
33446 CAAAATGTAACTTTTG-GAAGTTCGAGGGTA
1 -AAAATGTAATTTTTGAGAAGTTCGAGGGTA
* *
33476 AAAATGTATTTTTTGAGAAGTTCGA-GGTT
1 AAAATGTAATTTTTGAGAAGTTCGAGGGTA
* *
33505 AAAATGTAATTTTT-AGAAAGTTCGAGGATT
1 AAAATGTAATTTTTGAG-AAGTTCGAGGGTA
* *
33535 AAAATATAATTTTT-AGAAAGTTC-AGGGGTT
1 AAAATGTAATTTTTGAG-AAGTTCGA-GGGTA
*
33565 AAAATGTGATTTTTGA
1 AAAATGTAATTTTTGA
33581 AGAGTTTTGG
Statistics
Matches: 208, Mismatches: 35, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
28 2 0.01
29 106 0.51
30 99 0.48
31 1 0.00
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (30 bp):
AAAATGTAATTTTTGAGAAGTTCGAGGGTA
Found at i:33397 original size:59 final size:57
Alignment explanation
Indices: 33328--33579 Score: 209
Period size: 59 Copynumber: 4.3 Consensus size: 57
33318 GCTCGGGGGT
* * *
33328 AAAATGGTAATTTTTGGATGCTCGGGGGCAAAAATGTAATTTTTGAGAAGTTCAAATGTA
1 AAAAT-GTAATTTTTGGAAG-TCGGGGGTAAAAATGTAATTTTTGAGAAGTTC-AAGGTA
* * * * * *
33388 AAAATGTAATTTTTGGAAGTACGGGGGTAAAAATATAATTTTTGATAATTTTAGGGAA
1 AAAATGTAATTTTTGGAAGT-CGGGGGTAAAAATGTAATTTTTGAGAAGTTCAAGGTA
* * * * *
33446 CAAAATGTAACTTTTGGAAGTTCGAGGGTAAAAATGTATTTTTTGAGAAGTTCGAGGTT
1 -AAAATGTAATTTTTGGAAG-TCGGGGGTAAAAATGTAATTTTTGAGAAGTTCAAGGTA
* * * * * * *
33505 AAAATGTAATTTTTAGAAAGTTCGAGGATTAAAATATAATTTTT-AGAAAGTTCAGGGGTT
1 AAAATGTAATTTTT-GGAAG-TCGGGGGTAAAAATGTAATTTTTGAG-AAGTTCA-AGGTA
*
33565 AAAATGTGATTTTTG
1 AAAATGTAATTTTTG
33580 AAGAGTTTTG
Statistics
Matches: 157, Mismatches: 29, Indels: 13
0.79 0.15 0.07
Matches are distributed among these distances:
58 19 0.12
59 115 0.73
60 23 0.15
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.36
Consensus pattern (57 bp):
AAAATGTAATTTTTGGAAGTCGGGGGTAAAAATGTAATTTTTGAGAAGTTCAAGGTA
Found at i:33417 original size:29 final size:29
Alignment explanation
Indices: 33299--33617 Score: 203
Period size: 30 Copynumber: 10.8 Consensus size: 29
33289 AATTGATGGT
* *
33299 AAAATGGTAATTTTTGGATGCTCGGGGGT-
1 AAAAT-GTAATTTTTGGAAGTTCGGGGGTA
* * *
33328 AAAATGGTAATTTTTGGATGCTCGGGGGCA
1 AAAAT-GTAATTTTTGGAAGTTCGGGGGTA
****
33358 AAAATGTAATTTTTGAGAAGTTCAAATGTA
1 AAAATGTAATTTTTG-GAAGTTCGGGGGTA
*
33388 AAAATGTAATTTTTGGAAGTACGGGGGTA
1 AAAATGTAATTTTTGGAAGTTCGGGGGTA
* * *** *
33417 AAAATATAATTTTT-GATAATTTTAGGGAA
1 AAAATGTAATTTTTGGA-AGTTCGGGGGTA
* *
33446 CAAAATGTAACTTTTGGAAGTTCGAGGGTA
1 -AAAATGTAATTTTTGGAAGTTCGGGGGTA
* * *
33476 AAAATGTATTTTTTGAGAAGTTC-GAGGTT
1 AAAATGTAATTTTTG-GAAGTTCGGGGGTA
* * * *
33505 AAAATGTAATTTTTAGAAAGTTCGAGGATT
1 AAAATGTAATTTTT-GGAAGTTCGGGGGTA
* * * *
33535 AAAATATAATTTTTAGAAAGTTCAGGGGTT
1 AAAATGTAATTTTT-GGAAGTTCGGGGGTA
* * ** * *
33565 AAAATGTGATTTTTGAAGAGTTTTGGAGTC
1 AAAATGTAATTTTTGGA-AGTTCGGGGGTA
*
33595 AAAATATAATTTTTGGATAGTTC
1 AAAATGTAATTTTTGGA-AGTTC
33618 AGGGACCTTT
Statistics
Matches: 230, Mismatches: 51, Indels: 17
0.77 0.17 0.06
Matches are distributed among these distances:
28 2 0.01
29 104 0.45
30 122 0.53
31 2 0.01
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (29 bp):
AAAATGTAATTTTTGGAAGTTCGGGGGTA
Found at i:34664 original size:3 final size:3
Alignment explanation
Indices: 34656--34682 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
34646 TCGGCTCTCT
34656 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
34683 ATGTTATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:35383 original size:6 final size:6
Alignment explanation
Indices: 35372--35436 Score: 57
Period size: 6 Copynumber: 11.3 Consensus size: 6
35362 GAACATTATT
* * *
35372 AATTTA AATTTA GAA--TA AATTTA AACTTA AA-ATA AATTTA AACTTA
1 AATTTA AATTTA -AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
35418 AA-ATA AATTTA AATTTA AA
1 AATTTA AATTTA AATTTA AA
35437 AACAAATTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
4 2 0.04
5 10 0.21
6 34 0.71
7 2 0.04
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (6 bp):
AATTTA
Found at i:35394 original size:17 final size:17
Alignment explanation
Indices: 35372--35465 Score: 134
Period size: 17 Copynumber: 5.5 Consensus size: 17
35362 GAACATTATT
* *
35372 AATTTAAATTTAGAATA
1 AATTTAAACTTAAAATA
35389 AATTTAAACTTAAAATA
1 AATTTAAACTTAAAATA
35406 AATTTAAACTTAAAATA
1 AATTTAAACTTAAAATA
* *
35423 AATTTAAATTTAAAAACA
1 AATTTAAACTT-AAAATA
35441 AATTTAAACTTAAAATA
1 AATTTAAACTTAAAATA
*
35458 AATCTAAA
1 AATTTAAA
35466 AAAATGGTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
17 54 0.78
18 15 0.22
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.35
Consensus pattern (17 bp):
AATTTAAACTTAAAATA
Found at i:35451 original size:35 final size:34
Alignment explanation
Indices: 35372--35465 Score: 134
Period size: 35 Copynumber: 2.7 Consensus size: 34
35362 GAACATTATT
* * *
35372 AATTTAAATTTAGAATAAATTTAAACTTAAAATA
1 AATTTAAACTTAAAATAAATTTAAACTTAAAACA
*
35406 AATTTAAACTTAAAATAAATTTAAATTTAAAAACA
1 AATTTAAACTTAAAATAAATTTAAACTT-AAAACA
*
35441 AATTTAAACTTAAAATAAATCTAAA
1 AATTTAAACTTAAAATAAATTTAAA
35466 AAAATGGTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
34 25 0.46
35 29 0.54
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.35
Consensus pattern (34 bp):
AATTTAAACTTAAAATAAATTTAAACTTAAAACA
Found at i:37489 original size:14 final size:15
Alignment explanation
Indices: 37454--37494 Score: 59
Period size: 14 Copynumber: 2.8 Consensus size: 15
37444 AAACAAAATC
37454 AATAAA-AATTCCAA
1 AATAAATAATTCCAA
37468 ATATAAATAATTCC-A
1 A-ATAAATAATTCCAA
37483 AATAAATAATTC
1 AATAAATAATTC
37495 AAGGATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 12 0.48
15 7 0.28
16 6 0.24
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (15 bp):
AATAAATAATTCCAA
Found at i:39134 original size:5 final size:5
Alignment explanation
Indices: 39133--39213 Score: 58
Period size: 5 Copynumber: 15.2 Consensus size: 5
39123 TTAAAAATAA
*
39133 AAAAT AAAAA AAAAT AATAAAT AGAAAT AGAAAT GAAAAT AAAAT -AAAT
1 AAAAT AAAAT AAAAT -A-AAAT A-AAAT A-AAAT -AAAAT AAAAT AAAAT
* *
39182 AAAAT AAAA- ATAAAT GAAAT GAAAT GAAAAT A
1 AAAAT AAAAT A-AAAT AAAAT AAAAT -AAAAT A
39214 CGAAAAAAAG
Statistics
Matches: 64, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
4 5 0.08
5 34 0.53
6 20 0.31
7 5 0.08
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:39135 original size:6 final size:6
Alignment explanation
Indices: 39124--39195 Score: 58
Period size: 6 Copynumber: 11.7 Consensus size: 6
39114 ATAATTAAAT
* * *
39124 TAAAAA TAAAAA -ATAAAA -AAAAA TAATAAA TAGAAA TAGAAA TGAAAA
1 TAAAAA TAAAAA TA-AAAA TAAAAA TAA-AAA TAAAAA TAAAAA TAAAAA
*
39172 TAAAATA AATAAAA TAAAAA TAAA
1 TAAAA-A TA-AAAA TAAAAA TAAA
39196 TGAAATGAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
5 5 0.09
6 38 0.69
7 9 0.16
8 3 0.05
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (6 bp):
TAAAAA
Found at i:39177 original size:30 final size:29
Alignment explanation
Indices: 39111--39200 Score: 76
Period size: 30 Copynumber: 2.9 Consensus size: 29
39101 TAAGTTACAC
39111 AAAATAATTAAATTAAAAATAAAAAAT-AAAAA
1 AAAATAA-TAAA-T-AAAAT-AAAAATGAAAAA
* *
39143 AAAATAATAAATAGAAATAGAAATGAAAAT
1 AAAATAATAAATA-AAATAAAAATGAAAAA
*
39173 AAAATAAATAAAATAAAA-ATAAATGAAA
1 AAAAT-AAT-AAATAAAATAAAAATGAAA
39201 TGAAATGAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
29 6 0.12
30 23 0.45
31 10 0.20
32 12 0.24
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (29 bp):
AAAATAATAAATAAAATAAAAATGAAAAA
Found at i:39212 original size:35 final size:38
Alignment explanation
Indices: 39133--39222 Score: 98
Period size: 35 Copynumber: 2.3 Consensus size: 38
39123 TTAAAAATAA
39133 AAAATAAAAAAAAATAATAAATAGAAATAGAAATGAAAAT
1 AAAAT-AAAAAAAATAATAAATA-AAATAGAAATGAAAAT
*
39173 AAAATAAATAAAATAA-AAAT-AAAT-GAAATG-AAAT
1 AAAATAAAAAAAATAATAAATAAAATAGAAATGAAAAT
39207 GAAAATACGAAAAAAA
1 -AAAATA--AAAAAAA
39223 GGAAAATTAG
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
34 4 0.09
35 12 0.27
36 4 0.09
37 6 0.13
38 4 0.09
39 10 0.22
40 5 0.11
ACGTcount: A:0.74, C:0.01, G:0.08, T:0.17
Consensus pattern (38 bp):
AAAATAAAAAAAATAATAAATAAAATAGAAATGAAAAT
Done.