Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006597.1 Kokia drynarioides strain JFW-HI SEQ_121186, 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: 29546
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Warning! 16 characters in sequence are not A, C, G, or T
Found at i:3107 original size:29 final size:29
Alignment explanation
Indices: 3075--3162 Score: 88
Period size: 29 Copynumber: 3.0 Consensus size: 29
3065 AGTTTGAGGT
3075 TAAAACTTAATTTTGGAAAAGTTTAGGGG
1 TAAAACTTAATTTTGGAAAAGTTTAGGGG
* * *
3104 TAAAAATGTAATTTTGCAAAAGCTT-GGGG
1 TAAAACT-TAATTTTGGAAAAGTTTAGGGG
* * * *
3133 TCAAAACATGATTTTAGAGAAGTTTAGGGG
1 T-AAAACTTAATTTTGGAAAAGTTTAGGGG
3163 CCAAAATGTG
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
29 23 0.50
30 23 0.50
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.32
Consensus pattern (29 bp):
TAAAACTTAATTTTGGAAAAGTTTAGGGG
Found at i:3118 original size:30 final size:30
Alignment explanation
Indices: 3082--3495 Score: 265
Period size: 30 Copynumber: 14.0 Consensus size: 30
3072 GGTTAAAACT
* *
3082 TAATTTTGGAAAAGTTTAGGGGTAAAAATG
1 TAATTTTAGAAAAGTTTAGGGGTCAAAATG
* **
3112 TAATTTT-GCAAAAGCTT-GGGGTCAAAACA
1 TAATTTTAG-AAAAGTTTAGGGGTCAAAATG
* * *
3141 TGATTTTAGAGAAGTTTAGGGGCCAAAATG
1 TAATTTTAGAAAAGTTTAGGGGTCAAAATG
* * * * *
3171 TGA-TTTCGAGAAGGTTTTGGGATCAAAATG
1 TAATTTTAGA-AAAGTTTAGGGGTCAAAATG
* * * * *
3201 TGATTTTAGAGAAGTTTGGGGGTGAAAATA
1 TAATTTTAGAAAAGTTTAGGGGTCAAAATG
* * * *
3231 TGATTTTGGAAATGTTT-GAGGGTCAAAATA
1 TAATTTTAGAAAAGTTTAG-GGGTCAAAATG
* * * * * *
3261 TTATTTTAAAAAATTTTTGAGGTTAAAATG
1 TAATTTTAGAAAAGTTTAGGGGTCAAAATG
* * *
3291 TGATTTTAG-AAAGTTTTGGGATCAAAATG
1 TAATTTTAGAAAAGTTTAGGGGTCAAAATG
* * *
3320 TAATTTTAGAAAAGGTTAAGGGTTAAAATG
1 TAATTTTAGAAAAGTTTAGGGGTCAAAATG
* *
3350 -AACTTTTGGAAAAGTTTAGGGGTTAAAATG
1 TAA-TTTTAGAAAAGTTTAGGGGTCAAAATG
* * * * *
3380 AAATTTTGGGAAAGTTT-GGGGTAAAAATA
1 TAATTTTAGAAAAGTTTAGGGGTCAAAATG
* * **
3409 TAATTTTAAAAAAATTTA-GGGTGGAAATG
1 TAATTTTAGAAAAGTTTAGGGGTCAAAATG
* *
3438 TAATTTTA-AAGATGTTT-GGGGTTAAAATG
1 TAATTTTAGAA-AAGTTTAGGGGTCAAAATG
*
3467 TAATTTTAGATAAGTTT-GAGGGTCAAAAT
1 TAATTTTAGAAAAGTTTAG-GGGTCAAAAT
3496 ATGATTTTTA
Statistics
Matches: 301, Mismatches: 68, Indels: 30
0.75 0.17 0.08
Matches are distributed among these distances:
28 2 0.01
29 119 0.40
30 172 0.57
31 8 0.03
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (30 bp):
TAATTTTAGAAAAGTTTAGGGGTCAAAATG
Found at i:3139 original size:59 final size:58
Alignment explanation
Indices: 3065--3495 Score: 271
Period size: 59 Copynumber: 7.3 Consensus size: 58
3055 AATTTCGGAG
* * *
3065 AGTTTGAGGTTAAAACT-TAATTTTGGAAAAGTTTAGGGGTAAAAATGTAATTTTGCAAA
1 AGTTTGGGGTCAAAA-TGTAATTTTAGAAAAGTTTAGGGGTAAAAATGTAATTTTG-AAA
* ** * * ** * *
3124 AGCTTGGGGTCAAAACATGATTTTAGAGAAGTTTAGGGGCCAAAATGTGATTTCGAGAA
1 AGTTTGGGGTCAAAATGTAATTTTAGAAAAGTTTAGGGGTAAAAATGTAATTTTGA-AA
* * * * * * * *
3183 GGTTTTGGGATCAAAATGTGATTTTAGAGAAGTTTGGGGGTGAAAATATGATTTTGGAAA
1 AG-TTTGGGGTCAAAATGTAATTTTAGAAAAGTTTAGGGGTAAAAATGTAATTTT-GAAA
* * * * * * * * *
3243 TGTTTGAGGGTCAAAATATTATTTTAAAAAATTTTTGAGGTTAAAATGTGATTTT-AGAA
1 AGTTTG-GGGTCAAAATGTAATTTTAGAAAAGTTTAGGGGTAAAAATGTAATTTTGA-AA
* * * *
3302 AGTTTTGGGATCAAAATGTAATTTTAGAAAAGGTTAAGGGTTAAAATG-AACTTTTGGAAA
1 AG-TTTGGGGTCAAAATGTAATTTTAGAAAAGTTTAGGGGTAAAAATGTAA-TTTT-GAAA
* * * * * *
3362 AGTTTAGGGGTTAAAATGAAATTTTGGGAAAGTTT-GGGGTAAAAATATAATTTTAAAAA
1 AGTTT-GGGGTCAAAATGTAATTTTAGAAAAGTTTAGGGGTAAAAATGTAATTTT-GAAA
* * ** * * *
3421 AATTTAGGGTGGAAATGTAATTTTA-AAGATGTTT-GGGGTTAAAATGTAATTTTAGATA
1 AGTTTGGGGTCAAAATGTAATTTTAGAA-AAGTTTAGGGGTAAAAATGTAATTTT-GAAA
3479 AGTTTGAGGGTCAAAAT
1 AGTTTG-GGGTCAAAAT
3496 ATGATTTTTA
Statistics
Matches: 288, Mismatches: 70, Indels: 28
0.75 0.18 0.07
Matches are distributed among these distances:
57 1 0.00
58 47 0.16
59 120 0.42
60 117 0.41
61 3 0.01
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (58 bp):
AGTTTGGGGTCAAAATGTAATTTTAGAAAAGTTTAGGGGTAAAAATGTAATTTTGAAA
Found at i:3216 original size:119 final size:118
Alignment explanation
Indices: 3082--3377 Score: 324
Period size: 119 Copynumber: 2.5 Consensus size: 118
3072 GGTTAAAACT
* * *
3082 TAATTTTGGAAAAGTTTAGGGGTAAAAATGTAATTTTGCAAAAGCTTGGGGTCAAAACATGATTT
1 TAATTTTAGAAAAGTTTAGGGGTAAAAATGTAATTTTGGAAAAGTTTGGGGTCAAAACATGATTT
* * * *
3147 TAGAGAAGTTTAGGGGCCAAAATGTGATTTCGAGAAGGTTTTGGGATCAAAATG
66 TAAAAAAGTTTAGAGGCCAAAATGTGATTT-GAGAAAGTTTTGGGATCAAAATG
* * * * * * * * *
3201 TGATTTTAGAGAAGTTTGGGGGTGAAAATATGATTTTGGAAATGTTTGAGGGTCAAAATATTATT
1 TAATTTTAGAAAAGTTTAGGGGTAAAAATGTAATTTTGGAAAAGTTTG-GGGTCAAAACATGATT
* * ** *
3266 TTAAAAAATTTTTGAGGTTAAAATGTGATTTTAGAAAGTTTTGGGATCAAAATG
65 TTAAAAAAGTTTAGAGGCCAAAATGTGATTTGAGAAAGTTTTGGGATCAAAATG
* * * *
3320 TAATTTTAGAAAAGGTTAAGGGTTAAAATG-AACTTTTGGAAAAGTTTAGGGGTTAAAA
1 TAATTTTAGAAAAGTTTAGGGGTAAAAATGTAA-TTTTGGAAAAGTTT-GGGGTCAAAA
3378 TGAAATTTTG
Statistics
Matches: 143, Mismatches: 31, Indels: 6
0.79 0.17 0.03
Matches are distributed among these distances:
118 1 0.01
119 103 0.72
120 39 0.27
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.34
Consensus pattern (118 bp):
TAATTTTAGAAAAGTTTAGGGGTAAAAATGTAATTTTGGAAAAGTTTGGGGTCAAAACATGATTT
TAAAAAAGTTTAGAGGCCAAAATGTGATTTGAGAAAGTTTTGGGATCAAAATG
Found at i:4472 original size:22 final size:22
Alignment explanation
Indices: 4446--4517 Score: 101
Period size: 22 Copynumber: 3.3 Consensus size: 22
4436 AAAGTTTTGA
4446 AATAAATGCTAATAAAATGTAT
1 AATAAATGCTAATAAAATGTAT
**
4468 AATAAATGCTAATAAAAAATAT
1 AATAAATGCTAATAAAATGTAT
*
4490 AATAAATGCTAATATAAATG-CT
1 AATAAATGCTAATA-AAATGTAT
4512 AATAAA
1 AATAAA
4518 AGATATAATA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
22 41 0.93
23 3 0.07
ACGTcount: A:0.58, C:0.06, G:0.07, T:0.29
Consensus pattern (22 bp):
AATAAATGCTAATAAAATGTAT
Found at i:4494 original size:34 final size:35
Alignment explanation
Indices: 4455--4529 Score: 111
Period size: 34 Copynumber: 2.2 Consensus size: 35
4445 AAATAAATGC
4455 TAATAAAATG-T-ATAATAAATGCTAATAAAAAATA
1 TAATAAAATGCTAAT-ATAAATGCTAATAAAAAATA
*
4489 TAAT-AAATGCTAATATAAATGCTAATAAAAGATA
1 TAATAAAATGCTAATATAAATGCTAATAAAAAATA
4523 TAATAAA
1 TAATAAA
4530 TGATGTGTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
33 5 0.14
34 28 0.76
35 4 0.11
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.29
Consensus pattern (35 bp):
TAATAAAATGCTAATATAAATGCTAATAAAAAATA
Found at i:5124 original size:57 final size:57
Alignment explanation
Indices: 5015--5130 Score: 155
Period size: 57 Copynumber: 2.0 Consensus size: 57
5005 GAGATTGATT
* * * *
5015 TTTTTTTTTTGTAAGAGATTGGATGGTTACAATCTGTTCTTGGCGTGAGGTAAGAGA
1 TTTTTTTTTTATAAGAGATTGGATGGTTACAATATGCTCTTCGCGTGAGGTAAGAGA
*
5072 TTTTTTTTTTATAAGAGATTGGATGGTTGCAATATGCCTCTATCGCG-G-GGTAAGAGA
1 TTTTTTTTTTATAAGAGATTGGATGGTTACAATATG-CTCT-TCGCGTGAGGTAAGAGA
5129 TT
1 TT
5131 GCCTGATGGT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
57 44 0.85
58 4 0.08
59 4 0.08
ACGTcount: A:0.23, C:0.09, G:0.27, T:0.41
Consensus pattern (57 bp):
TTTTTTTTTTATAAGAGATTGGATGGTTACAATATGCTCTTCGCGTGAGGTAAGAGA
Found at i:5233 original size:78 final size:78
Alignment explanation
Indices: 5117--5753 Score: 681
Period size: 78 Copynumber: 8.2 Consensus size: 78
5107 GCCTCTATCG
* * * * ** *
5117 CGGGGTAAGAGATTGCCTGATGGTGATCTACCCCAGGCTCGGGGTAAAAGATCAAATGGTTACAA
1 CGGGGTAAGAGATTGGCTGATAGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGTTGCAA
* *
5182 CCTGTCCCAGGCT
66 TCTGTCCCAAGCT
* * ** * * *
5195 CGGGGTAAGAGATTGGCT-ACTCGTGATTTGCCTTAGGCTCGAGGTAAAAGATCGGATGGCTGCA
1 CGGGGTAAGAGATTGGCTGA-TAGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGTTGCA
5259 ATCTG-CCTCAAGCT
65 ATCTGTCC-CAAGCT
* * * * * * * * * *
5273 CGAGGTAAGAGATTGGTTAATGGTGATCTGCCCTAGGCTCGAGGTAAAAGATCAGATGGCTACAA
1 CGGGGTAAGAGATTGGCTGATAGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGTTGCAA
* **
5338 TCT-ACCCGTGGCT
66 TCTGTCCC-AAGCT
* * * * *
5351 CAGGGTAAGAGATTGACTGATGGTGATCTGCCCTAAGCTCGGGGTAAAAGATCAGATGGTTGCAA
1 CGGGGTAAGAGATTGGCTGATAGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGTTGCAA
* *
5416 TCTGTCTCAGGCT
66 TCTGTCCCAAGCT
*
5429 CGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGTTGCAA
1 CGGGGTAAGAGATTGGCTGATAGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGTTGCAA
*
5494 TCTGCCCCAAGCT
66 TCTGTCCCAAGCT
* * * *
5507 CGGGGTAAGAGATTAGTTGATAGTGATTTGCCCCAAGCTCGGGGTAAAAGATCGGA-GAGCTGCA
1 CGGGGTAAGAGATTGGCTGATAGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATG-GTTGCA
*
5571 ATTTGTCCCAAGCT
65 ATCTGTCCCAAGCT
* ** * * *
5585 CGAGGTAAGAGATTAACTAATAGTGATCTGCCCCAAGCTCTGGGTAAAAGATCGAATGGTTGCAA
1 CGGGGTAAGAGATTGGCTGATAGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGTTGCAA
**
5650 TCTACCCCAAGCT
66 TCTGTCCCAAGCT
* * **
5663 CGGGGTAAGAGATTGGCTGATAGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGAATGATTGTGA
1 CGGGGTAAGAGATTGGCTGATAGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGTTGCAA
* *
5728 TCTG-CCTCATGAT
66 TCTGTCC-CAAGCT
5741 CGGGGTAAGAGAT
1 CGGGGTAAGAGAT
5754 CGGAATCTTT
Statistics
Matches: 480, Mismatches: 70, Indels: 18
0.85 0.12 0.03
Matches are distributed among these distances:
77 7 0.01
78 469 0.98
79 4 0.01
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (78 bp):
CGGGGTAAGAGATTGGCTGATAGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGTTGCAA
TCTGTCCCAAGCT
Found at i:5555 original size:234 final size:233
Alignment explanation
Indices: 5119--5753 Score: 792
Period size: 234 Copynumber: 2.7 Consensus size: 233
5109 CTCTATCGCG
* * * * * *
5119 GGGTAAGAGATTGCCTGATGGTGATCTACCCCAGGCTCGGGGTAAAAGATCAAATGGTTACAACC
1 GGGTAAGAGATTGACTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCAGATGGTTGCAATC
* * ** * *
5184 TGTCCCAGGCTCGGGGTAAGAGATTGGCT-ACTCGTGATTTGCCTTAGGCTCGAGGTAAAAGATC
66 TGTCCCAGGCTCGGGGTAAGAGATTGGCTGA-TAGTGATCTGCCCCAAGCTCGGGGTAAAAGATC
* * * * * *
5248 GGATGGCTGCAATCTGCCTCAAGCTCGAGGTAAGAGATTGGTTAATGGTGATCTGCCCTAGGCTC
130 GGATGGTTGCAATCTGCCTCAAGCTCGGGGTAAGAGATTAGTTAATAGTGATCTGCCCCAAGCTC
**
5313 GAGGTAAAAGATCAGATG-GCTACAATCT-ACCCGTGGCTC
195 GAGGTAAAAGATCAGA-GAGCTACAATCTGACCC-AAGCTC
*
5352 AGGGTAAGAGATTGACTGATGGTGATCTGCCCTAAGCTCGGGGTAAAAGATCAGATGGTTGCAAT
1 -GGGTAAGAGATTGACTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCAGATGGTTGCAAT
* *
5417 CTGTCTCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATC
65 CTGTCCCAGGCTCGGGGTAAGAGATTGGCTGATAGTGATCTGCCCCAAGCTCGGGGTAAAAGATC
* * *
5482 GGATGGTTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTAGTTGATAGTGATTTGCCCCAAGCTC
130 GGATGGTTGCAATCTGCCTCAAGCTCGGGGTAAGAGATTAGTTAATAGTGATCTGCCCCAAGCTC
* * * * *
5547 GGGGTAAAAGATCGGAGAGCTGCAATTTGTCCCAAGCTC
195 GAGGTAAAAGATCAGAGAGCTACAATCTGACCCAAGCTC
* * * *
5586 GAGGTAAGAGATTAACTAATAGTGATCTGCCCCAAGCTCTGGGTAAAAGATC-GAATGGTTGCAA
1 G-GGTAAGAGATTGACTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCAG-ATGGTTGCAA
** *
5650 TCTACCCCAAGCTCGGGGTAAGAGATTGGCTGATAGTGATCTGCCCCAAGCTCGGGGTAAAAGAT
64 TCTGTCCCAGGCTCGGGGTAAGAGATTGGCTGATAGTGATCTGCCCCAAGCTCGGGGTAAAAGAT
* * ** * *
5715 CGAATGATTGTGATCTGCCTCATGATCGGGGTAAGAGAT
129 CGGATGGTTGCAATCTGCCTCAAGCTCGGGGTAAGAGAT
5754 CGGAATCTTT
Statistics
Matches: 349, Mismatches: 47, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
233 3 0.01
234 342 0.98
235 4 0.01
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (233 bp):
GGGTAAGAGATTGACTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCAGATGGTTGCAATC
TGTCCCAGGCTCGGGGTAAGAGATTGGCTGATAGTGATCTGCCCCAAGCTCGGGGTAAAAGATCG
GATGGTTGCAATCTGCCTCAAGCTCGGGGTAAGAGATTAGTTAATAGTGATCTGCCCCAAGCTCG
AGGTAAAAGATCAGAGAGCTACAATCTGACCCAAGCTC
Found at i:5754 original size:39 final size:39
Alignment explanation
Indices: 5348--5755 Score: 293
Period size: 39 Copynumber: 10.5 Consensus size: 39
5338 TCTACCCGTG
* * * * * *
5348 GCTCAGGGTAAGAGATTGACTGATGGTGATCTGCCCTAA
1 GCTCGGGGTAAAAGATCGAATGATTGTGATCTGCCCCAA
* ** * * *
5387 GCTCGGGGTAAAAGATC-AGATGGTTGCAATCTGTCTCAG
1 GCTCGGGGTAAAAGATCGA-ATGATTGTGATCTGCCCCAA
* * ** *
5426 GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAA
1 GCTCGGGGTAAAAGATCGAATGATTGTGATCTGCCCCAA
* * **
5465 GCTCGGGGTAAAAGATCGGATGGTTGCAATCTGCCCCAA
1 GCTCGGGGTAAAAGATCGAATGATTGTGATCTGCCCCAA
* * * * *
5504 GCTCGGGGTAAGAGAT-TAGTTGATAGTGATTTGCCCCAA
1 GCTCGGGGTAAAAGATCGA-ATGATTGTGATCTGCCCCAA
* * ** * *
5543 GCTCGGGGTAAAAGATCGGA-GAGCTGCAATTTGTCCCAA
1 GCTCGGGGTAAAAGATCGAATGA-TTGTGATCTGCCCCAA
* * * * *
5582 GCTCGAGGTAAGAGAT-TAACTAATAGTGATCTGCCCCAA
1 GCTCGGGGTAAAAGATCGAA-TGATTGTGATCTGCCCCAA
* * ** *
5621 GCTCTGGGTAAAAGATCGAATGGTTGCAATCTACCCCAA
1 GCTCGGGGTAAAAGATCGAATGATTGTGATCTGCCCCAA
* * ** *
5660 GCTCGGGGTAAGAGATTGGCTGATAGTGATCTGCCCCAA
1 GCTCGGGGTAAAAGATCGAATGATTGTGATCTGCCCCAA
* *
5699 GCTCGGGGTAAAAGATCGAATGATTGTGATCTGCCTCAT
1 GCTCGGGGTAAAAGATCGAATGATTGTGATCTGCCCCAA
* *
5738 GATCGGGGTAAGAGATCG
1 GCTCGGGGTAAAAGATCG
5756 GAATCTTTAA
Statistics
Matches: 273, Mismatches: 88, Indels: 16
0.72 0.23 0.04
Matches are distributed among these distances:
38 4 0.01
39 266 0.97
40 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.24
Consensus pattern (39 bp):
GCTCGGGGTAAAAGATCGAATGATTGTGATCTGCCCCAA
Found at i:11138 original size:30 final size:30
Alignment explanation
Indices: 10979--11130 Score: 143
Period size: 29 Copynumber: 5.2 Consensus size: 30
10969 CCTTCCTGTC
*
10979 AAAATGTGATTTTAAA-AAGATTTG-GGGTT
1 AAAATGTAATTTTAAATAAG-TTTGAGGGTT
* * *
11008 AAAATATAATTTTGGAA-AAG-TTGAGGGTG
1 AAAATGTAATTTT-AAATAAGTTTGAGGGTT
* *
11037 AAAATGTAATTTTAAATAAGTTT-AAGGTG
1 AAAATGTAATTTTAAATAAGTTTGAGGGTT
* * **
11066 AAAATGCAATTTTGAATAAGTTTGTCGGTT
1 AAAATGTAATTTTAAATAAGTTTGAGGGTT
* *
11096 AAAATGCAATTTTAAATAATTTTGAGGGTT
1 AAAATGTAATTTTAAATAAGTTTGAGGGTT
11126 AAAAT
1 AAAAT
11131 ATGATTTTTG
Statistics
Matches: 102, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
28 5 0.05
29 56 0.55
30 41 0.40
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.37
Consensus pattern (30 bp):
AAAATGTAATTTTAAATAAGTTTGAGGGTT
Found at i:13104 original size:24 final size:24
Alignment explanation
Indices: 13071--13128 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
13061 CGCTTTACTT
* * *
13071 GTTAATCACTTTATGTTTTTGCTC
1 GTTAACCACTTGACGTTTTTGCTC
13095 GTTAACCACTTGACGTTTTTGCTC
1 GTTAACCACTTGACGTTTTTGCTC
*
13119 GTCAACCACT
1 GTTAACCACT
13129 CTACGATCCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.19, C:0.24, G:0.14, T:0.43
Consensus pattern (24 bp):
GTTAACCACTTGACGTTTTTGCTC
Found at i:13749 original size:48 final size:49
Alignment explanation
Indices: 13647--13772 Score: 191
Period size: 48 Copynumber: 2.6 Consensus size: 49
13637 CACAAGACAC
* *
13647 TTCAACAAGACACGTATGTCTAACTCCTATCCATTAACTCGTAAGACTA
1 TTCAACAAGACACCTATGTCCAACTCCTATCCATTAACTCGTAAGACTA
* *
13696 TTCAACAAGACACCTATGTCGAACTCCTAT-CATTAACTCGTACGACTA
1 TTCAACAAGACACCTATGTCCAACTCCTATCCATTAACTCGTAAGACTA
* *
13744 TTCAACAAGACGCTTATGTCCAACTCCTA
1 TTCAACAAGACACCTATGTCCAACTCCTA
13773 CCACTAATCA
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
48 43 0.61
49 28 0.39
ACGTcount: A:0.33, C:0.29, G:0.10, T:0.28
Consensus pattern (49 bp):
TTCAACAAGACACCTATGTCCAACTCCTATCCATTAACTCGTAAGACTA
Found at i:14628 original size:23 final size:22
Alignment explanation
Indices: 14602--14657 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 22
14592 CTTCTTAATT
14602 ATTTGTGTTCAAATATTAATATG
1 ATTTGTGTT-AAATATTAATATG
* *
14625 ATTTATGCTTAAATATTAATATT
1 ATTTGTG-TTAAATATTAATATG
14648 ATTTGTGTTA
1 ATTTGTGTTA
14658 GAGTCTGTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.10
23 24 0.83
24 2 0.07
ACGTcount: A:0.34, C:0.04, G:0.11, T:0.52
Consensus pattern (22 bp):
ATTTGTGTTAAATATTAATATG
Found at i:14792 original size:228 final size:228
Alignment explanation
Indices: 14395--14873 Score: 922
Period size: 228 Copynumber: 2.1 Consensus size: 228
14385 ACAATTAACG
*
14395 TGATTTATGCTTAAATATTAATATAATTTGTGTTAGAGTCTGTTAAGTATAGTTAGTGATAGTTA
1 TGATTTATGCTTAAATATTAATATAATTTGTGTTAGAGTCTGTTAAATATAGTTAGTGATAGTTA
14460 AGAGTTTGTTAAAAGTAGTTATGGTTTGGTTATAATCTAGTTGTATAAATATAGTCATGGATTGA
66 AGAGTTTGTTAAAAGTAGTTATGGTTTGGTTATAATCTAGTTGTATAAATATAGTCATGGATTGA
14525 TGGTTTAGTATGAAAAAGATTGAATAATATCTTTGTTTCAATCATCACAGTTTTGTCGATGTTGT
131 TGGTTTAGTATGAAAAAGATTGAATAATATCTTTGTTTCAATCATCACAGTTTTGTCGATGTTGT
14590 AACTTCTTAATTATTTGTGTTCAAATATTAATA
196 AACTTCTTAATTATTTGTGTTCAAATATTAATA
*
14623 TGATTTATGCTTAAATATTAATATTATTTGTGTTAGAGTCTGTTAAATATAGTTAGTGATAGTTA
1 TGATTTATGCTTAAATATTAATATAATTTGTGTTAGAGTCTGTTAAATATAGTTAGTGATAGTTA
14688 AGAGTTTGTTAAAAGTAGTTATGGTTTGGTTATAATCTAGTTGTATAAATATAGTCATGGATTGA
66 AGAGTTTGTTAAAAGTAGTTATGGTTTGGTTATAATCTAGTTGTATAAATATAGTCATGGATTGA
14753 TGGTTTAGTATGAAAAAGATTGAATAATATCTTTGTTTCAATCATCACAGTTTTGTCGATGTTGT
131 TGGTTTAGTATGAAAAAGATTGAATAATATCTTTGTTTCAATCATCACAGTTTTGTCGATGTTGT
*
14818 AACTTCTTAATTATTTGTGTTCAAATATTAATG
196 AACTTCTTAATTATTTGTGTTCAAATATTAATA
*
14851 TGATCTATGCTTAAATATTAATA
1 TGATTTATGCTTAAATATTAATA
14874 ACCTTAACTC
Statistics
Matches: 247, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
228 247 1.00
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (228 bp):
TGATTTATGCTTAAATATTAATATAATTTGTGTTAGAGTCTGTTAAATATAGTTAGTGATAGTTA
AGAGTTTGTTAAAAGTAGTTATGGTTTGGTTATAATCTAGTTGTATAAATATAGTCATGGATTGA
TGGTTTAGTATGAAAAAGATTGAATAATATCTTTGTTTCAATCATCACAGTTTTGTCGATGTTGT
AACTTCTTAATTATTTGTGTTCAAATATTAATA
Found at i:15538 original size:6 final size:6
Alignment explanation
Indices: 15527--15554 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
15517 TTGAAATCAT
15527 TTTTTA TTTTTA TTTTTA TTTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTT
15555 AGGGGTCGTT
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:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:23830 original size:14 final size:14
Alignment explanation
Indices: 23792--23832 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
23782 AAAATGATAA
23792 ATTATATT-AATA-
1 ATTATATTAAATAT
*
23804 ATT-TATTATATAT
1 ATTATATTAAATAT
23817 ATTATATTAAATAT
1 ATTATATTAAATAT
23831 AT
1 AT
23833 ATTTATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 4 0.17
12 6 0.25
13 3 0.12
14 11 0.46
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
ATTATATTAAATAT
Found at i:23845 original size:16 final size:17
Alignment explanation
Indices: 23794--23851 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 17
23784 AATGATAAAT
* *
23794 TATATTAATAATTTATTA
1 TATATTTAT-ATTTAATA
*
23812 TATATATTATATTAAATA
1 TATAT-TTATATTTAATA
23830 TATATTTAT-TTTAATA
1 TATATTTATATTTAATA
23846 -ATATTT
1 TATATTT
23852 GAAATTAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
15 6 0.17
16 6 0.17
17 4 0.11
18 16 0.46
19 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TATATTTATATTTAATA
Found at i:23863 original size:28 final size:29
Alignment explanation
Indices: 23792--23864 Score: 71
Period size: 28 Copynumber: 2.5 Consensus size: 29
23782 AAAATGATAA
* *
23792 ATTATATTAATAATTTATTATATATATTAT
1 ATTAAATTAAT-ATTTATTATATATAATAT
*
23822 ATTAAA-TATATATTTATTTTA-ATAATAT
1 ATTAAATTA-ATATTTATTATATATAATAT
23850 -TTGAAATTAATATTT
1 ATT-AAATTAATATTT
23865 TAATATTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
27 2 0.05
28 15 0.41
29 13 0.35
30 7 0.19
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (29 bp):
ATTAAATTAATATTTATTATATATAATAT
Found at i:24955 original size:20 final size:20
Alignment explanation
Indices: 24916--24959 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
24906 TTTTAAGTTT
24916 TTTTTTAATTGTCTATATAAA
1 TTTTTTAATTGTCTATAT-AA
* *
24937 TTTTTTATTTTTCTA-ATAA
1 TTTTTTAATTGTCTATATAA
24956 TTTT
1 TTTT
24960 CAGATGATGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 2 0.10
21 13 0.62
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTTTTAATTGTCTATATAA
Done.