Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009928.1 Kokia drynarioides strain JFW-HI SEQ_124669, 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: 22802
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.33
Warning! 51 characters in sequence are not A, C, G, or T
Found at i:7617 original size:59 final size:57
Alignment explanation
Indices: 7544--7950 Score: 331
Period size: 59 Copynumber: 6.9 Consensus size: 57
7534 TTTGTGAACG
* * * *
7544 TTTGGGGTTAAAAATGGAATTTTTTAGACATTT-AGGGGTAAAAAAGTAA-TTTTGAGAGT
1 TTTGAGGTCAAAAATGGAA-TTTTTGGA-ATTTGA-GGGTAAAAAAGGAATTTTTG-GAGT
* * * *
7603 TTTGAGGT-AGAAAATGGAGTTTTTGGACATCTGAGGGTAAAAATGGAATTTTTTGAAGT
1 TTTGAGGTCA-AAAATGGAATTTTTGGA-ATTTGAGGGTAAAAAAGGAA-TTTTTGGAGT
* *
7662 TTTGGGGTCAAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAAAGGAATTTTTGGATGT
1 TTTGAGGTC-AAAAATGGAATTTTTGGAA-TTTGAGGGTAAAAAAGGAATTTTTGGA-GT
* * * *
7722 TTCGAGGTTAAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATGGAA-TTTTGGAAGT
1 TTTGAGGTCAAAAATGGAATTTTTGGAA-TTTGAGGGTAAAAAAGGAATTTTTGG-AGT
* * * *
7780 TTTAAGGTCAAAAATGGAATTTTTTTGAAGTTTGAGGGTAAAAATGGAATTTTTGGAAAT
1 TTTGAGGTCAAAAATGGAA-TTTTTGGAA-TTTGAGGGTAAAAAAGGAATTTTTGG-AGT
* * * * *
7840 TTT-AGGGTCAAAAATAGAA-TTTTGGAAGTTCGGGGGTAAAAATGTAATTTTTGGAAGT
1 TTTGA-GGTCAAAAATGGAATTTTTGGAA-TTTGAGGGTAAAAAAGGAATTTTTGG-AGT
* * * ** * *
7898 TTCGAGGTCGAAAATGGAATTTTTAGAAGTTCAAGGGTAAAAATGTAATTTTT
1 TTTGAGGTCAAAAATGGAATTTTTGGAA-TTTGAGGGTAAAAAAGGAATTTTT
7951 CGAATAGTTT
Statistics
Matches: 297, Mismatches: 37, Indels: 28
0.82 0.10 0.08
Matches are distributed among these distances:
58 96 0.32
59 130 0.44
60 70 0.24
61 1 0.00
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.36
Consensus pattern (57 bp):
TTTGAGGTCAAAAATGGAATTTTTGGAATTTGAGGGTAAAAAAGGAATTTTTGGAGT
Found at i:7669 original size:29 final size:29
Alignment explanation
Indices: 7523--7950 Score: 329
Period size: 29 Copynumber: 14.5 Consensus size: 29
7513 TTCTCGAGGC
7523 AAAATGGTAA-TTTTGTGAACG-TTTGGGGTTA
1 AAAATGG-AATTTTTG-GAA-GTTTTGGGG-TA
* *
7554 AAAATGGAATTTTTTAGACA-TTTAGGGGTA
1 AAAATGGAA-TTTTTGGA-AGTTTTGGGGTA
* * *
7584 AAAAAGTAA-TTTT-GAGAGTTTTGAGGTA
1 AAAATGGAATTTTTGGA-AGTTTTGGGGTA
* *
7612 GAAAATGGAGTTTTTGGACA--TCTGAGGGTA
1 -AAAATGGAATTTTTGGA-AGTTTTG-GGGTA
*
7642 AAAATGGAATTTTTTGAAGTTTTGGGGTCAA
1 AAAATGGAATTTTTGGAAGTTTTGGGGT--A
*
7673 AAAATGGAATTTTTGGAAG-TTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTTG-GGGTA
* * * *
7702 AAAAAGGAATTTTTGGATGTTTCGAGGTTA
1 AAAATGGAATTTTTGGAAGTTTTG-GGGTA
*
7732 AAAATGGAATTTTTGGAAGTTTGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTA
**
7761 AAAATGGAA-TTTTGGAAGTTTTAAGGTCA
1 AAAATGGAATTTTTGGAAGTTTTGGGGT-A
*
7790 AAAATGGAATTTTTTTGAAG-TTTGAGGGTA
1 AAAATGGAA-TTTTTGGAAGTTTTG-GGGTA
* *
7820 AAAATGGAATTTTTGGAAATTTTAGGGTCA
1 AAAATGGAATTTTTGGAAGTTTTGGGGT-A
* **
7850 AAAATAGAA-TTTTGGAAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTA
* * * *
7878 AAAATGTAATTTTTGGAAGTTTCGAGGTCG
1 AAAATGGAATTTTTGGAAGTTTTGGGGT-A
* ***
7908 AAAATGGAATTTTTAGAAGTTCAAGGGTA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTA
*
7937 AAAATGTAATTTTT
1 AAAATGGAATTTTT
7951 CGAATAGTTT
Statistics
Matches: 321, Mismatches: 53, Indels: 48
0.76 0.13 0.11
Matches are distributed among these distances:
27 3 0.01
28 36 0.11
29 123 0.38
30 102 0.32
31 52 0.16
32 5 0.02
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.36
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTTGGGGTA
Found at i:7705 original size:118 final size:115
Alignment explanation
Indices: 7523--7950 Score: 424
Period size: 118 Copynumber: 3.6 Consensus size: 115
7513 TTCTCGAGGC
* * * *
7523 AAAATGGTAA-TTTTGTGAACG-TTTGGGGTTAAAAATGGAATTTTTTAGACATTTAG-GGGTAA
1 AAAATGG-AATTTTTG-GAA-GTTTTGAGGTCAAAAATGGAATTTTTTAGA-AGTTCGAGGGTAA
* *
7585 AAAAGTAA-TTTTGAGAGTTTTGAGGTAGAAAATGGAGTTTTTGGACA-TCTGAGGGTA
62 AAAAGGAATTTTTG-GAGTTTTGAGGTA-AAAATGGA-TTTTTGGA-AGT-TGGGGGTA
* * *
7642 AAAATGGAATTTTTTGAAGTTTTGGGGTCAAAAAATGGAA-TTTTTGGAAGTTCGAGGGTAAAAA
1 AAAATGGAATTTTTGGAAGTTTTGAGGTC-AAAAATGGAATTTTTTAGAAGTTCGAGGGTAAAAA
*
7706 AGGAATTTTTGGATGTTTCGAGGTTAAAAATGGAATTTTTGGAAGTTTGGGGGTA
65 AGGAATTTTTGGA-GTTTTGAGG-TAAAAATGG-ATTTTTGGAAG-TTGGGGGTA
* * * *
7761 AAAATGGAA-TTTTGGAAGTTTTAAGGTCAAAAATGGAATTTTTTTGAAGTTTGAGGGTAAAAAT
1 AAAATGGAATTTTTGGAAGTTTTGAGGTCAAAAATGGAATTTTTTAGAAGTTCGAGGGTAAAAAA
* * *
7825 GGAATTTTTGGAAATTTT-AGGGTCAAAAATAGAATTTTGGAAGTTCGGGGGTA
66 GGAATTTTTGG-AGTTTTGA-GGT-AAAAATGGATTTTTGGAAGTT-GGGGGTA
* * * * *
7878 AAAATGTAATTTTTGGAAGTTTCGAGGTCGAAAATGGAA-TTTTTAGAAGTTCAAGGGTAAAAAT
1 AAAATGGAATTTTTGGAAGTTTTGAGGTCAAAAATGGAATTTTTTAGAAGTTCGAGGGTAAAAAA
*
7942 GTAATTTTT
66 GGAATTTTT
7951 CGAATAGTTT
Statistics
Matches: 267, Mismatches: 26, Indels: 34
0.82 0.08 0.10
Matches are distributed among these distances:
116 2 0.01
117 72 0.27
118 123 0.46
119 66 0.25
120 4 0.01
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.36
Consensus pattern (115 bp):
AAAATGGAATTTTTGGAAGTTTTGAGGTCAAAAATGGAATTTTTTAGAAGTTCGAGGGTAAAAAA
GGAATTTTTGGAGTTTTGAGGTAAAAATGGATTTTTGGAAGTTGGGGGTA
Found at i:8703 original size:129 final size:128
Alignment explanation
Indices: 8473--8729 Score: 496
Period size: 129 Copynumber: 2.0 Consensus size: 128
8463 ATTTTTCCCT
8473 TCTCTTTTTTAGAAAAACAAATTCACCCTTCAAAAAAGCTCTTTCCTTTCCCATGGTCGGCCAAA
1 TCTCTTTTTTAGAAAAACAAATTCACCCTTCAAAAAAGCTCTTTCCTTTCCCATGGTCGGCCAAA
*
8538 CTCCGGTCGGTCACCTCGTCGCCATCCACCGCACATCACCACCACACACCGTCGTCCGTCGCC
66 CTCCAGTCGGTCACCTCGTCGCCATCCACCGCACATCACCACCACACACCGTCGTCCGTCGCC
8601 NTCTCTTTTTTAGAAAAACAAATTCACCCTTCAAAAAAGCTCTTTCCTTTCCCATGGTCGGCCAA
1 -TCTCTTTTTTAGAAAAACAAATTCACCCTTCAAAAAAGCTCTTTCCTTTCCCATGGTCGGCCAA
8666 ACTCCAGTCGGTCACCTCGTCGCCATCCACCGCACATCACCACCACACACCGTCGTCCGTCGCC
65 ACTCCAGTCGGTCACCTCGTCGCCATCCACCGCACATCACCACCACACACCGTCGTCCGTCGCC
8730 GTCTTCGACC
Statistics
Matches: 127, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
129 127 1.00
ACGTcount: A:0.24, C:0.39, G:0.13, T:0.24
Consensus pattern (128 bp):
TCTCTTTTTTAGAAAAACAAATTCACCCTTCAAAAAAGCTCTTTCCTTTCCCATGGTCGGCCAAA
CTCCAGTCGGTCACCTCGTCGCCATCCACCGCACATCACCACCACACACCGTCGTCCGTCGCC
Found at i:12166 original size:12 final size:12
Alignment explanation
Indices: 12149--12218 Score: 54
Period size: 12 Copynumber: 5.5 Consensus size: 12
12139 ACAACAATAT
12149 AAATAAACAAAA
1 AAATAAACAAAA
12161 AAATAAA-AATAA
1 AAATAAACAA-AA
**
12173 AAATAAA-ATGCTA
1 AAATAAACA--AAA
12186 AAATAAACAAACA
1 AAATAAACAAA-A
12199 AATATAAACAATAA
1 AA-ATAAACAA-AA
12213 AAATAA
1 AAATAA
12219 TTGAGATTAG
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
11 2 0.04
12 17 0.36
13 15 0.32
14 12 0.26
15 1 0.02
ACGTcount: A:0.76, C:0.07, G:0.01, T:0.16
Consensus pattern (12 bp):
AAATAAACAAAA
Found at i:12166 original size:16 final size:15
Alignment explanation
Indices: 12129--12167 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
12119 AAATGGCATG
*
12129 AAAATAAATAACAAC
1 AAAATAAATAACAAA
*
12144 AATATAAATAAACAAA
1 AAAATAAAT-AACAAA
12160 AAAATAAA
1 AAAATAAA
12168 AATAAAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (15 bp):
AAAATAAATAACAAA
Found at i:12192 original size:5 final size:6
Alignment explanation
Indices: 12129--12180 Score: 52
Period size: 6 Copynumber: 8.5 Consensus size: 6
12119 AAATGGCATG
* * *
12129 AAAATA AATAACA ACAATA TAAATA AACAA-A AAAATA AAAATA AAAATA
1 AAAATA AA-AATA AAAATA AAAATA AA-AATA AAAATA AAAATA AAAATA
12178 AAA
1 AAA
12181 TGCTAAAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
5 2 0.05
6 29 0.78
7 6 0.16
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:12253 original size:15 final size:15
Alignment explanation
Indices: 12234--12275 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
12224 ATTAGACATG
*
12234 AAAATAAAT-GACAA
1 AAAATAAATAAACAA
12248 ATAAATAAATAAACAA
1 A-AAATAAATAAACAA
*
12264 AAAATAATTAAA
1 AAAATAAATAAA
12276 TTAAATGTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 1 0.04
15 18 0.75
16 5 0.21
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.19
Consensus pattern (15 bp):
AAAATAAATAAACAA
Found at i:12259 original size:19 final size:19
Alignment explanation
Indices: 12235--12292 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
12225 TTAGACATGA
12235 AAATAAATGACAAATAAAT
1 AAATAAATGACAAATAAAT
** * *
12254 AAATAAACAAAAAATAATT
1 AAATAAATGACAAATAAAT
*
12273 AAATTAAATGTCAGAATAAA
1 AAA-TAAATGACA-AATAAA
12293 CAATAAATAT
Statistics
Matches: 28, Mismatches: 9, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
19 18 0.64
20 5 0.18
21 5 0.18
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.22
Consensus pattern (19 bp):
AAATAAATGACAAATAAAT
Found at i:13221 original size:99 final size:99
Alignment explanation
Indices: 13118--13388 Score: 264
Period size: 99 Copynumber: 2.7 Consensus size: 99
13108 AGATTTGTCG
* * * ** *
13118 TCGCGGCTTCATTCTATTCCCTCTTTGATTTCAAAGTGTTAGATTCGTCGTTGTGACTTTAATCT
1 TCGCGGCTTCA-ACTATTCCCTCTTTGATTTTAAAGTGTAAGATTCGTCGTTGCAACTTCAATCT
13183 ATCCCTC-TTCATTTTTAAGGTATTAGGTCCGCCA
65 ATCCCTCTTTCATTTTTAAGGTATTAGGTCCGCCA
* * * * * * * *
13217 TCGCGGCTTTAACTTTTTCTTCTTTTG-TTTTAAGGTGTAAGATCCTTCATTGCAACTTCAATCT
1 TCGCGGCTTCAACTATTCCCTC-TTTGATTTTAAAGTGTAAGATTCGTCGTTGCAACTTCAATCT
* ** * *
13281 TTCCCTCTTTTGTTTTTAAGGTGTTAGGTCCGCCG
65 ATCCCTCTTTCATTTTTAAGGTATTAGGTCCGCCA
* ** *
13316 TTGCGGCTTCAAC-ATATCCCTCTTCT-ATTTTAAAGTGTAAGATTCGTCGTTGCGGCTTCAACC
1 TCGCGGCTTCAACTAT-TCCCTCTT-TGATTTTAAAGTGTAAGATTCGTCGTTGCAACTTCAATC
13379 T-TCCCTCTTT
64 TATCCCTCTTT
13389 GGTTTTAGGG
Statistics
Matches: 136, Mismatches: 31, Indels: 11
0.76 0.17 0.06
Matches are distributed among these distances:
98 53 0.39
99 83 0.61
ACGTcount: A:0.17, C:0.24, G:0.16, T:0.43
Consensus pattern (99 bp):
TCGCGGCTTCAACTATTCCCTCTTTGATTTTAAAGTGTAAGATTCGTCGTTGCAACTTCAATCTA
TCCCTCTTTCATTTTTAAGGTATTAGGTCCGCCA
Found at i:13290 original size:49 final size:49
Alignment explanation
Indices: 13096--14013 Score: 296
Period size: 49 Copynumber: 18.7 Consensus size: 49
13086 TTCACAGTTT
** ** *
13096 TTTTAAGGTGTAAGATTTGTCGTCGCGGCTTCATTCTATTCCCTC-TTTG
1 TTTTAAGGTGTAAGATCCGTCGTTACGGCTTCAATCT-TTCCCTCTTTTG
* * * * ** * * * *
13145 ATTTCAAAGTGTTAGATTCGTCGTTGTGACTTTAATCTATCCCTCTTCAT-
1 -TTTTAAGGTGTAAGATCCGTCGTTACGGCTTCAATCTTTCCCTCTT-TTG
* * * * * ** * * *
13195 TTTTAAGGTATTAGGTCCGCCATCGCGGCTTTAA-CTTTTTCTTCTTTTG
1 TTTTAAGGTGTAAGATCCGTCGTTACGGCTTCAATC-TTTCCCTCTTTTG
* * * **
13244 TTTTAAGGTGTAAGATCCTTCATTGCAACTTCAATCTTTCCCTCTTTTG
1 TTTTAAGGTGTAAGATCCGTCGTTACGGCTTCAATCTTTCCCTCTTTTG
* * * * * * *
13293 TTTTTAAGGTGTTAGGTCCGCCGTTGCGGCTTCAA-CATATCCCTCTTCTA
1 -TTTTAAGGTGTAAGATCCGTCGTTACGGCTTCAATC-TTTCCCTCTTTTG
* * * * *
13343 TTTTAAAGTGTAAGATTCGTCGTTGCGGCTTCAA-CCTTCCCTCTTTGG
1 TTTTAAGGTGTAAGATCCGTCGTTACGGCTTCAATCTTTCCCTCTTTTG
* * * * * * * * ***
13391 TTTTAGGGTGTTAGGTCCATCGTTATGACTTCAACCTATCCCTCTTCAA
1 TTTTAAGGTGTAAGATCCGTCGTTACGGCTTCAATCTTTCCCTCTTTTG
* * * *
13440 TTTTAAGGAGTAAGATCCATTGTTACGGCTTCAATCTTTCCCTCTTTAG
1 TTTTAAGGTGTAAGATCCGTCGTTACGGCTTCAATCTTTCCCTCTTTTG
* * ** * *
13489 TTTT-AGGATGTTAGATTCACCGTTACAGCTTCAATCTATT-CCTC-TTCG
1 TTTTAAGG-TGTAAGATCCGTCGTTACGGCTTCAATCT-TTCCCTCTTTTG
* ** * * * *
13537 ATTTTAAGGTGTTAGGCCCGTCATTACGGCTTCAACCTATCCCTC-TTCG
1 -TTTTAAGGTGTAAGATCCGTCGTTACGGCTTCAATCTTTCCCTCTTTTG
** * *
13586 ATTTTAAGGTGTAAGATCCGTCGTTGTGACTTTAATCTTTCCCT-TTTTAG
1 -TTTTAAGGTGTAAGATCCGTCGTTACGGCTTCAATCTTTCCCTCTTTT-G
** * * ** * * * ***
13636 TTTTTTTGGGTGTTAGGTCCACCGTTACAGCTTCAAACTATCCCTCTTCAA
1 --TTTTAAGGTGTAAGATCCGTCGTTACGGCTTCAATCTTTCCCTCTTTTG
* * * * * * *
13687 TTTCAAGGTGTAAGGTCCGCCGTTCCAGCTTCAACCTTT--CTCTTTTCAA
1 TTTTAAGGTGTAAGATCCGTCGTTACGGCTTCAATCTTTCCCTCTTTT--G
* * *
13736 TTTTAGGGT-TCTAGAT-C-TACTGTTACGACTTCAATCTATT-CCTC-TTTG
1 TTTTAAGGTGT-AAGATCCGT-C-GTTACGGCTTCAATCT-TTCCCTCTTTTG
** * * * * ** * * *
13784 ATTTTCGGGTGTTAGGTTCGTCATT-CAACTTCAACCTATCCCT-TTTCG
1 -TTTTAAGGTGTAAGATCCGTCGTTACGGCTTCAATCTTTCCCTCTTTTG
* * * * **
13832 ATTTTAAAGTGTAAGATCCATCGTTACGGCTGCAATCTTTTCCTCTTCAG
1 -TTTTAAGGTGTAAGATCCGTCGTTACGGCTTCAATCTTTCCCTCTTTTG
* * * * * ***
13882 TTTTAGGGTGTTAGGTCCGTTGTTACGACTTCAA-CTTATCCCTCTTCAA
1 TTTTAAGGTGTAAGATCCGTCGTTACGGCTTCAATCTT-TCCCTCTTTTG
* * * * * **
13931 ATTTAAGGTGTAAGGTCCGCCGTTACGGCTTCAACCTTTTCCTCTTCAG
1 TTTTAAGGTGTAAGATCCGTCGTTACGGCTTCAATCTTTCCCTCTTTTG
* *
13980 TTTT-AGGATGTTATG-TCCGTCGTTGCGGCTTCAA
1 TTTTAAGG-TG-TAAGATCCGTCGTTACGGCTTCAA
14014 CCTATCCTTC
Statistics
Matches: 642, Mismatches: 190, Indels: 73
0.71 0.21 0.08
Matches are distributed among these distances:
47 6 0.01
48 84 0.13
49 425 0.66
50 90 0.14
51 35 0.05
52 2 0.00
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.41
Consensus pattern (49 bp):
TTTTAAGGTGTAAGATCCGTCGTTACGGCTTCAATCTTTCCCTCTTTTG
Found at i:13522 original size:98 final size:97
Alignment explanation
Indices: 13244--14028 Score: 519
Period size: 98 Copynumber: 8.0 Consensus size: 97
13234 TCTTCTTTTG
* * * ** *
13244 TTTTAAGGTGTAAGATCCTTCATTGCAACTTCAATCTTTCCCTCTTTTGTTTTTAAGGTGTTAGG
1 TTTTAAGGTGTAAGATCCATCGTTACGGCTTCAATCTTTCCCTCTTTAG-TTTT-AGGTGTTAGG
* * * * *
13309 TCCGCCGTTGCGGCTTCAACATATCCCTCTTCTA
64 TCCGTCGTTACAGCTTCAACCTATCCCTCTTCAA
* * * * * *
13343 TTTTAAAGTGTAAGATTCGTCGTTGCGGCTTCAA-CCTTCCCTCTTTGGTTTTAGGGTGTTAGGT
1 TTTTAAGGTGTAAGATCCATCGTTACGGCTTCAATCTTTCCCTCTTTAGTTTTA-GGTGTTAGGT
* *
13407 CCATCGTTA-TGACTTCAACCTATCCCTCTTCAA
65 CCGTCGTTACAG-CTTCAACCTATCCCTCTTCAA
* * *
13440 TTTTAAGGAGTAAGATCCATTGTTACGGCTTCAATCTTTCCCTCTTTAGTTTTAGGATGTTAGAT
1 TTTTAAGGTGTAAGATCCATCGTTACGGCTTCAATCTTTCCCTCTTTAGTTTTAGG-TGTTAGGT
* ** * * *
13505 TCACCGTTACAGCTTCAATCTATTCCTCTTCGA
65 CCGTCGTTACAGCTTCAACCTATCCCTCTTCAA
* ** * * * * * * *
13538 TTTTAAGGTGTTAGGCCCGTCATTACGGCTTCAACCTATCCCTC-TTCGATTTTAAGGTGTAAGA
1 TTTTAAGGTGTAAGATCCATCGTTACGGCTTCAATCTTTCCCTCTTTAG-TTTT-AGGTGTTAGG
** * * * * * *
13602 TCCGTCGTT-GTGACTTTAATCTTTCCCTTTTTAGTT
64 TCCGTCGTTACAG-CTTCAACCTATCCCTCTTCA--A
** * * * * * * * * * *
13638 TTTTTGGGTGTTAGGTCCACCGTTACAGCTTCAAACTATCCCTCTTCAATTTCAAGGTGTAAGGT
1 TTTTAAGGTGTAAGATCCATCGTTACGGCTTCAATCTTTCCCTCTTTAGTTT-TAGGTGTTAGGT
* * * * *
13703 CCGCCGTTCCAGCTTCAACCTTTCTCTTTTCAA
65 CCGTCGTTACAGCTTCAACCTATCCCTCTTCAA
* * * * *
13736 TTTTAGGGT-TCTAGATCTA-CTGTTACGACTTCAATCTATT-CCTCTTT-GATTTTCGGGTGTT
1 TTTTAAGGTGT-AAGATCCATC-GTTACGGCTTCAATCT-TTCCCTCTTTAG-TTTT-AGGTGTT
* * * * *
13797 AGGTTCGTCATT-CAACTTCAACCTATCCCTTTTCGA
61 AGGTCCGTCGTTACAGCTTCAACCTATCCCTCTTCAA
* * * *
13833 TTTTAAAGTGTAAGATCCATCGTTACGGCTGCAATCTTTTCCTCTTCAGTTTTAGGGTGTTAGGT
1 TTTTAAGGTGTAAGATCCATCGTTACGGCTTCAATCTTTCCCTCTTTAGTTTTA-GGTGTTAGGT
* *
13898 CCGTTGTTAC-GACTTCAACTTATCCCTCTTCAA
65 CCGTCGTTACAG-CTTCAACCTATCCCTCTTCAA
* * ** * * * *
13931 ATTTAAGGTGTAAGGTCCGCCGTTACGGCTTCAACCTTTTCCTCTTCAGTTTTAGGATGTTATGT
1 TTTTAAGGTGTAAGATCCATCGTTACGGCTTCAATCTTTCCCTCTTTAGTTTTAGG-TGTTAGGT
* * *
13996 CCGTCGTTGCGGCTTCAACCTATCCTTCTTCAA
65 CCGTCGTTACAGCTTCAACCTATCCCTCTTCAA
14029 ACTCTATGAT
Statistics
Matches: 540, Mismatches: 119, Indels: 55
0.76 0.17 0.08
Matches are distributed among these distances:
96 4 0.01
97 149 0.28
98 279 0.52
99 34 0.06
100 72 0.13
101 2 0.00
ACGTcount: A:0.19, C:0.24, G:0.17, T:0.40
Consensus pattern (97 bp):
TTTTAAGGTGTAAGATCCATCGTTACGGCTTCAATCTTTCCCTCTTTAGTTTTAGGTGTTAGGTC
CGTCGTTACAGCTTCAACCTATCCCTCTTCAA
Found at i:13739 original size:149 final size:147
Alignment explanation
Indices: 13419--13782 Score: 394
Period size: 149 Copynumber: 2.5 Consensus size: 147
13409 ATCGTTATGA
* *
13419 CTTCAACCTATCCCTCTTCAATTTTAAGGAGTAAGATCCATTGTTACGGCTTCAATCTTTCCCTC
1 CTTCAACCTATCCCTCTTCAATTTTAAGGAGTAAGATCCATCGTTACGACTTCAATCTTTCCCTC
* * * * *
13484 TTTAGTTTTAGGATGTTAGATTCACCGTTACAGCTTCAATCTATTCCTCTTCGATTTTAAGGTGT
66 TTTAGTTTTAGGATGTTAGATCCACCGTTACAGCTTCAAACTATCCCTCTTCAATTTCAAGGTGT
* * *
13549 TAGGCCCGTCATTACGG
131 AAGGCCCGCCATTACAG
* * * ** * *
13566 CTTCAACCTATCCCTCTTCGATTTTAAGGTGTAAGATCCGTCGTTGTGACTTTAATCTTTCCCTT
1 CTTCAACCTATCCCTCTTCAATTTTAAGGAGTAAGATCCATCGTTACGACTTCAATCTTTCCCTC
* * *
13631 TTTAGTTTTTTTGGGTGTTAGGTCCACCGTTACAGCTTCAAACTATCCCTCTTCAATTTCAAGGT
66 TTTAG--TTTTAGGATGTTAGATCCACCGTTACAGCTTCAAACTATCCCTCTTCAATTTCAAGGT
* * *
13696 GTAAGGTCCGCCGTTCCAG
129 GTAAGGCCCGCCATTACAG
* * * * *
13715 CTTCAACCTTTCTCTTTTCAATTTT-AGG-GTTCTAGATCTA-CTGTTACGACTTCAATCTATT-
1 CTTCAACCTATCCCTCTTCAATTTTAAGGAG-T-AAGATCCATC-GTTACGACTTCAATCT-TTC
13776 CCTCTTT
62 CCTCTTT
13783 GATTTTCGGG
Statistics
Matches: 177, Mismatches: 34, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
147 62 0.35
148 5 0.03
149 108 0.61
150 2 0.01
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.40
Consensus pattern (147 bp):
CTTCAACCTATCCCTCTTCAATTTTAAGGAGTAAGATCCATCGTTACGACTTCAATCTTTCCCTC
TTTAGTTTTAGGATGTTAGATCCACCGTTACAGCTTCAAACTATCCCTCTTCAATTTCAAGGTGT
AAGGCCCGCCATTACAG
Found at i:14026 original size:49 final size:47
Alignment explanation
Indices: 13294--14027 Score: 309
Period size: 49 Copynumber: 15.0 Consensus size: 47
13284 CCTCTTTTGT
* * *
13294 TTTTAAGGTGTTAGGTCCGCCGTTGCGGCTTCAACATATCCCTCTTCTA-
1 TTTT-AGGTGTTAGGTCCGTCGTTACGGCTTCAACCTAT-CCTCTTC-AG
* * * * * **
13343 TTTTAAAGTGTAAGATTCGTCGTTGCGGCTTCAACCT-TCCCTCTTTGG
1 TTTT-AGGTGTTAGGTCCGTCGTTACGGCTTCAACCTAT-CCTCTTCAG
* * * *
13391 TTTTAGGGTGTTAGGTCCATCGTTATGACTTCAACCTATCCCTCTTCAA
1 TTTTA-GGTGTTAGGTCCGTCGTTACGGCTTCAACCTAT-CCTCTTCAG
* * * * * * * *
13440 TTTTAAGGAGTAAGATCCATTGTTACGGCTTCAATCTTTCCCTCTTTAG
1 TTTT-AGGTGTTAGGTCCGTCGTTACGGCTTCAACCTAT-CCTCTTCAG
* * ** * *
13489 TTTTAGGATGTTAGATTCACCGTTACAGCTTCAATCTATTCCTCTTC-G
1 TTTTAGG-TGTTAGGTCCGTCGTTACGGCTTCAACCTA-TCCTCTTCAG
* *
13537 ATTTTAAGGTGTTAGGCCCGTCATTACGGCTTCAACCTATCCCTCTTC-G
1 -TTTT-AGGTGTTAGGTCCGTCGTTACGGCTTCAACCTAT-CCTCTTCAG
* * ** * * * * * *
13586 ATTTTAAGGTGTAAGATCCGTCGTTGTGACTTTAATCTTTCCCTTTTTAG
1 -TTTT-AGGTGTTAGGTCCGTCGTTACGGCTTCAACCTAT-CCTCTTCAG
* ** * * *
13636 TTTTTTTGGGTGTTAGGTCCACCGTTACAGCTTCAAACTATCCCTCTTCAA
1 ---TTTTAGGTGTTAGGTCCGTCGTTACGGCTTCAACCTAT-CCTCTTCAG
* * * * * * * *
13687 TTTCAAGGTGTAAGGTCCGCCGTTCCAGCTTCAACCTTTCTCTTTTCAA
1 TTT-TAGGTGTTAGGTCCGTCGTTACGGCTTCAACCTATC-CTCTTCAG
* * * *
13736 TTTTAGG-GTTCTAGAT-C-TACTGTTACGACTTCAATCTATTCCTCTT-TG
1 TTTTAGGTG-T-TAGGTCCGT-C-GTTACGGCTTCAACCTA-TCCTCTTCAG
* * * ** *
13784 ATTTTCGGGTGTTAGGTTCGTCATT-CAACTTCAACCTATCCCTTTTC-G
1 -TTTT-AGGTGTTAGGTCCGTCGTTACGGCTTCAACCTAT-CCTCTTCAG
* * * * * * *
13832 ATTTTAAAGTGTAAGATCCATCGTTACGGCTGCAATCTTTTCCTCTTCAG
1 -TTTT-AGGTGTTAGGTCCGTCGTTACGGCTTCAA-CCTATCCTCTTCAG
* * * *
13882 TTTTAGGGTGTTAGGTCCGTTGTTACGACTTCAACTTATCCCTCTTCAAA
1 TTTTA-GGTGTTAGGTCCGTCGTTACGGCTTCAACCTAT-CCTCTTC-AG
* * * *
13932 TTTAAGGTGTAAGGTCCGCCGTTACGGCTTCAACCTTTTCCTCTTCAG
1 TTTTAGGTGTTAGGTCCGTCGTTACGGCTTCAACC-TATCCTCTTCAG
* *
13980 TTTTAGGATGTTATGTCCGTCGTTGCGGCTTCAACCTATCCTTCTTCA
1 TTTTAGG-TGTTAGGTCCGTCGTTACGGCTTCAACCTATCC-TCTTCA
14028 AACTCTATGA
Statistics
Matches: 514, Mismatches: 136, Indels: 70
0.71 0.19 0.10
Matches are distributed among these distances:
47 3 0.01
48 100 0.19
49 352 0.68
50 24 0.05
51 31 0.06
52 4 0.01
ACGTcount: A:0.19, C:0.24, G:0.17, T:0.40
Consensus pattern (47 bp):
TTTTAGGTGTTAGGTCCGTCGTTACGGCTTCAACCTATCCTCTTCAG
Found at i:19849 original size:19 final size:19
Alignment explanation
Indices: 19824--19909 Score: 59
Period size: 19 Copynumber: 4.4 Consensus size: 19
19814 AAATGGCATG
* * *
19824 AAAATAAATAACAACAATA
1 AAAATAAACAAAAAAAATA
*
19843 TAAATAAACAAAAAAAATA
1 AAAATAAACAAAAAAAATA
* *
19862 AAAAT-AA-AAATAAAATGCT
1 AAAATAAACAAAAAAAAT--A
*
19881 AAAATAAACAAACAAATATA
1 AAAATAAACAAA-AAAAATA
19901 AACAATAAA
1 AA-AATAAA
19910 AATAATTGAG
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
17 8 0.16
18 2 0.04
19 24 0.47
20 4 0.08
21 9 0.18
22 4 0.08
ACGTcount: A:0.74, C:0.08, G:0.01, T:0.16
Consensus pattern (19 bp):
AAAATAAACAAAAAAAATA
Found at i:19852 original size:13 final size:13
Alignment explanation
Indices: 19836--19914 Score: 67
Period size: 13 Copynumber: 6.1 Consensus size: 13
19826 AATAAATAAC
*
19836 AACAATATAAATA
1 AACAATAAAAATA
*
19849 AACAAAAAAAATA
1 AACAATAAAAATA
19862 AA-AATAAAAAT-
1 AACAATAAAAATA
*
19873 AA-AATGCTAAAATA
1 AACAAT--AAAAATA
19887 AACAA-ACAAATATA
1 AACAATA-AAA-ATA
19901 AACAATAAAAATA
1 AACAATAAAAATA
19914 A
1 A
19915 TTGAGATTAG
Statistics
Matches: 54, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
11 5 0.09
12 8 0.15
13 25 0.46
14 13 0.24
15 3 0.06
ACGTcount: A:0.75, C:0.08, G:0.01, T:0.16
Consensus pattern (13 bp):
AACAATAAAAATA
Found at i:19864 original size:6 final size:6
Alignment explanation
Indices: 19824--19876 Score: 52
Period size: 6 Copynumber: 8.5 Consensus size: 6
19814 AAATGGCATG
* * * *
19824 AAAATA AATAACA ACAATA TAAATA AACAAAA AAAATA AAAATA AAAATA
1 AAAATA AA-AATA AAAATA AAAATA AA-AATA AAAATA AAAATA AAAATA
19874 AAA
1 AAA
19877 TGCTAAAATA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
6 28 0.76
7 9 0.24
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:19866 original size:38 final size:39
Alignment explanation
Indices: 19824--19911 Score: 101
Period size: 38 Copynumber: 2.3 Consensus size: 39
19814 AAATGGCATG
19824 AAAATAAATAACAACAAT-AT-AAATAAACAAA-AAAAATA
1 AAAATAAA-AACAA-AATGATAAAATAAACAAACAAAAATA
* * *
19862 AAAATAAAAATAAAATGCTAAAATAAACAAACAAATATA
1 AAAATAAAAACAAAATGATAAAATAAACAAACAAAAATA
19901 AACAATAAAAA
1 AA-AATAAAAA
19912 TAATTGAGAT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
36 3 0.07
37 5 0.12
38 19 0.44
39 8 0.19
40 8 0.19
ACGTcount: A:0.75, C:0.08, G:0.01, T:0.16
Consensus pattern (39 bp):
AAAATAAAAACAAAATGATAAAATAAACAAACAAAAATA
Found at i:19973 original size:25 final size:25
Alignment explanation
Indices: 19933--19988 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
19923 AGGCATGAAA
19933 ATAAATGACAAATAAATAAATAAAT
1 ATAAATGACAAATAAATAAATAAAT
* *
19958 -TAAATGTCAGAATAAATAACTAAAT
1 ATAAATGACA-AATAAATAAATAAAT
19983 ATAAAT
1 ATAAAT
19989 AATAATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 8 0.30
25 14 0.52
26 5 0.19
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.27
Consensus pattern (25 bp):
ATAAATGACAAATAAATAAATAAAT
Found at i:22781 original size:2 final size:2
Alignment explanation
Indices: 22774--22802 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
22764 TTGAAATGTG
22774 AT 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 AT A
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.