Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015258.1 Kokia drynarioides strain JFW-HI SEQ_130303, 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: 342652
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 809 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:256636 original size:29 final size:28
Alignment explanation
Indices: 256553--256722 Score: 146
Period size: 29 Copynumber: 5.8 Consensus size: 28
256543 AATAAGGGTC
* * *
256553 AAAAATGGAATTTTTTGAAGTTTGGGGT
1 AAAAATGGAATTTTTGGAAGTTCGAGGT
* **
256581 AAAAATGGTAATTTTTGAAAAAATCGAGGT
1 AAAAATGG-AATTTTTG-GAAGTTCGAGGT
256611 CAAAAATGGAATTTTTGGAAGTTCGAGGGT
1 -AAAAATGGAATTTTTGGAAGTTCGA-GGT
*
256641 -AAAATGGTAATTTTTGGAAGTTTCAAGGT
1 AAAAATGG-AATTTTTGGAAG-TTCGAGGT
* *
256670 CAAAAAT-GAAATTTTGGAAAGTTCGCGGGT
1 -AAAAATGGAATTTTTGG-AAGTTCG-AGGT
*
256700 AAAAATGTAATTTTTGGATAGTT
1 AAAAATGGAATTTTTGGA-AGTT
256723 TATAGACTTT
Statistics
Matches: 115, Mismatches: 15, Indels: 22
0.76 0.10 0.14
Matches are distributed among these distances:
28 15 0.13
29 46 0.40
30 41 0.36
31 13 0.11
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (28 bp):
AAAAATGGAATTTTTGGAAGTTCGAGGT
Found at i:257839 original size:18 final size:18
Alignment explanation
Indices: 257792--257839 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
257782 TATTTTTTAT
*
257792 TTATTATTTATTA-AATA
1 TTATTAGTTATTATAATA
257809 TTA-TAGTTATTATCAATA
1 TTATTAGTTATTAT-AATA
257827 TTATTA-TTATTAT
1 TTATTAGTTATTAT
257840 TATTATCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 8 0.30
17 3 0.11
18 14 0.52
19 2 0.07
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (18 bp):
TTATTAGTTATTATAATA
Found at i:257870 original size:27 final size:27
Alignment explanation
Indices: 257829--257880 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
257819 TATCAATATT
*
257829 ATTATTATTATTATT-ATCATTAAAATA
1 ATTATTATTACTATTAAT-ATTAAAATA
*
257856 ATTATTATTGCTATTAATATTAAAA
1 ATTATTATTACTATTAATATTAAAA
257881 CGTTATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (27 bp):
ATTATTATTACTATTAATATTAAAATA
Found at i:259286 original size:194 final size:193
Alignment explanation
Indices: 258939--259514 Score: 839
Period size: 194 Copynumber: 3.0 Consensus size: 193
258929 TTTGGTGTCG
* * * * *
258939 TTGATTTGGTCTACTTCTTAGTATCTTATCAGGAAGATGACTGCATCGCTTGTTTCAATCCGCTT
1 TTGAGTTGGTATACTTCTTTGTATCTTATCAGGAAGATGAC-GCCTCACTTGTTTCAATCCGCTT
* * * * *
259004 CTTTGTACCTCATCAGGAAGACAAATTTGGTCTACTTCTCAGTATTTCATCAGGAAGCTAACCAT
65 CTCTGTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACTAT
* * *
259069 TTTATTGCTTCGACCTACTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGAAGATTTGTTCGCA
130 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGTTCGCA
* * *
259133 TTGAGTTGGTATACTTCTTTGTATCTTATCAGGAAGATAATCGCCTCAATGGTTTCAATCCGCTT
1 TTGAGTTGGTATACTTCTTTGTATCTTATCAGGAAGATGA-CGCCTCACTTGTTTCAATCCGCTT
* *
259198 CTCTGTACCTTATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACTAT
65 CTCTGTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACTAT
* * * * *
259263 TTTATTGCTTCGACCTGCTTCTCAATATTTGATCATGAAGCTAGGGTTCGAAGATTTATTCGCA
130 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGTTCGCA
* * *
259327 TTGAGTTGGTATACTTCTCTATATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCCGCTT
1 TTGAGTTGGTATACTTCTTTGTATCTTATCAGGAAGATGA-CGCCTCACTTGTTTCAATCCGCTT
* * *
259392 CTCTGTACCTCATCAGGAAGACGAATTTAGTCCACTTCTCAGTATGTCATCGGGAAGCTAACCT-
65 CTCTGTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAA-CTA
*
259456 TTTTATTGCTTCGACCTGCTTCTCAGTACCTCATCAGGAAGCTAGGGTTCGAAGATTTG
129 TTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTG
259515 CTCATATTAA
Statistics
Matches: 339, Mismatches: 41, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
194 336 0.99
195 3 0.01
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (193 bp):
TTGAGTTGGTATACTTCTTTGTATCTTATCAGGAAGATGACGCCTCACTTGTTTCAATCCGCTTC
TCTGTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACTATT
TTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTGTTCGCA
Found at i:271462 original size:29 final size:27
Alignment explanation
Indices: 271425--271503 Score: 70
Period size: 28 Copynumber: 2.8 Consensus size: 27
271415 TAAACACTCG
* *
271425 GGGGCTAAATGGTAATTTTGGGAAAGTTC
1 GGGGTTAAATGGTAATTTTGGG-AA-TCC
* *
271454 GGGGTTAAAATGG-AATTTTTGGCATCC
1 GGGGTT-AAATGGTAATTTTGGGAATCC
*
271481 GAGGGTAAAATGGTAATTTTGGG
1 G-GGGTTAAATGGTAATTTTGGG
271504 GAAAATTGGG
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
27 9 0.22
28 13 0.32
29 13 0.32
30 6 0.15
ACGTcount: A:0.28, C:0.06, G:0.34, T:0.32
Consensus pattern (27 bp):
GGGGTTAAATGGTAATTTTGGGAATCC
Found at i:271617 original size:29 final size:30
Alignment explanation
Indices: 271574--271682 Score: 123
Period size: 30 Copynumber: 3.6 Consensus size: 30
271564 AAACGAGGGT
271574 AAAATGGTAATTTTTGAAAGTTTCGAGGACA
1 AAAATGG-AATTTTTGAAAGTTTCGAGGACA
* * **
271605 AAAATAGAATTTTTGGAAG-TTCG-GGGGA
1 AAAATGGAATTTTTGAAAGTTTCGAGGACA
* *
271633 AAAATGGTAATTTTTTAAAGTTTCGAGGTCA
1 AAAATGG-AATTTTTGAAAGTTTCGAGGACA
*
271664 AAAATGGAATTTTGGAAAG
1 AAAATGGAATTTTTGAAAG
271683 CTCGAGGGTA
Statistics
Matches: 64, Mismatches: 11, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
28 9 0.14
29 14 0.22
30 25 0.39
31 16 0.25
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.32
Consensus pattern (30 bp):
AAAATGGAATTTTTGAAAGTTTCGAGGACA
Found at i:271689 original size:29 final size:31
Alignment explanation
Indices: 271574--271682 Score: 111
Period size: 31 Copynumber: 3.6 Consensus size: 31
271564 AAACGAGGGT
* *
271574 AAAATGGTAATTTTTGAAAGTTTCGAGGACA
1 AAAATGGTAATTTTGGAAAGTTTCGAGGTCA
* **
271605 AAAATAG-AATTTTTGG-AAG-TTCG-GGGGA
1 AAAATGGTAA-TTTTGGAAAGTTTCGAGGTCA
**
271633 AAAATGGTAATTTTTTAAAGTTTCGAGGTCA
1 AAAATGGTAATTTTGGAAAGTTTCGAGGTCA
271664 AAAATGG-AATTTTGGAAAG
1 AAAATGGTAATTTTGGAAAG
271683 CTCGAGGGTA
Statistics
Matches: 62, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
28 13 0.21
29 9 0.15
30 19 0.31
31 21 0.34
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.32
Consensus pattern (31 bp):
AAAATGGTAATTTTGGAAAGTTTCGAGGTCA
Found at i:271695 original size:29 final size:29
Alignment explanation
Indices: 271431--271697 Score: 139
Period size: 29 Copynumber: 9.1 Consensus size: 29
271421 CTCGGGGGCT
*
271431 AAATGGTAATTTTGGGAAAGTTCG-GGGTTA
1 AAATGG-AATTTT-GGAAAGTTCGAGGGTAA
* *
271461 AAATGGAATTTTTGG-CA-TCCGAGGGT-A
1 AAATGGAA-TTTTGGAAAGTTCGAGGGTAA
*
271488 AAATGGTAATTTTGGGGAAAATT-G-GGGTCAA
1 AAATGG-AATTTT--GGAAAGTTCGAGGGT-AA
* *
271519 AAATGGAATTTTTG-AAGTT-TAGGGGTAA
1 AAATGGAATTTTGGAAAGTTCGA-GGGTAA
***
271547 AATACT--AATTTTGGAAAAAACGAGGGT-A
1 AA-A-TGGAATTTTGGAAAGTTCGAGGGTAA
* **
271575 AAATGGTAATTTTTGAAAGTTTCGAGGACAA
1 AAATGG-AATTTTGGAAAG-TTCGAGGGTAA
* *
271606 AAATAGAATTTTTGG-AAGTTCG-GGGGAA
1 AAATGGAA-TTTTGGAAAGTTCGAGGGTAA
**
271634 AAATGGTAATTTTTTAAAGTTTCGA-GGTCAA
1 AAATGG-AATTTTGGAAAG-TTCGAGGGT-AA
*
271665 AAATGGAATTTTGGAAAGCTCGAGGGTAA
1 AAATGGAATTTTGGAAAGTTCGAGGGTAA
271694 AAAT
1 AAAT
271698 AAAAATTTTG
Statistics
Matches: 181, Mismatches: 29, Indels: 55
0.68 0.11 0.21
Matches are distributed among these distances:
26 1 0.01
27 19 0.10
28 35 0.19
29 50 0.28
30 49 0.27
31 27 0.15
ACGTcount: A:0.37, C:0.05, G:0.27, T:0.31
Consensus pattern (29 bp):
AAATGGAATTTTGGAAAGTTCGAGGGTAA
Found at i:272793 original size:7 final size:7
Alignment explanation
Indices: 272781--272811 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
272771 TCTTCCTTTT
272781 TTATTTA
1 TTATTTA
272788 TTATTTA
1 TTATTTA
272795 TTATTTA
1 TTATTTA
272802 TTATTTA
1 TTATTTA
272809 TTA
1 TTA
272812 AATATTATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TTATTTA
Found at i:274020 original size:17 final size:17
Alignment explanation
Indices: 273985--274027 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
273975 TGAAAAAGTA
*
273985 GTTACAAGAATATGAAAG
1 GTTA-AAGAAGATGAAAG
*
274003 GTTAAAGAAGATGGAAG
1 GTTAAAGAAGATGAAAG
274020 GTTAAAGA
1 GTTAAAGA
274028 TCAAGGGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.49, C:0.02, G:0.28, T:0.21
Consensus pattern (17 bp):
GTTAAAGAAGATGAAAG
Found at i:276648 original size:34 final size:34
Alignment explanation
Indices: 276610--276676 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
276600 GGTAATAACC
* *
276610 TCAACTTTTTACTCTCATTAACGAGCTAACAAAT
1 TCAACTTTCTACTCTCATTAACAAGCTAACAAAT
*
276644 TCAACTTTCTACTCTCATTAACAAGTTAACAAA
1 TCAACTTTCTACTCTCATTAACAAGCTAACAAA
276677 CTTCCAAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.34
Consensus pattern (34 bp):
TCAACTTTCTACTCTCATTAACAAGCTAACAAAT
Found at i:277428 original size:12 final size:12
Alignment explanation
Indices: 277411--277535 Score: 65
Period size: 12 Copynumber: 10.1 Consensus size: 12
277401 ATAACATCTA
277411 AACAACAAAAAT
1 AACAACAAAAAT
* *
277423 AACAACCAAAAC
1 AACAACAAAAAT
* *
277435 AGCAGCAAAAAT
1 AACAACAAAAAT
*
277447 AACAGCAAGCAACATT
1 AACAACAA--AA-A-T
* *
277463 AAAAAAATAAAAAT
1 --AACAACAAAAAT
*
277477 AGCAACAAAAAT
1 AACAACAAAAAT
*
277489 AGCAA-AAAAAT
1 AACAACAAAAAT
* *
277500 AACAGCAAAAAC
1 AACAACAAAAAT
*
277512 AAC-ACGAAAAT
1 AACAACAAAAAT
*
277523 AACAACCAAAAT
1 AACAACAAAAAT
277535 A
1 A
277536 GTAAAAAACA
Statistics
Matches: 85, Mismatches: 20, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
11 17 0.20
12 55 0.65
14 3 0.04
15 2 0.02
16 3 0.04
18 5 0.06
ACGTcount: A:0.67, C:0.18, G:0.06, T:0.08
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:277497 original size:23 final size:23
Alignment explanation
Indices: 277471--277543 Score: 74
Period size: 23 Copynumber: 3.2 Consensus size: 23
277461 TTAAAAAAAT
*
277471 AAAAATAGCAACAAAAATAGCAA
1 AAAAATAACAACAAAAATAGCAA
* * * *
277494 AAAAATAACAGCAAAAACAACAC
1 AAAAATAACAACAAAAATAGCAA
* * *
277517 GAAAATAACAACCAAAATAGTAA
1 AAAAATAACAACAAAAATAGCAA
277540 AAAA
1 AAAA
277544 CACAAAACAG
Statistics
Matches: 37, Mismatches: 13, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.70, C:0.15, G:0.07, T:0.08
Consensus pattern (23 bp):
AAAAATAACAACAAAAATAGCAA
Found at i:277506 original size:26 final size:26
Alignment explanation
Indices: 277441--277507 Score: 64
Period size: 26 Copynumber: 2.5 Consensus size: 26
277431 AAACAGCAGC
* *
277441 AAAAATAACAGCAAGCAACATTAAAA
1 AAAAATAACAGCAAGCAAAAATAAAA
* * *
277467 AAATAAAAATAGCAA-CAAAAATAGCAA
1 AAA-AATAACAGCAAGCAAAAATA-AAA
277494 AAAAATAACAGCAA
1 AAAAATAACAGCAA
277508 AAACAACACG
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
26 18 0.56
27 14 0.44
ACGTcount: A:0.69, C:0.13, G:0.07, T:0.10
Consensus pattern (26 bp):
AAAAATAACAGCAAGCAAAAATAAAA
Found at i:277555 original size:17 final size:17
Alignment explanation
Indices: 277529--277562 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
277519 AAATAACAAC
*
277529 CAAAATAGTAAAAAACA
1 CAAAACAGTAAAAAACA
277546 CAAAACAGTAAAAAACA
1 CAAAACAGTAAAAAACA
277563 GCAACCAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.71, C:0.15, G:0.06, T:0.09
Consensus pattern (17 bp):
CAAAACAGTAAAAAACA
Found at i:282122 original size:20 final size:20
Alignment explanation
Indices: 282097--282137 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
282087 TCTTCTTTTT
282097 TTTATTAGATGAGG-GATTAA
1 TTTATTAGATG-GGAGATTAA
282117 TTTATTAGATGGGAGATTAA
1 TTTATTAGATGGGAGATTAA
282137 T
1 T
282138 CGGGTCGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.34, C:0.00, G:0.24, T:0.41
Consensus pattern (20 bp):
TTTATTAGATGGGAGATTAA
Found at i:285320 original size:15 final size:14
Alignment explanation
Indices: 285300--285329 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
285290 ACGACTTAAG
285300 AAACAAATAAAAAAA
1 AAACAAA-AAAAAAA
285315 AAACAAAAAAAAAA
1 AAACAAAAAAAAAA
285329 A
1 A
285330 CAAAGGATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.90, C:0.07, G:0.00, T:0.03
Consensus pattern (14 bp):
AAACAAAAAAAAAA
Found at i:285325 original size:12 final size:12
Alignment explanation
Indices: 285308--285333 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
285298 AGAAACAAAT
285308 AAAAAAAAAACA
1 AAAAAAAAAACA
285320 AAAAAAAAAACA
1 AAAAAAAAAACA
285332 AA
1 AA
285334 GGATACTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAACA
Found at i:286169 original size:32 final size:30
Alignment explanation
Indices: 286131--286199 Score: 75
Period size: 32 Copynumber: 2.2 Consensus size: 30
286121 ATTACAAAAT
* * *
286131 AATCATTTAACTATTTGAAAGTTTTTTATTTA
1 AATCATTGAACTATATGAAAG--CTTTATTTA
* *
286163 AGTCATTGAAGTATATGAAAGCTTTATTTA
1 AATCATTGAACTATATGAAAGCTTTATTTA
286193 AATCATT
1 AATCATT
286200 AGATTCTTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
30 14 0.45
32 17 0.55
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.46
Consensus pattern (30 bp):
AATCATTGAACTATATGAAAGCTTTATTTA
Found at i:289237 original size:162 final size:164
Alignment explanation
Indices: 288956--289253 Score: 415
Period size: 162 Copynumber: 1.8 Consensus size: 164
288946 GCACAATGAC
* * * ** *
288956 GCATTGACTCGAGTCCTGTAGAGGTAAAGCCCCGAAAGGCGAGTGTATCTAACAATCTAGGTTAG
1 GCATTGACTCGAGTCCTATAGAGGCAAAGCCCCAAAAGGCGAGTAAATCTAACAATCTAGGATAG
* * *
289021 AAAAAGATCATCATTGCTCGAGTCAGGCTTCCCTCTCTAATGGAAGCAAGGAAGAGACTTTGGCA
66 AAAAAGATCATCATTGCTCGAATCAGGCCTCCCTCTCTAATGGAAGCAAGGAAGAGACTTTGACA
289086 CAAACGCGACTGGTACCAACTCAAGCAAAACAAG
131 CAAACGCGACTGGTACCAACTCAAGCAAAACAAG
* * *
289120 GCATTTACTCGAGTCTTATAGAGGCAAAGCCCCAAAAGGTGAGTAAATCTAACAATCTA-GATA-
1 GCATTGACTCGAGTCCTATAGAGGCAAAGCCCCAAAAGGCGAGTAAATCTAACAATCTAGGATAG
* * *
289183 AAAAA-ATTCATCATTGCTTGAATCTA-GCCTCCTTGTCTAATGGAAGCAAGGAAGAGACTTTGA
66 AAAAAGA-TCATCATTGCTCGAATC-AGGCCTCCCTCTCTAATGGAAGCAAGGAAGAGACTTTGA
289246 CACAAACG
129 CACAAACG
289254 TGAGACTCGG
Statistics
Matches: 117, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
161 1 0.01
162 61 0.52
163 4 0.03
164 51 0.44
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.22
Consensus pattern (164 bp):
GCATTGACTCGAGTCCTATAGAGGCAAAGCCCCAAAAGGCGAGTAAATCTAACAATCTAGGATAG
AAAAAGATCATCATTGCTCGAATCAGGCCTCCCTCTCTAATGGAAGCAAGGAAGAGACTTTGACA
CAAACGCGACTGGTACCAACTCAAGCAAAACAAG
Found at i:301562 original size:21 final size:21
Alignment explanation
Indices: 301537--301592 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
301527 AACAGATGAT
*
301537 TTTTTATTACTATTTTTATAA
1 TTTTTATTAATATTTTTATAA
* * *
301558 TTTTTAATAATTTTTTTATGA
1 TTTTTATTAATATTTTTATAA
301579 TTTTTA-TAAT-TTTT
1 TTTTTATTAATATTTT
301593 CATACCTTGC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.13
20 4 0.13
21 23 0.74
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (21 bp):
TTTTTATTAATATTTTTATAA
Found at i:301567 original size:10 final size:9
Alignment explanation
Indices: 301548--301592 Score: 54
Period size: 9 Copynumber: 4.7 Consensus size: 9
301538 TTTTATTACT
301548 ATTTTTATA
1 ATTTTTATA
301557 ATTTTTAATA
1 ATTTTT-ATA
*
301567 ATTTTTTTATG
1 A--TTTTTATA
301578 ATTTTTATA
1 ATTTTTATA
301587 ATTTTT
1 ATTTTT
301593 CATACCTTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
9 19 0.61
10 4 0.13
11 3 0.10
12 5 0.16
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (9 bp):
ATTTTTATA
Found at i:304690 original size:52 final size:52
Alignment explanation
Indices: 304610--304846 Score: 397
Period size: 52 Copynumber: 4.6 Consensus size: 52
304600 AAAAGGGTTT
* *
304610 GATGACTAAGTGTCATCGTGAGTATATGAATCTTTTACGGATTATGAGGTCC
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCC
*
304662 GGTGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCC
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCC
304714 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCC
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCC
* * *
304766 GATGGCTATGTGTCATCGTGAGTATATGAATCC-TTATGGATTACGAGGTCC
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCC
*
304817 G-TGACTATGTGTCATCGTGAGTGTATGAAT
1 GATGACTATGTGTCATCGTGAGTATATGAAT
304847 GAAATGAAAT
Statistics
Matches: 176, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
50 27 0.15
51 17 0.10
52 132 0.75
ACGTcount: A:0.24, C:0.14, G:0.27, T:0.35
Consensus pattern (52 bp):
GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCC
Found at i:312688 original size:25 final size:25
Alignment explanation
Indices: 312659--312709 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
312649 TAAATTAAGA
312659 TCTAAAATATAGCATTTGAAAATAG
1 TCTAAAATATAGCATTTGAAAATAG
312684 TCTAAAATATAGCATTTGAAAATAG
1 TCTAAAATATAGCATTTGAAAATAG
312709 T
1 T
312710 AAGTTATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.33
Consensus pattern (25 bp):
TCTAAAATATAGCATTTGAAAATAG
Found at i:315449 original size:14 final size:15
Alignment explanation
Indices: 315422--315451 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
315412 TTTATGTTTT
315422 AATAAAAGAAAAAAC
1 AATAAAAGAAAAAAC
315437 AATAAAA-AAAAAAC
1 AATAAAAGAAAAAAC
315451 A
1 A
315452 GTTATTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.83, C:0.07, G:0.03, T:0.07
Consensus pattern (15 bp):
AATAAAAGAAAAAAC
Found at i:319921 original size:29 final size:29
Alignment explanation
Indices: 319879--319965 Score: 138
Period size: 29 Copynumber: 3.0 Consensus size: 29
319869 CTCAGAGCCC
319879 CCCATGTGCAATGCTATAAGTTATTTAGA
1 CCCATGTGCAATGCTATAAGTTATTTAGA
* *
319908 CCCATGTGCAATGCTACAAGTGATTTAGA
1 CCCATGTGCAATGCTATAAGTTATTTAGA
* *
319937 CTCATGTGCAATGCTATAAGTTATATAGA
1 CCCATGTGCAATGCTATAAGTTATTTAGA
319966 AAGTGCTTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Consensus pattern (29 bp):
CCCATGTGCAATGCTATAAGTTATTTAGA
Found at i:323006 original size:13 final size:15
Alignment explanation
Indices: 322968--323018 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
322958 TATTTGATAA
*
322968 ATTGAAAATTTAAGT
1 ATTGAAATTTTAAGT
*
322983 ATTGAATTTTTAA-T
1 ATTGAAATTTTAAGT
322997 ATT-AAATTTTATAAGT
1 ATTGAAA-TTT-TAAGT
323013 ATTGAA
1 ATTGAA
323019 TTTATATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
13 2 0.07
14 7 0.24
15 14 0.48
16 4 0.14
17 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (15 bp):
ATTGAAATTTTAAGT
Found at i:323020 original size:16 final size:15
Alignment explanation
Indices: 322976--323021 Score: 67
Period size: 14 Copynumber: 3.1 Consensus size: 15
322966 AAATTGAAAA
322976 TTTAAGTATTGAATT
1 TTTAAGTATTGAATT
*
322991 TTTAA-TATTAAATT
1 TTTAAGTATTGAATT
323005 TTATAAGTATTGAATT
1 TT-TAAGTATTGAATT
323021 T
1 T
323022 ATATTAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 10 0.37
15 8 0.30
16 9 0.33
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (15 bp):
TTTAAGTATTGAATT
Found at i:323024 original size:15 final size:15
Alignment explanation
Indices: 322978--323024 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
322968 ATTGAAAATT
*
322978 TAAGTATTGAATTTT
1 TAAGTATTGAATTTA
*
322993 TAA-TATTAAATTTTA
1 TAAGTATTGAA-TTTA
323008 TAAGTATTGAATTTA
1 TAAGTATTGAATTTA
323023 TA
1 TA
323025 TTAAAATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 6 0.22
15 15 0.56
16 6 0.22
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (15 bp):
TAAGTATTGAATTTA
Found at i:323031 original size:28 final size:29
Alignment explanation
Indices: 322978--323035 Score: 84
Period size: 27 Copynumber: 2.0 Consensus size: 29
322968 ATTGAAAATT
322978 TAAGTATTGAATTTTTAATATTAAATTTTA
1 TAAGTATTGAA-TTTTAATATTAAATTTTA
*
323008 TAAGTATTGAA-TTT-ATATTAAAATTTA
1 TAAGTATTGAATTTTAATATTAAATTTTA
323035 T
1 T
323036 TTTTAAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 13 0.48
28 3 0.11
30 11 0.41
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (29 bp):
TAAGTATTGAATTTTAATATTAAATTTTA
Found at i:330083 original size:22 final size:22
Alignment explanation
Indices: 330046--330100 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 22
330036 AATAATTGAC
* *
330046 TAATAATTTTCAATAA-AATTT
1 TAATAATTTTAAAAAATAATTT
330067 T-AT-ATTTTAAAAAATAATTT
1 TAATAATTTTAAAAAATAATTT
330087 TAATAATTTTAAAA
1 TAATAATTTTAAAA
330101 TATTTGTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 9 0.31
20 8 0.28
21 3 0.10
22 9 0.31
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TAATAATTTTAAAAAATAATTT
Done.