Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008360.1 Kokia drynarioides strain JFW-HI SEQ_123027, 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: 24189
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.34
Warning! 117 characters in sequence are not A, C, G, or T
Found at i:4693 original size:16 final size:16
Alignment explanation
Indices: 4672--4710 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
4662 GTCTGTACTC
4672 AAACCCCATATAGGTG
1 AAACCCCATATAGGTG
* *
4688 AAACCCCATGTATGTG
1 AAACCCCATATAGGTG
*
4704 AATCCCC
1 AAACCCC
4711 TACAAACCCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.33, C:0.31, G:0.15, T:0.21
Consensus pattern (16 bp):
AAACCCCATATAGGTG
Found at i:4733 original size:23 final size:21
Alignment explanation
Indices: 4699--4752 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 21
4689 AACCCCATGT
4699 ATGTGAATCCCCTACAAACCCTC
1 ATGTGAA-CCCCTACAAA-CCTC
* *
4722 ATGTGTAACCCCTGCGAACCTC
1 ATGTG-AACCCCTACAAACCTC
4744 ATGTGAACC
1 ATGTGAACC
4753 ATGCAAACCC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 4 0.14
22 9 0.32
23 13 0.46
24 2 0.07
ACGTcount: A:0.28, C:0.35, G:0.15, T:0.22
Consensus pattern (21 bp):
ATGTGAACCCCTACAAACCTC
Found at i:4858 original size:26 final size:27
Alignment explanation
Indices: 4801--4862 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
4791 CCCCCAGGCG
* *
4801 AACCCATGTAAGCGAACCCCATGTGTGTA
1 AACCCATGTAAGCGAA--CCATGTATGCA
*
4830 AACCCATGTATGCGAA-CATGTATGCA
1 AACCCATGTAAGCGAACCATGTATGCA
4856 AACCCAT
1 AACCCAT
4863 ATGCAAATCC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 15 0.50
29 15 0.50
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (27 bp):
AACCCATGTAAGCGAACCATGTATGCA
Found at i:5052 original size:28 final size:28
Alignment explanation
Indices: 5012--5084 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 28
5002 TAGTAACATG
* *
5012 CGAACCCTCATAGGCGAGCCCCTGTATA
1 CGAACCCTTATAGGCGAGCCCCTATATA
* * *
5040 CGAAACCTTATAGGCAAGCCCCTATATG
1 CGAACCCTTATAGGCGAGCCCCTATATA
5068 CGAACCCTTATAGGCGA
1 CGAACCCTTATAGGCGA
5085 ACCCAGATGT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.29, C:0.32, G:0.21, T:0.19
Consensus pattern (28 bp):
CGAACCCTTATAGGCGAGCCCCTATATA
Found at i:5079 original size:14 final size:14
Alignment explanation
Indices: 5009--5108 Score: 60
Period size: 14 Copynumber: 7.2 Consensus size: 14
4999 ATGTAGTAAC
*
5009 ATGCGAACCCTCAT
1 ATGCGAACCCTTAT
* * * *
5023 AGGCGAGCCCCTGT
1 ATGCGAACCCTTAT
* *
5037 ATACGAAACCTTAT
1 ATGCGAACCCTTAT
* *
5051 AGGC-AAGCCCCTAT
1 ATGCGAA-CCCTTAT
5065 ATGCGAACCCTTAT
1 ATGCGAACCCTTAT
* **
5079 AGGCGAACCCAGAT
1 ATGCGAACCCTTAT
*
5093 GTGCGAACCC-TAT
1 ATGCGAACCCTTAT
5106 ATG
1 ATG
5109 TGTTAACCTA
Statistics
Matches: 60, Mismatches: 24, Indels: 5
0.67 0.27 0.06
Matches are distributed among these distances:
13 6 0.10
14 52 0.87
15 2 0.03
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (14 bp):
ATGCGAACCCTTAT
Found at i:5097 original size:28 final size:28
Alignment explanation
Indices: 5009--5103 Score: 86
Period size: 28 Copynumber: 3.4 Consensus size: 28
4999 ATGTAGTAAC
* * *
5009 ATGCGAACCCTCATAGGCGAGCCCCTG-T
1 ATGCGAACCCTTATAGGCAAG-CCCAGAT
* * **
5037 ATACGAAACCTTATAGGCAAGCCCCTAT
1 ATGCGAACCCTTATAGGCAAGCCCAGAT
5065 ATGCGAACCCTTATAGGCGAA-CCCAGAT
1 ATGCGAACCCTTATAGGC-AAGCCCAGAT
*
5093 GTGCGAACCCT
1 ATGCGAACCCT
5104 ATATGTGTTA
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
27 3 0.06
28 49 0.91
29 2 0.04
ACGTcount: A:0.28, C:0.32, G:0.21, T:0.19
Consensus pattern (28 bp):
ATGCGAACCCTTATAGGCAAGCCCAGAT
Found at i:5118 original size:14 final size:15
Alignment explanation
Indices: 5091--5139 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
5081 GCGAACCCAG
*
5091 ATGTGCGAACCCTAT
1 ATGTGTGAACCCTAT
*
5106 ATGTGTTAA-CCTAT
1 ATGTGTGAACCCTAT
5120 ATGTGTGAACCCTAT
1 ATGTGTGAACCCTAT
5135 ATGTG
1 ATGTG
5140 CAAACCCTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
14 13 0.43
15 17 0.57
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (15 bp):
ATGTGTGAACCCTAT
Found at i:5145 original size:15 final size:15
Alignment explanation
Indices: 5066--5148 Score: 84
Period size: 14 Copynumber: 5.7 Consensus size: 15
5056 AGCCCCTATA
5066 TGCGAACCCT-TATAG
1 TGCGAACCCTATAT-G
*
5081 -GCGAACCC-AGATG
1 TGCGAACCCTATATG
5094 TGCGAACCCTATATG
1 TGCGAACCCTATATG
**
5109 TGTTAA-CCTATATG
1 TGCGAACCCTATATG
*
5123 TGTGAACCCTATATG
1 TGCGAACCCTATATG
*
5138 TGCAAACCCTA
1 TGCGAACCCTA
5149 CTTATGTATG
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
13 1 0.02
14 31 0.54
15 25 0.44
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (15 bp):
TGCGAACCCTATATG
Found at i:6419 original size:16 final size:15
Alignment explanation
Indices: 6397--6440 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
6387 AAAGTAAATA
*
6397 TTTATTTGAATTATT
1 TTTATTTGAATTAAT
* *
6412 TATTATTTTAAATAAT
1 T-TTATTTGAATTAAT
6428 TTTATTTGAATTA
1 TTTATTTGAATTA
6441 CTTACTTAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (15 bp):
TTTATTTGAATTAAT
Found at i:7677 original size:42 final size:42
Alignment explanation
Indices: 7630--7711 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
7620 GAGGAAAGAA
*
7630 TGCCCGTTTGTTTTGATTTTCATGGAGAATTGAAGTCGTGCC
1 TGCCCGTTTGTTTCGATTTTCATGGAGAATTGAAGTCGTGCC
7672 TGCCCGTTTGTTTCGATTTTCATGGAGAATTGAAGTCGTG
1 TGCCCGTTTGTTTCGATTTTCATGGAGAATTGAAGTCGTG
7712 ACCAACACGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.17, C:0.16, G:0.27, T:0.40
Consensus pattern (42 bp):
TGCCCGTTTGTTTCGATTTTCATGGAGAATTGAAGTCGTGCC
Found at i:8276 original size:30 final size:30
Alignment explanation
Indices: 8184--8487 Score: 209
Period size: 30 Copynumber: 10.2 Consensus size: 30
8174 GCAAAAATGG
* * *
8184 AATTTTTGGAAA-TTTAAGAGT-AAAATGGT
1 AATTTTTGGAAAGTTTGAGGGTCAAAAT-AT
* *
8213 AA-TTTTCGAGAAG-TTG-GGGTCAAAAATAG
1 AATTTTTGGA-AAGTTTGAGGGTC-AAAATAT
*
8242 AATTTTTGGAAAATTTGAGGGTCAAAATAT
1 AATTTTTGGAAAGTTTGAGGGTCAAAATAT
* * * *
8272 AATTTTTTGATAGTTTGAGGGTAAAAATGT
1 AATTTTTGGAAAGTTTGAGGGTCAAAATAT
* * *
8302 AATTTTTGTG-AACTTTGAAGG-CAAAATTGT
1 AATTTTTG-GAAAGTTTGAGGGTCAAAA-TAT
* *
8332 AA-TTTTGTG-AAGTTTTGAGGGTAAAAATGT
1 AATTTTTG-GAAAG-TTTGAGGGTCAAAATAT
* * *
8362 AATTTTTGGAAATTTTGGGGGTTAAAATAT
1 AATTTTTGGAAAGTTTGAGGGTCAAAATAT
*
8392 AATTTTTTGGAAAGTTT-AGGGGT-AAAGATGT
1 AA-TTTTTGGAAAGTTTGA-GGGTCAAA-ATAT
* *
8423 AATTTTTGGAAAGTTTAAGGGTTAAAATAT
1 AATTTTTGGAAAGTTTGAGGGTCAAAATAT
* *
8453 AATTTTTAGAAAG-TTCAGGGGTCAAAATAT
1 AATTTTTGGAAAGTTTGA-GGGTCAAAATAT
*
8483 GATTT
1 AATTT
8488 CTAGATAGTT
Statistics
Matches: 223, Mismatches: 33, Indels: 37
0.76 0.11 0.13
Matches are distributed among these distances:
28 9 0.04
29 26 0.12
30 145 0.65
31 43 0.19
ACGTcount: A:0.36, C:0.02, G:0.23, T:0.38
Consensus pattern (30 bp):
AATTTTTGGAAAGTTTGAGGGTCAAAATAT
Found at i:8426 original size:61 final size:61
Alignment explanation
Indices: 8176--8480 Score: 267
Period size: 60 Copynumber: 5.1 Consensus size: 61
8166 TCTCAGGGGC
* * * * *
8176 AAAAATGGAATTTTTGG-AAATTTAAGAGT-AAAATGGTAA-TTTTCGAGAAG-TT-G-GGGT
1 AAAAATGTAATTTTTGGAAAATTTGAGGGTCAAAAT-ATAATTTTTTGA-AAGTTTAGAGGGT
*
8233 CAAAAATAG-AATTTTTGGAAAATTTGAGGGTCAAAATATAATTTTTTGATAGTTT-GAGGGT
1 -AAAAAT-GTAATTTTTGGAAAATTTGAGGGTCAAAATATAATTTTTTGAAAGTTTAGAGGGT
* * * * *
8294 AAAAATGTAATTTTTGTG-AACTTTGAAGG-CAAAATTGTAATTTTGTG-AAGTTTTGAGGGT
1 AAAAATGTAATTTTTG-GAAAATTTGAGGGTCAAAA-TATAATTTTTTGAAAGTTTAGAGGGT
* * *
8354 AAAAATGTAATTTTTGGAAATTTTGGGGGTTAAAATATAATTTTTTGGAAAGTTTAG-GGGT
1 AAAAATGTAATTTTTGGAAAATTTGAGGGTCAAAATATAATTTTTT-GAAAGTTTAGAGGGT
* * * * * *
8415 AAAGATGTAATTTTTGGAAAGTTTAAGGGTTAAAATATAATTTTTAGAAAGTTCAG-GGGT
1 AAAAATGTAATTTTTGGAAAATTTGAGGGTCAAAATATAATTTTTTGAAAGTTTAGAGGGT
*
8475 CAAAAT
1 AAAAAT
8481 ATGATTTCTA
Statistics
Matches: 208, Mismatches: 25, Indels: 26
0.80 0.10 0.10
Matches are distributed among these distances:
58 15 0.07
59 28 0.13
60 103 0.50
61 55 0.26
62 7 0.03
ACGTcount: A:0.37, C:0.02, G:0.23, T:0.37
Consensus pattern (61 bp):
AAAAATGTAATTTTTGGAAAATTTGAGGGTCAAAATATAATTTTTTGAAAGTTTAGAGGGT
Found at i:9519 original size:13 final size:13
Alignment explanation
Indices: 9478--9543 Score: 64
Period size: 13 Copynumber: 5.2 Consensus size: 13
9468 TCCTTTTTTT
9478 TTATTT-TTATTA
1 TTATTTATTATTA
* * *
9490 ATATTTATTAATG
1 TTATTTATTATTA
*
9503 TTATTTATTACTA
1 TTATTTATTATTA
*
9516 TTATTAATTATTA
1 TTATTTATTATTA
*
9529 TTA-TTATCATTA
1 TTATTTATTATTA
9541 TTA
1 TTA
9544 ATCGTTTTTA
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
12 15 0.35
13 28 0.65
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (13 bp):
TTATTTATTATTA
Found at i:9522 original size:22 final size:21
Alignment explanation
Indices: 9483--9553 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 21
9473 TTTTTTTATT
9483 TTTATTAATATTTATTAATGTTA
1 TTTATT-ATA-TTATTAATGTTA
*
9506 TTTATTACTATTATTAATTATTA
1 TTTATTA-TATTATTAA-TGTTA
9529 -TTATTATCATTATTAATCGTT-
1 TTTATTAT-ATTATTAAT-GTTA
9550 TTTA
1 TTTA
9554 AAATAAACAA
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
21 2 0.05
22 27 0.66
23 12 0.29
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.61
Consensus pattern (21 bp):
TTTATTATATTATTAATGTTA
Found at i:9528 original size:3 final size:3
Alignment explanation
Indices: 9478--9543 Score: 51
Period size: 3 Copynumber: 21.0 Consensus size: 3
9468 TCCTTTTTTT
* * * * *
9478 TTA TTT TTA TTA ATA TTTA TTA ATG TTA TTTA TTA CTA TTA TTAA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA -TTA TTA TTA TTA TT-A TTA
*
9526 TTA TTA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA
9544 ATCGTTTTTA
Statistics
Matches: 48, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
3 40 0.83
4 8 0.17
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:10143 original size:17 final size:17
Alignment explanation
Indices: 10121--10164 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
10111 TTATTAATTT
10121 AAATAAATTTAAACTTA
1 AAATAAATTTAAACTTA
**
10138 AAATAAATTTAATTTTA
1 AAATAAATTTAAACTTA
10155 AAATAAATTT
1 AAATAAATTT
10165 CAATTCTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATAAATTTAAACTTA
Found at i:10843 original size:155 final size:155
Alignment explanation
Indices: 10671--10983 Score: 491
Period size: 155 Copynumber: 2.0 Consensus size: 155
10661 GGTTCGAAGA
*
10671 TTTGCTCACTTTGAGCCTGATTTCATTGATTTGGTCTCCTTCTCAGTATCTCATCAGGAAGATGA
1 TTTGCTCACTTTGAGCCTGATTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGA
** * * * *
10736 TTGCATTGTTTGTTTTGATCCACTTCTCTGTGTCTTATCAGGAAGACGGATCTGGTTCACTTCTC
66 CCGCATTGTTTGTTTTGATCCACTTCTCTGTGTCTCATAAGGAAGACGAATCTAGTTCACTTCTC
*
10801 TATATCTCATCAAGAAGGTAACCTC
131 TATATCTCACCAAGAAGGTAACCTC
* * *
10826 TTTGCTTACTTTGAGCCTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGATGATGA
1 TTTGCTCACTTTGAGCCTGATTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGA
* *
10891 CCGTATTGTTTGTTTTGATCCACTTCTCTGTGTCTCATAAGGAAGATGAATCTAGTTCACTTCTC
66 CCGCATTGTTTGTTTTGATCCACTTCTCTGTGTCTCATAAGGAAGACGAATCTAGTTCACTTCTC
* *
10956 TGTATCTCACCAGGAAGGTAACCTC
131 TATATCTCACCAAGAAGGTAACCTC
10981 TTT
1 TTT
10984 ATTGCTTCAA
Statistics
Matches: 143, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
155 143 1.00
ACGTcount: A:0.20, C:0.21, G:0.18, T:0.40
Consensus pattern (155 bp):
TTTGCTCACTTTGAGCCTGATTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGA
CCGCATTGTTTGTTTTGATCCACTTCTCTGTGTCTCATAAGGAAGACGAATCTAGTTCACTTCTC
TATATCTCACCAAGAAGGTAACCTC
Found at i:11046 original size:85 final size:85
Alignment explanation
Indices: 10951--11106 Score: 215
Period size: 85 Copynumber: 1.8 Consensus size: 85
10941 TCTAGTTCAC
* * * * * * *
10951 TTCTCTGTATCTCACCAGGAAGGTAACC-TCTTTATTGCTTCAACTTGTTTCTTAGTATCTCATC
1 TTCTCAGTATCTCACCAGGAAGCTAACCAT-TTTATTACTTCAACCTGCTTCTCAATATCTCATC
11015 AGGAAGACGAATTTGGTCAAT
65 AGGAAGACGAATTTGGTCAAT
* *
11036 TTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACTTCGACCTGCTTCTCAATATCTCATCA
1 TTCTCAGTATCTCACCAGGAAGCTAACCATTTTATTACTTCAACCTGCTTCTCAATATCTCATCA
11101 GGAAGA
66 GGAAGA
11107 TGAGGTTCGA
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
85 60 0.98
86 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (85 bp):
TTCTCAGTATCTCACCAGGAAGCTAACCATTTTATTACTTCAACCTGCTTCTCAATATCTCATCA
GGAAGACGAATTTGGTCAAT
Found at i:11269 original size:209 final size:209
Alignment explanation
Indices: 11005--11395 Score: 570
Period size: 209 Copynumber: 1.9 Consensus size: 209
10995 TTGTTTCTTA
* *
11005 GTATCTCATCAGGAAGACGAATTTGGTCAATTTCTCAGTATCTCATCAGGAAGCTAACCATTTTA
1 GTATCTCATCAGGAAGACGAATCTGGTCAACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTA
* * *
11070 TTACTTCGACCTGCTTCTCAATATCTCATCAGGAAGAT-GAGGTTCGAAGATTTGCTCACTTTGA
66 TTACTTCAACCTGCTTCACAATATCTCATCAGGAAGATAGA-GTTCGAAGATCTGCTCACTTTGA
* * * *
11134 GCCTAATTTCTTTGATTTGGTCCACTTCTCAGTACCTCATCAGGAAGATGACCACATCTCTTGTT
130 GCCTAATTTCATCGAGTTGGTACACTTCTCAGTACCTCATCAGGAAGATGACCACATCTCTTGTT
11199 TTGATCCACTTCTCT
195 TTGATCCACTTCTCT
* *
11214 GTATCTCATCAGGAAGACGGATCTGGTCCACTTCTCAGTATCTCATCTA-GAAGCTAACCATTTT
1 GTATCTCATCAGGAAGACGAATCTGGTCAACTTCTCAGTATCTCATC-AGGAAGCTAACCATTTT
* * * *
11278 ATTGCTTCAACCTGCTTCACAGTATCTCATTAGGAAGCTAGAGTTCGAAGATCTGCTCACTTTGA
65 ATTACTTCAACCTGCTTCACAATATCTCATCAGGAAGATAGAGTTCGAAGATCTGCTCACTTTGA
** * * *
11343 GCCTGGTTTCATCGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACC
130 GCCTAATTTCATCGAGTTGGTACACTTCTCAGTACCTCATCAGGAAGATGACC
11396 GCCTCATTAT
Statistics
Matches: 160, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
209 157 0.98
210 3 0.02
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.34
Consensus pattern (209 bp):
GTATCTCATCAGGAAGACGAATCTGGTCAACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTA
TTACTTCAACCTGCTTCACAATATCTCATCAGGAAGATAGAGTTCGAAGATCTGCTCACTTTGAG
CCTAATTTCATCGAGTTGGTACACTTCTCAGTACCTCATCAGGAAGATGACCACATCTCTTGTTT
TGATCCACTTCTCT
Found at i:23372 original size:29 final size:29
Alignment explanation
Indices: 23339--23418 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 29
23329 AAAATACGAC
*
23339 TTTTGGATGCTC-GGAGGTAAAATGGTAAT
1 TTTTGGAGGCTCAGG-GGTAAAATGGTAAT
* *
23368 TTTTGGAGGTTCAGGGGTAAAATGGTGAT
1 TTTTGGAGGCTCAGGGGTAAAATGGTAAT
** *
23397 TTTTGGAATCTTAGGGGTAAAA
1 TTTTGGAGGCTCAGGGGTAAAA
23419 AAAGGAATTT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 41 0.95
30 2 0.05
ACGTcount: A:0.28, C:0.05, G:0.33, T:0.35
Consensus pattern (29 bp):
TTTTGGAGGCTCAGGGGTAAAATGGTAAT
Found at i:23509 original size:30 final size:30
Alignment explanation
Indices: 23357--23707 Score: 170
Period size: 30 Copynumber: 11.8 Consensus size: 30
23347 GCTCGGAGGT
** *
23357 AAAATGGTAATTTTTGG-AGGTTCAGGGGT-
1 AAAAT-GTAATTTTTGGAAAATTTAGGGGTC
* *
23386 AAAATGGTGATTTTTGG--AATCTTAGGGGTAA
1 AAAAT-GTAATTTTTGGAAAAT-TTAGGGGT-C
* * * *
23417 AAAAAGGAATTTTTAG-AAATTTATGGG-C
1 AAAATGTAATTTTTGGAAAATTTAGGGGTC
* * * * *
23445 AAAATGGTAA-TTTTCGAGAAGTTCGAGGTC
1 AAAAT-GTAATTTTTGGAAAATTTAGGGGTC
* * *
23475 AAAATGGAATTTTTGGAAAATTTCGGGGTT
1 AAAATGTAATTTTTGGAAAATTTAGGGGTC
* * * *
23505 AAAATATATTTTTTGGAAAGTTTAAGGG-C
1 AAAATGTAATTTTTGGAAAATTTAGGGGTC
** * *
23534 AAAATGTAATTTTTGTG-AAGGTCAAGGGT-
1 AAAATGTAATTTTTG-GAAAATTTAGGGGTC
** * *
23563 AATAATGTAATTTTTGTGAAGTTTTGGGGGGTA
1 AA-AATGTAATTTTTG-GAAAATTT-AGGGGTC
23596 AAAATGTAATTTTTGGAAAATTTAGGGGTC
1 AAAATGTAATTTTTGGAAAATTTAGGGGTC
* * *
23626 AAAATATAA-TTTTGGAAAGTTTAGAGG-C
1 AAAATGTAATTTTTGGAAAATTTAGGGGTC
* * *
23654 AAAATGCAATTTTTGG-AAAGTTCGAGGGTC
1 AAAATGTAATTTTTGGAAAATTTAG-GGGTC
* * * *
23684 AAAATATGATTTCTGGACAATTTA
1 AAAATGTAATTTTTGGAAAATTTA
23708 AGGACCTTTT
Statistics
Matches: 243, Mismatches: 61, Indels: 34
0.72 0.18 0.10
Matches are distributed among these distances:
28 23 0.09
29 83 0.34
30 99 0.41
31 19 0.08
32 17 0.07
33 2 0.01
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (30 bp):
AAAATGTAATTTTTGGAAAATTTAGGGGTC
Found at i:23537 original size:29 final size:30
Alignment explanation
Indices: 23424--23710 Score: 175
Period size: 30 Copynumber: 9.7 Consensus size: 30
23414 TAAAAAAAGG
* *
23424 AATTTTTAGAAA-TTTATGGG-CAAAATGGT
1 AATTTTTGGAAAGTTTAAGGGTCAAAAT-GT
* ** *
23453 AA-TTTTCGAGAAGTTCGA-GGTCAAAATGG
1 AATTTTTGGA-AAGTTTAAGGGTCAAAATGT
* ** * *
23482 AATTTTTGGAAAATTTCGGGGTTAAAATAT
1 AATTTTTGGAAAGTTTAAGGGTCAAAATGT
*
23512 ATTTTTTGGAAAGTTTAAGGG-CAAAATGT
1 AATTTTTGGAAAGTTTAAGGGTCAAAATGT
* *
23541 AATTTTTGTG-AAGGTCAAGGGT-AATAATGT
1 AATTTTTG-GAAAGTTTAAGGGTCAA-AATGT
** *
23571 AATTTTTGTG-AAGTTTTGGGGGGTAAAAATGT
1 AATTTTTG-GAAAG-TTT-AAGGGTCAAAATGT
* * *
23603 AATTTTTGGAAAATTTAGGGGTCAAAATAT
1 AATTTTTGGAAAGTTTAAGGGTCAAAATGT
*
23633 AA-TTTTGGAAAGTTT-AGAGG-CAAAATGC
1 AATTTTTGGAAAGTTTAAG-GGTCAAAATGT
** *
23661 AATTTTTGGAAAGTTCGAGGGTCAAAATAT
1 AATTTTTGGAAAGTTTAAGGGTCAAAATGT
* *
23691 GATTTCTGGACAA-TTTAAGG
1 AATTTTTGGA-AAGTTTAAGG
23711 ACCTTTTGGG
Statistics
Matches: 200, Mismatches: 41, Indels: 33
0.73 0.15 0.12
Matches are distributed among these distances:
28 15 0.08
29 65 0.32
30 92 0.46
31 7 0.04
32 19 0.09
33 2 0.01
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (30 bp):
AATTTTTGGAAAGTTTAAGGGTCAAAATGT
Found at i:23602 original size:32 final size:30
Alignment explanation
Indices: 23534--23610 Score: 91
Period size: 32 Copynumber: 2.5 Consensus size: 30
23524 GTTTAAGGGC
23534 AAAATGTAATTTTTGTGAAGGTCAAGGGTA
1 AAAATGTAATTTTTGTGAAGGTCAAGGGTA
* * ***
23564 ATAATGTAATTTTTGTGAAGTTTTGGGGGGTA
1 AAAATGTAATTTTTGTGAAG--GTCAAGGGTA
23596 AAAATGTAATTTTTG
1 AAAATGTAATTTTTG
23611 GAAAATTTAG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 19 0.49
32 20 0.51
ACGTcount: A:0.32, C:0.01, G:0.26, T:0.40
Consensus pattern (30 bp):
AAAATGTAATTTTTGTGAAGGTCAAGGGTA
Done.