Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011652.1 Kokia drynarioides strain JFW-HI SEQ_126644, 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: 34916
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Warning! 71 characters in sequence are not A, C, G, or T
Found at i:12520 original size:19 final size:18
Alignment explanation
Indices: 12476--12522 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
12466 ATTGTAAATA
*
12476 TTTTT-ATAATCTTTTAT
1 TTTTTAATAATATTTTAT
**
12493 TTTAAAATAATATTTATAT
1 TTTTTAATAATATTT-TAT
12512 TTTTTAATAAT
1 TTTTTAATAAT
12523 TTCAAATTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
17 3 0.13
18 8 0.35
19 12 0.52
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTTAATAATATTTTAT
Found at i:21121 original size:17 final size:17
Alignment explanation
Indices: 21101--21135 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
21091 AAATAATATA
21101 ATTTATTTAATGATTTT
1 ATTTATTTAATGATTTT
21118 ATTTATTTAATGATTTT
1 ATTTATTTAATGATTTT
21135 A
1 A
21136 GTTAATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (17 bp):
ATTTATTTAATGATTTT
Found at i:21648 original size:5 final size:5
Alignment explanation
Indices: 21638--21680 Score: 68
Period size: 5 Copynumber: 8.6 Consensus size: 5
21628 CAATTTCTTC
* *
21638 GAACG GAACG GAACG GAACG GAACG AAACG GAACA GAACG GAA
1 GAACG GAACG GAACG GAACG GAACG GAACG GAACG GAACG GAA
21681 AATCGTATTC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.47, C:0.19, G:0.35, T:0.00
Consensus pattern (5 bp):
GAACG
Found at i:21953 original size:849 final size:844
Alignment explanation
Indices: 19981--22482 Score: 3561
Period size: 845 Copynumber: 3.0 Consensus size: 844
19971 ATGGCACGGG
* * *
19981 ACGGAAAACCGTAATCCTGATCTCATGTAAAACATGAAAGTATATAAGCTTCTCCCCAACGATTT
1 ACGGAAAACCGTATTCCTGATCTCATGTAAAACATGAAAGTATATAAGCTTCTCCCTAAGGATTT
* * * * * * * *
20046 AAATAGTGGTCGGATAGCGGAAAAACGGCCGCTATATAGCAGTAGCGATG-CTGTCCGAAACCGC
66 AAATAGCGATCGGATAGCGGAATAGCGACTGCTATATAGCAGTAACGGTGTC-GTCCGAAACCGC
* *
20110 TATTGACAAAAATAGCGGTGTGAAGCAGAATCACACCAATAGCGGTGGATCACGCCCGCAATTTA
130 TATTGACGAAAATAGCGGTGTGAAGCAGAATCACACCAATAGCGGTGGATCACG-GCGCAATTTA
* * *
20175 ACGGGTAACGGTCAATTGCGGCAATAGCAGGCCACTATTTCCGTTATTGTTCAGTTACGGTAAAA
194 ACGGGTAACGGCCAATTGCGGCAATAGCAGGCCGCTATTTCCGTTATTGTTCCGTTACGGTAAAA
20240 -TTAAAAAATAATATAATTTAAATTATATGATTTTATTTATTTAATGATTTTAGTTAATATAAAA
259 TTTAAAAAATAATATAATTTAAATTATATGATTTTATTTATTTAATGATTTTAGTTAATATAAAA
* ** * * *
20304 TTCACGGCCGTGATACCCGCAGTGACCATAATAGTATCCGTTATGTCCATAACCGCGATAAACTC
324 TTCACGACCGTGATACCCGCAGTGACCGCAATAGTATCCGTTATGTTCGTAACCGCGATAAACAC
*
20369 AACAC-AACTGAAAACGCTACCTACATATCCTTGCTTTTTCAAATTTGAAAACCCCATACTTGAT
389 AACGCGAAC-GAAAACGCTACCTACATATCCTTGCTTTTTCAAATTTGAAAACCCCATACTTGAT
* * *
20433 TCTCCAAAATGAAAAACA-CAATTTTCTTCCCCTATTGAGATTGCAATCTACCCTTTCTCAACTA
453 TCTCCAAAATGAAAAA-AGCAATTTTCTTTCCCTATTGAAATTGCAATCTCCCCTTTCTCAACTA
* *
20497 AACAAACAGCACCATTCTTTTTCTATCCAAGTTCGATATAAAATTTACCGTGGAAAACTCAAATC
517 AACGAACAGCACCATT-TTTTTCTATCCAAGTTTGATATAAAATTTACCGTGGAAAACTCAAATC
*
20562 CCTTATCCTGAGCATTTGGATCACATGGGCCTATTATAGAACCATCATTAAACCCATTTCCCCCT
581 CCTTATCTTGAGCATTTGGATCACATGGGCCTATTATAGAACCATCATTAAACCCATTTCCCCCT
* *
20627 TGTATAGATGACGGCCCAACATTTACATTATTGGGCCTTAAAGCTTTAAAACCAGCTTTAGGTCC
646 TGTATAGATGACGGCCCAACATTTACATTATT-GGCCCTAAAGCTTTAAAACCAACTTTAGGTCC
* * *
20692 ACTGCCTAGTATAATACCTTTGCCTTTAAGCCTAGTTG-CCCTTATCTTTCCCAAATTAGGTTCC
710 ACTACCAAGTATAATACCTTTGCCTTTAAGCCTAGTTGCCCCCT-TCTTTCCCAAATTAGGTTCC
*
20756 CTTTGATCAGAATCTCTAGATTTAGCCTTCAATTTCTTCAAATGAAACGAAACGGAAAGACACGA
774 CTTTGATCAGAATCTCTAGATTTAGCCTTCAATTTCTTCAAACGAAACGAAACGGAAAGACACGA
*
20821 CACGAA
839 AACGAA
*
20827 AC-AAAAACCGTATTCCTGATCTCATGTAAAACATGAAAGTATATAAGCTTCTCCCTAAGGATTT
1 ACGGAAAACCGTATTCCTGATCTCATGTAAAACATGAAAGTATATAAGCTTCTCCCTAAGGATTT
* * * *
20891 AAATAGCGATCGGATAGCGGAATAGCGA-TCGCTATATAGCAATAACAGTGTCGTCCAAAACTGC
66 AAATAGCGATCGGATAGCGGAATAGCGACT-GCTATATAGCAGTAACGGTGTCGTCCGAAACCGC
* * * **
20955 TATTGCCGAAAATAGCGATGTGAAGCGGAATCACACCAATAGCGGTGGATCGTGGCCGCAATTTA
130 TATTGACGAAAATAGCGGTGTGAAGCAGAATCACACCAATAGCGGTGGATCACGG-CGCAATTTA
* * * * * * *
21020 ACGGGTAACGGCAAATTACGGCAATAGCGGGCCGCTATTTCCATTATTGTTTCATTACAGTAAAA
194 ACGGGTAACGGCCAATTGCGGCAATAGCAGGCCGCTATTTCCGTTATTGTTCCGTTACGGTAAAA
* *
21085 TTAAAAAAATAATATAATTT-ATTTA-ATGATTTTATTTATTTAATGATTTTAGTTAATATAAAA
259 TTTAAAAAATAATATAATTTAAATTATATGATTTTATTTATTTAATGATTTTAGTTAATATAAAA
* * * ** *
21148 TTCACGACCGTGCTACCCGCAGTGGCTGCAATAGTATCCGTTATGTTCGTAATTGCGATAAACGC
324 TTCACGACCGTGATACCCGCAGTGACCGCAATAGTATCCGTTATGTTCGTAACCGCGATAAACAC
* * ** * * *
21213 AACGCGATCGAAAACGCGACCTACGCAACCTTGTTTTTTCAAATTTGAAAACCTCATACTTGATT
389 AACGCGAACGAAAACGCTACCTACATATCCTTGCTTTTTCAAATTTGAAAACCCCATACTTGATT
* *
21278 CTCCAAAATGAAAAAAGCAATTTTCTTTCCCTGTTGAAATTGTAATCTCCCCTTTCTCAACTAAA
454 CTCCAAAATGAAAAAAGCAATTTTCTTTCCCTATTGAAATTGCAATCTCCCCTTTCTCAACTAAA
*
21343 CGAACAGCACCATGTTTTATTCTATCCAAGTTTGATATAAAATTTACGGTGGAAAACTCAAATCC
519 CGAACAGCACCAT-TTTT-TTCTATCCAAGTTTGATATAAAATTTACCGTGGAAAACTCAAATCC
** * *
21408 CTTATCTTGAGCATTTGGATCACATAAGCCTATTACAGAACCATTATTAAACCCA-TTCCGCCCT
582 CTTATCTTGAGCATTTGGATCACATGGGCCTATTATAGAACCATCATTAAACCCATTTCC-CCCT
*
21472 TGTATAGATGATGGCCCAACATTTACATTATTGGCCCTAAAGCTTT-AAACCAACTTTAGGTCCA
646 TGTATAGATGACGGCCCAACATTTACATTATTGGCCCTAAAGCTTTAAAACCAACTTTAGGTCCA
* *
21536 CTACCAAGTATAATACCTTTGCCTTTAAGCCTAATTGCCCCCTTCTTTCCCAAATTAGGTTTCCT
711 CTACCAAGTATAATACCTTTGCCTTTAAGCCTAGTTGCCCCCTTCTTTCCCAAATTAGGTTCCCT
* * * *
21601 TTGATCAGAATCTCTAGATTTAGCCTTCAATTTCTTCGAACGGAACGGAACGGAACGGA-ACGAA
776 TTGATCAGAATCTCTAGATTTAGCCTTCAATTTCTTCAAACGAAACGAAACGGAA-AGACACGAA
21665 ACGGAACAGA
840 AC-G---A-A
* *
21675 ACGGAAAATCGTATTCCTGATCTCATGTAAGACATGAAAGTATATAAGCTTCTCCCTAAGGATTT
1 ACGGAAAACCGTATTCCTGATCTCATGTAAAACATGAAAGTATATAAGCTTCTCCCTAAGGATTT
* * *
21740 AAATAGCGATCGAATAGCGGAATAGCGACTGCTATATTGCAGTAATGGTGTCGTCCGAAACCGCT
66 AAATAGCGATCGGATAGCGGAATAGCGACTGCTATATAGCAGTAACGGTGTCGTCCGAAACCGCT
* * * * * *
21805 ATTGTCGAAAATAGCGGTTTGAAGCAAAATTACACCAATAGCGATGGATCACGAGCGTAATTTAA
131 ATTGACGAAAATAGCGGTGTGAAGCAGAATCACACCAATAGCGGTGGATCACG-GCGCAATTTAA
* * * ** * *
21870 TGAGTAACGGCCAATTGCGACAATAGCAAACCGCTATTTTCGTTATTATTCCGTTACGGTAAAAT
195 CGGGTAACGGCCAATTGCGGCAATAGCAGGCCGCTATTTCCGTTATTGTTCCGTTACGGTAAAAT
21935 TTAAAAAATAATATAATTTAAATTATATG-TTTTATTTATTTAATGATTTTAGTTAATATAAAAT
260 TTAAAAAATAATATAATTTAAATTATATGATTTTATTTATTTAATGATTTTAGTTAATATAAAAT
* *
21999 TCACAACCGTGATACCCGCAGTGACCGCAATAGTATCCATTATG-TCTGTAACCGCGATAAACAC
325 TCACGACCGTGATACCCGCAGTGACCGCAATAGTATCCGTTATGTTC-GTAACCGCGATAAACAC
* * * * *
22063 AATGCGACCGAAAACGCTAGCTACATTTCCTTGCTTTTTCAAATTTGGAAACCCCA-ACCTTGAT
389 AACGCGAACGAAAACGCTACCTACATATCCTTGCTTTTTCAAATTTGAAAACCCCATA-CTTGAT
* * *
22127 TCTCCAAAATGAAAAACGCAATTTT-TTGTCCTTATTGAAATTACAATCTCCCCTTTCTCAACTA
453 TCTCCAAAATGAAAAAAGCAATTTTCTT-TCCCTATTGAAATTGCAATCTCCCCTTTCTCAACTA
* *
22191 AACGAATAGCACCATTTTTTTCTATCCAAGTTTGATATAAAATTTACCGTGGAAAACTCAAATCT
517 AACGAACAGCACCATTTTTTTCTATCCAAGTTTGATATAAAATTTACCGTGGAAAACTCAAATCC
* *
22256 CTTATCTTAAGCATTTGGATCACA-GGGTCTATTATAGAACCATCATTAAACCCATTTCCCCCTT
582 CTTATCTTGAGCATTTGGATCACATGGGCCTATTATAGAACCATCATTAAACCCATTTCCCCCTT
* ** * * *
22320 ATATAGATGACAACCCAACATTTACATTACTAGG-CCTTAAGCTTTAAAACCAACTTTAGGTTCA
647 GTATAGATGACGGCCCAACATTTACATTA-TTGGCCCTAAAGCTTTAAAACCAACTTTAGGTCCA
22384 CTACCAAGTATAATACCTTTGCC---AAGCCTAGTTGCCCCCTTCTTTCCCAAATTAGGTTCCCT
711 CTACCAAGTATAATACCTTTGCCTTTAAGCCTAGTTGCCCCCTTCTTTCCCAAATTAGGTTCCCT
*
22446 TTGATCAGAATCTCTAGATTTAACCTTCAATTTCTTC
776 TTGATCAGAATCTCTAGATTTAGCCTTCAATTTCTTC
22483 CCTAAATCAC
Statistics
Matches: 1469, Mismatches: 160, Indels: 55
0.87 0.10 0.03
Matches are distributed among these distances:
843 130 0.09
844 243 0.17
845 428 0.29
846 21 0.01
847 66 0.04
848 117 0.08
849 246 0.17
850 215 0.15
851 3 0.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (844 bp):
ACGGAAAACCGTATTCCTGATCTCATGTAAAACATGAAAGTATATAAGCTTCTCCCTAAGGATTT
AAATAGCGATCGGATAGCGGAATAGCGACTGCTATATAGCAGTAACGGTGTCGTCCGAAACCGCT
ATTGACGAAAATAGCGGTGTGAAGCAGAATCACACCAATAGCGGTGGATCACGGCGCAATTTAAC
GGGTAACGGCCAATTGCGGCAATAGCAGGCCGCTATTTCCGTTATTGTTCCGTTACGGTAAAATT
TAAAAAATAATATAATTTAAATTATATGATTTTATTTATTTAATGATTTTAGTTAATATAAAATT
CACGACCGTGATACCCGCAGTGACCGCAATAGTATCCGTTATGTTCGTAACCGCGATAAACACAA
CGCGAACGAAAACGCTACCTACATATCCTTGCTTTTTCAAATTTGAAAACCCCATACTTGATTCT
CCAAAATGAAAAAAGCAATTTTCTTTCCCTATTGAAATTGCAATCTCCCCTTTCTCAACTAAACG
AACAGCACCATTTTTTTCTATCCAAGTTTGATATAAAATTTACCGTGGAAAACTCAAATCCCTTA
TCTTGAGCATTTGGATCACATGGGCCTATTATAGAACCATCATTAAACCCATTTCCCCCTTGTAT
AGATGACGGCCCAACATTTACATTATTGGCCCTAAAGCTTTAAAACCAACTTTAGGTCCACTACC
AAGTATAATACCTTTGCCTTTAAGCCTAGTTGCCCCCTTCTTTCCCAAATTAGGTTCCCTTTGAT
CAGAATCTCTAGATTTAGCCTTCAATTTCTTCAAACGAAACGAAACGGAAAGACACGAAACGAA
Found at i:27328 original size:18 final size:18
Alignment explanation
Indices: 27307--27345 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
27297 TTTTTATACT
* *
27307 TTTTTATATTTTTATTAA
1 TTTTTAAATATTTATTAA
*
27325 TTTTTAAATATTTATTTA
1 TTTTTAAATATTTATTAA
27343 TTT
1 TTT
27346 ATTGTTTGAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTAAATATTTATTAA
Found at i:31001 original size:119 final size:119
Alignment explanation
Indices: 30794--31105 Score: 403
Period size: 119 Copynumber: 2.6 Consensus size: 119
30784 CCTCTTTTTA
* * * *
30794 ATCTGATTAAAAAAAATCAAATTTTTTGGTGTTAACCATGCAATGGTCGACACCTCTTTTTTGTC
1 ATCTGA-TAAAAAAAATCAAATTTTTGGGTGTTAGCCATGCAATGGTCGACACCCCTTTTTTATC
*
30859 AGATAAAAAATACAATTTGTTTGTGTTGGTCATACAATGGTCGACATCCCTATTT
65 AGATAAAAAATACAATTTGTTTGTGTTGGCCATACAATGGTCGACATCCCTATTT
* * * * * *
30914 ATCTGATAAAAAAATTTAAAATTTTGGGTGTT-GCCACGCAATGGCCGACACCCCTTTTTTTATT
1 ATCTGATAAAAAAAATCAAATTTTTGGGTGTTAGCCATGCAATGGTCGACACCCC-TTTTTTATC
* * * * *
30978 AGATCAAAAATTCAATTTTTTTGTTTTGGCCATGCAATGGTCGACATCCCTATTT
65 AGATAAAAAATACAATTTGTTTGTGTTGGCCATACAATGGTCGACATCCCTATTT
* * * * *
31033 ATCTGATAAAAAAAATCAATTTTTTGGGTGTTAGTCATGCAATGGTCGACA-CCCTCTGTTCTCA
1 ATCTGATAAAAAAAATCAAATTTTTGGGTGTTAGCCATGCAATGGTCGACACCCCTTTTTTATCA
31097 GATAAAAAA
66 GATAAAAAA
31106 ATTGTATTTT
Statistics
Matches: 162, Mismatches: 28, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
118 32 0.20
119 109 0.67
120 21 0.13
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.36
Consensus pattern (119 bp):
ATCTGATAAAAAAAATCAAATTTTTGGGTGTTAGCCATGCAATGGTCGACACCCCTTTTTTATCA
GATAAAAAATACAATTTGTTTGTGTTGGCCATACAATGGTCGACATCCCTATTT
Found at i:31023 original size:60 final size:59
Alignment explanation
Indices: 30756--31117 Score: 277
Period size: 60 Copynumber: 6.1 Consensus size: 59
30746 AAAAAAAAAA
* * * * * *
30756 TTTGGTGTTGACCATGCAATGATCTACACCTCTTTTTAATCTGATTAAAAAAAATCAAATTT
1 TTTGGTGTTGGCCATGCAATGGTCGACACCCCTATTT-ATCTGA-TAAAAAAATTC-AATTT
** * * * * *
30818 TTTGGTGTTAACCATGCAATGGTCGACACCTCTTTTTTGTCAGAT-AAAAAATACAATTT
1 TTTGGTGTTGGCCATGCAATGGTCGACACC-CCTATTTATCTGATAAAAAAATTCAATTT
* * * * *
30877 GTTT-GTGTTGGTCATACAATGGTCGACATCCCTATTTATCTGATAAAAAAATTTAAAATT
1 -TTTGGTGTTGGCCATGCAATGGTCGACACCCCTATTTATCTGATAAAAAAA-TTCAATTT
* * * * *
30937 TTGGGTGTT-GCCACGCAATGGCCGACACCCCTTTTTTTAT-TAGAT-CAAAAATTCAATTT
1 TTTGGTGTTGGCCATGCAATGGTCGACACCCC--TATTTATCT-GATAAAAAAATTCAATTT
* * * *
30996 TTTTGTTTTGGCCATGCAATGGTCGACATCCCTATTTATCTGATAAAAAAAATCAATTT
1 TTTGGTGTTGGCCATGCAATGGTCGACACCCCTATTTATCTGATAAAAAAATTCAATTT
* * * * * **
31055 TTTGGGTGTTAGTCATGCAATGGTCGACACCCTCT-GTTCTCAGATAAAAAAATTGTATTT
1 TTT-GGTGTTGGCCATGCAATGGTCGACACCC-CTATTTATCTGATAAAAAAATTCAATTT
31115 TTT
1 TTT
31118 ATCTGACAAA
Statistics
Matches: 236, Mismatches: 51, Indels: 28
0.75 0.16 0.09
Matches are distributed among these distances:
58 19 0.08
59 79 0.33
60 90 0.38
61 12 0.05
62 31 0.13
63 5 0.02
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (59 bp):
TTTGGTGTTGGCCATGCAATGGTCGACACCCCTATTTATCTGATAAAAAAATTCAATTT
Found at i:32777 original size:13 final size:12
Alignment explanation
Indices: 32757--32796 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 12
32747 TTTATTTTAA
32757 TTTAATTTAATT
1 TTTAATTTAATT
32769 TTATAATTTAATT
1 TT-TAATTTAATT
32782 CTTTAAATTTAATT
1 -TTT-AATTTAATT
32796 T
1 T
32797 CAATTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.08
13 12 0.48
14 11 0.44
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTAATTTAATT
Found at i:32780 original size:5 final size:5
Alignment explanation
Indices: 32742--32804 Score: 53
Period size: 5 Copynumber: 13.0 Consensus size: 5
32732 AATTTAAAAG
* * *
32742 TTTAA TTTAT TTTAA TTTAA TTTAA TTT-- TATAA TTTAA TTCT-- TTAAA
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TT-TAA TTTAA
32789 TTTAA TTTCAA TTTAA
1 TTTAA TTT-AA TTTAA
32805 AAGTATCATG
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
3 2 0.04
4 2 0.04
5 36 0.78
6 6 0.13
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (5 bp):
TTTAA
Found at i:32972 original size:19 final size:20
Alignment explanation
Indices: 32923--32972 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
32913 ACTTGAAAAA
32923 ATTTTCATATAATTTAAGTATT
1 ATTTTCAT-T-ATTTAAGTATT
32945 ATTTT-ATTATTTAAGT-TT
1 ATTTTCATTATTTAAGTATT
*
32963 TTTTTCATTA
1 ATTTTCATTA
32973 AAAATAGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 6 0.23
19 12 0.46
20 1 0.04
21 2 0.08
22 5 0.19
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (20 bp):
ATTTTCATTATTTAAGTATT
Found at i:34625 original size:25 final size:23
Alignment explanation
Indices: 34609--34808 Score: 258
Period size: 23 Copynumber: 8.7 Consensus size: 23
34599 AGCATGTCTC
34609 GTGCTCTCTGTTATTAGCACTGTGT
1 GTGCTCTCTG--ATTAGCACTGTGT
34634 GTGCTCTCTGATTAGCACTGTGT
1 GTGCTCTCTGATTAGCACTGTGT
*
34657 GTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTGTGT
* *
34680 GTGCTCTCTGATTAGTACTTTGT
1 GTGCTCTCTGATTAGCACTGTGT
* * *
34703 GTACTCTCTGTTTAGCATTGTGT
1 GTGCTCTCTGATTAGCACTGTGT
*
34726 GTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTGTGT
* * * *
34749 GTGCTCTCTAATTTGTACTTTGT
1 GTGCTCTCTGATTAGCACTGTGT
* *
34772 GTACTCTCTGTTTAGCACTGTGT
1 GTGCTCTCTGATTAGCACTGTGT
34795 GTGCTCTCT-ATTAG
1 GTGCTCTCTGATTAG
34809 TATTTTGGTA
Statistics
Matches: 153, Mismatches: 22, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
22 4 0.03
23 139 0.91
25 10 0.07
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.45
Consensus pattern (23 bp):
GTGCTCTCTGATTAGCACTGTGT
Found at i:34725 original size:69 final size:69
Alignment explanation
Indices: 34609--34825 Score: 312
Period size: 69 Copynumber: 3.1 Consensus size: 69
34599 AGCATGTCTC
* * * *
34609 GTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCA
1 GTGCTCTCTG--ATTAGTACTTTGTGTACTCTCTGTTTAGCACTGTGTGTGCTCTCTGATTAGCA
34674 CTTTGT
64 CTTTGT
*
34680 GTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCATTGTGTGTGCTCTCTGATTAGCACT
1 GTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACTGTGTGTGCTCTCTGATTAGCACT
34745 TTGT
66 TTGT
* * * *
34749 GTGCTCTCTAATTTGTACTTTGTGTACTCTCTGTTTAGCACTGTGTGTGCTCTCT-ATTAGTATT
1 GTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACTGTGTGTGCTCTCTGATTAGCACT
34813 TTG-
66 TTGT
*
34816 GTACTCTCTG
1 GTGCTCTCTG
34826 TTTGTTCCGT
Statistics
Matches: 134, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
67 8 0.06
68 10 0.07
69 106 0.79
71 10 0.07
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.46
Consensus pattern (69 bp):
GTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACTGTGTGTGCTCTCTGATTAGCACT
TTGT
Done.