Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003438.1 Kokia drynarioides strain JFW-HI SEQ_116217, 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: 47095
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:11292 original size:8 final size:8
Alignment explanation
Indices: 11279--11323 Score: 90
Period size: 8 Copynumber: 5.6 Consensus size: 8
11269 GAACAGAGAC
11279 GTGAAAGA
1 GTGAAAGA
11287 GTGAAAGA
1 GTGAAAGA
11295 GTGAAAGA
1 GTGAAAGA
11303 GTGAAAGA
1 GTGAAAGA
11311 GTGAAAGA
1 GTGAAAGA
11319 GTGAA
1 GTGAA
11324 GTGAAGTGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.38, T:0.13
Consensus pattern (8 bp):
GTGAAAGA
Found at i:15270 original size:715 final size:713
Alignment explanation
Indices: 14233--16361 Score: 3029
Period size: 715 Copynumber: 3.0 Consensus size: 713
14223 CGTGACAAGA
* * * * * *
14233 GAACACC-AAGCAATTGAGGTTTGGTAGTAACACAAAATATTGGACCTTTGAACGACCTTCATTT
1 GAACACCGAA-CAATCGAGGTTTGGTAGTAACACAAAATACTGGACCTTTGTATGACCCTCAGTT
* *
14297 GGTTATTTTGATTTGAACTTCGATCAATCGATCTTTAATGCTGGGAACACTTACAGGGGAATGAT
65 GGTTATTTTGATTTGAACTTCGATCAACCGATGTTTAATGCTGGGAACACTTACA-GGGAATGAT
* * * *
14362 ATCAAGTTTTGGCGATTGGCAATCTTCAATAATTGATTTTAGTTGTTTTAACAACTATACAATAA
129 ATTAAGTTTTAGCG-TTGGCAATCTTCAACAATTGATTTTAGTTGTTTTAACAACTATACAAGAA
* ** *
14427 GTGATTATGTACTCCTTATGATGTCCACTGGAAAAGGGACATCCAACCTTGAAGATGTTGGTGGG
193 GTGATTATGTACTCCTTATAATGTCCACCAGAAAAGGGACATCCAAACTTGAAGATGTTGGTGGG
* * *
14492 GTTGAGAATGAAGAGGGCACTGAATTCAATG-CTGATCCAATCCGAGAACCCAGTGCAGATAGAT
258 GTTGAGAACGAAGAGGGCATTGAATTCAATGTC-GATCCAATCCGAGAACCCGGTGCAGATAGAT
*
14556 CAAAAATTACATTATTTTCTAAATCGGAGTCAGTTCCAAATGAACCATAAGATGGAGGTTTAGAC
322 CAAAAATTACATTATTTTTTAAATCGGAGTCAGTTCCAAATGAACCATAAGATGGAGGTTTAGAC
14621 AGTGGAAGTCCGAATGAAGATGCCGAAGAAAATCCACTATTCAAGGTGTACTTGTTGGAAATATA
387 AGTGGAAGTCCGAATGAAGATGCCGAAGAAAATCCACTATTCAAGGTGTACTTGTTGGAAATATA
* * *
14686 ATCTACCGCAAAACATGTATGTTAGCACTGCCTGGGAAAAATCAAGAATTAAATATAAAATCAGA
452 ATCTACTGCAAAACAAGTATGTTAGCACTGCCTGGGAAAGATCAAGAATTAAATATAAAATCAGA
* * * ** *
14751 AATTTCTGTGCCATGGTAAATCTACTGCCTTAGAAACGAATTCACCCTGACCAGCATAATCGTGT
517 AATTTCTGTGCCATGGTAAATCTACTGCCTTAAAAACGAATTCACCCTGATCGGTGTAATCGCGT
* *
14816 AGTGGACGTTGTCCCTCAAGTTTAACATAGTCCTTTGATATTTGTACACCCGAATATGGAAGATG
582 AGTGGACGTTGTCCCTCAAGTTTAACACAGTCCTTTGATATTCGTACACCCGAATATGGAAGATG
*
14881 GAACTCAATTGGTGCTGCTCTTCTTGCGAAATCACAGTAGGAACAATTCCCAAGAAAGCTTGGAG
647 GAACTCAATTGGTGCTGCTCTTCTTGAGAAATCACAGTAGGAACAATTCCCAAGAAAGCTTGGAG
14946 GG
712 GG
* *
14948 GAACACCGAACAATCGAGGTTTGGTAATAACACGAAATACTGGACCTTTGTATGACCCTCAGTTG
1 GAACACCGAACAATCGAGGTTTGGTAGTAACACAAAATACTGGACCTTTGTATGACCCTCAGTTG
* *
15013 GTTATTTTGATTTGAATTTCGATCAACCAATGTTTAATGCTGGGAACACTTACATGGGAATGATA
66 GTTATTTTGATTTGAACTTCGATCAACCGATGTTTAATGCTGGGAACACTTACA-GGGAATGATA
* *
15078 TTAAGTTTTAGCGGTTGGCAATCTTCAACAATTGATTTTAGTTGTTTTAACAACTACAGAAGAAG
130 TTAAGTTTTAGC-GTTGGCAATCTTCAACAATTGATTTTAGTTGTTTTAACAACTATACAAGAAG
* *
15143 TGATTATGTACTCCTTACAATGTCCACCAGTAAAGGGACATCCAAACTTGAAGATGTTGGTGGGG
194 TGATTATGTACTCCTTATAATGTCCACCAGAAAAGGGACATCCAAACTTGAAGATGTTGGTGGGG
* * * * *
15208 TTGAGAACAAAGAGGGCATTGGATTCAGTGTCGATCCAATCCGAGAACCTGGTGCAGATAGATTA
259 TTGAGAACGAAGAGGGCATTGAATTCAATGTCGATCCAATCCGAGAACCCGGTGCAGATAGATCA
* * *
15273 AAAATTACATTATTTTTTGAACCGGAGTCAGTTCCAAGTGAACCATAAGATGGAGGTTTAGACAG
324 AAAATTACATTATTTTTTAAATCGGAGTCAGTTCCAAATGAACCATAAGATGGAGGTTTAGACAG
* *
15338 TGGAAGTCCGAATAAAGTTGCCGAAGAAAATCCACTATTCAAGGTGTACTTGTTGGAAATATAAT
389 TGGAAGTCCGAATGAAGATGCCGAAGAAAATCCACTATTCAAGGTGTACTTGTTGGAAATATAAT
* * * *
15403 CTACTGTAAAACAAATTTGTTAGCACTGCCTGGGAAAGATCAAGAATTAAATATAAAATCAAAAA
454 CTACTGCAAAACAAGTATGTTAGCACTGCCTGGGAAAGATCAAGAATTAAATATAAAATCAGAAA
* * * * * * *
15468 TTCCTATGTCGTGGTAAATCTATTGCCTTAAAAATGAATCCACCCTGATCGGTGTAATCGCGTAG
519 TTTCTGTGCCATGGTAAATCTACTGCCTTAAAAACGAATTCACCCTGATCGGTGTAATCGCGTAG
* * * *
15533 TGAACGTTGTCCCCCAAGTTTAACACAATCCTTTGATATTCGTACACCTGAATATGGAAGATGGA
584 TGGACGTTGTCCCTCAAGTTTAACACAGTCCTTTGATATTCGTACACCCGAATATGGAAGATGGA
* * * * * *
15598 ACTCAATTGGTGCTGTTATTCTCGAGAAATCACAGTAAGAACAATTCCCAAGAAAGCTTGAAGAG
649 ACTCAATTGGTGCTGCTCTTCTTGAGAAATCACAGTAGGAACAATTCCCAAGAAAGCTTGGAGGG
* * *
15663 GAACACCGAACAATCAAGGTTTGGTAGTAACACAAAATACTGGACCTTTGTATGAACCTTAGTTG
1 GAACACCGAACAATCGAGGTTTGGTAGTAACACAAAATACTGGACCTTTGTATGACCCTCAGTTG
* *
15728 GTTACTTTGATTTGAACTTAGATCAACCGATGTTTAATGCTGGGAACACTTACAGGG---GA-A-
66 GTTATTTTGATTTGAACTTCGATCAACCGATGTTTAATGCTGGGAACACTTACAGGGAATGATAT
*
15788 T--G----A----TAGCAATCTTCAACAATTGATTTTAGTTGTTTTAACAACTATACAAGAAGTG
131 TAAGTTTTAGCGTTGGCAATCTTCAACAATTGATTTTAGTTGTTTTAACAACTATACAAGAAGTG
* ** * *
15843 ATTATGTACTCCTTATTATGTTTACCAAAAAAGGGACATCC-AACATTGAAGAGGTTGGTGGGGT
196 ATTATGTACTCCTTATAATGTCCACCAGAAAAGGGACATCCAAAC-TTGAAGATGTTGGTGGGGT
** *
15907 TGAGAACGAAGAGGGCATTGAATTCAATGTCGATCCAATATGAGAACCCGGTGTAGATAGATCAA
260 TGAGAACGAAGAGGGCATTGAATTCAATGTCGATCCAATCCGAGAACCCGGTGCAGATAGATCAA
* * * * *
15972 AAATTAGATTTTTTTTTTAATTGGAGTCAGTTCCAAATGAACCATAAGATGGAGGTTTAGACACT
325 AAATTACATTATTTTTTAAATCGGAGTCAGTTCCAAATGAACCATAAGATGGAGGTTTAGACAGT
* * * * * * *
16037 GGAAGTTCGGACGAAGATGCCGAAGAAAATTCACTATTTAATGTATACTTGTTGGAAATATAATC
390 GGAAGTCCGAATGAAGATGCCGAAGAAAATCCACTATTCAAGGTGTACTTGTTGGAAATATAATC
* * * * * * *
16102 TGCTGCAAAATACGTCTGTTAGCACTACCTGAGAAAGATCAAGAATTAAATATAAAATTAGAAA-
455 TACTGCAAAACAAGTATGTTAGCACTGCCTGGGAAAGATCAAGAATTAAATATAAAATCAGAAAT
* * *
16166 TTCTTGTGCCATGGTAAATCTTCTACCTTAAAAACGAATTCACCCTGATTGGTGTAATCGCGTAG
520 TTC-TGTGCCATGGTAAATCTACTGCCTTAAAAACGAATTCACCCTGATCGGTGTAATCGCGTAG
**
16231 TGGACGTCATCCCTCAAGTTTAACACAG-CTCTTTGATATTCGTACACCCGAATATGGAAGATGG
584 TGGACGTTGTCCCTCAAGTTTAACACAGTC-CTTTGATATTCGTACACCCGAATATGGAAGATGG
* * *
16295 AACTCAATTGGTACTGCTCTTCTTGAGAAATCACAGTAGGAACAATTCCCAGGAAAACTTGGAGG
648 AACTCAATTGGTGCTGCTCTTCTTGAGAAATCACAGTAGGAACAATTCCCAAGAAAGCTTGGAGG
16360 G
713 G
16361 G
1 G
16362 TTACAGTCAG
Statistics
Matches: 1258, Mismatches: 150, Indels: 29
0.88 0.10 0.02
Matches are distributed among these distances:
697 6 0.00
698 493 0.39
703 1 0.00
707 1 0.00
709 1 0.00
710 1 0.00
711 2 0.00
714 3 0.00
715 746 0.59
716 4 0.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.29
Consensus pattern (713 bp):
GAACACCGAACAATCGAGGTTTGGTAGTAACACAAAATACTGGACCTTTGTATGACCCTCAGTTG
GTTATTTTGATTTGAACTTCGATCAACCGATGTTTAATGCTGGGAACACTTACAGGGAATGATAT
TAAGTTTTAGCGTTGGCAATCTTCAACAATTGATTTTAGTTGTTTTAACAACTATACAAGAAGTG
ATTATGTACTCCTTATAATGTCCACCAGAAAAGGGACATCCAAACTTGAAGATGTTGGTGGGGTT
GAGAACGAAGAGGGCATTGAATTCAATGTCGATCCAATCCGAGAACCCGGTGCAGATAGATCAAA
AATTACATTATTTTTTAAATCGGAGTCAGTTCCAAATGAACCATAAGATGGAGGTTTAGACAGTG
GAAGTCCGAATGAAGATGCCGAAGAAAATCCACTATTCAAGGTGTACTTGTTGGAAATATAATCT
ACTGCAAAACAAGTATGTTAGCACTGCCTGGGAAAGATCAAGAATTAAATATAAAATCAGAAATT
TCTGTGCCATGGTAAATCTACTGCCTTAAAAACGAATTCACCCTGATCGGTGTAATCGCGTAGTG
GACGTTGTCCCTCAAGTTTAACACAGTCCTTTGATATTCGTACACCCGAATATGGAAGATGGAAC
TCAATTGGTGCTGCTCTTCTTGAGAAATCACAGTAGGAACAATTCCCAAGAAAGCTTGGAGGG
Found at i:23608 original size:31 final size:31
Alignment explanation
Indices: 23570--23720 Score: 197
Period size: 31 Copynumber: 4.9 Consensus size: 31
23560 TTAATATAAC
23570 ATTTGGTACCTAAACTTGACATTTTTTTCTA
1 ATTTGGTACCTAAACTTGACATTTTTTTCTA
23601 ATTTGGTACCTAAACTTGACATTTTTTTCTA
1 ATTTGGTACCTAAACTTGACATTTTTTTCTA
*
23632 ATTTGGTACCTAAACTT----TTTTTTGGTCCA
1 ATTTGGTACCTAAACTTGACATTTTTT--TCTA
*
23661 ATTTGGTA-CTCAAACTTGACA-CTTTTTCTTA
1 ATTTGGTACCT-AAACTTGACATTTTTTTC-TA
23692 ATTTGGTACCTAAACTTGACACTTTTTTT
1 ATTTGGTACCTAAACTTGACA-TTTTTTT
23721 TTTAAGTTGA
Statistics
Matches: 105, Mismatches: 4, Indels: 20
0.81 0.03 0.16
Matches are distributed among these distances:
27 6 0.06
28 2 0.02
29 17 0.16
30 2 0.02
31 67 0.64
32 6 0.06
33 5 0.05
ACGTcount: A:0.25, C:0.17, G:0.11, T:0.48
Consensus pattern (31 bp):
ATTTGGTACCTAAACTTGACATTTTTTTCTA
Found at i:23678 original size:60 final size:59
Alignment explanation
Indices: 23570--23708 Score: 176
Period size: 60 Copynumber: 2.3 Consensus size: 59
23560 TTAATATAAC
* *
23570 ATTTGGTACCTAAACTTGACATTTTTTTCTAATTTGGTACCTAAACTTGACA-TTTTTTTCTA
1 ATTTGGTACCTAAACTT---ATTTTTTTCCAATTTGGTACCTAAACTTGACACTTTTTCT-TA
23632 ATTTGGTACCTAAACTT-TTTTTTGGTCCAATTTGGTA-CTCAAACTTGACACTTTTTCTTA
1 ATTTGGTACCTAAACTTATTTTTT--TCCAATTTGGTACCT-AAACTTGACACTTTTTCTTA
23692 ATTTGGTACCTAAACTT
1 ATTTGGTACCTAAACTT
23709 GACACTTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 10
0.86 0.02 0.12
Matches are distributed among these distances:
58 6 0.08
59 2 0.03
60 40 0.56
61 6 0.08
62 17 0.24
ACGTcount: A:0.25, C:0.17, G:0.11, T:0.47
Consensus pattern (59 bp):
ATTTGGTACCTAAACTTATTTTTTTCCAATTTGGTACCTAAACTTGACACTTTTTCTTA
Found at i:23744 original size:91 final size:91
Alignment explanation
Indices: 23570--23792 Score: 292
Period size: 91 Copynumber: 2.4 Consensus size: 91
23560 TTAATATAAC
* *
23570 ATTTGGTACCTAAACTTGACATTTTTTTCTAATTTGGTACCTAAACTTGACATTTTTTTCTAATT
1 ATTTGGTACCTAAACTTGACACTTTTTTCTAATTTGGTACCTAAACTTGACATTTTTTTCTAAGT
* * *
23635 TGGTACCTAAACTTTTTTTTG-GTCCA
66 TGATACCTAAAC-ATTTTTGGAGTCCA
*
23661 ATTTGGTA-CTCAAACTTGACAC-TTTTTCTTAATTTGGTACCTAAACTTGACACTTTTTTTTTT
1 ATTTGGTACCT-AAACTTGACACTTTTTTC-TAATTTGGTACCTAAACTTGACA--TTTTTTTCT
*
23724 AAGTTGATACTTAAA-ATTTTTGGAGTCCA
62 AAGTTGATACCTAAACATTTTTGGAGTCCA
* *
23753 ATTTGGTACCTGAACTTGACTCTTTTTTCTAATTTGGTAC
1 ATTTGGTACCTAAACTTGACACTTTTTTCTAATTTGGTAC
23793 TTATTCTTTT
Statistics
Matches: 116, Mismatches: 9, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
90 8 0.07
91 47 0.41
92 33 0.28
93 28 0.24
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.47
Consensus pattern (91 bp):
ATTTGGTACCTAAACTTGACACTTTTTTCTAATTTGGTACCTAAACTTGACATTTTTTTCTAAGT
TGATACCTAAACATTTTTGGAGTCCA
Found at i:24060 original size:60 final size:60
Alignment explanation
Indices: 23951--24136 Score: 232
Period size: 60 Copynumber: 3.1 Consensus size: 60
23941 ATTTAGGTAT
* * * * * *
23951 CAAATTGAATCTAAAAAAAAGCTTAGGTACCAAATT-AGGAAAAGATGTCAAGTTTAGGTAC
1 CAAATTGAGTCT-AAAAAAAGTTTAAGTACCAAATTAAGAAAAAG-TGTCAAGTTCAAGTAC
*
24012 CAAATTGAGTCTAAAAAAAGTTTAAGTACCAAATTAAGAAAAAGTGTCAAGTTCAAGTAT
1 CAAATTGAGTCTAAAAAAAGTTTAAGTACCAAATTAAGAAAAAGTGTCAAGTTCAAGTAC
** * *
24072 CAAATT-AGGTAAAAAAAAAGTTTAAGTATCAAATTAAGAAAAACTGTCAAGTTCAAGTAC
1 CAAATTGA-GTCTAAAAAAAGTTTAAGTACCAAATTAAGAAAAAGTGTCAAGTTCAAGTAC
24132 CAAAT
1 CAAAT
24137 GTTACATTAA
Statistics
Matches: 111, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
59 1 0.01
60 92 0.83
61 18 0.16
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.25
Consensus pattern (60 bp):
CAAATTGAGTCTAAAAAAAGTTTAAGTACCAAATTAAGAAAAAGTGTCAAGTTCAAGTAC
Found at i:24070 original size:31 final size:30
Alignment explanation
Indices: 23977--24136 Score: 116
Period size: 31 Copynumber: 5.3 Consensus size: 30
23967 AAAAGCTTAG
* * *
23977 GTACCAAATTAGGAAAAGATGTCAAGTTTAG
1 GTACCAAATTAAGAAAA-ATGTCAAGTTCAA
* *
24008 GTACCAAATTGAGTCTAAAAA----AAGTTTAA
1 GTACCAAATTAAG---AAAAATGTCAAGTTCAA
24037 GTACCAAATTAAGAAAAAGTGTCAAGTTCAA
1 GTACCAAATTAAGAAAAA-TGTCAAGTTCAA
* * ** *
24068 GTATCAAATTAGGTAAAAA--AAAAGTTTAA
1 GTACCAAATTAAG-AAAAATGTCAAGTTCAA
*
24097 GTATCAAATTAAGAAAAACTGTCAAGTTCAA
1 GTACCAAATTAAGAAAAA-TGTCAAGTTCAA
24128 GTACCAAAT
1 GTACCAAAT
24137 GTTACATTAA
Statistics
Matches: 102, Mismatches: 15, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
26 5 0.05
28 5 0.05
29 38 0.37
31 44 0.43
32 5 0.05
33 1 0.01
34 4 0.04
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.26
Consensus pattern (30 bp):
GTACCAAATTAAGAAAAATGTCAAGTTCAA
Found at i:24101 original size:29 final size:28
Alignment explanation
Indices: 24024--24114 Score: 101
Period size: 29 Copynumber: 3.1 Consensus size: 28
24014 AATTGAGTCT
*
24024 AAAAAAAGTTTAAGTACCAAATTAAGAA
1 AAAAAAAGTTTAAGTATCAAATTAAGAA
** * *
24052 AAAGTGTCAAGTTCAAGTATCAAATTAGGTAA
1 AAA---AAAAGTTTAAGTATCAAATTAAG-AA
24084 AAAAAAAGTTTAAGTATCAAATTAAGAA
1 AAAAAAAGTTTAAGTATCAAATTAAGAA
24112 AAA
1 AAA
24115 CTGTCAAGTT
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
28 8 0.16
29 19 0.38
31 18 0.36
32 5 0.10
ACGTcount: A:0.56, C:0.07, G:0.13, T:0.24
Consensus pattern (28 bp):
AAAAAAAGTTTAAGTATCAAATTAAGAA
Found at i:24289 original size:48 final size:48
Alignment explanation
Indices: 24218--24314 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
24208 TGACCGTTGG
24218 GGGAAAGCATTTCTAGCTAGAGATATTTTCAACTTATGTGGCAAAAAC
1 GGGAAAGCATTTCTAGCTAGAGATATTTTCAACTTATGTGGCAAAAAC
*
24266 GGGAAAGCATTTCTAGCTGGAGATATTTTCAACTTATGTGGCAAAAAC
1 GGGAAAGCATTTCTAGCTAGAGATATTTTCAACTTATGTGGCAAAAAC
24314 G
1 G
24315 CTTCTAACTA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (48 bp):
GGGAAAGCATTTCTAGCTAGAGATATTTTCAACTTATGTGGCAAAAAC
Found at i:24684 original size:9 final size:9
Alignment explanation
Indices: 24672--24762 Score: 60
Period size: 9 Copynumber: 9.9 Consensus size: 9
24662 AGAAAAATCA
24672 ATAAAATTT
1 ATAAAATTT
*
24681 ATAAAAATT
1 ATAAAATTT
**
24690 ATTAATTTTT
1 A-TAAAATTT
24700 AATAAAA--T
1 -ATAAAATTT
**
24708 ATAAAATAAG
1 ATAAAAT-TT
*
24718 AAAAAATTT
1 ATAAAATTT
*
24727 ATAAAAATT
1 ATAAAATTT
*
24736 ATAAAAATT
1 ATAAAATTT
24745 ATAAAATTTT
1 ATAAAA-TTT
24755 ATAAAATT
1 ATAAAATT
24763 GTAAGAAAAT
Statistics
Matches: 63, Mismatches: 13, Indels: 12
0.72 0.15 0.14
Matches are distributed among these distances:
7 6 0.10
8 1 0.02
9 33 0.52
10 22 0.35
11 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (9 bp):
ATAAAATTT
Found at i:24741 original size:19 final size:19
Alignment explanation
Indices: 24719--24818 Score: 77
Period size: 19 Copynumber: 5.3 Consensus size: 19
24709 TAAAATAAGA
24719 AAAAATTTATAAAAATTAT
1 AAAAATTTATAAAAATTAT
*
24738 AAAAA-TTAT-AAAATTTT
1 AAAAATTTATAAAAATTAT
24755 ATAAAATTGTA-AGAAAATTAT
1 A-AAAATT-TATA-AAAATTAT
*
24776 AAAAAATGTA-AAGAAA-TAT
1 -AAAAATTTATAA-AAATTAT
*
24795 -AAAATTTGTAAAAAATTAT
1 AAAAATTTAT-AAAAATTAT
24814 AAAAA
1 AAAAA
24819 ATATCATACA
Statistics
Matches: 65, Mismatches: 5, Indels: 21
0.71 0.05 0.23
Matches are distributed among these distances:
17 14 0.22
18 11 0.17
19 15 0.23
20 12 0.18
21 12 0.18
22 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (19 bp):
AAAAATTTATAAAAATTAT
Found at i:24819 original size:10 final size:10
Alignment explanation
Indices: 24718--24820 Score: 76
Period size: 10 Copynumber: 10.7 Consensus size: 10
24708 ATAAAATAAG
24718 AAAAAATT-T
1 AAAAAATTAT
24727 ATAAAAATTAT
1 A-AAAAATTAT
24738 -AAAAATTAT
1 AAAAAATTAT
*
24747 --AAAATTTT
1 AAAAAATTAT
* *
24755 ATAAAATTGT
1 AAAAAATTAT
24765 AAGAAAATTAT
1 AA-AAAATTAT
24776 AAAAAATGTA-
1 AAAAAAT-TAT
*
24786 AAGAAA-TAT
1 AAAAAATTAT
* *
24795 -AAAATTTGT
1 AAAAAATTAT
24804 AAAAAATTAT
1 AAAAAATTAT
24814 AAAAAAT
1 AAAAAAT
24821 ATCATACAAA
Statistics
Matches: 75, Mismatches: 10, Indels: 17
0.74 0.10 0.17
Matches are distributed among these distances:
8 12 0.16
9 12 0.16
10 39 0.52
11 12 0.16
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:25111 original size:8 final size:9
Alignment explanation
Indices: 25012--25111 Score: 59
Period size: 9 Copynumber: 11.6 Consensus size: 9
25002 TTTATAATTT
*
25012 TTTTTATGA
1 TTTTTATAA
25021 TTTTTATAAA
1 TTTTTAT-AA
* *
25031 ATTTTACAA
1 TTTTTATAA
25040 TTTTTATAA
1 TTTTTATAA
*
25049 TTTTTATAT
1 TTTTTATAA
25058 TTTATTA-AA
1 TTT-TTATAA
* *
25067 ATTTAATAA
1 TTTTTATAA
*
25076 -TTTTGTAA
1 TTTTTATAA
*
25084 CTTTTAT--
1 TTTTTATAA
*
25091 TTATTATAA
1 TTTTTATAA
25100 -TTTTAT-A
1 TTTTTATAA
25107 TTTTT
1 TTTTT
25112 TTTGCTACAT
Statistics
Matches: 69, Mismatches: 15, Indels: 15
0.70 0.15 0.15
Matches are distributed among these distances:
7 6 0.09
8 17 0.25
9 37 0.54
10 9 0.13
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:25426 original size:87 final size:87
Alignment explanation
Indices: 25212--25528 Score: 331
Period size: 89 Copynumber: 3.6 Consensus size: 87
25202 TTAATAGTTA
* * * * * *
25212 AAGGTCTTTTTGATGCATTTTGACAGTTCAATTACCGAATTGAGTGTAAAAAAA-AAA-A-CTTA
1 AAGGTTTTTTTGATGCATTTTGAAATTTCAAGTACCCAATTAAGTGTAAAAAAAGAAAGAGCTTA
* *
25274 ATTGCTTTTTTTTGAAAAAATTTT
66 ATTGC-TTTTTTTG-AAAAGTTTG
* * * * * * *
25298 AGGGTTTTTTTTATGTATTTTTTAAAGTTT-AAATACTCAATTGAGTGTAAAAAAAGAAAGAGCT
1 AAGGTTTTTTTGATGCA-TTTTGAAA-TTTCAAGTACCCAATTAAGTGTAAAAAAAGAAAGAGCT
25362 TAATTGCTTTTTTTGAAAAGTTTG
64 TAATTGCTTTTTTTGAAAAGTTTG
* * *
25386 AAGGTTTTTTTGATGCATTTTGAAATTTCAAGTACCCAATTAAGTGCAAAAAAAGGGCAAGGGCT
1 AAGGTTTTTTTGATGCATTTTGAAATTTCAAGTACCCAATTAAGTGTAAAAAAA--GAAAGAGCT
*
25451 TAATTGATTTTTTTGAAAAGTTTG
64 TAATTGCTTTTTTTGAAAAGTTTG
* * *
25475 AAGGCTTTTTTT-ATGTATTTTGAAAATTCAAGTACTCAATTAAGTG-AAAAAAAG
1 AAGG-TTTTTTTGATGCATTTTGAAATTTCAAGTACCCAATTAAGTGTAAAAAAAG
25529 GGTTTAATTT
Statistics
Matches: 196, Mismatches: 26, Indels: 18
0.82 0.11 0.08
Matches are distributed among these distances:
86 17 0.09
87 56 0.29
88 33 0.17
89 74 0.38
90 16 0.08
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.40
Consensus pattern (87 bp):
AAGGTTTTTTTGATGCATTTTGAAATTTCAAGTACCCAATTAAGTGTAAAAAAAGAAAGAGCTTA
ATTGCTTTTTTTGAAAAGTTTG
Found at i:35268 original size:61 final size:62
Alignment explanation
Indices: 35168--35310 Score: 166
Period size: 62 Copynumber: 2.3 Consensus size: 62
35158 CTTTTATAAA
* * * * * * *
35168 AAATATATTTAAATTTTTTAGAGTTAGGACTACATTGAC-AAATTTTGTAAATATTGAAGG-T
1 AAATTTATTGAAA-TTTTTAGAATTAGAACTACATTGACAAAATTTTATAAACATTGAGGGCT
35229 CAAATTTATTGAAATTTTTAGAATTAGAACTAACA-TGACAAAATTTTATAAACATTGAGGGCT
1 -AAATTTATTGAAATTTTTAGAATTAGAACT-ACATTGACAAAATTTTATAAACATTGAGGGCT
*
35292 AAATTTATTGAATTTTTTA
1 AAATTTATTGAAATTTTTA
35311 TATTTAAGAT
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
61 19 0.27
62 50 0.71
63 1 0.01
ACGTcount: A:0.41, C:0.06, G:0.13, T:0.41
Consensus pattern (62 bp):
AAATTTATTGAAATTTTTAGAATTAGAACTACATTGACAAAATTTTATAAACATTGAGGGCT
Found at i:46737 original size:18 final size:17
Alignment explanation
Indices: 46702--46749 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 17
46692 CAACAACAAC
*
46702 AATAATAATAATA--AT
1 AATAATAATAATATTGT
46717 AATAATAATAAATATTGT
1 AATAATAAT-AATATTGT
*
46735 AATAATGATAATATT
1 AATAATAATAATATT
46750 AATTAATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 9 0.32
16 4 0.14
17 6 0.21
18 9 0.32
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (17 bp):
AATAATAATAATATTGT
Found at i:46737 original size:27 final size:28
Alignment explanation
Indices: 46707--46777 Score: 94
Period size: 27 Copynumber: 2.6 Consensus size: 28
46697 ACAACAATAA
46707 TAATAATAATAATAATAATAAATATTG-
1 TAATAATAATAATAATAATAAATATTGT
* * *
46734 TAATAATGATAATATTAATTAATATTGT
1 TAATAATAATAATAATAATAAATATTGT
46762 TAATAATAA-AA-AATAA
1 TAATAATAATAATAATAA
46778 AACCGAAAGG
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
26 4 0.11
27 26 0.68
28 8 0.21
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (28 bp):
TAATAATAATAATAATAATAAATATTGT
Found at i:46770 original size:3 final size:3
Alignment explanation
Indices: 46702--46727 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
46692 CAACAACAAC
46702 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
46728 ATATTGTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Done.