Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008740.1 Kokia drynarioides strain JFW-HI SEQ_123422, 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: 120446
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:8997 original size:30 final size:30
Alignment explanation
Indices: 8961--9050 Score: 112
Period size: 30 Copynumber: 3.1 Consensus size: 30
8951 CCAAATAAAC
8961 TAGACTTATTTTATTTTATTTTAATTAGAA
1 TAGACTTATTTTATTTTATTTTAATTAGAA
* *
8991 TAGACTTCTTTCATTTTATTTTAATTAGAA
1 TAGACTTATTTTATTTTATTTTAATTAGAA
* * * *
9021 TAG-GTCA-TCTATTCTATTTTAATTAGAA
1 TAGACTTATTTTATTTTATTTTAATTAGAA
9049 TA
1 TA
9051 AGATTTTTCA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
28 20 0.38
29 1 0.02
30 31 0.60
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (30 bp):
TAGACTTATTTTATTTTATTTTAATTAGAA
Found at i:27348 original size:8 final size:8
Alignment explanation
Indices: 27337--27795 Score: 195
Period size: 8 Copynumber: 57.5 Consensus size: 8
27327 AATTGTTTTT
27337 AATAATTA
1 AATAATTA
* *
27345 AATATTTC
1 AATAATTA
* *
27353 ATTAAATA
1 AATAATTA
* *
27361 ATTAAATA
1 AATAATTA
*
27369 ATTAATTA
1 AATAATTA
* *
27377 AAGAAATA
1 AATAATTA
*
27385 AATTTATTA
1 AA-TAATTA
*
27394 AATAAATA
1 AATAATTA
27402 AATAATTA
1 AATAATTA
27410 AATAATTA
1 AATAATTA
*
27418 AATAGTTA
1 AATAATTA
27426 AATAATTA
1 AATAATTA
27434 AATAATTA
1 AATAATTA
* *
27442 AATATTTGG
1 AATAATT-A
** * *
27451 GTTATTTTT
1 AATA-ATTA
*
27460 AATCATTA
1 AATAATTA
27468 AAT-ATT-
1 AATAATTA
27474 --TAATTA
1 AATAATTA
27480 AATAATTA
1 AATAATTA
27488 AATAATTA
1 AATAATTA
* *
27496 AATATTTT
1 AATAATTA
** ** *
27504 GGTTTTTT
1 AATAATTA
27512 AATAATTA
1 AATAATTA
27520 AATAATTA
1 AATAATTA
27528 AATAATTA
1 AATAATTA
*
27536 AACAATTA
1 AATAATTA
* *
27544 AATATTTGG
1 AATAATT-A
* ** *
27553 ATTGTTTTT
1 AAT-AATTA
27562 AATAATTA
1 AATAATTA
27570 AATAATTA
1 AATAATTA
*
27578 AATAGTTA
1 AATAATTA
27586 AATAATTA
1 AATAATTA
27594 AATAATTA
1 AATAATTA
* *
27602 AATATTTGG
1 AATAATT-A
** * *
27611 GTTATTTTT
1 AATA-ATTA
27620 AATAATTA
1 AATAATTA
27628 AAT-ATT-
1 AATAATTA
27634 --TAATTA
1 AATAATTA
27640 AATAATTA
1 AATAATTA
27648 AATAATTA
1 AATAATTA
*
27656 AATGATTA
1 AATAATTA
* *
27664 AATATTTT
1 AATAATTA
** ** *
27672 GGTTTTTT
1 AATAATTA
27680 AATAATTA
1 AATAATTA
27688 AATAATTA
1 AATAATTA
*
27696 AATATTTGA
1 AATAATT-A
** ** *
27705 GTTGTTTTT
1 AAT-AATTA
27714 AATAATTA
1 AATAATTA
27722 AATAATTA
1 AATAATTA
27730 AATAATTA
1 AATAATTA
*
27738 AATATTTGA
1 AATAATT-A
** * *
27747 GTTATTTTT
1 AATA-ATTA
27756 AATAATTA
1 AATAATTA
*
27764 AAT-ATTT
1 AATAATTA
27771 AATAA-T-
1 AATAATTA
27777 -ATAATTA
1 AATAATTA
27784 AATAATTA
1 AATAATTA
27792 AATA
1 AATA
27796 TTAGAGTTGT
Statistics
Matches: 337, Mismatches: 91, Indels: 46
0.71 0.19 0.10
Matches are distributed among these distances:
4 2 0.01
5 10 0.03
6 1 0.00
7 13 0.04
8 272 0.81
9 24 0.07
10 15 0.04
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.45
Consensus pattern (8 bp):
AATAATTA
Found at i:27587 original size:58 final size:56
Alignment explanation
Indices: 27512--27699 Score: 261
Period size: 58 Copynumber: 3.2 Consensus size: 56
27502 TTGGTTTTTT
*
27512 AATAATTAAATAATTAAATAATTAAACAATTAAATATTTGGATTGTTTTTAATAATTA
1 AATAATTAAATAATTAAATAATTAAATAATTAAATATTTGG-TT-TTTTTAATAATTA
*
27570 AATAATTAAATAGTTAAATAATTAAATAATTAAATATTTGGGTTATTTTTAATAATTAA
1 AATAATTAAATAATTAAATAATTAAATAATTAAATATTT-GGTT-TTTTTAATAATT-A
*
27629 ATATTTAATTAAATAATTAAATAATTAAATGATTAAATATTTTGG-TTTTTTAATAATTA
1 A-A--TAATTAAATAATTAAATAATTAAATAATTAAATA-TTTGGTTTTTTTAATAATTA
27688 AATAATTAAATA
1 AATAATTAAATA
27700 TTTGAGTTGT
Statistics
Matches: 119, Mismatches: 5, Indels: 14
0.86 0.04 0.10
Matches are distributed among these distances:
56 10 0.08
58 52 0.44
59 6 0.05
60 13 0.11
61 1 0.01
62 34 0.29
63 3 0.03
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.45
Consensus pattern (56 bp):
AATAATTAAATAATTAAATAATTAAATAATTAAATATTTGGTTTTTTTAATAATTA
Found at i:27602 original size:160 final size:165
Alignment explanation
Indices: 27402--27699 Score: 525
Period size: 160 Copynumber: 1.8 Consensus size: 165
27392 TAAATAAATA
*
27402 AATAATTAAATAATTAAATAGTTAAATAATTAAATAATTAAATATTTGGGTTATTTTTAATCATT
1 AATAATTAAATAATTAAATAGTTAAATAATTAAATAATTAAATATTTGGGTTATTTTTAATAATT
27467 AAATATTTAATTAAATAATT-A-AA-T-A-ATTAAATATTTTGGTTTTTTAATAATTAAATAATT
66 AAATATTTAATTAAATAATTAATAATTAAGATTAAATATTTTGGTTTTTTAATAATTAAATAATT
27527 AAATAATTAAACAATTAAATATTTGGATTGTTTTT
131 AAATAATTAAACAATTAAATATTTGGATTGTTTTT
27562 AATAATTAAATAATTAAATAGTTAAATAATTAAATAATTAAATATTTGGGTTATTTTTAATAATT
1 AATAATTAAATAATTAAATAGTTAAATAATTAAATAATTAAATATTTGGGTTATTTTTAATAATT
27627 AAATATTTAATTAAATAATTAAATAATTAAATGATTAAATATTTTGGTTTTTTAATAATTAAATA
66 AAATATTTAATTAAATAATT-AATAATT-AA-GATTAAATATTTTGGTTTTTTAATAATTAAATA
27692 ATTAAATA
128 ATTAAATA
27700 TTTGAGTTGT
Statistics
Matches: 129, Mismatches: 1, Indels: 8
0.93 0.01 0.06
Matches are distributed among these distances:
160 84 0.65
162 1 0.01
163 2 0.02
164 1 0.01
166 1 0.01
168 40 0.31
ACGTcount: A:0.48, C:0.01, G:0.05, T:0.46
Consensus pattern (165 bp):
AATAATTAAATAATTAAATAGTTAAATAATTAAATAATTAAATATTTGGGTTATTTTTAATAATT
AAATATTTAATTAAATAATTAATAATTAAGATTAAATATTTTGGTTTTTTAATAATTAAATAATT
AAATAATTAAACAATTAAATATTTGGATTGTTTTT
Found at i:27629 original size:42 final size:42
Alignment explanation
Indices: 27578--27776 Score: 204
Period size: 42 Copynumber: 4.5 Consensus size: 42
27568 TAAATAATTA
* *
27578 AATAGTTAAATAATTAAATAATTAAATATTTGGGTTATTTTT
1 AATAATTAAATAATTAAATAATTAAATATTTGAGTTATTTTT
27620 AATAATTAAATATTTAATTAAATAATTAAATAATTAAATGA-TTAAATATTTT
1 AATAATT-AA-A--TAATTAAATAATTAAAT-ATT---TGAGTT--AT-TTTT
** ** * *
27672 GGTTTTTTAATAATTAAATAATTAAATATTTGAGTTGTTTTT
1 AATAATTAAATAATTAAATAATTAAATATTTGAGTTATTTTT
27714 AATAATTAAATAATTAAATAATTAAATATTTGAGTTATTTTT
1 AATAATTAAATAATTAAATAATTAAATATTTGAGTTATTTTT
*
27756 AATAATTAAAT-ATTTAATAAT
1 AATAATTAAATAATTAAATAAT
27777 ATAATTAAAT
Statistics
Matches: 130, Mismatches: 15, Indels: 25
0.76 0.09 0.15
Matches are distributed among these distances:
41 9 0.07
42 57 0.44
43 3 0.02
44 4 0.03
45 2 0.02
46 17 0.13
47 6 0.05
48 17 0.13
49 2 0.02
50 3 0.02
51 3 0.02
52 7 0.05
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (42 bp):
AATAATTAAATAATTAAATAATTAAATATTTGAGTTATTTTT
Found at i:27695 original size:152 final size:156
Alignment explanation
Indices: 27402--27741 Score: 503
Period size: 160 Copynumber: 2.2 Consensus size: 156
27392 TAAATAAATA
*
27402 AATAATTAAATAATTAAATAGTTAAATAATTAAATAATTAAATATTTGGGTTATTTTTAATCATT
1 AATAATTAAATAATTAAATAGTTAAATAATTAAATAATTAAATATTTGGGTTATTTTTAATAATT
*** *
27467 AAATATTTAATTAAATAATTAAATAATTAAATATTTTGGTTTTTTAATAATTAAATAATTAAATA
66 AAATATTTAATTAAATAATTAAATAATTAAATATTTAAATATTTTAAT-ATT--AT-ATTAAATA
27532 ATTAAACAATTAAATATTTG-GATTGTTTTT
127 ATTAAACAATTAAATATTTGAG-TTGTTTTT
27562 AATAATTAAATAATTAAATAGTTAAATAATTAAATAATTAAATATTTGGGTTATTTTTAATAATT
1 AATAATTAAATAATTAAATAGTTAAATAATTAAATAATTAAATATTTGGGTTATTTTTAATAATT
**
27627 AAATATTTAATTAAATAATTAAATAATTAAATGA-TTAAATATTTTGGT-TT-T-TT-AATAATT
66 AAATATTTAATTAAATAATTAAATAATTAAAT-ATTTAAATATTTTAATATTATATTAAATAATT
*
27687 AAATAATTAAATATTTGAGTTGTTTTT
130 AAACAATTAAATATTTGAGTTGTTTTT
*
27714 AATAATTAAATAATTAAATAATTAAATA
1 AATAATTAAATAATTAAATAGTTAAATA
27742 TTTGAGTTAT
Statistics
Matches: 169, Mismatches: 9, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
152 58 0.34
153 3 0.02
155 1 0.01
158 2 0.01
160 104 0.62
161 1 0.01
ACGTcount: A:0.48, C:0.01, G:0.06, T:0.46
Consensus pattern (156 bp):
AATAATTAAATAATTAAATAGTTAAATAATTAAATAATTAAATATTTGGGTTATTTTTAATAATT
AAATATTTAATTAAATAATTAAATAATTAAATATTTAAATATTTTAATATTATATTAAATAATTA
AACAATTAAATATTTGAGTTGTTTTT
Found at i:27764 original size:26 final size:26
Alignment explanation
Indices: 27730--27821 Score: 105
Period size: 26 Copynumber: 3.5 Consensus size: 26
27720 TAAATAATTA
27730 AATAATTAAATATTTGAGTTATTTTT
1 AATAATTAAATATTTGAGTTATTTTT
* * *
27756 AATAATTAAATATTT-AATAATATAATTA
1 AATAATTAAATATTTGAGT--TAT-TTTT
* *
27784 AATAATTAAATATTAGAGTTGTTTTT
1 AATAATTAAATATTTGAGTTATTTTT
27810 AATAATTAAATA
1 AATAATTAAATA
27822 ATTATTTTGT
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
25 2 0.04
26 29 0.54
27 5 0.09
28 16 0.30
29 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (26 bp):
AATAATTAAATATTTGAGTTATTTTT
Found at i:27773 original size:136 final size:130
Alignment explanation
Indices: 27578--27825 Score: 390
Period size: 136 Copynumber: 1.9 Consensus size: 130
27568 TAAATAATTA
* *
27578 AATAGTTAAATAATTAAATAATTAAATATTTGGGTTATTTTTAATAATTAAATATTTAATTAA-A
1 AATAATTAAATAATTAAATAATTAAATATTTGAGTTATTTTTAATAATTAAATATTTAA-TAATA
* *
27642 TAATTAAATAATTAAATGATTAAATATTTTGGTTTTTTAATAATTAAATAATTAAATATTTGAGT
65 TAATTAAATAATTAAAT-ATT--AGA-GTT-G-TTTTTAATAATTAAATAATTAAATATTTGAGT
27707 TGTTTTT
124 TGTTTTT
27714 AATAATTAAATAATTAAATAATTAAATATTTGAGTTATTTTTAATAATTAAATATTTAATAATAT
1 AATAATTAAATAATTAAATAATTAAATATTTGAGTTATTTTTAATAATTAAATATTTAATAATAT
27779 AATTAAATAATTAAATATTAGAGTTGTTTTTAATAATTAAATAATTA
66 AATTAAATAATTAAATATTAGAGTTGTTTTTAATAATTAAATAATTA
27826 TTTTGTAGAA
Statistics
Matches: 107, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
130 21 0.20
131 1 0.01
132 2 0.02
133 2 0.02
135 6 0.06
136 75 0.70
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (130 bp):
AATAATTAAATAATTAAATAATTAAATATTTGAGTTATTTTTAATAATTAAATATTTAATAATAT
AATTAAATAATTAAATATTAGAGTTGTTTTTAATAATTAAATAATTAAATATTTGAGTTGTTTTT
Found at i:28001 original size:19 final size:20
Alignment explanation
Indices: 27977--28016 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
27967 CATTATGATG
*
27977 ATTTTATTGATATTT-TTTA
1 ATTTTATTAATATTTATTTA
27996 ATTTTATTAATATTTATTTA
1 ATTTTATTAATATTTATTTA
28016 A
1 A
28017 AAATTTGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (20 bp):
ATTTTATTAATATTTATTTA
Found at i:37420 original size:49 final size:49
Alignment explanation
Indices: 37313--37420 Score: 130
Period size: 49 Copynumber: 2.2 Consensus size: 49
37303 GGATTAGAAA
* * * *
37313 TTGAGGATTTTGAGGATTGAGAGAGGATAAAATATCAGAGATTTTTCAAT
1 TTGAGG-TTTGGAGGATTGAGAAAAGAGAAAATATCAGAGATTTTTCAAT
*
37363 TT-AGGGTTTGGAGGATTGAGAAAAGAGAAAATATTAGAGA-TTTTCTAAT
1 TTGA-GGTTTGGAGGATTGAGAAAAGAGAAAATATCAGAGATTTTTC-AAT
37412 TTGAGGTTT
1 TTGAGGTTT
37421 AGGGATTTGA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
48 5 0.10
49 40 0.80
50 5 0.10
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (49 bp):
TTGAGGTTTGGAGGATTGAGAAAAGAGAAAATATCAGAGATTTTTCAAT
Found at i:37650 original size:43 final size:43
Alignment explanation
Indices: 37532--37642 Score: 136
Period size: 42 Copynumber: 2.6 Consensus size: 43
37522 CTATTGCCAT
* * * *
37532 ACTTTTAGCGGCGTTTTTCTCATAAATGCCGTTAATAAC-CTAG
1 ACTTTTTGCGGTGTTTTTCTCATAAATGTCGTTAAT-GCTCTAG
* *
37575 ACTTTTTACGGTG-TTTTCTCATTAATGTCGTTAATGCTCTAG
1 ACTTTTTGCGGTGTTTTTCTCATAAATGTCGTTAATGCTCTAG
*
37617 ATTTTTTGCGGTGTTTTTCTCATAAA
1 ACTTTTTGCGGTGTTTTTCTCATAAA
37643 CATCGTTATT
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
41 1 0.02
42 35 0.61
43 21 0.37
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.45
Consensus pattern (43 bp):
ACTTTTTGCGGTGTTTTTCTCATAAATGTCGTTAATGCTCTAG
Found at i:37682 original size:41 final size:41
Alignment explanation
Indices: 37621--37699 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
37611 CTCTAGATTT
* * *
37621 TTTGCGGTGTTTTTCTCATAAACATCGTTATTGCTTTATCA
1 TTTGCGGCGTTTTTCACATAAACATCGCTATTGCTTTATCA
*
37662 TTTGCGGCGTTTTTCACATAAACGTCGCTATTGCTTTA
1 TTTGCGGCGTTTTTCACATAAACATCGCTATTGCTTTA
37700 CCGCTAGTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.19, C:0.19, G:0.16, T:0.46
Consensus pattern (41 bp):
TTTGCGGCGTTTTTCACATAAACATCGCTATTGCTTTATCA
Found at i:39136 original size:43 final size:43
Alignment explanation
Indices: 39089--39171 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
39079 TTTTTCCACC
* * * *
39089 TTTAACGGCATTTTTCCCGTAAACGCCTCTAATGCTCTTAACG
1 TTTAACGACATTTTTCCCATAAACACCGCTAATGCTCTTAACG
**
39132 TTTAACGATGTTTTTCCCATAAACACCGCTAATGCTCTTA
1 TTTAACGACATTTTTCCCATAAACACCGCTAATGCTCTTA
39172 CCTTTAGTGG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.25, C:0.27, G:0.12, T:0.36
Consensus pattern (43 bp):
TTTAACGACATTTTTCCCATAAACACCGCTAATGCTCTTAACG
Found at i:39198 original size:41 final size:41
Alignment explanation
Indices: 39144--39406 Score: 305
Period size: 41 Copynumber: 6.4 Consensus size: 41
39134 TAACGATGTT
* * *
39144 TTTCC-CATAAACACCGCTAATGCTCTTACCTTTAGTGGCG
1 TTTCCTCATAAACGCCGCTAATGCTCTGACCTTTAGCGGCG
* * * *
39184 TTTTCTTATAAACACCGCTATTGCTCTGACCTTTAGCGGCG
1 TTTCCTCATAAACGCCGCTAATGCTCTGACCTTTAGCGGCG
** * * **
39225 TTTCCTCATAAACGTAGCTAATGCTCTAACCTTTAGAGGAA
1 TTTCCTCATAAACGCCGCTAATGCTCTGACCTTTAGCGGCG
** * *
39266 TTTCCTCATAAACGTAGCTAATGCTCTGACCTTTAACGGTG
1 TTTCCTCATAAACGCCGCTAATGCTCTGACCTTTAGCGGCG
*
39307 TTTCCTCATAAACGCCGCTAATGCTCTGACCTTTAGCGACG
1 TTTCCTCATAAACGCCGCTAATGCTCTGACCTTTAGCGGCG
* * *
39348 TTTCCTCATAAACGCCACTAATGCTCTGATCTTTAGTGGCG
1 TTTCCTCATAAACGCCGCTAATGCTCTGACCTTTAGCGGCG
39389 TTTTTCCT-ATAAACGCCG
1 --TTTCCTCATAAACGCCG
39407 TTAAAAATGC
Statistics
Matches: 190, Mismatches: 30, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
40 4 0.02
41 171 0.90
42 9 0.05
43 6 0.03
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (41 bp):
TTTCCTCATAAACGCCGCTAATGCTCTGACCTTTAGCGGCG
Found at i:40660 original size:21 final size:21
Alignment explanation
Indices: 40634--40677 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
40624 TTCAGTCCGT
40634 TAAGTTCATATGGTTAAATTC
1 TAAGTTCATATGGTTAAATTC
40655 TAAGTTCATATGGTTAAATTC
1 TAAGTTCATATGGTTAAATTC
40676 TA
1 TA
40678 TCTTAAACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (21 bp):
TAAGTTCATATGGTTAAATTC
Found at i:50166 original size:21 final size:21
Alignment explanation
Indices: 50128--50185 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
50118 CTGTGCAGAT
* ** *
50128 TTCTACCGGTACCTGTATTAG
1 TTCTACCGATACAAGTATGAG
*
50149 TTCTACCGATACAAGTATGAT
1 TTCTACCGATACAAGTATGAG
50170 TTCTACC-ACTACAAGT
1 TTCTACCGA-TACAAGT
50186 CATGCAACTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 1 0.03
21 30 0.97
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (21 bp):
TTCTACCGATACAAGTATGAG
Found at i:56780 original size:52 final size:52
Alignment explanation
Indices: 56716--56955 Score: 235
Period size: 51 Copynumber: 4.6 Consensus size: 52
56706 GCTATAAACG
* **
56716 AAAGGGTCCGATGACTAAGTGTCATCGTGAGTAAACAAATCCTTTACGGATT
1 AAAGAGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* *
56768 AAAGGGTTCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGA--
1 AAAGAGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * * *
56818 ACACGAGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATGGATT
1 A-AAGAGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* *
56871 AAA-AGTCCGATGACTCAA-TGTCATCGTAAG-AATATGAATTCCTATACGGA--
1 AAAGAGTCCGATGACT-AAGTGTCATCGTGAGTAA-ATGAA-TCCTTTACGGATT
* *
56921 ACAAGAGGTCCAATGATTATA-TGTCATCGTGAGTA
1 A-AAGA-GTCCGATGACTA-AGTGTCATCGTGAGTA
56956 TTAAATGAAA
Statistics
Matches: 157, Mismatches: 20, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
50 4 0.03
51 71 0.45
52 59 0.38
53 22 0.14
54 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.28
Consensus pattern (52 bp):
AAAGAGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:56919 original size:103 final size:104
Alignment explanation
Indices: 56720--56955 Score: 284
Period size: 103 Copynumber: 2.3 Consensus size: 104
56710 TAAACGAAAG
* * * *
56720 GGTCCGATGACTAAGTGTCATCGTGAGTAAACAAATCCTTTACGGATTAAAGGGTTCGATGACTA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAACAAATCCATGACGGATTAAAGAGTCCGATGACTA
* * *
56785 AGTGTCATCGTGAGTAAATGAATCCTTTACGGAACACGA
66 AGTGTCATCGTAAGTAAATGAATCCTATACGGAACAAGA
* ** *
56824 -GTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATGGATTAAA-AGTCCGATGACTC
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAACAAATCCATGACGGATTAAAGAGTCCGATGACT-
56887 AA-TGTCATCGTAAG-AATATGAATTCCTATACGGAACAAGA
65 AAGTGTCATCGTAAGTAA-ATGAA-TCCTATACGGAACAAGA
* *
56927 GGTCCAATGATTATA-TGTCATCGTGAGTA
1 GGTCCGATGACTA-AGTGTCATCGTGAGTA
56956 TTAAATGAAA
Statistics
Matches: 113, Mismatches: 14, Indels: 10
0.82 0.10 0.07
Matches are distributed among these distances:
101 2 0.02
102 26 0.23
103 61 0.54
104 23 0.20
105 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (104 bp):
GGTCCGATGACTAAGTGTCATCGTGAGTAAACAAATCCATGACGGATTAAAGAGTCCGATGACTA
AGTGTCATCGTAAGTAAATGAATCCTATACGGAACAAGA
Found at i:61738 original size:27 final size:28
Alignment explanation
Indices: 61701--61772 Score: 80
Period size: 27 Copynumber: 2.6 Consensus size: 28
61691 TCATGATTGG
61701 TTTATTGATTTATTTC-TTTTGTTTATTT-
1 TTTATT-ATTTATTTCTTTTTG-TTATTTA
*
61729 TTCT-TTATTTGTTTCTTTTTGTTATTTA
1 TT-TATTATTTATTTCTTTTTGTTATTTA
61757 TTTATT-TTTATTTCTT
1 TTTATTATTTATTTCTT
61773 CAACTTATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
27 24 0.63
28 13 0.34
29 1 0.03
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.76
Consensus pattern (28 bp):
TTTATTATTTATTTCTTTTTGTTATTTA
Found at i:61753 original size:17 final size:18
Alignment explanation
Indices: 61718--61765 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
61708 ATTTATTTCT
*
61718 TTTGTTTATTTTTCTTTA
1 TTTGTTTATTTTTCGTTA
*
61736 TTTGTTTCTTTTT-GTTA
1 TTTGTTTATTTTTCGTTA
*
61753 TTTATTTATTTTT
1 TTTGTTTATTTTT
61766 ATTTCTTCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
17 14 0.54
18 12 0.46
ACGTcount: A:0.10, C:0.04, G:0.06, T:0.79
Consensus pattern (18 bp):
TTTGTTTATTTTTCGTTA
Found at i:62802 original size:12 final size:12
Alignment explanation
Indices: 62785--62831 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
62775 ATCAAAATAA
62785 AAAAACAAAATT
1 AAAAACAAAATT
*
62797 AAAAACAAGAAAT
1 AAAAACAA-AATT
*
62810 AAAATGCAAAATT
1 AAAA-ACAAAATT
62823 -AAAACAAAA
1 AAAAACAAAA
62832 AAATTAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
11 5 0.17
12 11 0.38
13 10 0.34
14 3 0.10
ACGTcount: A:0.74, C:0.09, G:0.04, T:0.13
Consensus pattern (12 bp):
AAAAACAAAATT
Found at i:71220 original size:18 final size:18
Alignment explanation
Indices: 71197--71234 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
71187 CTACCCCACC
71197 ATAATTTTCCTAGGCATG
1 ATAATTTTCCTAGGCATG
*
71215 ATAATTTTCCTAGGCTTG
1 ATAATTTTCCTAGGCATG
71233 AT
1 AT
71235 CCTCTTGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (18 bp):
ATAATTTTCCTAGGCATG
Found at i:74719 original size:42 final size:41
Alignment explanation
Indices: 74629--74743 Score: 126
Period size: 42 Copynumber: 2.7 Consensus size: 41
74619 AATCAATTTT
*
74629 ATGCTC-TATCGAGTCATAAGTCTTCCTTTAATCATAATCTC
1 ATGCTCAT-TCGAGTCATGAGTCTTCCTTTAATCATAATCTC
* * *
74670 ATTCTCATCTCGAGACATGAGTCTTCCTTTAATCAT-ATTTCC
1 ATGCTCAT-TCGAGTCATGAGTCTTCCTTTAATCATAATCT-C
*
74712 ATGCTCATTCCGAGTCAAGAGTCTTCCATTTA
1 ATGCTCATT-CGAGTCATGAGTCTTCC-TTTA
74744 TACAATTTTT
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
41 9 0.15
42 49 0.79
43 4 0.06
ACGTcount: A:0.25, C:0.25, G:0.11, T:0.38
Consensus pattern (41 bp):
ATGCTCATTCGAGTCATGAGTCTTCCTTTAATCATAATCTC
Found at i:76296 original size:14 final size:14
Alignment explanation
Indices: 76279--76305 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
76269 ATTACAAGAA
76279 TAGAATTTTTATTC
1 TAGAATTTTTATTC
76293 TAGAATTTTTATT
1 TAGAATTTTTATT
76306 AATCAAGCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.04, G:0.07, T:0.59
Consensus pattern (14 bp):
TAGAATTTTTATTC
Found at i:77937 original size:21 final size:21
Alignment explanation
Indices: 77899--77942 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
77889 TTCAAACAAA
77899 AACTTGTAACTTTTTTTTCTC
1 AACTTGTAACTTTTTTTTCTC
* *
77920 AACTT-TAAGTTTTATTTTTTC
1 AACTTGTAACTTTT-TTTTCTC
77941 AA
1 AA
77943 AAAAAGTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.25, C:0.14, G:0.05, T:0.57
Consensus pattern (21 bp):
AACTTGTAACTTTTTTTTCTC
Found at i:83402 original size:27 final size:27
Alignment explanation
Indices: 83344--83403 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
83334 GGCCAAAGGC
* *
83344 CAAAATGTTTACAAAAGATAGGAATGA
1 CAAACTGTTTACAAAAGAAAGGAATGA
*
83371 CAAACTGTTTACAAAATAAAGGAATGA
1 CAAACTGTTTACAAAAGAAAGGAATGA
83398 CAAACT
1 CAAACT
83404 ATTGCCAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.52, C:0.12, G:0.15, T:0.22
Consensus pattern (27 bp):
CAAACTGTTTACAAAAGAAAGGAATGA
Found at i:84432 original size:11 final size:11
Alignment explanation
Indices: 84416--84453 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
84406 AACAACATCC
84416 AACATAAAGCT
1 AACATAAAGCT
84427 AACATAAAAGCT
1 AACAT-AAAGCT
*
84439 AACATAAAGCC
1 AACATAAAGCT
84450 AACA
1 AACA
84454 ACAAATAGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.58, C:0.21, G:0.08, T:0.13
Consensus pattern (11 bp):
AACATAAAGCT
Found at i:84438 original size:12 final size:12
Alignment explanation
Indices: 84416--84446 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
84406 AACAACATCC
84416 AACAT-AAAGCT
1 AACATAAAAGCT
84427 AACATAAAAGCT
1 AACATAAAAGCT
84439 AACATAAA
1 AACATAAA
84447 GCCAACAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.61, C:0.16, G:0.06, T:0.16
Consensus pattern (12 bp):
AACATAAAAGCT
Found at i:86335 original size:33 final size:33
Alignment explanation
Indices: 86298--86365 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
86288 ACAAATTACT
*
86298 CATCACTATCAGACCACAAACAAACATTTAATA
1 CATCACTATCAAACCACAAACAAACATTTAATA
*
86331 CATCACTATCAAACCAGAAACAAACATTTAATA
1 CATCACTATCAAACCACAAACAAACATTTAATA
86364 CA
1 CA
86366 ACAAATGCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.50, C:0.26, G:0.03, T:0.21
Consensus pattern (33 bp):
CATCACTATCAAACCACAAACAAACATTTAATA
Found at i:86377 original size:33 final size:33
Alignment explanation
Indices: 86305--86377 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
86295 ACTCATCACT
* * *
86305 ATCAGACCACAAACAAACATTTAATACATCACT
1 ATCAAACCACAAACAAACATTTAATACAACACA
*
86338 ATCAAACCAGAAACAAACATTTAATACAACA-A
1 ATCAAACCACAAACAAACATTTAATACAACACA
86370 ATGCAAAC
1 AT-CAAAC
86378 ACTTTAACCA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 2 0.06
33 33 0.94
ACGTcount: A:0.53, C:0.25, G:0.04, T:0.18
Consensus pattern (33 bp):
ATCAAACCACAAACAAACATTTAATACAACACA
Found at i:86578 original size:17 final size:17
Alignment explanation
Indices: 86558--86594 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
86548 TATAGAGCAT
*
86558 ATATATCTGCATAAACA
1 ATATATCTACATAAACA
86575 ATATATCTACATAAACA
1 ATATATCTACATAAACA
86592 ATA
1 ATA
86595 GGCAATTGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.51, C:0.16, G:0.03, T:0.30
Consensus pattern (17 bp):
ATATATCTACATAAACA
Found at i:86977 original size:47 final size:47
Alignment explanation
Indices: 86870--86987 Score: 166
Period size: 47 Copynumber: 2.5 Consensus size: 47
86860 TTGCAATCAG
* * *
86870 AATCCAAATCAAAATCGAAAAAACCCTAAATAAAAAATCAAAATAAA
1 AATCCAAATCAAATTTGAATAAACCCTAAATAAAAAATCAAAATAAA
* *
86917 AATCCAAATCAAATTTGAATAAACCCTAAATTAAAAATCACAATAAA
1 AATCCAAATCAAATTTGAATAAACCCTAAATAAAAAATCAAAATAAA
*
86964 TAT-CAATATCAAATTTGAATAAAC
1 AATCCAA-ATCAAATTTGAATAAAC
86988 ATAAGATAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
46 3 0.05
47 61 0.95
ACGTcount: A:0.59, C:0.16, G:0.03, T:0.22
Consensus pattern (47 bp):
AATCCAAATCAAATTTGAATAAACCCTAAATAAAAAATCAAAATAAA
Found at i:104525 original size:16 final size:16
Alignment explanation
Indices: 104504--104534 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
104494 ATAATGTGAA
104504 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
104520 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
104535 GGATCCATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:105579 original size:37 final size:37
Alignment explanation
Indices: 105499--105579 Score: 110
Period size: 37 Copynumber: 2.2 Consensus size: 37
105489 ATATTCCTGT
* * *
105499 AGCGATAGTTTTGGGTGAAATCTGGAAGTGCTCATGC
1 AGCGACAGTTTTGGGCGAAATCTAGAAGTGCTCATGC
*
105536 -GACGACAGTTTTGGGCGTAATCTAGAAGTGCTCATGC
1 AG-CGACAGTTTTGGGCGAAATCTAGAAGTGCTCATGC
105573 AGCGACA
1 AGCGACA
105580 TTAGTAGTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
36 1 0.03
37 36 0.95
38 1 0.03
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (37 bp):
AGCGACAGTTTTGGGCGAAATCTAGAAGTGCTCATGC
Found at i:108804 original size:16 final size:16
Alignment explanation
Indices: 108783--108813 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
108773 ATAGTGTGAA
108783 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
108799 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
108814 GGATCCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:109798 original size:37 final size:37
Alignment explanation
Indices: 109757--109835 Score: 131
Period size: 37 Copynumber: 2.1 Consensus size: 37
109747 CCAAAAATAT
*
109757 TCATGTGGCGACAGTTTTGGGTGCAATCTAGAAGTGC
1 TCATGTGGCGACAGTTTTGGGCGCAATCTAGAAGTGC
* *
109794 TCATGTGGTGATAGTTTTGGGCGCAATCTAGAAGTGC
1 TCATGTGGCGACAGTTTTGGGCGCAATCTAGAAGTGC
109831 TCATG
1 TCATG
109836 CAATGACATT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.22, C:0.15, G:0.32, T:0.32
Consensus pattern (37 bp):
TCATGTGGCGACAGTTTTGGGCGCAATCTAGAAGTGC
Found at i:118601 original size:12 final size:12
Alignment explanation
Indices: 118584--118619 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
118574 ATCGAATTTT
*
118584 ACACATGCACAC
1 ACACATACACAC
118596 ACACATACACAC
1 ACACATACACAC
*
118608 ACACACACACAC
1 ACACATACACAC
118620 CTATATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.47, C:0.44, G:0.03, T:0.06
Consensus pattern (12 bp):
ACACATACACAC
Found at i:118838 original size:22 final size:23
Alignment explanation
Indices: 118813--118886 Score: 93
Period size: 22 Copynumber: 3.3 Consensus size: 23
118803 TGGACAAGCC
118813 ACCACATAATTGTCGATAAAC-G
1 ACCACATAATTGTCGATAAACTG
118835 ACCACATAATTG-CAGATAAACTG
1 ACCACATAATTGTC-GATAAACTG
* *
118858 -CCACATAATTGTAGATAAAGTG
1 ACCACATAATTGTCGATAAACTG
118880 -CCACATA
1 ACCACATA
118887 TCTTCCTCCT
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
21 1 0.02
22 45 0.96
23 1 0.02
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.23
Consensus pattern (23 bp):
ACCACATAATTGTCGATAAACTG
Done.