Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013786.1 Kokia drynarioides strain JFW-HI SEQ_128814, 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: 120827
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 4 characters in sequence are not A, C, G, or T
Found at i:4993 original size:17 final size:17
Alignment explanation
Indices: 4971--5009 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
4961 AGGTGGAGAA
* *
4971 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
4988 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
5005 CTTGT
1 CTTGT
5010 CAATGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:7624 original size:3 final size:3
Alignment explanation
Indices: 7616--7667 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
7606 CTTTTATTTA
* * *
7616 ATT ATT ATT ATT ATT ATT ATT GTT ATT ACT ATT ATAT ACT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT
7662 ATT ATT
1 ATT ATT
7668 TAAAACAGTG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 40 0.95
4 2 0.05
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:12320 original size:14 final size:14
Alignment explanation
Indices: 12303--12340 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
12293 TTGCTGTTTT
12303 TTGTTGTTTTGATG
1 TTGTTGTTTTGATG
12317 TTGTTGTTTTGATG
1 TTGTTGTTTTGATG
12331 TTGTTGTTTT
1 TTGTTGTTTT
12341 TACTGTTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.05, C:0.00, G:0.26, T:0.68
Consensus pattern (14 bp):
TTGTTGTTTTGATG
Found at i:12326 original size:22 final size:22
Alignment explanation
Indices: 12281--12332 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
12271 AAAAATTATA
*
12281 TTGTTGTTTTGGTTGCTGTTTT
1 TTGTTGTTTTGGATGCTGTTTT
*
12303 TTGTTGTTTT-GATGTTGTTGTT
1 TTGTTGTTTTGGATGCTGTT-TT
*
12325 TTGATGTT
1 TTGTTGTT
12333 GTTGTTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 7 0.27
22 19 0.73
ACGTcount: A:0.04, C:0.02, G:0.27, T:0.67
Consensus pattern (22 bp):
TTGTTGTTTTGGATGCTGTTTT
Found at i:21356 original size:15 final size:15
Alignment explanation
Indices: 21338--21369 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
21328 CTAAATTCTT
21338 GAAAATAAAATTATA
1 GAAAATAAAATTATA
*
21353 GAAACTAAAATTATA
1 GAAAATAAAATTATA
21368 GA
1 GA
21370 CTTATGACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.09, T:0.25
Consensus pattern (15 bp):
GAAAATAAAATTATA
Found at i:21441 original size:19 final size:19
Alignment explanation
Indices: 21417--21453 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
21407 TATTATTACT
*
21417 ATATTTATAATTATAATAA
1 ATATTTATAATTAAAATAA
*
21436 ATATTTATTATTAAAATA
1 ATATTTATAATTAAAATA
21454 TTAATATTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATTTATAATTAAAATAA
Found at i:21454 original size:15 final size:15
Alignment explanation
Indices: 21399--21455 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
21389 TTTATACTAC
21399 AAAATATTTATTATT
1 AAAATATTTATTATT
** *
21414 ACTATATTTATAATTATA
1 AAAATA-TT-T-ATTATT
21432 ATAAATATTTATTATT
1 A-AAATATTTATTATT
21448 AAAATATT
1 AAAATATT
21456 AATATTGAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
15 11 0.34
16 8 0.25
17 2 0.06
18 8 0.25
19 3 0.09
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (15 bp):
AAAATATTTATTATT
Found at i:21519 original size:16 final size:16
Alignment explanation
Indices: 21488--21524 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
21478 ATGTGAAGAA
21488 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
21504 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
21520 TATTA
1 TATTA
21525 AAAAATTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:21581 original size:16 final size:16
Alignment explanation
Indices: 21535--21584 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
21525 AAAAATTGAA
21535 ATATTAAATAATTTATT
1 ATATT-AATAATTTATT
**
21552 A-A--AATAATAAATT
1 ATATTAATAATTTATT
21565 ATATTAATAATTTATT
1 ATATTAATAATTTATT
21581 ATAT
1 ATAT
21585 GATTAAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
13 10 0.38
14 1 0.04
16 14 0.54
17 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATTAATAATTTATT
Found at i:21594 original size:26 final size:27
Alignment explanation
Indices: 21519--21581 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 27
21509 TTAAAATTTA
*
21519 TTATTAAAA-AATTGAAATATTAAATAAT
1 TTATTAAAATAA-TAAAATATT-AATAAT
21547 TTATTAAAATAATAAATTATATTAATAAT
1 TTATTAAAATAATAAA--ATATTAATAAT
21576 TTATTA
1 TTATTA
21582 TATGATTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
28 12 0.39
29 14 0.45
30 5 0.16
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (27 bp):
TTATTAAAATAATAAAATATTAATAAT
Found at i:21601 original size:26 final size:26
Alignment explanation
Indices: 21519--21602 Score: 73
Period size: 28 Copynumber: 3.0 Consensus size: 26
21509 TTAAAATTTA
21519 TTATTAAAA-AATTGAAATATTAAATAAT
1 TTATTAAAATAA-T-AAATA-TAAATAAT
21547 TTATTAAAATAATAAATTATATTAATAAT
1 TTATTAAAATAATAAA-TATA--AATAAT
* *
21576 TTATT-ATATGATTAAATATAAATAAT
1 TTATTAAAAT-AATAAATATAAATAAT
21602 T
1 T
21603 AAATAGGTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
26 7 0.14
27 5 0.10
28 19 0.39
29 18 0.37
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (26 bp):
TTATTAAAATAATAAATATAAATAAT
Found at i:21874 original size:19 final size:19
Alignment explanation
Indices: 21850--21888 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
21840 GATCTCTAAG
21850 TTATTTTTTATTAATCAAA
1 TTATTTTTTATTAATCAAA
*
21869 TTATTTTTTGTTAATCAAA
1 TTATTTTTTATTAATCAAA
21888 T
1 T
21889 ATAAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (19 bp):
TTATTTTTTATTAATCAAA
Found at i:22037 original size:2 final size:2
Alignment explanation
Indices: 22030--22079 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
22020 AACCGTTCTA
22030 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22072 AT AT AT AT
1 AT AT AT AT
22080 TTTACCTTTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22690 original size:17 final size:18
Alignment explanation
Indices: 22649--22692 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
22639 ATAGTAATTT
*
22649 TTAAAAGTATTTTTGACA
1 TTAAAAATATTTTTGACA
22667 -TATAAAATATTTTTGA-A
1 TTA-AAAATATTTTTGACA
22684 TTAAAAATA
1 TTAAAAATA
22693 ATGCTAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (18 bp):
TTAAAAATATTTTTGACA
Found at i:27509 original size:15 final size:15
Alignment explanation
Indices: 27489--27545 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
27479 GTTTGATAAA
27489 CTGAAAAATTAAGTT
1 CTGAAAAATTAAGTT
*
27504 CTGAAAAAATAAGTGT
1 CTGAAAAATTAAGT-T
*
27520 -TGAACAAA-TAAGTA
1 CTGAA-AAATTAAGTT
27534 CTGAAAAATTAA
1 CTGAAAAATTAA
27546 TTGTTAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 3 0.08
15 29 0.81
16 4 0.11
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (15 bp):
CTGAAAAATTAAGTT
Found at i:27532 original size:30 final size:30
Alignment explanation
Indices: 27490--27550 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
27480 TTTGATAAAC
*
27490 TGAAAAATTAAGTTCTGAAAAAATAAGTGT
1 TGAAAAATTAAGTACTGAAAAAATAAGTGT
* *
27520 TGAACAAA-TAAGTACTGAAAAATTAATTGT
1 TGAA-AAATTAAGTACTGAAAAAATAAGTGT
27550 T
1 T
27551 AAATTTAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 24 0.89
31 3 0.11
ACGTcount: A:0.49, C:0.05, G:0.15, T:0.31
Consensus pattern (30 bp):
TGAAAAATTAAGTACTGAAAAAATAAGTGT
Found at i:33327 original size:22 final size:23
Alignment explanation
Indices: 33302--33345 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
33292 ATTATAACAA
*
33302 ATTT-AAAAATAAGGGAAAATAC
1 ATTTAAAAAATAAGGAAAAATAC
33324 ATTTAAAAAATAAGGAAAAATA
1 ATTTAAAAAATAAGGAAAAATA
33346 TTTGATATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.64, C:0.02, G:0.11, T:0.23
Consensus pattern (23 bp):
ATTTAAAAAATAAGGAAAAATAC
Found at i:42874 original size:26 final size:26
Alignment explanation
Indices: 42845--43070 Score: 167
Period size: 26 Copynumber: 8.7 Consensus size: 26
42835 ATCGTAAACA
*
42845 AATATATAGCAAGCCTT-GAGCTGGTG
1 AATATATAGC-AGGCTTCGAGCTGGTG
* **
42871 AATATATAGCAAGCCTT-GAGCCAGTG
1 AATATATAGC-AGGCTTCGAGCTGGTG
* * *
42897 AATAAATAGCAGGCTTCGAGCTGATA
1 AATATATAGCAGGCTTCGAGCTGGTG
* * *
42923 AATAAATAGCAGGCTTCGACCTGATG
1 AATATATAGCAGGCTTCGAGCTGGTG
* * *
42949 AATA-ATTAACAGGCTTCGAGCCGATG
1 AATATA-TAGCAGGCTTCGAGCTGGTG
**
42975 AATATATAATAGGCCTT-GAGTCT-GTG
1 AATATATAGCAGG-CTTCGAG-CTGGTG
* *
43001 AATA-ATTAGAAGACTTCGAGCTGGTG
1 AATATA-TAGCAGGCTTCGAGCTGGTG
* *
43027 AATAAATAGCAGGCTTCAAGCTGGTG
1 AATATATAGCAGGCTTCGAGCTGGTG
* *
43053 ATTATATAACAGGCTTCG
1 AATATATAGCAGGCTTCG
43071 TGCCGGTGTA
Statistics
Matches: 165, Mismatches: 26, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
25 12 0.07
26 147 0.89
27 6 0.04
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (26 bp):
AATATATAGCAGGCTTCGAGCTGGTG
Found at i:43063 original size:104 final size:104
Alignment explanation
Indices: 42869--43075 Score: 263
Period size: 104 Copynumber: 2.0 Consensus size: 104
42859 CTTGAGCTGG
* * *
42869 TGAATATATAGCAAGCCTTGAGCCAGTGAATAAATAGCAGGCTTCGAGCTGATAAATAAATAGCA
1 TGAATATATAACAAGCCTTGAGCCAGTGAATAAATAGAAGACTTCGAGCTGATAAATAAATAGCA
*
42934 GGCTTCGACCTGATGAATAATTAACAGGCTTCGAGCCGA
66 GGCTTCAACCTGATGAATAATTAACAGGCTTCGAGCCGA
* * * * * * *
42973 TGAATATATAATAGGCCTTGAGTCTGTGAATAATTAGAAGACTTCGAGCTGGTGAATAAATAGCA
1 TGAATATATAACAAGCCTTGAGCCAGTGAATAAATAGAAGACTTCGAGCTGATAAATAAATAGCA
* * * *
43038 GGCTTCAAGCTGGTG-ATTATATAACAGGCTTCGTGCCG
66 GGCTTCAACCTGATGAATAAT-TAACAGGCTTCGAGCCG
43076 GTGTATGGTT
Statistics
Matches: 87, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
103 4 0.05
104 83 0.95
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.26
Consensus pattern (104 bp):
TGAATATATAACAAGCCTTGAGCCAGTGAATAAATAGAAGACTTCGAGCTGATAAATAAATAGCA
GGCTTCAACCTGATGAATAATTAACAGGCTTCGAGCCGA
Found at i:46635 original size:18 final size:18
Alignment explanation
Indices: 46604--46656 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
46594 TTAAATTTTC
*
46604 AAAAATATATAATGTAGAA
1 AAAAAT-TAAAATGTAGAA
*
46623 AAAAATTAAAATGTTTCGAA
1 AAAAATTAAAATG--TAGAA
46643 AAAAA-TAAAATGTA
1 AAAAATTAAAATGTA
46657 TGACAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 1 0.03
18 6 0.21
19 13 0.45
20 9 0.31
ACGTcount: A:0.62, C:0.02, G:0.09, T:0.26
Consensus pattern (18 bp):
AAAAATTAAAATGTAGAA
Found at i:46752 original size:19 final size:20
Alignment explanation
Indices: 46730--46771 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
46720 TTAATACCTA
*
46730 TTAATTTTTATA-AAATTTT
1 TTAATTTATATATAAATTTT
*
46749 TTAATTTATATATATATTTT
1 TTAATTTATATATAAATTTT
46769 TTA
1 TTA
46772 TTTCTTAAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTAATTTATATATAAATTTT
Found at i:48148 original size:22 final size:21
Alignment explanation
Indices: 48089--48149 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
48079 AAGAAATATA
* *
48089 TAAAAATACAT-AAATAACTT
1 TAAAAATATATAAAATAAATT
48109 TAAAAA-ATATAATAATAAATT
1 TAAAAATATATAA-AATAAATT
48130 TAAAAATATATAAACATAAA
1 TAAAAATATATAAA-ATAAA
48150 AAAAATCAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 3 0.09
20 7 0.20
21 14 0.40
22 11 0.31
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (21 bp):
TAAAAATATATAAAATAAATT
Found at i:48217 original size:27 final size:26
Alignment explanation
Indices: 48164--48227 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 26
48154 ATCAAGAAAT
48164 AATAAATTTTAAAATATAAAAAAGAA
1 AATAAATTTTAAAATATAAAAAAGAA
* * * *
48190 AATAAATATTTTAAGTATAATAATGAA
1 AATAAAT-TTTAAAATATAAAAAAGAA
*
48217 ATTAAATTTTA
1 AATAAATTTTA
48228 TATTAATATT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
26 10 0.32
27 21 0.68
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (26 bp):
AATAAATTTTAAAATATAAAAAAGAA
Found at i:48251 original size:22 final size:22
Alignment explanation
Indices: 48226--48269 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
48216 AATTAAATTT
48226 TATATTAATATTAAATAAAAAA
1 TATATTAATATTAAATAAAAAA
48248 TATATTAATATTAAATAAAAAA
1 TATATTAATATTAAATAAAAAA
48270 AACACCTCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
TATATTAATATTAAATAAAAAA
Found at i:62388 original size:15 final size:15
Alignment explanation
Indices: 62370--62399 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
62360 AATTATTACC
*
62370 CCCAAAATTCATGCA
1 CCCAAAATTAATGCA
62385 CCCAAAATTAATGCA
1 CCCAAAATTAATGCA
62400 TACATGAATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.30, G:0.07, T:0.20
Consensus pattern (15 bp):
CCCAAAATTAATGCA
Found at i:63384 original size:15 final size:15
Alignment explanation
Indices: 63366--63416 Score: 68
Period size: 15 Copynumber: 3.3 Consensus size: 15
63356 ACGGGTAGAA
*
63366 AGAAAATTAAAAGAG
1 AGAAAAATAAAAGAG
63381 AGAAGAAATAAATAGA-
1 AGAA-AAATAAA-AGAG
63397 AGAAAAATAAAAGAG
1 AGAAAAATAAAAGAG
63412 AGAAA
1 AGAAA
63417 GGGGAAGTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 3 0.09
15 16 0.50
16 10 0.31
17 3 0.09
ACGTcount: A:0.71, C:0.00, G:0.20, T:0.10
Consensus pattern (15 bp):
AGAAAAATAAAAGAG
Found at i:93813 original size:6 final size:6
Alignment explanation
Indices: 93802--93835 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
93792 CTTCTTCAAT
93802 GATTGG GATTGG GATTGG GATTGG GATTGG GATT
1 GATTGG GATTGG GATTGG GATTGG GATTGG GATT
93836 TATTTATCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.47, T:0.35
Consensus pattern (6 bp):
GATTGG
Found at i:95261 original size:22 final size:22
Alignment explanation
Indices: 95218--95281 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 22
95208 TTAGTATTAG
** *
95218 TTTTT-TTTATTTCAATAAAAT
1 TTTTTATTTATTTTTATATAAT
95239 TTTTTATTTATTTTTATATAAT
1 TTTTTATTTATTTTTATATAAT
* * * *
95261 TTTATAATTATATTTACATAA
1 TTTTTATTTATTTTTATATAA
95282 ATTTGTTTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
21 5 0.14
22 30 0.86
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTTTATTTATTTTTATATAAT
Found at i:99904 original size:19 final size:20
Alignment explanation
Indices: 99856--99905 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
99846 AGGTAGAATA
*
99856 TAAAAATATA-AATATAATT
1 TAAAAATAAATAATATAATT
* *
99875 T-AAATTTAATAATA-AATT
1 TAAAAATAAATAATATAATT
99893 TAAAAATAAATAA
1 TAAAAATAAATAA
99906 CAAGTATACT
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAAAATAAATAATATAATT
Found at i:100257 original size:22 final size:22
Alignment explanation
Indices: 100232--100281 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
100222 GAAATTTAAA
100232 ACAAAACATTATAAGGAGAGTT
1 ACAAAACATTATAAGGAGAGTT
*
100254 ACAAAACATTATGAGGAGAGTT
1 ACAAAACATTATAAGGAGAGTT
*
100276 TCAAAA
1 ACAAAA
100282 TAAAAATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.50, C:0.10, G:0.18, T:0.22
Consensus pattern (22 bp):
ACAAAACATTATAAGGAGAGTT
Found at i:100691 original size:22 final size:22
Alignment explanation
Indices: 100666--100712 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
100656 CGATATGAGG
100666 AAAAATAAAA-AAAACAGAATT
1 AAAAATAAAATAAAACAGAATT
100687 AAAAATAAAATAAAACAGAATT
1 AAAAATAAAATAAAACAGAATT
100709 AAAA
1 AAAA
100713 GAAATAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.15
Consensus pattern (22 bp):
AAAAATAAAATAAAACAGAATT
Found at i:119482 original size:30 final size:30
Alignment explanation
Indices: 119419--119675 Score: 231
Period size: 30 Copynumber: 8.6 Consensus size: 30
119409 ATTTAACCCT
* * *
119419 AAAATTGCAATTTAACCCT-AAACTT-TGCA
1 AAAATTACATTTTAACCCTCAAACTTCT-CC
* *
119448 AAAATTATATTTTAACCCCCAAACTTCTCC
1 AAAATTACATTTTAACCCTCAAACTTCTCC
* ** *
119478 AAAATTACATTTTAACTCTTGAACTTCTCG
1 AAAATTACATTTTAACCCTCAAACTTCTCC
* * *
119508 AAAATTACATTTTGA-CATCGAACTTCTCC
1 AAAATTACATTTTAACCCTCAAACTTCTCC
* * *
119537 AAAATTACATTTTGACCCCCAAACTT-TCTT
1 AAAATTACATTTTAACCCTCAAACTTCTC-C
** * *
119567 AAAATCCCATTTTAACCTTCAAACTTCTCT
1 AAAATTACATTTTAACCCTCAAACTTCTCC
119597 AAAATTACATTTTAACCCTCAAACTT-TCCC
1 AAAATTACATTTTAACCCTCAAACTTCT-CC
*
119627 AAAATTACATTTTAACCC-CAAAC-TCATCT
1 AAAATTACATTTTAACCCTCAAACTTC-TCC
*
119656 AAAATTACCATTTTACCCCT
1 AAAATTA-CATTTTAACCCT
119676 GAACATCTAA
Statistics
Matches: 187, Mismatches: 31, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
28 1 0.01
29 56 0.30
30 127 0.68
31 3 0.02
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (30 bp):
AAAATTACATTTTAACCCTCAAACTTCTCC
Found at i:119555 original size:89 final size:89
Alignment explanation
Indices: 119419--119670 Score: 264
Period size: 89 Copynumber: 2.8 Consensus size: 89
119409 ATTTAACCCT
* * * * * * *
119419 AAAATTGCAATTTAACCCT-AAACTTTGCAAAAATTATATTTTAACCCCCAAACTTCTCCAAAAT
1 AAAATTACATTTTAACCATCAAACTTTCCCAAAATTACATTTT-ACCCCCAAACTTCTCTAAAAT
*
119483 TACATTTTAACTCTT-GAACTTCTCG
65 TACATTTTAAC-CTTCAAACTTCTCG
* *
119508 AAAATTACATTTTGA-CATCGAAC-TTCTCCAAAATTACATTTTGACCCCCAAACTT-TCTTAAA
1 AAAATTACATTTTAACCATCAAACTTTC-CCAAAATTACATTTT-ACCCCCAAACTTCTC-TAAA
** *
119570 ATCCCATTTTAACCTTCAAACTTCTCT
63 ATTACATTTTAACCTTCAAACTTCTCG
* *
119597 AAAATTACATTTTAACCCTCAAACTTTCCCAAAATTACATTTTAACCCCAAAC-TCATCTAAAAT
1 AAAATTACATTTTAACCATCAAACTTTCCCAAAATTACATTTTACCCCCAAACTTC-TCTAAAAT
119661 TACCATTTTA
65 TA-CATTTTA
119671 CCCCTGAACA
Statistics
Matches: 134, Mismatches: 20, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
88 10 0.07
89 91 0.68
90 30 0.22
91 3 0.02
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (89 bp):
AAAATTACATTTTAACCATCAAACTTTCCCAAAATTACATTTTACCCCCAAACTTCTCTAAAATT
ACATTTTAACCTTCAAACTTCTCG
Found at i:119660 original size:119 final size:119
Alignment explanation
Indices: 119456--119674 Score: 282
Period size: 119 Copynumber: 1.8 Consensus size: 119
119446 CAAAAATTAT
* ** *
119456 ATTTTAACCCCCAAACTTCTCCAAAATTACATTTTAACTCTTGAACTTCTCGAAAATTACATTTT
1 ATTTTAACCCCCAAACTTCTCCAAAATTACATTTTAACCCTCAAACTTCTCCAAAATTACATTTT
* * *
119521 GACATCGAACTTCTCCAAAATTA-CATTTTGACCCCCAAACTTTCTTAAAATCCC
66 AACACCAAACTTCTCCAAAATTACCATTTT-ACCCCCAAACTTTCTTAAAATCCC
** *
119575 ATTTTAACCTTCAAACTTCTCTAAAATTACATTTTAACCCTCAAACTT-TCCCAAAATTACATTT
1 ATTTTAACCCCCAAACTTCTCCAAAATTACATTTTAACCCTCAAACTTCT-CCAAAATTACATTT
* *
119639 TAACCCCAAAC-TCATCTAAAATTACCATTTTACCCC
65 TAACACCAAACTTC-TCCAAAATTACCATTTTACCCC
119675 TGAACATCTA
Statistics
Matches: 85, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
118 3 0.04
119 76 0.89
120 6 0.07
ACGTcount: A:0.35, C:0.28, G:0.02, T:0.35
Consensus pattern (119 bp):
ATTTTAACCCCCAAACTTCTCCAAAATTACATTTTAACCCTCAAACTTCTCCAAAATTACATTTT
AACACCAAACTTCTCCAAAATTACCATTTTACCCCCAAACTTTCTTAAAATCCC
Found at i:119696 original size:119 final size:120
Alignment explanation
Indices: 119447--119726 Score: 281
Period size: 119 Copynumber: 2.4 Consensus size: 120
119437 TAAACTTTGC
* * ** *
119447 AAAAATTA-TATTTTAACCCCCAAACTTCTCCAAAATTACATTTTAACTCTTGAACTTCTCGAAA
1 AAAAATTACCATTTTAACCCCCAAACTTCTCCAAAATTACATTTTAACCCTCAAACTTCTCCAAA
* * * *
119511 ATTACATTTTGACATCGAACTTCTCCAAAATTACATTTTGACCCCCAAACTTTCT
66 ATTACATTTTAACACCAAACTTCTCCAAAATTACATTTTGACCCCCAAACTATCT
* * ** *
119566 TAAAA-TCCCATTTTAACCTTCAAACTTCTCTAAAATTACATTTTAACCCTCAAACTT-TCCCAA
1 AAAAATTACCATTTTAACCCCCAAACTTCTCCAAAATTACATTTTAACCCTCAAACTTCT-CCAA
* * **
119629 AATTACATTTTAACCCCAAAC-TCATCTAAAATTACCATTTT-ACCCCTGAAC-ATCT
65 AATTACATTTTAACACCAAACTTC-TCCAAAATTA-CATTTTGACCCCCAAACTATCT
* *
119684 AAAAATTACCA-TTCAACCCCCAAA-TT-TCCAAAAGTCACATTTT
1 AAAAATTACCATTTTAACCCCCAAACTTCTCCAAAA-TTACATTTT
119727 CGATCTCAAA
Statistics
Matches: 130, Mismatches: 25, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
116 6 0.05
117 10 0.08
118 21 0.16
119 87 0.67
120 6 0.05
ACGTcount: A:0.37, C:0.27, G:0.03, T:0.34
Consensus pattern (120 bp):
AAAAATTACCATTTTAACCCCCAAACTTCTCCAAAATTACATTTTAACCCTCAAACTTCTCCAAA
ATTACATTTTAACACCAAACTTCTCCAAAATTACATTTTGACCCCCAAACTATCT
Done.