Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014274.1 Kokia drynarioides strain JFW-HI SEQ_129307, 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: 333927
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 167 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:218158 original size:30 final size:28
Alignment explanation
Indices: 218113--218188 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 28
218103 CAAATTTTTA
*
218113 TTTTTTTT-AGCTTTTAAG-GATCAAAAT
1 TTTTTTTTCAACTTTTAAGAGATC-AAAT
* *
218140 ATTTTTTTATCAATTTTTAAGAGATCTAAT
1 -TTTTTTT-TCAACTTTTAAGAGATCAAAT
218170 TTTTTTTTCAACTTTTAAG
1 TTTTTTTTCAACTTTTAAG
218189 TAATCTAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 18 0.44
29 8 0.20
30 11 0.27
31 4 0.10
ACGTcount: A:0.29, C:0.08, G:0.08, T:0.55
Consensus pattern (28 bp):
TTTTTTTTCAACTTTTAAGAGATCAAAT
Found at i:218171 original size:28 final size:28
Alignment explanation
Indices: 218140--218196 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
218130 GGATCAAAAT
*
218140 ATTTTTTTATCAATTTTTAAG-AGATCTA
1 ATTTTTTTATCAACTTTTAAGTA-ATCTA
*
218168 ATTTTTTTTTCAACTTTTAAGTAATCTA
1 ATTTTTTTATCAACTTTTAAGTAATCTA
218196 A
1 A
218197 AACCTTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 25 0.96
29 1 0.04
ACGTcount: A:0.32, C:0.09, G:0.05, T:0.54
Consensus pattern (28 bp):
ATTTTTTTATCAACTTTTAAGTAATCTA
Found at i:223613 original size:128 final size:129
Alignment explanation
Indices: 223384--223618 Score: 400
Period size: 128 Copynumber: 1.8 Consensus size: 129
223374 ATTTTTGAAA
* * *
223384 TATTTTCCACTTTAGTCCTTTCGTATTTTTATGGTGTTACAATTTAATACTTTTCCATTTTTAAT
1 TATTTTCCACTTTAGTCCTTCCGCATTTTTATGGTGTTACAATTTAATACTTTTACATTTTTAAT
* *
223449 TATTTTAATTTGGCCCATTAATTCTAATTTCTTTACAGTTCGGTCCGCGTGTTTTTATTTATGT
66 TATTTTAATTTAGCCCATTAATTCTAATTTCTTTACAATTCGGTCCGCGTGTTTTTATTTATGT
* *
223513 TATTTTCTACTTTAGTCCTTCCGCA-TTTTATGGTGTTACAATTTAGTACTTTTACATTTTTAAT
1 TATTTTCCACTTTAGTCCTTCCGCATTTTTATGGTGTTACAATTTAATACTTTTACATTTTTAAT
223577 TATTTTAATTTAGCCCATTAATTCTAATTTCTTTACAATTCG
66 TATTTTAATTTAGCCCATTAATTCTAATTTCTTTACAATTCG
223619 ATCCTTTCTT
Statistics
Matches: 99, Mismatches: 7, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
128 77 0.78
129 22 0.22
ACGTcount: A:0.22, C:0.16, G:0.09, T:0.53
Consensus pattern (129 bp):
TATTTTCCACTTTAGTCCTTCCGCATTTTTATGGTGTTACAATTTAATACTTTTACATTTTTAAT
TATTTTAATTTAGCCCATTAATTCTAATTTCTTTACAATTCGGTCCGCGTGTTTTTATTTATGT
Found at i:223727 original size:16 final size:15
Alignment explanation
Indices: 223706--223735 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
223696 TGATCTCACT
223706 TTTTATTTGTGTATTA
1 TTTTATTTGT-TATTA
223722 TTTTATTTGTTATT
1 TTTTATTTGTTATT
223736 TAATTTTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.73
Consensus pattern (15 bp):
TTTTATTTGTTATTA
Found at i:223783 original size:27 final size:27
Alignment explanation
Indices: 223740--223821 Score: 76
Period size: 31 Copynumber: 2.9 Consensus size: 27
223730 GTTATTTAAT
* *
223740 TTTC-TTTATTTTCTTTATTTATTGATC
1 TTTCATTTA-TTTATTTATTTATTGATA
* *
223767 TTTCATTTATTTATTTATGTTGTTTATA
1 TTTCATTTATTTATTTAT-TTATTGATA
223795 TTCTCACCTTTATTTATTTATTTATTG
1 TT-TCA--TTTATTTATTTATTTATTG
223822 TTTTTATGTA
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
27 12 0.27
28 12 0.27
29 3 0.07
30 4 0.09
31 13 0.30
ACGTcount: A:0.18, C:0.10, G:0.05, T:0.67
Consensus pattern (27 bp):
TTTCATTTATTTATTTATTTATTGATA
Found at i:233135 original size:16 final size:16
Alignment explanation
Indices: 233107--233148 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
233097 ATACTATTTT
233107 TAATATGATATAGA-CA
1 TAATAT-ATATAGATCA
*
233123 TAATATATGATAGATTA
1 TAATATAT-ATAGATCA
233140 TAATATATA
1 TAATATATA
233149 CAATCTAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 2 0.09
16 12 0.52
17 9 0.39
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (16 bp):
TAATATATATAGATCA
Found at i:238663 original size:29 final size:29
Alignment explanation
Indices: 238558--238664 Score: 92
Period size: 29 Copynumber: 3.6 Consensus size: 29
238548 ACTTAAATTT
** *
238558 TTTTTATAATTTTTA-TAAAATTTTACGAT
1 TTTTTATAATTTTTATTAAAA-TTTAATAA
* *
238587 TTTTTATAA-TTTTAATAGAATTTAAATAA
1 TTTTTATAATTTTTATTAAAATTT-AATAA
* *
238616 TTTTTTTATATTTTCTTATTAAAATCTAATAA
1 --TTTTTATAATTT-TTATTAAAATTTAATAA
238648 TTTTTATAATTTTTATT
1 TTTTTATAATTTTTATT
238665 TATTTCAATT
Statistics
Matches: 63, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
28 8 0.13
29 20 0.32
30 11 0.17
31 8 0.13
32 7 0.11
33 9 0.14
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.60
Consensus pattern (29 bp):
TTTTTATAATTTTTATTAAAATTTAATAA
Found at i:248416 original size:40 final size:40
Alignment explanation
Indices: 248367--248446 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
248357 TTAACAATAA
*
248367 GATGTCGATCATATGCTCAAAATTGATTTTTAAAATTATC
1 GATGTCGATCATATGCTCAAAATCGATTTTTAAAATTATC
*
248407 GATGTCGATCATATGCTTAAAATCGATTTTTAAAATTATC
1 GATGTCGATCATATGCTCAAAATCGATTTTTAAAATTATC
248447 TCTTTTAACT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (40 bp):
GATGTCGATCATATGCTCAAAATCGATTTTTAAAATTATC
Found at i:249662 original size:51 final size:54
Alignment explanation
Indices: 249543--249667 Score: 136
Period size: 53 Copynumber: 2.4 Consensus size: 54
249533 TTTCATTTAA
* ** *
249543 TACTCACGATGACA-TATAGTCATTGGACCTCTTGTTCCGTATAGGAATTCATGT
1 TACTCACGATGACACTA-AGTCATCGGACCTCTTAATCCATATAGGAATTCATGT
*
249597 T-CTCAGGATGACACTAAGTCATCGGACCT-TTAATCCATCAT-GG-ATTCAT-T
1 TACTCACGATGACACTAAGTCATCGGACCTCTTAATCCAT-ATAGGAATTCATGT
*
249647 TACTCACGATGACACTTAGTC
1 TACTCACGATGACACTAAGTC
249668 TGATTCATTT
Statistics
Matches: 61, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
50 2 0.03
51 23 0.38
52 8 0.13
53 25 0.41
54 3 0.05
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (54 bp):
TACTCACGATGACACTAAGTCATCGGACCTCTTAATCCATATAGGAATTCATGT
Found at i:249675 original size:30 final size:30
Alignment explanation
Indices: 249639--249697 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
249629 ATCCATCATG
249639 GATTCATTTACTCACGATGACACTTAGTCT
1 GATTCATTTACTCACGATGACACTTAGTCT
249669 GATTCATTTACTCACGATGACACTTAGTC
1 GATTCATTTACTCACGATGACACTTAGTC
249698 ATCGGACCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.36
Consensus pattern (30 bp):
GATTCATTTACTCACGATGACACTTAGTCT
Found at i:249740 original size:82 final size:81
Alignment explanation
Indices: 249589--249749 Score: 243
Period size: 82 Copynumber: 2.0 Consensus size: 81
249579 CCGTATAGGA
* * *
249589 ATTCATGTTCTCAGGATGACACTAAGTCATCGGACCTTTAATCCATCATGGATTCATTTACTCAC
1 ATTCATGTTCTCACGATGACACTAAGTCATCGGACCTTTAATCCATAAAGGATTCATTTACTCAC
249654 GATGACACTTAGTCTG
66 GATGACACTTAGTCTG
* *
249670 ATTCAT-TTACTCACGATGACACTTAGTCATCGGACCCTTTAATCCGTAAAGGATTCATTTACTC
1 ATTCATGTT-CTCACGATGACACTAAGTCATCGGA-CCTTTAATCCATAAAGGATTCATTTACTC
*
249734 ATGATGACACTTAGTC
64 ACGATGACACTTAGTC
249750 ATCGGACCCT
Statistics
Matches: 72, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
80 2 0.03
81 29 0.40
82 41 0.57
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.34
Consensus pattern (81 bp):
ATTCATGTTCTCACGATGACACTAAGTCATCGGACCTTTAATCCATAAAGGATTCATTTACTCAC
GATGACACTTAGTCTG
Found at i:249747 original size:52 final size:52
Alignment explanation
Indices: 249669--249813 Score: 281
Period size: 52 Copynumber: 2.8 Consensus size: 52
249659 CACTTAGTCT
249669 GATTCATTTACTCACGATGACACTTAGTCATCGGACCCTTTAATCCGTAAAG
1 GATTCATTTACTCACGATGACACTTAGTCATCGGACCCTTTAATCCGTAAAG
*
249721 GATTCATTTACTCATGATGACACTTAGTCATCGGACCCTTTAATCCGTAAAG
1 GATTCATTTACTCACGATGACACTTAGTCATCGGACCCTTTAATCCGTAAAG
249773 GATTCATTTACTCACGATGACACTTAGTCATCGGACCCTTT
1 GATTCATTTACTCACGATGACACTTAGTCATCGGACCCTTT
249814 CGTTTATAGC
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 91 1.00
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (52 bp):
GATTCATTTACTCACGATGACACTTAGTCATCGGACCCTTTAATCCGTAAAG
Found at i:249761 original size:134 final size:134
Alignment explanation
Indices: 249543--249801 Score: 375
Period size: 134 Copynumber: 1.9 Consensus size: 134
249533 TTTCATTTAA
* *
249543 TACTCACGATGACATATAGTCATTGGACCTCTTGTTCCGTATAGGAATTCATGTTCTCAGGATGA
1 TACTCACGATGACATATAGTCATCGGACCTCTTGTTCCGTAAAGGAATTCATGTTCTCAGGATGA
* *
249608 CACTAAGTCATCGGACCTTTAATCCATCATGGATTCATTTACTCACGATGACACTTAGTCTGATT
66 CACTAAGTCATCGGACCTTTAATCCATAAAGGATTCATTTACTCACGATGACACTTAGTCTGATT
249673 CATT
131 CATT
*
249677 TACTCACGATGACACT-TAGTCATCGGACC-CTT-TAATCCGTAAAGG-ATTCAT-TTACTCATG
1 TACTCACGATGACA-TATAGTCATCGGACCTCTTGT--TCCGTAAAGGAATTCATGTT-CTCAGG
* *
249737 ATGACACTTAGTCATCGGACCCTTTAATCCGTAAAGGATTCATTTACTCACGATGACACTTAGTC
62 ATGACACTAAGTCATCGGA-CCTTTAATCCATAAAGGATTCATTTACTCACGATGACACTTAGTC
249802 ATCGGACCCT
Statistics
Matches: 113, Mismatches: 7, Indels: 10
0.87 0.05 0.08
Matches are distributed among these distances:
132 3 0.03
133 32 0.28
134 77 0.68
135 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.33
Consensus pattern (134 bp):
TACTCACGATGACATATAGTCATCGGACCTCTTGTTCCGTAAAGGAATTCATGTTCTCAGGATGA
CACTAAGTCATCGGACCTTTAATCCATAAAGGATTCATTTACTCACGATGACACTTAGTCTGATT
CATT
Found at i:253543 original size:14 final size:14
Alignment explanation
Indices: 253512--253552 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
253502 GGTGGCAATG
*
253512 AAGGGGGAAGAGGG
1 AAGGGGGAAGAGGA
253526 AAGGGGGAAG-GGA
1 AAGGGGGAAGAGGA
*
253539 AA-AGGGAAGAGGA
1 AAGGGGGAAGAGGA
253552 A
1 A
253553 TTTTCTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 6 0.25
13 8 0.33
14 10 0.42
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (14 bp):
AAGGGGGAAGAGGA
Found at i:272122 original size:17 final size:17
Alignment explanation
Indices: 272085--272124 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
272075 TAATTTAGTC
**
272085 AAAAGAAAATAAAAACTT
1 AAAA-AAAATAAAAAAAT
272103 AAAAAAAATAAAAAAAT
1 AAAAAAAATAAAAAAAT
272120 AAAAA
1 AAAAA
272125 CAAAAATAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.12
Consensus pattern (17 bp):
AAAAAAAATAAAAAAAT
Found at i:274077 original size:41 final size:41
Alignment explanation
Indices: 274017--274107 Score: 164
Period size: 41 Copynumber: 2.2 Consensus size: 41
274007 TTTTATTTTA
*
274017 ACAAGAATTCTAGTCACCCAATTCTAACAATCTTCACCTTG
1 ACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACCTTG
*
274058 ACAAGAATTCTAGTTACCCAATTCTAACAATCTCCACCTTG
1 ACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACCTTG
274099 ACAAGAATT
1 ACAAGAATT
274108 TTCTACGAAC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.36, C:0.27, G:0.08, T:0.29
Consensus pattern (41 bp):
ACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACCTTG
Found at i:283815 original size:44 final size:43
Alignment explanation
Indices: 283696--283820 Score: 169
Period size: 43 Copynumber: 2.9 Consensus size: 43
283686 TGAGAGTTGG
* * * *
283696 AACATTGTTTTCTACTATTGAAAGTATGTGATTGATTGCGAGG
1 AACATTGTTTCCTATTATTGAAAGTATGTGATTGATTGAGAGA
* *
283739 AACATTGTTTCTTATTATTGAAAGCATGTGATTGATTGAGAGA
1 AACATTGTTTCCTATTATTGAAAGTATGTGATTGATTGAGAGA
* *
283782 AACATTGTTTCCCTATTATTAAAAGTATATGATTGATTG
1 AACATTGTTT-CCTATTATTGAAAGTATGTGATTGATTG
283821 TGAGCATGAT
Statistics
Matches: 71, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
43 47 0.66
44 24 0.34
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (43 bp):
AACATTGTTTCCTATTATTGAAAGTATGTGATTGATTGAGAGA
Found at i:284069 original size:28 final size:27
Alignment explanation
Indices: 284009--284071 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
283999 TATAGAGGAG
* *
284009 ATTGGCGATCTTTATTGCATTATATGTT
1 ATTGGC-ATCTCTATCGCATTATATGTT
284037 ATTGGCATCTCTATCGCATTAT-TCGTT
1 ATTGGCATCTCTATCGCATTATAT-GTT
284064 ATTTGGCA
1 A-TTGGCA
284072 GATTTTCTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 1 0.03
27 18 0.58
28 12 0.39
ACGTcount: A:0.21, C:0.16, G:0.17, T:0.46
Consensus pattern (27 bp):
ATTGGCATCTCTATCGCATTATATGTT
Found at i:284115 original size:46 final size:46
Alignment explanation
Indices: 284062--284150 Score: 126
Period size: 46 Copynumber: 1.9 Consensus size: 46
284052 GCATTATTCG
* *
284062 TTATTTGGCAGATTTTC-TACACTATTGATCATTTAGTGGTTTTTAA
1 TTATTTGGCAGA-CTTCATACACTATTGATCATTCAGTGGTTTTTAA
* *
284108 TTATTTGGCAGACTTCATTCACTATTGATTATTCAGTGGTTTT
1 TTATTTGGCAGACTTCATACACTATTGATCATTCAGTGGTTTT
284151 ACCACATCGA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 3 0.08
46 35 0.92
ACGTcount: A:0.22, C:0.12, G:0.16, T:0.49
Consensus pattern (46 bp):
TTATTTGGCAGACTTCATACACTATTGATCATTCAGTGGTTTTTAA
Found at i:292508 original size:220 final size:220
Alignment explanation
Indices: 292099--292524 Score: 488
Period size: 220 Copynumber: 1.9 Consensus size: 220
292089 TCCTATACAA
* *
292099 TATAAAGCTAAAAGGCTAATATACTAAAAAAGACTTAAACTAGTATACTTGGTTCAAATAAACTC
1 TATAAAGCCAAAAGGCTAATATACTAAAAAAGACTTAAACTAGTAAACTTGGTTCAAATAAACTC
* * *
292164 TTATGTTTATTTTTTGGTAACTAAATAACTCCTACTTTTATTTATATTCATGTAAACCCTTAATT
66 TTATG-TTATTTTGTGGTAACTAAATAACTCCTACTTTGATTTATATTCATGTAAACCCTTAACT
** * * * *
292229 TTAACTAAAAATACTTTTGGAGAAACTCAATACCAAGTTACAATCAATATTCTTGAGATATTTAG
130 AAAACTAAAAATACTTTTGGAGAAACCCAATACCAAGTTACAACCAATATTCATGAGATATTAAG
*
292294 TTATCAATATCCGATTTTTTTTCTAT
195 CTATCAATATCCGATTTTTTTTCTAT
* * * * * * *
292320 TATATAGCCAAAAGGCTAATGTACTAAAGTAGGCCTTAAACTAGTAAACTTTGTTCAAATAAGC-
1 TATAAAGCCAAAAGGCTAATATACTAAA-AAAGACTTAAACTAGTAAACTTGGTTCAAATAAACT
* * *
292384 CTTTATG-T-TTTTGT-GTCACTAAATAAGTCCTATACTTTGATTTGA-ATTCATGTAAGCCCTT
65 C-TTATGTTATTTTGTGGTAACTAAATAACTCC--TACTTTGATTT-ATATTCATGTAAACCCTT
* * * *
292445 -ACTAAAAGTAAAACT-CTTTTTGGAGAAACCCAAATACCAAGTTACAACCAGTGTTCATGAGAT
126 AACTAAAACTAAAAATAC-TTTTGGAGAAACCC-AATACCAAGTTACAACCAATATTCATGAGAT
*
292508 ATTAAGCTGTCAATATC
189 ATTAAGCTATCAATATC
292525 GAATATTAGT
Statistics
Matches: 171, Mismatches: 27, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
218 15 0.09
219 28 0.16
220 67 0.39
221 27 0.16
222 34 0.20
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (220 bp):
TATAAAGCCAAAAGGCTAATATACTAAAAAAGACTTAAACTAGTAAACTTGGTTCAAATAAACTC
TTATGTTATTTTGTGGTAACTAAATAACTCCTACTTTGATTTATATTCATGTAAACCCTTAACTA
AAACTAAAAATACTTTTGGAGAAACCCAATACCAAGTTACAACCAATATTCATGAGATATTAAGC
TATCAATATCCGATTTTTTTTCTAT
Found at i:295584 original size:3 final size:3
Alignment explanation
Indices: 295578--295610 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
295568 ATGTAATTTA
295578 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
295611 CGGCGGCGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.67, T:0.33
Consensus pattern (3 bp):
TGG
Found at i:300096 original size:21 final size:21
Alignment explanation
Indices: 300072--300123 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
300062 GAGTTTTTAG
300072 TATAGGTAGAAGCATGACTTA
1 TATAGGTAGAAGCATGACTTA
*
300093 TATAGGTAGAAGCATGACTTG
1 TATAGGTAGAAGCATGACTTA
*
300114 TATCGGTAGA
1 TATAGGTAGA
300124 TGTCTCACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.35, C:0.10, G:0.27, T:0.29
Consensus pattern (21 bp):
TATAGGTAGAAGCATGACTTA
Found at i:301058 original size:2 final size:2
Alignment explanation
Indices: 301051--301076 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
301041 ATCATGGCCA
301051 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
301077 GTTATTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:304850 original size:16 final size:16
Alignment explanation
Indices: 304831--304878 Score: 53
Period size: 17 Copynumber: 3.0 Consensus size: 16
304821 GATCGATCTG
*
304831 TTTATGTAATATATTT
1 TTTATTTAATATATTT
**
304847 TTTATTTTTTATAATTT
1 TTTATTTAATAT-ATTT
304864 TTTATTTAAT-TATTT
1 TTTATTTAATATATTT
304879 AATTTCACGA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 4 0.15
16 10 0.38
17 12 0.46
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (16 bp):
TTTATTTAATATATTT
Found at i:309565 original size:30 final size:29
Alignment explanation
Indices: 309524--309587 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
309514 TATACAGTTA
* * *
309524 ATTACTTTAAATAATATTGTTTCTATTTTT
1 ATTATTTTAAAT-ATATTATTTCTATTTTG
* *
309554 ATTATTTTAAATTTTTTATTTCTATTTTG
1 ATTATTTTAAATATATTATTTCTATTTTG
309583 ATTAT
1 ATTAT
309588 AATTTAATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 18 0.62
30 11 0.38
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (29 bp):
ATTATTTTAAATATATTATTTCTATTTTG
Found at i:310184 original size:53 final size:53
Alignment explanation
Indices: 310125--310228 Score: 131
Period size: 53 Copynumber: 2.0 Consensus size: 53
310115 TTTTAGTTAA
* *
310125 AAAAATATTTT-TTCAA-AGTATTTTTATATGTCAAAAACACTTTTGAAAAATTT
1 AAAAATATTTTATTCAATAATA-TTTT-TATCTCAAAAACACTTTTGAAAAATTT
* * *
310178 AAAAATATTTTATTTAATAATATTTTTATCTCAAAAATACTTTTGAGAAAT
1 AAAAATATTTTATTCAATAATATTTTTATCTCAAAAACACTTTTGAAAAAT
310229 AATGCTAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
53 33 0.75
54 8 0.18
55 3 0.07
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (53 bp):
AAAAATATTTTATTCAATAATATTTTTATCTCAAAAACACTTTTGAAAAATTT
Found at i:310206 original size:16 final size:15
Alignment explanation
Indices: 310174--310203 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
310164 CTTTTGAAAA
310174 ATTTAAAAATATTTT
1 ATTTAAAAATATTTT
*
310189 ATTTAATAATATTTT
1 ATTTAAAAATATTTT
310204 TATCTCAAAA
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:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTAAAAATATTTT
Found at i:311277 original size:20 final size:20
Alignment explanation
Indices: 311264--311309 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
311254 TGAGTTTAAG
311264 TCATAAACAGTGAGATTATA
1 TCATAAACAGTGAGATTATA
* * *
311284 TCATGAACAGTGATAATATA
1 TCATAAACAGTGAGATTATA
311304 T-ATAAA
1 TCATAAA
311310 TACTCGAATG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.48, C:0.09, G:0.13, T:0.30
Consensus pattern (20 bp):
TCATAAACAGTGAGATTATA
Found at i:313835 original size:29 final size:31
Alignment explanation
Indices: 313788--313848 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 31
313778 AGATCCCCAC
313788 ACTTACCCAAAATCACAATTA-AGCCCTTAA
1 ACTTACCCAAAATCACAATTAGAGCCCTTAA
* * *
313818 ACTT-CCCAAATTCCCAATTAGATCCCTTAA
1 ACTTACCCAAAATCACAATTAGAGCCCTTAA
313848 A
1 A
313849 TAAAATTAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.39, C:0.31, G:0.03, T:0.26
Consensus pattern (31 bp):
ACTTACCCAAAATCACAATTAGAGCCCTTAA
Found at i:317582 original size:29 final size:30
Alignment explanation
Indices: 317549--317605 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
317539 AAATAGAATT
*
317549 TTTAAAAATAATTATAATTT-AATTACACA
1 TTTAAAAATAATTAGAATTTGAATTACACA
317578 TTTAAAAATAATTAGAATTTGAATTACA
1 TTTAAAAATAATTAGAATTTGAATTACA
317606 ATTATTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (30 bp):
TTTAAAAATAATTAGAATTTGAATTACACA
Found at i:323518 original size:23 final size:23
Alignment explanation
Indices: 323492--323566 Score: 68
Period size: 23 Copynumber: 3.4 Consensus size: 23
323482 TTTTAAAAAA
*
323492 GTTATAAAATAGTTTGCTAAACC
1 GTTATAAAATAGTTTGTTAAACC
* * **
323515 G-T-TAGAA-AGTTTTTTAAAAAA
1 GTTATAAAATAGTTTGTT-AAACC
323536 GTTATAAAATAGTTTGTTAAACC
1 GTTATAAAATAGTTTGTTAAACC
323559 GTTA-AAAA
1 GTTATAAAA
323567 GTTTTCATTT
Statistics
Matches: 39, Mismatches: 9, Indels: 9
0.68 0.16 0.16
Matches are distributed among these distances:
20 6 0.15
21 8 0.21
22 6 0.15
23 12 0.31
24 7 0.18
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.36
Consensus pattern (23 bp):
GTTATAAAATAGTTTGTTAAACC
Found at i:323532 original size:44 final size:44
Alignment explanation
Indices: 323482--323571 Score: 162
Period size: 44 Copynumber: 2.0 Consensus size: 44
323472 AATCACTTAA
*
323482 TTTTAAAAAAGTTATAAAATAGTTTGCTAAACCGTTAGAAAGTT
1 TTTTAAAAAAGTTATAAAATAGTTTGCTAAACCGTTAAAAAGTT
*
323526 TTTTAAAAAAGTTATAAAATAGTTTGTTAAACCGTTAAAAAGTT
1 TTTTAAAAAAGTTATAAAATAGTTTGCTAAACCGTTAAAAAGTT
323570 TT
1 TT
323572 CATTTAAGTC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (44 bp):
TTTTAAAAAAGTTATAAAATAGTTTGCTAAACCGTTAAAAAGTT
Found at i:325950 original size:21 final size:21
Alignment explanation
Indices: 325924--325966 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
325914 TTCTCCTTAA
325924 TTTTTTATATTTAAATTTTTT
1 TTTTTTATATTTAAATTTTTT
* *
325945 TTTTTTATATTTTAGTTTTTT
1 TTTTTTATATTTAAATTTTTT
325966 T
1 T
325967 CTAGTTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (21 bp):
TTTTTTATATTTAAATTTTTT
Found at i:326026 original size:23 final size:25
Alignment explanation
Indices: 325983--326037 Score: 87
Period size: 24 Copynumber: 2.3 Consensus size: 25
325973 TTTGTCTGCT
325983 TTTGTGGCACGCTTTTTCCTCTACC
1 TTTGTGGCACGCTTTTTCCTCTACC
*
326008 -TTGTGGCATGC-TTTTCCTCTACC
1 TTTGTGGCACGCTTTTTCCTCTACC
326031 TTTGTGG
1 TTTGTGG
326038 TAGATTTGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 12 0.43
24 16 0.57
ACGTcount: A:0.07, C:0.27, G:0.20, T:0.45
Consensus pattern (25 bp):
TTTGTGGCACGCTTTTTCCTCTACC
Found at i:326506 original size:28 final size:27
Alignment explanation
Indices: 326440--326508 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 27
326430 CATATTATTC
*
326440 AAAAATATAAAAATATATAAAAGAATT
1 AAAAATATATAAATATATAAAAGAATT
* *
326467 AAAAAAATTATAAATTTATAAAAGAATAT
1 AAAAATA-TATAAATATATAAAAGAAT-T
**
326496 ATCAATATATAAA
1 AAAAATATATAAA
326509 AACTAAAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
27 6 0.18
28 23 0.68
29 5 0.15
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (27 bp):
AAAAATATATAAATATATAAAAGAATT
Found at i:326620 original size:11 final size:11
Alignment explanation
Indices: 326603--326646 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 11
326593 TTTGTATCTA
326603 AATTTTTT-TT
1 AATTTTTTATT
326613 ATATTTTTTATT
1 A-ATTTTTTATT
326625 AATTTTTATATTT
1 AATTTTT-TA-TT
326638 AATTTTTTA
1 AATTTTTTA
326647 AATAAATATG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 1 0.03
11 13 0.43
12 7 0.23
13 9 0.30
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
AATTTTTTATT
Found at i:326639 original size:13 final size:12
Alignment explanation
Indices: 326591--326646 Score: 53
Period size: 12 Copynumber: 4.7 Consensus size: 12
326581 GTCTGGGTTC
* *
326591 ATTTTGTATCTA
1 ATTTTTTATTTA
*
326603 AATTTTT-TTTA
1 ATTTTTTATTTA
326614 TATTTTTTA-TTA
1 -ATTTTTTATTTA
326626 ATTTTTATATTTA
1 ATTTTT-TATTTA
326639 ATTTTTTA
1 ATTTTTTA
326647 AATAAATATG
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
11 9 0.25
12 18 0.50
13 9 0.25
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (12 bp):
ATTTTTTATTTA
Found at i:329050 original size:49 final size:50
Alignment explanation
Indices: 328997--329111 Score: 151
Period size: 52 Copynumber: 2.3 Consensus size: 50
328987 AAACTTAATC
* * *
328997 AATTTAATTTTAAATTAATATAATACTTATC-AAGATAAATATTAGATTA
1 AATTTAATATTAAATTAATAGAATACTTATCTAAGATAAATATTAAATTA
* *
329046 AATTTAATATTAAATTAATAGAATATTTATCTTGTAGATAAATATTAAATTA
1 AATTTAATATTAAATTAATAGAATACTTATC-T-AAGATAAATATTAAATTA
*
329098 TATTTAATATTAAA
1 AATTTAATATTAAA
329112 ATAGTCACTT
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
49 28 0.49
52 29 0.51
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (50 bp):
AATTTAATATTAAATTAATAGAATACTTATCTAAGATAAATATTAAATTA
Found at i:329108 original size:17 final size:20
Alignment explanation
Indices: 329086--329134 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
329076 CTTGTAGATA
329086 AATATTAAATTA-T-A-TTT
1 AATATTAAATTAGTCACTTT
*
329103 AATATTAAAATAGTCACTTT
1 AATATTAAATTAGTCACTTT
*
329123 AATAGTAAATTA
1 AATATTAAATTA
329135 ATAAAATACT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 11 0.42
18 1 0.04
19 1 0.04
20 13 0.50
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (20 bp):
AATATTAAATTAGTCACTTT
Found at i:332535 original size:17 final size:16
Alignment explanation
Indices: 332513--332582 Score: 77
Period size: 17 Copynumber: 4.1 Consensus size: 16
332503 CAAACTCATT
332513 TTAAATTTATTTTAAGA
1 TTAAATTTATTTTAA-A
*
332530 TTAAATTTGTTTTAAAA
1 TTAAATTTATTTT-AAA
332547 TTTAAATTTATTTTAAA
1 -TTAAATTTATTTTAAA
* *
332564 TTTAATTTAAGTTTAAA
1 TTAAATTT-ATTTTAAA
332581 TT
1 TT
332583 TATTTTCAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
16 7 0.15
17 25 0.54
18 14 0.30
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (16 bp):
TTAAATTTATTTTAAA
Found at i:332553 original size:18 final size:18
Alignment explanation
Indices: 332512--332572 Score: 83
Period size: 17 Copynumber: 3.6 Consensus size: 18
332502 CCAAACTCAT
*
332512 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAAAA
*
332530 -TTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAAAA
332547 TTTAAATTTATTTT-AAA
1 TTTAAATTTATTTTAAAA
332564 TTT-AATTTA
1 TTTAAATTTA
332573 AGTTTAAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
16 6 0.15
17 21 0.54
18 12 0.31
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
TTTAAATTTATTTTAAAA
Found at i:332555 original size:6 final size:6
Alignment explanation
Indices: 332544--332584 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
332534 ATTTGTTTTA
* *
332544 AAATTT AAATTT -ATTTT AAATTT -AATTT AAGTTT AAATTT A
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT A
332585 TTTTCAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
5 9 0.31
6 20 0.69
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (6 bp):
AAATTT
Found at i:332560 original size:46 final size:46
Alignment explanation
Indices: 332510--332614 Score: 149
Period size: 46 Copynumber: 2.3 Consensus size: 46
332500 GTCCAAACTC
* *
332510 ATTTTAAATTTATTTTAAGATTAAATTTGTTTTAAAATTT-AAATTT
1 ATTTTAAATTTAATTTAAGATTAAATTTATTTTAAAATTTCAAA-TT
* *
332556 ATTTTAAATTTAATTTAAGTTTAAATTTATTTTCAAATTTCAAATT
1 ATTTTAAATTTAATTTAAGATTAAATTTATTTTAAAATTTCAAATT
*
332602 ATTATAAATTTAA
1 ATTTTAAATTTAA
332615 AATAAATTAC
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
46 50 0.94
47 3 0.06
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (46 bp):
ATTTTAAATTTAATTTAAGATTAAATTTATTTTAAAATTTCAAATT
Found at i:332561 original size:11 final size:11
Alignment explanation
Indices: 332545--332584 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
332535 TTTGTTTTAA
332545 AATTTAAATTT
1 AATTTAAATTT
*
332556 ATTTTAAATTT
1 AATTTAAATTT
*
332567 AATTTAAGTTT
1 AATTTAAATTT
332578 AAATTTA
1 -AATTTA
332585 TTTTCAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
11 19 0.76
12 6 0.24
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:332562 original size:29 final size:28
Alignment explanation
Indices: 332530--332595 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 28
332520 TATTTTAAGA
**
332530 TTAAATTTGTTTTAAAATTTAAATTTATT
1 TTAAATTTAATTT-AAATTTAAATTTATT
*
332559 TTAAATTTAATTTAAGTTTAAATTTATT
1 TTAAATTTAATTTAAATTTAAATTTATT
332587 TTCAAATTT
1 TT-AAATTT
332596 CAAATTATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 16 0.48
29 17 0.52
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.58
Consensus pattern (28 bp):
TTAAATTTAATTTAAATTTAAATTTATT
Found at i:332579 original size:35 final size:34
Alignment explanation
Indices: 332512--332584 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 34
332502 CCAAACTCAT
332512 TTTAAATTTATTTTAAGATTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAAGATTAAATTTGTTTT-AAA
*
332547 TTTAAATTTATTTTAA-ATTTAATTTAAG-TTTAAA
1 TTTAAATTTATTTTAAGATTAAATTT--GTTTTAAA
332581 TTTA
1 TTTA
332585 TTTTCAAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
34 15 0.43
35 19 0.54
36 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (34 bp):
TTTAAATTTATTTTAAGATTAAATTTGTTTTAAA
Found at i:332613 original size:29 final size:28
Alignment explanation
Indices: 332547--332602 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 28
332537 TGTTTTAAAA
*
332547 TTTAAATTTATTTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAATTTAAATTAAG
332575 TTTAAATTTATTTTCAAATTTCAAATTA
1 TTTAAATTTATTTT-AAATTT-AAATTA
332603 TTATAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 14 0.56
29 6 0.24
30 5 0.20
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (28 bp):
TTTAAATTTATTTTAAATTTAAATTAAG
Done.