Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010316.1 Kokia drynarioides strain JFW-HI SEQ_125178, 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: 389999
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 37 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:300583 original size:90 final size:92
Alignment explanation
Indices: 300444--300711 Score: 350
Period size: 90 Copynumber: 3.0 Consensus size: 92
300434 TTTGGGGTCG
** * * *
300444 AAAATGGAGA-TTTTGGAAG-TTCGAGGGTAAAAATGGGATTTTTAAAAGTTTTAAGGGTAAAAA
1 AAAATGGA-ATTTTTGGAAGTTTTAAGGGTAAAAATGGAATTTTTAGAAGTTTTAGGGGTAAAAA
* *
300507 TAGAATTTTTAAAAGTTTCATGG-GT-A
65 TGGAATTTTTAGAAGTTTCATGGAGTCA
* ** *
300533 AAAATGGAATTTTTGGAATTTTTGGGGGTAAAAATCGAATTTTTAGAAGTTTTAGGGGTAAAAAT
1 AAAATGGAATTTTTGGAAGTTTTAAGGGTAAAAATGGAATTTTTAGAAGTTTTAGGGGTAAAAAT
300598 GGAATTTTTAGAAGTTT--TGGAGTCA
66 GGAATTTTTAGAAGTTTCATGGAGTCA
* * *
300623 AAAATGGAATTTTTGGAAGTTTTAAGGGTAAAAATGGAATTCTTGGAAGTTTTTGGGGTAAAAAT
1 AAAATGGAATTTTTGGAAGTTTTAAGGGTAAAAATGGAATTTTTAGAAGTTTTAGGGGTAAAAAT
*
300688 GGAATTTTTAGAAGTTTCAGGGAG
66 GGAATTTTTAGAAGTTTCATGGAG
300712 CCTCCAAGGC
Statistics
Matches: 156, Mismatches: 17, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
88 4 0.03
89 18 0.12
90 130 0.83
92 4 0.03
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.35
Consensus pattern (92 bp):
AAAATGGAATTTTTGGAAGTTTTAAGGGTAAAAATGGAATTTTTAGAAGTTTTAGGGGTAAAAAT
GGAATTTTTAGAAGTTTCATGGAGTCA
Found at i:302544 original size:17 final size:17
Alignment explanation
Indices: 302522--302562 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
302512 TCTTTAATTC
302522 AATTTAAAATCAATTTA
1 AATTTAAAATCAATTTA
* *
302539 AATTTAAACTTAATTTA
1 AATTTAAAATCAATTTA
302556 AATTTAA
1 AATTTAA
302563 GTTTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTTAAAATCAATTTA
Found at i:302809 original size:30 final size:31
Alignment explanation
Indices: 302740--302817 Score: 83
Period size: 30 Copynumber: 2.5 Consensus size: 31
302730 GCATAAAGTT
*
302740 AAAGTTCATGTATCAA-ATTGAATATTAAATC
1 AAAGTTCATGTAT-AATTTTGAATATTAAATC
302771 ATAA-TTCATGTATAATTTTG-ATA-TATAATC
1 A-AAGTTCATGTATAATTTTGAATATTA-AATC
*
302801 AAAGTTCATGTAAAATT
1 AAAGTTCATGTATAATT
302818 GCACTAAAGT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
29 4 0.10
30 22 0.54
31 13 0.32
32 2 0.05
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.40
Consensus pattern (31 bp):
AAAGTTCATGTATAATTTTGAATATTAAATC
Found at i:305705 original size:9 final size:9
Alignment explanation
Indices: 305691--305724 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
305681 AAAAAATTCA
*
305691 TTTAAATTT
1 TTTAAAATT
305700 TTTAAAATT
1 TTTAAAATT
305709 TTTAAAA-T
1 TTTAAAATT
305717 TTTAAAAT
1 TTTAAAAT
305725 AAAAATGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TTTAAAATT
Found at i:309990 original size:20 final size:21
Alignment explanation
Indices: 309954--309995 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
309944 GTATAACATT
309954 ATTATTTAATGTATTTATAAC
1 ATTATTTAATGTATTTATAAC
*
309975 ATTATTT-ATTTATTTATAAC
1 ATTATTTAATGTATTTATAAC
309995 A
1 A
309996 ATTCTTCACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (21 bp):
ATTATTTAATGTATTTATAAC
Found at i:311124 original size:24 final size:24
Alignment explanation
Indices: 311077--311124 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
311067 ATGTATATTC
* * *
311077 AACCTTTCATCTCCTTTGATCTTT
1 AACCTTTCATCTCATTTAACCTTT
*
311101 AACCTTTCATCTTATTTAACCTTT
1 AACCTTTCATCTCATTTAACCTTT
311125 CATATTTTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.21, C:0.27, G:0.02, T:0.50
Consensus pattern (24 bp):
AACCTTTCATCTCATTTAACCTTT
Found at i:316405 original size:17 final size:17
Alignment explanation
Indices: 316383--316424 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
316373 CTCCCTTAAC
*
316383 CTTTAACCTTTCATCTT
1 CTTTAACCTTTCATATT
316400 CTTTAACCTTTCATATT
1 CTTTAACCTTTCATATT
316417 CTTGTAAC
1 CTT-TAAC
316425 TACTTTTTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.21, C:0.26, G:0.02, T:0.50
Consensus pattern (17 bp):
CTTTAACCTTTCATATT
Found at i:326689 original size:12 final size:13
Alignment explanation
Indices: 326668--326696 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
326658 AATTGATTTT
326668 AAAAAGGAAAAAG
1 AAAAAGGAAAAAG
326681 AAAAA-GAAAAAG
1 AAAAAGGAAAAAG
326693 AAAA
1 AAAA
326697 TAAGAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAAAGGAAAAAG
Found at i:326701 original size:20 final size:19
Alignment explanation
Indices: 326668--326705 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
326658 AATTGATTTT
*
326668 AAAAAGGAAAAAGAAAAAG
1 AAAAAGAAAAAAGAAAAAG
326687 AAAAAGAAAATAAGAAAAA
1 AAAAAGAAAA-AAGAAAAA
326706 TAGAAATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.03
Consensus pattern (19 bp):
AAAAAGAAAAAAGAAAAAG
Found at i:327837 original size:43 final size:43
Alignment explanation
Indices: 327776--327880 Score: 174
Period size: 43 Copynumber: 2.4 Consensus size: 43
327766 TGCATATTCT
*
327776 CCACAGCTTGTGTGAGCAGCATCGTGTAGCCCCACATCTCGAC
1 CCACAGCTCGTGTGAGCAGCATCGTGTAGCCCCACATCTCGAC
* *
327819 CCACAACTCGTGTGAGCAGCATCGTGTAGCCCCACATCTTGAC
1 CCACAGCTCGTGTGAGCAGCATCGTGTAGCCCCACATCTCGAC
*
327862 CCACAGCTCATGTGAGCAG
1 CCACAGCTCGTGTGAGCAG
327881 GCCCATTTTA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.23, C:0.34, G:0.23, T:0.20
Consensus pattern (43 bp):
CCACAGCTCGTGTGAGCAGCATCGTGTAGCCCCACATCTCGAC
Found at i:330530 original size:14 final size:14
Alignment explanation
Indices: 330513--330539 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
330503 AAAATAAAAA
330513 TAAAAAATTTTATC
1 TAAAAAATTTTATC
330527 TAAAAAATTTTAT
1 TAAAAAATTTTAT
330540 GCAATTATTT
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:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (14 bp):
TAAAAAATTTTATC
Found at i:332121 original size:13 final size:13
Alignment explanation
Indices: 332103--332129 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
332093 GAGGAGAGTT
332103 ACAAAACATTATA
1 ACAAAACATTATA
332116 ACAAAACATTATA
1 ACAAAACATTATA
332129 A
1 A
332130 GGAGAGTTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.15, G:0.00, T:0.22
Consensus pattern (13 bp):
ACAAAACATTATA
Found at i:337096 original size:22 final size:22
Alignment explanation
Indices: 337068--337113 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
337058 TTTAAAATAT
*
337068 AACATTATGGGGAGAGTTACAA
1 AACATTATGAGGAGAGTTACAA
337090 AACATTATGAGGAGAGTTACAA
1 AACATTATGAGGAGAGTTACAA
337112 AA
1 AA
337114 TAATGTTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.46, C:0.09, G:0.24, T:0.22
Consensus pattern (22 bp):
AACATTATGAGGAGAGTTACAA
Found at i:338490 original size:7 final size:8
Alignment explanation
Indices: 338463--338489 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
338453 TTGAAATTTC
338463 AAAATTCA
1 AAAATTCA
338471 AAAATTCA
1 AAAATTCA
338479 AAAATTCA
1 AAAATTCA
338487 AAA
1 AAA
338490 TGATTAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (8 bp):
AAAATTCA
Found at i:338726 original size:3 final size:3
Alignment explanation
Indices: 338720--338767 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
338710 AATAATATAA
338720 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
338768 TGTATGTGCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:348746 original size:25 final size:25
Alignment explanation
Indices: 348709--348789 Score: 80
Period size: 26 Copynumber: 3.3 Consensus size: 25
348699 GAAGCGCATA
*
348709 AGTGCTGGGGAAACAGAAGCACATCA-
1 AGTGCT-GTGAAACAGAAGCACA-CAC
*
348735 AGTGCTGTGAAACAGTAGGCACACAC
1 AGTGCTGTGAAACAG-AAGCACACAC
*
348761 AGTGC--TG-AACAGAAGCACACAT
1 AGTGCTGTGAAACAGAAGCACACAC
348783 AGTGCTG
1 AGTGCTG
348790 AACAGTAAGC
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
22 13 0.28
23 5 0.11
24 2 0.04
25 10 0.21
26 17 0.36
ACGTcount: A:0.36, C:0.21, G:0.28, T:0.15
Consensus pattern (25 bp):
AGTGCTGTGAAACAGAAGCACACAC
Found at i:348779 original size:22 final size:22
Alignment explanation
Indices: 348720--348799 Score: 83
Period size: 22 Copynumber: 3.5 Consensus size: 22
348710 GTGCTGGGGA
348720 AACAG-AAGCACATCAAGTGCTGTG
1 AACAGTAAGCACA-CAAGTGC--TG
*
348744 AAACAGTAGGCACACACAGTGCTG
1 -AACAGTAAGCACACA-AGTGCTG
348768 AACAG-AAGCACACATAGTGCTG
1 AACAGTAAGCACACA-AGTGCTG
348790 AACAGTAAGC
1 AACAGTAAGC
348800 GCGCTAGCGT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
22 20 0.41
23 9 0.18
24 2 0.04
25 7 0.14
26 11 0.22
ACGTcount: A:0.40, C:0.23, G:0.24, T:0.14
Consensus pattern (22 bp):
AACAGTAAGCACACAAGTGCTG
Found at i:352804 original size:13 final size:11
Alignment explanation
Indices: 352776--352818 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
352766 AGTTAAATAT
352776 TATTTTATTAA
1 TATTTTATTAA
352787 TATTTTACTTAGA
1 TATTTTA-TTA-A
*
352800 TA-TTTATTAT
1 TATTTTATTAA
352810 TATTTTATT
1 TATTTTATT
352819 TAGAAAATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 2 0.07
11 16 0.57
12 7 0.25
13 3 0.11
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:352805 original size:23 final size:23
Alignment explanation
Indices: 352779--352822 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
352769 TAAATATTAT
352779 TTTATTAATATTTTACTTAGATA
1 TTTATTAATATTTTACTTAGATA
* *
352802 TTTATTATTATTTTATTTAGA
1 TTTATTAATATTTTACTTAGA
352823 AAATGATAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (23 bp):
TTTATTAATATTTTACTTAGATA
Found at i:354112 original size:2 final size:2
Alignment explanation
Indices: 354105--354167 Score: 108
Period size: 2 Copynumber: 31.5 Consensus size: 2
354095 ATTCTAATAA
354105 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
* *
354147 AT AT AT AT AG AT AT AG AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
354168 AAGGATGTGG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:370172 original size:20 final size:20
Alignment explanation
Indices: 370149--370187 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
370139 GGAGAAGAAG
*
370149 AAAAAGAAAAGAAA-TAAAT
1 AAAAAGAAAAAAAATTAAAT
370168 AAAAAGAAAAAAAATTAAAT
1 AAAAAGAAAAAAAATTAAAT
370188 TGTTCAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (20 bp):
AAAAAGAAAAAAAATTAAAT
Found at i:371551 original size:93 final size:93
Alignment explanation
Indices: 371387--371578 Score: 303
Period size: 93 Copynumber: 2.1 Consensus size: 93
371377 TGGATCTAAG
* * * * *
371387 TTTAAACCTTGAAAACGACATTGTTTGGAGGGGCAGCCACACACCTCGAAGTTTTAGTTTGAGTT
1 TTTATACCTTGAAAACGACATTATTTGGAGGGGCAGCCACACACCCCGAAGTTCTAGTTCGAGTT
371452 CCATCTTGCATAAATCATATGTGAGTTA
66 CCATCTTGCATAAATCATATGTGAGTTA
* * *
371480 TTTATACCTTGGAGACGGCATTATTTGGAGGGGCAGCCACACACCCCGAAGTTCTAGTTCGAGTT
1 TTTATACCTTGAAAACGACATTATTTGGAGGGGCAGCCACACACCCCGAAGTTCTAGTTCGAGTT
371545 CCATCTTGCATAAATCATATGTGAGTTA
66 CCATCTTGCATAAATCATATGTGAGTTA
*
371573 TCTATA
1 TTTATA
371579 TTTATCCCAA
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 90 1.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.32
Consensus pattern (93 bp):
TTTATACCTTGAAAACGACATTATTTGGAGGGGCAGCCACACACCCCGAAGTTCTAGTTCGAGTT
CCATCTTGCATAAATCATATGTGAGTTA
Found at i:372313 original size:22 final size:22
Alignment explanation
Indices: 372271--372314 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
372261 ACCTAATGAT
*
372271 TAAATAATTTTTAATATTTTTA
1 TAAATAATTTTTAATAGTTTTA
*
372293 TAAAT-ATTTATTCATAGTTTTA
1 TAAATAATTT-TTAATAGTTTTA
372315 AATTCTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
TAAATAATTTTTAATAGTTTTA
Found at i:375213 original size:58 final size:56
Alignment explanation
Indices: 375054--375213 Score: 164
Period size: 58 Copynumber: 2.8 Consensus size: 56
375044 AAAAATTTGG
* * * * * *
375054 TGTTGGCTAATGCTTGGTCGACACCACCTTTTTTGT-TAAATAAAATTTTTTTTGG
1 TGTTGGCCAATGCTTGGTCGACACCATCTTTTTTATCTAAAAAAAATTTTTTTCGC
*
375109 TGTTGGCC-ATGCATTGGTCGACACCAGTATTTTTTATC-AAAGAAAAATATTTTTTCGC
1 TGTTGGCCAATGC-TTGGTCGACACCA-TCTTTTTTATCTAAA-AAAAAT-TTTTTTCGC
** *
375167 TGTTGGCCAATGCTTGACCGACATCATCTTTTTTATCTAATAAAAAA
1 TGTTGGCCAATGCTTGGTCGACACCATCTTTTTTATCTAA-AAAAAA
375214 ACAAATTTTT
Statistics
Matches: 86, Mismatches: 11, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
54 4 0.05
55 20 0.23
56 10 0.12
57 15 0.17
58 32 0.37
59 5 0.06
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (56 bp):
TGTTGGCCAATGCTTGGTCGACACCATCTTTTTTATCTAAAAAAAATTTTTTTCGC
Found at i:375235 original size:61 final size:59
Alignment explanation
Indices: 375095--375237 Score: 148
Period size: 58 Copynumber: 2.4 Consensus size: 59
375085 TTTGTTAAAT
* ** *
375095 AAAATTTTTTTTGGTGTTGGCC-ATGCATTGGTCGACACCAGTATTTTTTATCAAAGAA
1 AAAAATTTTTTTGGTGTTGGCCAATGCATTGACCGACACCAGTATTTTTTATCAAAAAA
* * * * *
375153 AAATATTTTTTCGCTGTTGGCCAATGC-TTGACCGACATCA-TCTTTTTTATCTAATAAAAA
1 AAAAATTTTTTTGGTGTTGGCCAATGCATTGACCGACACCAGTATTTTTTATC--A-AAAAA
375213 AACAAATTTTTTTGGTGTTGGCCAA
1 AA-AAATTTTTTTGGTGTTGGCCAA
375238 CCACCTTTTT
Statistics
Matches: 68, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
57 10 0.15
58 28 0.41
59 5 0.07
60 6 0.09
61 19 0.28
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (59 bp):
AAAAATTTTTTTGGTGTTGGCCAATGCATTGACCGACACCAGTATTTTTTATCAAAAAA
Found at i:379339 original size:17 final size:16
Alignment explanation
Indices: 379317--379351 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
379307 ATTTGTGTAA
*
379317 AAATTAATTTGAAAATT
1 AAATTAAGTTG-AAATT
379334 AAATTAAGTTGAAATT
1 AAATTAAGTTGAAATT
379350 AA
1 AA
379352 TTTCAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (16 bp):
AAATTAAGTTGAAATT
Found at i:379598 original size:131 final size:127
Alignment explanation
Indices: 379486--379734 Score: 306
Period size: 131 Copynumber: 1.9 Consensus size: 127
379476 AAATTTGCAA
*
379486 AAAAAAAATAACTTTTA-AAATT-AATTTAAAATTATTTAAATAAAAATATTATTATAATATTTC
1 AAAAAAAATAA--TTTACAAATTAAATTTAAAATTATTTAAATAAAAAAATTATTATAATATTTC
* * ***
379549 AATTCATATAAAATAATATGTTGATTTGATAATACATTATTTATCAAATTCAAAATTTTGATTTG
64 AATTCATATAAAATAAT-TGTTGATTTGACAATACATTATTTACCAAATTCAAAATTCAAATTTG
* * * *
379614 ACAATACATTATTTACCAAATTCAAAATTTAAAATTATTTAAATAAAAAAATTATTATAATATTT
1 AAAAAAAATAATTTA-CAAATT--AAATTTAAAATTATTTAAATAAAAAAATTATTATAATATTT
* * *
379679 CAATTTATATCAAATAATTGTTGATTTGACAATATATTATTTACCAAATT-AAAATT
63 CAATTCATATAAAATAATTGTTGATTTGACAATACATTATTTACCAAATTCAAAATT
379735 TTAAAATTAT
Statistics
Matches: 106, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
126 4 0.04
128 12 0.11
129 6 0.06
130 29 0.27
131 55 0.52
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (127 bp):
AAAAAAAATAATTTACAAATTAAATTTAAAATTATTTAAATAAAAAAATTATTATAATATTTCAA
TTCATATAAAATAATTGTTGATTTGACAATACATTATTTACCAAATTCAAAATTCAAATTTG
Found at i:379611 original size:37 final size:37
Alignment explanation
Indices: 379569--379643 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
379559 AAATAATATG
* *
379569 TTGATTTGATAATACATTATTTATCAAATTCAAAATT
1 TTGATTTGACAATACATTATTTACCAAATTCAAAATT
379606 TTGATTTGACAATACATTATTTACCAAATTCAAAATT
1 TTGATTTGACAATACATTATTTACCAAATTCAAAATT
379643 T
1 T
379644 AAAATTATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.44
Consensus pattern (37 bp):
TTGATTTGACAATACATTATTTACCAAATTCAAAATT
Found at i:379812 original size:51 final size:51
Alignment explanation
Indices: 379757--379907 Score: 124
Period size: 51 Copynumber: 3.1 Consensus size: 51
379747 AAATAAAAAG
379757 ATTATTATAATATTTCAATTTTTATCAAATAATGTATTGATTTTACAATAC
1 ATTATTATAATATTTCAATTTTTATCAAATAATGTATTGATTTTACAATAC
* ** * ** * *
379808 ATTATT-TACCA-AATTCAA--AAT-TC-AA-AAT-TATTTA-AATA-AAAAG
1 ATTATTATA--ATATTTCAATTTTTATCAAATAATGTATTGATTTTACAATAC
* *
379851 ATTATTATAATATTTCAATTTTTATCAAATAATGTGTTGATTTGACAATAC
1 ATTATTATAATATTTCAATTTTTATCAAATAATGTATTGATTTTACAATAC
379902 ATTATT
1 ATTATT
379908 TACCAAAATA
Statistics
Matches: 70, Mismatches: 18, Indels: 24
0.62 0.16 0.21
Matches are distributed among these distances:
42 1 0.01
43 15 0.21
44 4 0.06
45 6 0.09
46 5 0.07
47 4 0.06
48 5 0.07
49 5 0.07
50 3 0.04
51 21 0.30
52 1 0.01
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (51 bp):
ATTATTATAATATTTCAATTTTTATCAAATAATGTATTGATTTTACAATAC
Found at i:379848 original size:94 final size:94
Alignment explanation
Indices: 379606--379914 Score: 541
Period size: 94 Copynumber: 3.3 Consensus size: 94
379596 ATTCAAAATT
*
379606 TTGATTTGACAATACATTATTTACCAAATTCAAAATTTAAAATTATTTAAATAAAAAAATTATTA
1 TTGATTTGACAATACATTATTTACCAAATTCAAAATTTAAAATTATTTAAATAAAAAGATTATTA
*
379671 TAATATTTCAATTTATATCAAATAAT-TG
66 TAATATTTCAATTTTTATCAAATAATGTG
*
379699 TTGATTTGACAATATATTATTTACCAAATT-AAAATTTTAAAATTATTTAAATAAAAAGATTATT
1 TTGATTTGACAATACATTATTTACCAAATTCAAAA-TTTAAAATTATTTAAATAAAAAGATTATT
*
379763 ATAATATTTCAATTTTTATCAAATAATGTA
65 ATAATATTTCAATTTTTATCAAATAATGTG
* *
379793 TTGATTTTACAATACATTATTTACCAAATTCAAAATTCAAAATTATTTAAATAAAAAGATTATTA
1 TTGATTTGACAATACATTATTTACCAAATTCAAAATTTAAAATTATTTAAATAAAAAGATTATTA
379858 TAATATTTCAATTTTTATCAAATAATGTG
66 TAATATTTCAATTTTTATCAAATAATGTG
379887 TTGATTTGACAATACATTATTTACCAAA
1 TTGATTTGACAATACATTATTTACCAAA
379915 ATAACCTTAA
Statistics
Matches: 204, Mismatches: 9, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
92 4 0.02
93 83 0.41
94 113 0.55
95 4 0.02
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (94 bp):
TTGATTTGACAATACATTATTTACCAAATTCAAAATTTAAAATTATTTAAATAAAAAGATTATTA
TAATATTTCAATTTTTATCAAATAATGTG
Found at i:380011 original size:22 final size:22
Alignment explanation
Indices: 379983--380030 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
379973 AGCATTGGAC
379983 CACCCAAATTCCAACTCACCAA
1 CACCCAAATTCCAACTCACCAA
* * *
380005 CACCCAAATTCTAGCTCACCAC
1 CACCCAAATTCCAACTCACCAA
380027 CACC
1 CACC
380031 TTTCGACTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.35, C:0.48, G:0.02, T:0.15
Consensus pattern (22 bp):
CACCCAAATTCCAACTCACCAA
Found at i:381927 original size:12 final size:13
Alignment explanation
Indices: 381899--381931 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
381889 AATTTCACTT
*
381899 ATTAAATATAAAT
1 ATTAAATATAAAC
381912 ATTAAA-ATAAAC
1 ATTAAATATAAAC
381924 ATTAAATA
1 ATTAAATA
381932 ATGAATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (13 bp):
ATTAAATATAAAC
Found at i:382138 original size:17 final size:18
Alignment explanation
Indices: 382104--382139 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
382094 TGAATTTCTA
382104 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
382122 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
382139 T
1 T
382140 AACTTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:389116 original size:12 final size:13
Alignment explanation
Indices: 389088--389120 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
389078 AATTTCACTT
*
389088 ATTAAATATAAAT
1 ATTAAATATAAAC
389101 ATTAAA-ATAAAC
1 ATTAAATATAAAC
389113 ATTAAATA
1 ATTAAATA
389121 ATGAATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (13 bp):
ATTAAATATAAAC
Found at i:389327 original size:17 final size:18
Alignment explanation
Indices: 389293--389328 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
389283 TGAATTTCTA
389293 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
389311 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
389328 T
1 T
389329 AACTTATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:389742 original size:15 final size:15
Alignment explanation
Indices: 389700--389742 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
389690 AATCCTAGTT
*
389700 TCCCCTTTTTCTTTT
1 TCCCCTTTTTCTTTC
389715 TCCTTCCTTTTTCTTTC
1 TCC--CCTTTTTCTTTC
*
389732 TCCCCTGTTTC
1 TCCCCTTTTTC
389743 GTTTGAGCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 10 0.42
17 14 0.58
ACGTcount: A:0.00, C:0.37, G:0.02, T:0.60
Consensus pattern (15 bp):
TCCCCTTTTTCTTTC
Done.