Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000776.1 Kokia drynarioides strain JFW-HI SEQ_111833, 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: 139163
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 13 characters in sequence are not A, C, G, or T
Found at i:1212 original size:15 final size:14
Alignment explanation
Indices: 1192--1227 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
1182 TAAATAAGAT
1192 ATTTAAATATTAAA
1 ATTTAAATATTAAA
*
1206 ATGTTAAATATTCAA
1 AT-TTAAATATTAAA
1221 ATTTAAA
1 ATTTAAA
1228 AAAAAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (14 bp):
ATTTAAATATTAAA
Found at i:3335 original size:6 final size:6
Alignment explanation
Indices: 3326--3376 Score: 84
Period size: 6 Copynumber: 8.3 Consensus size: 6
3316 TTGTCTTAAA
*
3326 ATCCCC ATCCCC ATCCCC ATCCCC ATCCCC ATCCCC ATTCCC AGTCCCC
1 ATCCCC ATCCCC ATCCCC ATCCCC ATCCCC ATCCCC ATCCCC A-TCCCC
3375 AT
1 AT
3377 ATGCTTCCAT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
6 37 0.88
7 5 0.12
ACGTcount: A:0.18, C:0.61, G:0.02, T:0.20
Consensus pattern (6 bp):
ATCCCC
Found at i:3641 original size:6 final size:6
Alignment explanation
Indices: 3630--3661 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
3620 TTGGCCACTC
*
3630 CCTCCA CCTCCA CCTCCA CCTCCA CCACCA CC
1 CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CC
3662 CCAACCACCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.19, C:0.69, G:0.00, T:0.12
Consensus pattern (6 bp):
CCTCCA
Found at i:7221 original size:22 final size:21
Alignment explanation
Indices: 7196--7257 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 21
7186 AATGGAGATA
*
7196 AAAACTAAACTCCAAAAACCT
1 AAAACTAAACTCCAAAAACAT
7217 GAAAAC-AAAC-CCACAAAACAT
1 -AAAACTAAACTCCA-AAAACAT
7238 AAACACTAAATTCTCCAAAA
1 AAA-ACTAAA--CTCCAAAA
7258 GTGTTAGGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
20 6 0.18
21 12 0.36
22 8 0.24
24 4 0.12
25 3 0.09
ACGTcount: A:0.58, C:0.27, G:0.02, T:0.13
Consensus pattern (21 bp):
AAAACTAAACTCCAAAAACAT
Found at i:9348 original size:24 final size:23
Alignment explanation
Indices: 9330--9404 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 23
9320 AGTTTGACTC
9330 AAACAAATAAACAAAGTTTAATTG
1 AAACAAATAAA-AAAGTTTAATTG
*
9354 AAACAAATAAATAGAGTTTAATTG
1 AAACAAATAAA-AAAGTTTAATTG
*
9378 AAACAAATAAAAAGAGTTTAACTG
1 AAACAAATAAAAA-AGTTTAATTG
9402 AAA
1 AAA
9405 GATTATTTCT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 1 0.02
24 45 0.98
ACGTcount: A:0.59, C:0.07, G:0.11, T:0.24
Consensus pattern (23 bp):
AAACAAATAAAAAAGTTTAATTG
Found at i:11029 original size:29 final size:28
Alignment explanation
Indices: 10969--11038 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 28
10959 AGATGAGTGC
** *
10969 AAAATTATAAAAAAATTTAAACATTGTA
1 AAAATTATAAAAAAAACTAAACATTATA
*
10997 AAAATTATTAAAAAAAACTAAATATTATTA
1 AAAATTA-TAAAAAAAACTAAACATTA-TA
*
11027 AAACATTGTAAA
1 AAA-ATTATAAA
11039 TATTATAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
28 7 0.21
29 15 0.44
30 9 0.26
31 3 0.09
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.31
Consensus pattern (28 bp):
AAAATTATAAAAAAAACTAAACATTATA
Found at i:11038 original size:20 final size:20
Alignment explanation
Indices: 10987--11048 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
10977 AAAAAAATTT
*
10987 AAACATTGTAAAAATTATTA
1 AAACATTGTAAATATTATTA
* ***
11007 AAAAAAACTAAATATTATTA
1 AAACATTGTAAATATTATTA
11027 AAACATTGTAAATATTA-TA
1 AAACATTGTAAATATTATTA
11046 AAA
1 AAA
11049 TTTTAAATAT
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
19 5 0.15
20 28 0.85
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.32
Consensus pattern (20 bp):
AAACATTGTAAATATTATTA
Found at i:11042 original size:17 final size:16
Alignment explanation
Indices: 11022--11064 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
11012 AACTAAATAT
11022 TATTAAAACATTGTAAA
1 TATTAAAA-ATTGTAAA
*
11039 TATTATAAAATTTTAAA
1 TATTA-AAAATTGTAAA
11056 TATGTAAAA
1 TAT-TAAAA
11065 GATTATTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (16 bp):
TATTAAAAATTGTAAA
Found at i:11096 original size:9 final size:9
Alignment explanation
Indices: 10969--11099 Score: 52
Period size: 10 Copynumber: 13.8 Consensus size: 9
10959 AGATGAGTGC
10969 AAAATTATAAA
1 AAAATTAT--A
10980 AAAATT-TA
1 AAAATTATA
* *
10988 AACATTGTA
1 AAAATTATA
10997 AAAATTATTA
1 AAAATTA-TA
**
11007 AAAAAAACTA
1 AAAATTA-TA
*
11017 AATATTATTA
1 AAAATTA-TA
*
11027 AAACATTGTA
1 AAA-ATTATA
*
11037 AATATTAT-
1 AAAATTATA
*
11045 AAAATTTTA
1 AAAATTATA
*
11054 AATATGTA-A
1 AAAAT-TATA
*
11063 AAGATTATTA
1 AAAATTA-TA
*
11073 ATAATTTATA
1 A-AAATTATA
11083 TAAAATTATA
1 -AAAATTATA
11093 AAAATTA
1 AAAATTA
11100 ATAGTTTTGC
Statistics
Matches: 89, Mismatches: 22, Indels: 20
0.68 0.17 0.15
Matches are distributed among these distances:
8 14 0.16
9 27 0.30
10 34 0.38
11 14 0.16
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (9 bp):
AAAATTATA
Found at i:11434 original size:21 final size:20
Alignment explanation
Indices: 11412--11486 Score: 73
Period size: 21 Copynumber: 3.8 Consensus size: 20
11402 AAAACTATTA
11412 TTTTTTTATAATTTTATAAT
1 TTTTTTTATAATTTTATAAT
* ** *
11432 ATTTATAAATATTTTTATAAT
1 -TTTTTTTATAATTTTATAAT
* *
11453 TTTTATTA-ATTTTTA-AAT
1 TTTTTTTATAATTTTATAAT
11471 TTTTTTTATAATTTTA
1 TTTTTTTATAATTTTA
11487 CACACTCATA
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
18 10 0.23
19 13 0.30
20 4 0.09
21 16 0.37
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTTTTATAATTTTATAAT
Found at i:11449 original size:29 final size:29
Alignment explanation
Indices: 11414--11486 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 29
11404 AACTATTATT
11414 TTTTTATAATTTTA-TAATATTTATAAA-TA
1 TTTTTATAATTTTATTAAT-TTT-TAAATTA
*
11443 TTTTTATAATTTTTATTAATTTTTAAATTT
1 TTTTTATAA-TTTTATTAATTTTTAAATTA
11473 TTTTTATAATTTTA
1 TTTTTATAATTTTA
11487 CACACTCATA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
29 18 0.45
30 18 0.45
31 4 0.10
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (29 bp):
TTTTTATAATTTTATTAATTTTTAAATTA
Found at i:11485 original size:10 final size:9
Alignment explanation
Indices: 11414--11474 Score: 63
Period size: 8 Copynumber: 6.6 Consensus size: 9
11404 AACTATTATT
11414 TTTTTATAA
1 TTTTTATAA
11423 -TTTTATAA
1 TTTTTATAA
*
11431 TATTTATAAATA
1 T-TTT-TATA-A
11443 TTTTTATAA
1 TTTTTATAA
11452 TTTTTATTAA
1 TTTTTA-TAA
11462 TTTTTA-AA
1 TTTTTATAA
11470 TTTTT
1 TTTTT
11475 TTTATAATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
8 15 0.33
9 7 0.16
10 15 0.33
11 6 0.13
12 2 0.04
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TTTTTATAA
Found at i:11921 original size:81 final size:80
Alignment explanation
Indices: 11750--11921 Score: 247
Period size: 81 Copynumber: 2.1 Consensus size: 80
11740 TGCACTTTAC
* * * *
11750 CCCCTAAAATTGATACAATTTTGATTTAATCCTTTAAAAATTACTTTTTTACTATCATAAAAATT
1 CCCCTAAAAATGATAAAATTTTGATCTAATACTTTAAAAATTACTTTTTTACTATCATAAAAATT
11815 ACAATTTAACTTCGG
66 ACAATTTAACTTCGG
*
11830 CCCTCGAAAAATGATAAAATTTTGATCTAATACTTTAAAAATTA-TATTTTTACTATCATAAAAA
1 CCC-CTAAAAATGATAAAATTTTGATCTAATACTTTAAAAATTACT-TTTTTACTATCATAAAAA
* *
11894 TTACAATTTACCTTCAGT
64 TTACAATTTAACTTC-GG
11912 CCCCTAAAAA
1 CCCCTAAAAA
11922 AATTTTCTGA
Statistics
Matches: 81, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
80 4 0.05
81 73 0.90
82 4 0.05
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.38
Consensus pattern (80 bp):
CCCCTAAAAATGATAAAATTTTGATCTAATACTTTAAAAATTACTTTTTTACTATCATAAAAATT
ACAATTTAACTTCGG
Found at i:12252 original size:30 final size:30
Alignment explanation
Indices: 12186--12264 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 30
12176 GTTCTTCATC
* *
12186 CATGCTCGCAACA-TCAGTGTTTGCAGCAT
1 CATGCTCGCAACATTCAGTGTTCGCAGAAT
*
12215 CAGTGCTCGCAACATTTA-TGTTCGCAGAAGT
1 CA-TGCTCGCAACATTCAGTGTTCGCAGAA-T
*
12246 CATGCTCGCAGCATT-AGTG
1 CATGCTCGCAACATTCAGTG
12265 ATCACGACAT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
29 3 0.07
30 34 0.81
31 5 0.12
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.28
Consensus pattern (30 bp):
CATGCTCGCAACATTCAGTGTTCGCAGAAT
Found at i:12259 original size:45 final size:45
Alignment explanation
Indices: 12208--12302 Score: 109
Period size: 45 Copynumber: 2.1 Consensus size: 45
12198 ATCAGTGTTT
* * * * *
12208 GCAGCATCAGTGCTCGCAACATTTATGTTCGCAGAAGTCATGCTC
1 GCAGCATCAGTGATCACAACATTCATGTTAGCACAAGTCATGCTC
* * * *
12253 GCAGCATTAGTGATCACGACATTCATGTTAGCACTAGTCATGCTT
1 GCAGCATCAGTGATCACAACATTCATGTTAGCACAAGTCATGCTC
12298 GCAGC
1 GCAGC
12303 TCCTTCAAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.27
Consensus pattern (45 bp):
GCAGCATCAGTGATCACAACATTCATGTTAGCACAAGTCATGCTC
Found at i:12761 original size:79 final size:79
Alignment explanation
Indices: 12593--12764 Score: 274
Period size: 79 Copynumber: 2.2 Consensus size: 79
12583 AAGCTAAAAA
* * *
12593 AATTTTTAGGGAGCGAAGTTAAATTGTAATTTTTACTATAGTAAAAATGCAATTTTTAAAGGATT
1 AATTTTTAGGGGGCGAAGTTAAATTGTAATTTTTACGATAGTAAAAATGC-ATATTTAAAGGATT
12658 AAATCAAAATTTTAT
65 AAATCAAAATTTTAT
* *
12673 CATTTTTAGGGGGTCGAAGTTAAATTGTAATTTTTAGGATAGTAAAAATGC-TATTTAAAGGATT
1 AATTTTTAGGGGG-CGAAGTTAAATTGTAATTTTTACGATAGTAAAAATGCATATTTAAAGGATT
12737 AAATCAAAATTTTAT
65 AAATCAAAATTTTAT
12752 AATTTTTAGGGGG
1 AATTTTTAGGGGG
12765 GTCAAATGCA
Statistics
Matches: 85, Mismatches: 6, Indels: 3
0.90 0.06 0.03
Matches are distributed among these distances:
79 39 0.46
80 11 0.13
81 35 0.41
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (79 bp):
AATTTTTAGGGGGCGAAGTTAAATTGTAATTTTTACGATAGTAAAAATGCATATTTAAAGGATTA
AATCAAAATTTTAT
Found at i:12968 original size:22 final size:22
Alignment explanation
Indices: 12943--12988 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
12933 AGTTAGAGGG
*
12943 ATATTTGATTAATAAATATTTA
1 ATATCTGATTAATAAATATTTA
12965 ATATCTGATTAATAAATATTTA
1 ATATCTGATTAATAAATATTTA
12987 AT
1 AT
12989 CATGATTTAT
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:0.02, G:0.04, T:0.48
Consensus pattern (22 bp):
ATATCTGATTAATAAATATTTA
Found at i:38241 original size:16 final size:16
Alignment explanation
Indices: 38220--38251 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
38210 TGTTATCAGC
38220 TGCCATTTAAAAACTT
1 TGCCATTTAAAAACTT
38236 TGCCATTTAAAAACTT
1 TGCCATTTAAAAACTT
38252 AAGAGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.38
Consensus pattern (16 bp):
TGCCATTTAAAAACTT
Found at i:41833 original size:195 final size:197
Alignment explanation
Indices: 41474--41850 Score: 465
Period size: 195 Copynumber: 1.9 Consensus size: 197
41464 TCTCGTATAT
* *
41474 GTTTTCTATTCTAGAGGGAGAATATCTTTTATACAACGCAACGGAGGATAGCTTTCTTCCCCCGC
1 GTTTTCTATTCTAGAGGGAG-ATATCTTTTATACAACGCAACGGAGGATAGCTTACATCCCCCGC
* *** * * * *
41539 TTCATTTTTTTTGGTTTGATTTCCATCTGACCCTACACCCCTTCTTCTACAATCTTCTTAATAAT
65 TTCATTGTTTTTGGGCCGATTTCCATATAACCCTACACCCCTTCTTCTACAATCTTCTTAACAAC
* * **
41604 TATAAGTTGGCCCCGAGCCACCTTTCTATTACCTCTTGGTGGTTGGCTATTTTTGACTTCGCGTA
130 TATAAGTTGGCCCAGAGCCACCTTTCTATTACCTCTTGCTAATTGGCTATTTTTGACTTCGCGTA
41669 CGA
195 CGA
* * * * * *
41672 GTTTTCTATTCTTGA-GGAG-TATCTTTTATACGACGCCACGGAGGATGGCTTACATCCGCCTCT
1 GTTTTCTATTCTAGAGGGAGATATCTTTTATACAACGCAACGGAGGATAGCTTACATCCCCCGCT
* *
41735 TCA-TGTTTTTGAGGCCGATTTCCATATAACCTTACACCCCTTCTTCTACAATCTTCTTAACGAC
66 TCATTGTTTTTG-GGCCGATTTCCATATAACCCTACACCCCTTCTTCTACAATCTTCTTAACAAC
** * *
41799 TATAAGTTGGCTTTAG-GCCAGCTTTCTCTTACCTCTTGCTAATTGGCTATTT
130 TATAAGTTGGC-CCAGAGCCACCTTTCTATTACCTCTTGCTAATTGGCTATTT
41851 CTTACTTTTT
Statistics
Matches: 151, Mismatches: 26, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
194 7 0.05
195 125 0.83
196 1 0.01
197 4 0.03
198 14 0.09
ACGTcount: A:0.20, C:0.25, G:0.16, T:0.39
Consensus pattern (197 bp):
GTTTTCTATTCTAGAGGGAGATATCTTTTATACAACGCAACGGAGGATAGCTTACATCCCCCGCT
TCATTGTTTTTGGGCCGATTTCCATATAACCCTACACCCCTTCTTCTACAATCTTCTTAACAACT
ATAAGTTGGCCCAGAGCCACCTTTCTATTACCTCTTGCTAATTGGCTATTTTTGACTTCGCGTAC
GA
Found at i:44252 original size:15 final size:15
Alignment explanation
Indices: 44232--44262 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
44222 GTATTATCCT
44232 TATTTGCTGTGGGGG
1 TATTTGCTGTGGGGG
*
44247 TATTTGTTGTGGGGG
1 TATTTGCTGTGGGGG
44262 T
1 T
44263 GAGTTATGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.06, C:0.03, G:0.45, T:0.45
Consensus pattern (15 bp):
TATTTGCTGTGGGGG
Found at i:47446 original size:30 final size:30
Alignment explanation
Indices: 47410--47498 Score: 124
Period size: 30 Copynumber: 3.0 Consensus size: 30
47400 CAAGAATCTG
* *
47410 AGGATACTGCTCTTATTATCCCTCTACTTA
1 AGGATACTGCTCTTATTGTCCCTCTACCTA
*
47440 AGGATACTGCTCTTATTGTCCCTCTACCTG
1 AGGATACTGCTCTTATTGTCCCTCTACCTA
* * *
47470 AGGATACTCCTCCTATTGTCCCTCCACCT
1 AGGATACTGCTCTTATTGTCCCTCTACCT
47499 CGTTCAAACT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.19, C:0.33, G:0.12, T:0.36
Consensus pattern (30 bp):
AGGATACTGCTCTTATTGTCCCTCTACCTA
Found at i:48375 original size:28 final size:28
Alignment explanation
Indices: 48343--48396 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
48333 TTCTTATGAC
48343 TTTTTATA-ATTCTTACT-ATTTTTAAATA
1 TTTTTATATATT-TTA-TAATTTTTAAATA
*
48371 TTTTTTTATATTTTATAATTTTTAAA
1 TTTTTATATATTTTATAATTTTTAAA
48397 ACTAACAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 1 0.04
28 19 0.83
29 3 0.13
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (28 bp):
TTTTTATATATTTTATAATTTTTAAATA
Found at i:58130 original size:30 final size:30
Alignment explanation
Indices: 58065--58181 Score: 128
Period size: 30 Copynumber: 3.9 Consensus size: 30
58055 TTCAAGAACT
* * * *
58065 TGAGGATACTACTCCTATCGTCCC-ACACC
1 TGAGGATACTCCTCCTACCATCCCTCCACC
*
58094 TGAGGATACTCCTCCTACCATCCCTCCACT
1 TGAGGATACTCCTCCTACCATCCCTCCACC
** *
58124 TGAGGATACTCCTGTTACTATCCCTCCACC
1 TGAGGATACTCCTCCTACCATCCCTCCACC
* **
58154 TGAGGATACTCCTCTTACTGTCCCTCCA
1 TGAGGATACTCCTCCTACCATCCCTCCA
58182 GTCTCTTCCC
Statistics
Matches: 76, Mismatches: 11, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
29 21 0.28
30 55 0.72
ACGTcount: A:0.21, C:0.38, G:0.13, T:0.28
Consensus pattern (30 bp):
TGAGGATACTCCTCCTACCATCCCTCCACC
Found at i:60447 original size:30 final size:30
Alignment explanation
Indices: 60334--60445 Score: 143
Period size: 30 Copynumber: 3.7 Consensus size: 30
60324 AGAACTTGAC
* * *
60334 GATACTGCTCCTACTGTCCCTCCACTTGAG
1 GATACTCCTCCTACTATCCCTCCACCTGAG
* * **
60364 GATACTCCTCCTACTGTCCCTCCAACTGTT
1 GATACTCCTCCTACTATCCCTCCACCTGAG
* *
60394 GATACTCCTCCTCCTATCCCTCTACCTGAG
1 GATACTCCTCCTACTATCCCTCCACCTGAG
60424 GATACTCCTCCTACTATCCCTC
1 GATACTCCTCCTACTATCCCTC
60446 TAATCTCTTC
Statistics
Matches: 70, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 70 1.00
ACGTcount: A:0.17, C:0.41, G:0.11, T:0.31
Consensus pattern (30 bp):
GATACTCCTCCTACTATCCCTCCACCTGAG
Found at i:68337 original size:30 final size:29
Alignment explanation
Indices: 68296--68367 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 29
68286 GGATACTGCT
* *
68296 TACTGTCCCTCCACCTGAGGATACTCCACC
1 TACTATCCCTCCACCTAAGGATA-TCCACC
* *
68326 TACTATCCCTCCACTTAAGGATATCCGCC
1 TACTATCCCTCCACCTAAGGATATCCACC
*
68355 TACTATCCTTCCA
1 TACTATCCCTCCA
68368 GTCTCTTCCC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 17 0.46
30 20 0.54
ACGTcount: A:0.22, C:0.40, G:0.10, T:0.28
Consensus pattern (29 bp):
TACTATCCCTCCACCTAAGGATATCCACC
Found at i:70874 original size:30 final size:30
Alignment explanation
Indices: 70826--70913 Score: 131
Period size: 30 Copynumber: 2.9 Consensus size: 30
70816 ATCAAGAACT
* * *
70826 TGAGAATACTACTTCTACTGTCCCTCCACC
1 TGAGGATACTCCTCCTACTGTCCCTCCACC
*
70856 TGAGGATACTCCTCCTACTATCCCTCCACC
1 TGAGGATACTCCTCCTACTGTCCCTCCACC
*
70886 TAAGGATACTCCTCCTACTGTCCCTCCA
1 TGAGGATACTCCTCCTACTGTCCCTCCA
70914 GTCTCTTCCC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.22, C:0.40, G:0.10, T:0.28
Consensus pattern (30 bp):
TGAGGATACTCCTCCTACTGTCCCTCCACC
Found at i:72155 original size:21 final size:22
Alignment explanation
Indices: 72129--72170 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
72119 TAATCTCAAA
*
72129 AATTTAT-TTCTTTTTGTTCTC
1 AATTTATGTTCTTTTTCTTCTC
*
72150 AATTTATGTTTTTTTTCTTCT
1 AATTTATGTTCTTTTTCTTCT
72171 TGAAACTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
AATTTATGTTCTTTTTCTTCTC
Found at i:73434 original size:30 final size:30
Alignment explanation
Indices: 73398--73485 Score: 122
Period size: 30 Copynumber: 2.9 Consensus size: 30
73388 CTTTTCAAGA
* *
73398 ACTTAAGGATACTGCTCCAACTATCCCTCC
1 ACTTAAGGATACTCCTCCTACTATCCCTCC
* *
73428 ACTTAAGAATACACCTCCTACTATCCCTCC
1 ACTTAAGGATACTCCTCCTACTATCCCTCC
* *
73458 ACTTGAGGATACTCCGCCTACTATCCCT
1 ACTTAAGGATACTCCTCCTACTATCCCT
73486 TCAGTCTCTT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.26, C:0.38, G:0.09, T:0.27
Consensus pattern (30 bp):
ACTTAAGGATACTCCTCCTACTATCCCTCC
Found at i:74753 original size:23 final size:22
Alignment explanation
Indices: 74709--74753 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
74699 CAGGATTTTT
**
74709 TTCTTTTTCTTCTCAATTTATG
1 TTCTTTTTCTTCTCAAACTATG
*
74731 TTCTTTTTCTTCCTGAAACTATG
1 TTCTTTTTCTT-CTCAAACTATG
74754 GTTAAGTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.16, C:0.20, G:0.07, T:0.58
Consensus pattern (22 bp):
TTCTTTTTCTTCTCAAACTATG
Found at i:75986 original size:30 final size:30
Alignment explanation
Indices: 75952--76025 Score: 112
Period size: 30 Copynumber: 2.5 Consensus size: 30
75942 TTTAAGAACT
* * *
75952 TGAGGGTACTGCTCCTACTGTCCCTCCACC
1 TGAGGATACTCCTCCTACTATCCCTCCACC
75982 TGAGGATACTCCTCCTACTATCCCTCCACC
1 TGAGGATACTCCTCCTACTATCCCTCCACC
*
76012 TGAGTATACTCCTC
1 TGAGGATACTCCTC
76026 ATTTTGTCCC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.18, C:0.39, G:0.15, T:0.28
Consensus pattern (30 bp):
TGAGGATACTCCTCCTACTATCCCTCCACC
Found at i:76036 original size:30 final size:30
Alignment explanation
Indices: 75952--76037 Score: 100
Period size: 30 Copynumber: 2.9 Consensus size: 30
75942 TTTAAGAACT
* * *
75952 TGAGGGTACTGCTCCTACTGTCCCTCCACC
1 TGAGGATACTCCTCATACTGTCCCTCCACC
* *
75982 TGAGGATACTCCTCCTACTATCCCTCCACC
1 TGAGGATACTCCTCATACTGTCCCTCCACC
* **
76012 TGAGTATACTCCTCATTTTGTCCCTC
1 TGAGGATACTCCTCATACTGTCCCTC
76038 TAGTTTCTTC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.16, C:0.38, G:0.14, T:0.31
Consensus pattern (30 bp):
TGAGGATACTCCTCATACTGTCCCTCCACC
Found at i:81002 original size:30 final size:30
Alignment explanation
Indices: 80944--81031 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 30
80934 TTCAAGAACT
* * * *
80944 TGAGGATAATGCTCCTACTGTCCCTCCACC
1 TGAGGATACTCCTCCTACTATACCTCCACC
*
80974 TGAGGATACTCCTCCTACTATACGTCCACC
1 TGAGGATACTCCTCCTACTATACCTCCACC
* * *
81004 TTAAGATACTCCTCCTACTATATCTCCA
1 TGAGGATACTCCTCCTACTATACCTCCA
81032 ATCTCTTCCC
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.24, C:0.35, G:0.11, T:0.30
Consensus pattern (30 bp):
TGAGGATACTCCTCCTACTATACCTCCACC
Found at i:81343 original size:218 final size:221
Alignment explanation
Indices: 80927--81352 Score: 547
Period size: 218 Copynumber: 1.9 Consensus size: 221
80917 TCGAGGTTGG
*
80927 TCGTCCTTTCAAGAACTTGAGGATAATGCTCCTACTGTCCCTCCACCTGAGGATACTCCTCCTAC
1 TCGTCCTTTCAAGAACTTGAGGATAATACTCCTACTGTCCCTCCACCTGAGGATACTCCTCCTAC
* * * **
80992 TATACGTCCACCTTAAGATACTCCTCCTACTATATCTCCAATCTCTTCCCTCATTCCTATGGTTG
66 TATACCTCCACCTTAAGATACTACTCCTACTATACCTCCAATCTCTTCCCTCATTCCTACAGTTG
* * * *
81057 AGGAGACCTTATCTCACGATGAGTCCGTAAGAATTCGTCTCTTCCCTCTAGTTTATGATATCTAA
131 AGGAGACCTCATCTAACGATGAGTCCGTAAGAATTAGTCTCCTCCCTCTAGTTTATGATATCTAA
*
81122 GTACACTGAAGCTTATATGTGCCAGC
196 GTACACTAAAGCTTATATGTGCCAGC
* * * * * *
81148 TCGTCCTTTTAAGAACTTGAGGATACTACTCCTGCTGTCCCTCCAGCTGAGGATACTCCTCTTAT
1 TCGTCCTTTCAAGAACTTGAGGATAATACTCCTACTGTCCCTCCACCTGAGGATACTCCTCCTAC
* * * * * * *
81213 TATCCCTGCACC-TAAGA-A-TACTCCTACTGTCCCTCCAGTCTCTTCCCT-AGTTTCTGCAGTT
66 TATACCTCCACCTTAAGATACTACTCCTACTATACCTCCAATCTCTTCCCTCA-TTCCTACAGTT
* * * *
81274 GAGGAGACCTCATCTAACGATGAGTTCGTAGGAATTATTCTCCTCCCTCTAGTTTATGAT-TGTT
130 GAGGAGACCTCATCTAACGATGAGTCCGTAAGAATTAGTCTCCTCCCTCTAGTTTATGATAT-CT
81338 AAGTACACTAAAGCT
194 AAGTACACTAAAGCT
81353 CGTGTGCGCC
Statistics
Matches: 175, Mismatches: 28, Indels: 7
0.83 0.13 0.03
Matches are distributed among these distances:
217 2 0.01
218 100 0.57
219 1 0.01
220 5 0.03
221 67 0.38
ACGTcount: A:0.23, C:0.29, G:0.15, T:0.33
Consensus pattern (221 bp):
TCGTCCTTTCAAGAACTTGAGGATAATACTCCTACTGTCCCTCCACCTGAGGATACTCCTCCTAC
TATACCTCCACCTTAAGATACTACTCCTACTATACCTCCAATCTCTTCCCTCATTCCTACAGTTG
AGGAGACCTCATCTAACGATGAGTCCGTAAGAATTAGTCTCCTCCCTCTAGTTTATGATATCTAA
GTACACTAAAGCTTATATGTGCCAGC
Found at i:83769 original size:30 final size:30
Alignment explanation
Indices: 83733--83820 Score: 113
Period size: 30 Copynumber: 2.9 Consensus size: 30
83723 TTCAAGAACT
* *
83733 TGAGGATAATGCTCCTACTGTCCCTCCACC
1 TGAGGATAATCCTCCTACTATCCCTCCACC
* * *
83763 TGAGGATATTCCTCATACTATCCATCCACC
1 TGAGGATAATCCTCCTACTATCCCTCCACC
* *
83793 TCAGGATACTCCTCCTACTATCCCTCCA
1 TGAGGATAATCCTCCTACTATCCCTCCA
83821 ATCTCTTCTC
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.23, C:0.38, G:0.11, T:0.28
Consensus pattern (30 bp):
TGAGGATAATCCTCCTACTATCCCTCCACC
Found at i:86738 original size:835 final size:832
Alignment explanation
Indices: 85129--86795 Score: 2250
Period size: 835 Copynumber: 2.0 Consensus size: 832
85119 GAGCCACAAA
*
85129 TTATGGTCACCGAAAAAAAGTGCAGGTGCACCACCACACTAACATTGACTGTGCGGGGGATAAAG
1 TTATGGTCACCGAAAAAAAGTGCAAGTGCACCACCACACTAACATTGACTGTGCGGGGGATAAAG
* * *
85194 ATCCCCAACTTCGCATACGAGTTCTCTATTCCTTAGATGGAGCATCTTTTATGCAAGGCCACAGA
66 ATCCCCAACTTCGCATACGAGTTCTCCATTCCTTAGAGGGAGCATCTTTTATGCAAGGCCACAAA
* * ** * * *
85259 GGATATCTTTCTTCTTCTGTTTTATGCTTTAGAGGTCAGTTTTCATCTGCTCTTACACACCTTCT
131 GAATACCTTTCTTCTTCTACTTTATGCTTTAGAGGTCAGTTTCCATATGCTCTCACACACCTTCT
* ** *
85324 TCTACAATCCTCTTAACTAGTACAAGCTTTCTTCGGGTCAGCTTTCTAATTTCTCTTGATGGTTG
196 TCTACAATCCTCTTAACGAGTACAAGCTGGCTCCGGGTCAGCTTTCTAATTTCTCTTGATGGTTG
* * *
85389 GTTACCCTACTTTCTCGACTGCTGCCAACACGATGAGATACCAATGATCATCGTTTTCTAAAATC
261 GTTACCCTACTTTCTCGACTGCTGCCAACACAACGAGATACCAATGATAATCGTTTTCTAAAATC
* * * * *
85454 TTTATAAGTTGAAACGCGGTGAAGGAGAGGACTTCATGGGCTTCTGTTACTTTAACTCTTGCACT
326 TCTATAACTTGAAACGCAGTGAAGGAGAGGACTTCAGGGGCTTCTGTTACTTTAACCCTTGCACT
*
85519 GGATTGAGAAAATCCATCCGAAACAATACATCTAGTCTTCACCTGAACTGCCACAAGTATATCAT
391 AGATTGAGAAAATCCATCCGAAACAATACATCTAGTCTTCACCTGAACTGCCACAAGTATATCAT
* ** ** *
85584 GATTAGTAGTAAGTTTAGGGATGGTTTTGGGTTTAATACCAAGTAGTTTTTTCAAACTAAAGACG
456 GATTAGCACCAAGTTTAGGGATGGTTTCAGGTTTAATACCAAGTAGTTTTTTCAAACTAAAGACA
* * *
85649 TGCGAAAATATAAGTGATCTCTTGATGTAGAAGGATCTCTTGAACAATTTAATATGCTAAAACTG
521 TGCGAAAATATAAGCGATCTCTTGAAGTAGAAGGATATCTTGAACAATTTAATATGCTAAAACTG
*
85714 GGGGACGTATTGACTTTTGAGACCCTCGTTACTGCATGTAATATCTTCAAATTTTGTATGGAAGG
586 GGGGACGTATTGACTTTGGAGACCCTCGTTACTG-ATGTAATATCTTCAAATTTTGTATGGAAGG
* * * *
85779 TCGTAGTCCTAACGGTTGGAGGTTGGCCGATAACAAAGCAGTCGCTCGATTCATTGGCGTAGTGC
650 TCGCAGTCCTAACGGTTGGAGGTTGGCCGATAACAAAGCAGTCACTCGATTCATCGGCATAGTGC
** *
85844 TTGAGGAAGATGCTAAGCCCCACCACTTTAGTGATCAATTGGTTTACACTTCAGTTGGGAAAAAG
715 TTGAGGAAGATGCTAAGCCCCACCACTCCAGCGATCAATTGGTTTACACTTCAGTTGGGAAAAAG
* *
85909 GAGGAGCCTATTAATTATTTCTACACTTATTGCAACATGAAACCTCGTTCATC
780 GAGGAGCCTATTAATTATTTCTACACTTACTGCAACATGAAACCTCATTCATC
* * * * * *
85962 TTATGGTCATCGAAAAAAAGTGCAAGTGTACCACCACACTGACTTTGATTGTGCGGGGGATAGAG
1 TTATGGTCACCGAAAAAAAGTGCAAGTGCACCACCACACTAACATTGACTGTGCGGGGGATAAAG
* * *
86027 ATTCCCAACTTCGCATACGAGTTCTCCATT-CTTGAGGGGGAGCATCTTTTATGCAAGGCCATAA
66 ATCCCCAACTTCGCATACGAGTTCTCCATTCCTT-AGAGGGAGCATCTTTTATGCAAGGCCACAA
* * *
86091 AGAATACCTTTCTTCTTCTACTTTATGCTTTTGAGGTCGGTTTCCATATGCT-TCCACACCCCTT
130 AGAATACCTTTCTTCTTCTACTTTATGCTTTAGAGGTCAGTTTCCATATGCTCT-CACACACCTT
* * * ** *
86155 CTTTTACAATTCTCTTAACGAGTACAAGCTGGCTCCGGG-CTAGCTTTTTGGTTTCTCTTGGTGG
194 CTTCTACAATCCTCTTAACGAGTACAAGCTGGCTCCGGGTC-AGCTTTCTAATTTCTCTTGATGG
** * * * *
86219 TTGGTTGTGTCCTACTTTCTCGACTGCTGCCAACGCAACGAGATATCAATGATAATTGTTTTCTG
258 TTGG-T-TACCCTACTTTCTCGACTGCTGCCAACACAACGAGATACCAATGATAATCGTTTTCTA
* * * *
86284 AAATCTCTATCACTTGAAAGGCAGTGAATGAGAGGACTTCAGGGGCTTTTGTTACTTTAACCCTT
321 AAATCTCTATAACTTGAAACGCAGTGAAGGAGAGGACTTCAGGGGCTTCTGTTACTTTAACCCTT
* * * * * *
86349 GCATTAGATTGTGAAAAT-TATTTCGAAACAATACATCTAGTCTTCGCTTGAACTGCCACAAGTA
386 GCACTAGATTGAGAAAATCCA-TCCGAAACAATACATCTAGTCTTCACCTGAACTGCCACAAGTA
* * * * * *
86413 TATCATGATTAGCACCAAGTTTGGGGATGGTTTCAGGTTTAATACCGAGTGGTTTTTTCCAGCTG
450 TATCATGATTAGCACCAAGTTTAGGGATGGTTTCAGGTTTAATACCAAGTAGTTTTTTCAAACTA
* * *
86478 AGGACATGTGAAAATATAAGCGATCTCTTGAAGTAGAAGGATATGTT-AGACAATTTAATATGCT
515 AAGACATGCGAAAATATAAGCGATCTCTTGAAGTAGAAGGATATCTTGA-ACAATTTAATATGCT
* * * *
86542 AAAAGTGGGTGTCGTGTTGACTTTGGAGACCCTCGTTACCATG-TGTAATATCTTCAAATTTTGT
579 AAAACTGGGGGACGTATTGACTTTGGAGACCCTCGTTA-C-TGATGTAATATCTTCAAATTTTGT
* ** ** *
86606 ATGGAAGGTTGCAGTCCTAACGAG-TGGAGGTTGGGTGATAATGAGGCAGTCACTCGATTCATCG
642 ATGGAAGGTCGCAGTCCTAACG-GTTGGAGGTTGGCCGATAACAAAGCAGTCACTCGATTCATCG
* ** * * **
86670 GCATAGTGCTTGAGGAATATGCTTGGCCCCACCACTCCAGCGATCAGTTGGTTTACATTTTGGTT
706 GCATAGTGCTTGAGGAAGATGCTAAGCCCCACCACTCCAGCGATCAATTGGTTTACACTTCAGTT
*
86735 GGGAAAAATGAGGAGCCTATTAATTATTTCTACACTTACTGCAACATGAAACCTCATTCAT
771 GGGAAAAAGGAGGAGCCTATTAATTATTTCTACACTTACTGCAACATGAAACCTCATTCAT
86796 GTGTCTTGCT
Statistics
Matches: 720, Mismatches: 104, Indels: 18
0.86 0.12 0.02
Matches are distributed among these distances:
832 5 0.01
833 220 0.31
834 3 0.00
835 488 0.68
836 2 0.00
837 2 0.00
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.33
Consensus pattern (832 bp):
TTATGGTCACCGAAAAAAAGTGCAAGTGCACCACCACACTAACATTGACTGTGCGGGGGATAAAG
ATCCCCAACTTCGCATACGAGTTCTCCATTCCTTAGAGGGAGCATCTTTTATGCAAGGCCACAAA
GAATACCTTTCTTCTTCTACTTTATGCTTTAGAGGTCAGTTTCCATATGCTCTCACACACCTTCT
TCTACAATCCTCTTAACGAGTACAAGCTGGCTCCGGGTCAGCTTTCTAATTTCTCTTGATGGTTG
GTTACCCTACTTTCTCGACTGCTGCCAACACAACGAGATACCAATGATAATCGTTTTCTAAAATC
TCTATAACTTGAAACGCAGTGAAGGAGAGGACTTCAGGGGCTTCTGTTACTTTAACCCTTGCACT
AGATTGAGAAAATCCATCCGAAACAATACATCTAGTCTTCACCTGAACTGCCACAAGTATATCAT
GATTAGCACCAAGTTTAGGGATGGTTTCAGGTTTAATACCAAGTAGTTTTTTCAAACTAAAGACA
TGCGAAAATATAAGCGATCTCTTGAAGTAGAAGGATATCTTGAACAATTTAATATGCTAAAACTG
GGGGACGTATTGACTTTGGAGACCCTCGTTACTGATGTAATATCTTCAAATTTTGTATGGAAGGT
CGCAGTCCTAACGGTTGGAGGTTGGCCGATAACAAAGCAGTCACTCGATTCATCGGCATAGTGCT
TGAGGAAGATGCTAAGCCCCACCACTCCAGCGATCAATTGGTTTACACTTCAGTTGGGAAAAAGG
AGGAGCCTATTAATTATTTCTACACTTACTGCAACATGAAACCTCATTCATC
Found at i:87772 original size:20 final size:20
Alignment explanation
Indices: 87744--87782 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
87734 AGTTTTAGGA
87744 AGAAAAAAA-AACAAAAATTG
1 AGAAAAAAAGAA-AAAAATTG
*
87764 AGAACAAAAGAAAAAAATT
1 AGAAAAAAAGAAAAAAATT
87783 TCTGAGATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.74, C:0.05, G:0.10, T:0.10
Consensus pattern (20 bp):
AGAAAAAAAGAAAAAAATTG
Found at i:88987 original size:80 final size:80
Alignment explanation
Indices: 88816--88986 Score: 267
Period size: 80 Copynumber: 2.1 Consensus size: 80
88806 AATTACACTT
* * **
88816 GACCCCTAAAAATGATGAAATTTTTATTTAATCCTTTAAATTTGCATTTTTACTATCATAAAAAT
1 GACCCCTAAAAATGATAAAATTTTGATTTAATCCTTTAAAACTGCATTTTTACTATCATAAAAAT
88881 TACAATTTAACTTTTC
66 TACAATTTAAC-TTTC
88897 --CCTCCTAAAAATGATAAAATTTTGATTTAATCCTTTAAAACTGCATTTTTACTATCATAAAAA
1 GACC-CCTAAAAATGATAAAATTTTGATTTAATCCTTTAAAACTGCATTTTTACTATCATAAAAA
88960 TTACAATTTAA-TTTC
65 TTACAATTTAACTTTC
88975 GACCCCTAAAAA
1 GACCCCTAAAAA
88987 AATTTTTTGC
Statistics
Matches: 83, Mismatches: 4, Indels: 8
0.87 0.04 0.08
Matches are distributed among these distances:
78 4 0.05
79 10 0.12
80 69 0.83
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.40
Consensus pattern (80 bp):
GACCCCTAAAAATGATAAAATTTTGATTTAATCCTTTAAAACTGCATTTTTACTATCATAAAAAT
TACAATTTAACTTTC
Found at i:96328 original size:18 final size:20
Alignment explanation
Indices: 96302--96344 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
96292 ACAATTACCG
96302 TTATAACATAAAT-TTATAT
1 TTATAACATAAATATTATAT
96321 TTAT-ACATAAATAATTATAT
1 TTATAACATAAAT-ATTATAT
96341 TTAT
1 TTAT
96345 CTAATATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.36
19 4 0.18
20 10 0.45
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATAACATAAATATTATAT
Found at i:98975 original size:10 final size:10
Alignment explanation
Indices: 98932--98988 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
98922 ATAAAATCAT
* *
98932 AAAATTATAT
1 AAAAATATAA
98942 AAAAAT-TAA
1 AAAAATATAA
*
98951 AATAATATTTAA
1 AA-AA-ATATAA
*
98963 AAAACTATAA
1 AAAAATATAA
98973 AAAAATATAA
1 AAAAATATAA
98983 AAAAAT
1 AAAAAT
98989 TCAAGAGCAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
9 4 0.10
10 26 0.67
11 4 0.10
12 5 0.13
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (10 bp):
AAAAATATAA
Found at i:99137 original size:25 final size:24
Alignment explanation
Indices: 99075--99142 Score: 73
Period size: 25 Copynumber: 2.8 Consensus size: 24
99065 CAGAAAATAT
*
99075 TAAAAATGATAAAAAATATTTAAAA
1 TAAAAATTATAAAAAA-ATTTAAAA
*
99100 TAAAAATTGTAAAAAAATTTAAATA
1 TAAAAATTATAAAAAAATTTAAA-A
** *
99125 TTGAAGTTATAAAAAAAT
1 TAAAAATTATAAAAAAAT
99143 ATTATAAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
24 7 0.19
25 29 0.81
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (24 bp):
TAAAAATTATAAAAAAATTTAAAA
Found at i:100060 original size:26 final size:26
Alignment explanation
Indices: 100028--100077 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
100018 TTTTATTAAA
* *
100028 ATTTTAAATAATTTTAATAATTTTGT
1 ATTTTAAAAAAATTTAATAATTTTGT
*
100054 ATTTTAAAAAAATTTCATAATTTT
1 ATTTTAAAAAAATTTAATAATTTT
100078 TTACAATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (26 bp):
ATTTTAAAAAAATTTAATAATTTTGT
Found at i:102492 original size:18 final size:18
Alignment explanation
Indices: 102469--102505 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
102459 TAAAATTCCC
102469 AACAAGATCAAGTATGGT
1 AACAAGATCAAGTATGGT
102487 AACAAGATCAAGTATGGT
1 AACAAGATCAAGTATGGT
102505 A
1 A
102506 CATTTCAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.22, T:0.22
Consensus pattern (18 bp):
AACAAGATCAAGTATGGT
Found at i:104627 original size:30 final size:30
Alignment explanation
Indices: 104585--104643 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
104575 ATTAATTTAC
*
104585 TAAACTTTTTAATATAAATTCAATACTTAT
1 TAAACTTTTTAATAAAAATTCAATACTTAT
104615 TAAA-TTTATTAATAAAAATTCAATACTTA
1 TAAACTTT-TTAATAAAAATTCAATACTTA
104644 ATTATTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 3 0.11
30 24 0.89
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.44
Consensus pattern (30 bp):
TAAACTTTTTAATAAAAATTCAATACTTAT
Found at i:104721 original size:3 final size:3
Alignment explanation
Indices: 104713--104745 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
104703 AGCTTTTTAA
104713 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
104746 GTTGTTTATA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:113559 original size:24 final size:24
Alignment explanation
Indices: 113531--113593 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
113521 AGAAATAATC
113531 TTTCAGTTAAACTCTGTTTATTTA
1 TTTCAGTTAAACTCTGTTTATTTA
* *
113555 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTATTTA
* *
113579 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
113594 TATTAGTCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.25, C:0.14, G:0.10, T:0.51
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTATTTA
Found at i:113946 original size:23 final size:23
Alignment explanation
Indices: 113920--113964 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
113910 GGTATCAGAG
113920 TTAGTTCGATTTTCGTAAATCAT
1 TTAGTTCGATTTTCGTAAATCAT
*
113943 TTAGTTTGATTTTCGTAAATCA
1 TTAGTTCGATTTTCGTAAATCA
113965 GCCCGTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.11, G:0.13, T:0.49
Consensus pattern (23 bp):
TTAGTTCGATTTTCGTAAATCAT
Found at i:115533 original size:24 final size:25
Alignment explanation
Indices: 115474--115544 Score: 78
Period size: 24 Copynumber: 3.0 Consensus size: 25
115464 AGAAATAATA
115474 TTTT-AGTCAAACTCTGTTTAATTG
1 TTTTAAGTCAAACTCTGTTTAATTG
* * *
115498 TTTCAA-TTAAACTCTGTTT-ATTT
1 TTTTAAGTCAAACTCTGTTTAATTG
115521 TTTTAAGTCAAACTCT-TATTAATT
1 TTTTAAGTCAAACTCTGT-TTAATT
115545 TAGATTATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
23 9 0.24
24 25 0.66
25 4 0.11
ACGTcount: A:0.28, C:0.13, G:0.07, T:0.52
Consensus pattern (25 bp):
TTTTAAGTCAAACTCTGTTTAATTG
Found at i:119920 original size:30 final size:31
Alignment explanation
Indices: 119876--119947 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 31
119866 TAATAAATGC
119876 TAAAATTATAATTTGATCATTTTAAAAAAATA
1 TAAAATTATAATTTGATC-TTTTAAAAAAATA
* *
119908 -AAAATT-TGATTTGATCTTTTAAAAAATTA
1 TAAAATTATAATTTGATCTTTTAAAAAAATA
119937 TAAAATTATAA
1 TAAAATTATAA
119948 ACTATTGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 12 0.34
30 15 0.43
31 8 0.23
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (31 bp):
TAAAATTATAATTTGATCTTTTAAAAAAATA
Found at i:126234 original size:29 final size:31
Alignment explanation
Indices: 126185--126249 Score: 84
Period size: 29 Copynumber: 2.2 Consensus size: 31
126175 GATAGACTTG
*
126185 AATT-TTAAAGTCTGAAAAATA-GATGGACTA
1 AATTCTTAAAGTCTGAAAAATATAAT-GACTA
126215 AATTCTTAAAGT-T-AAAAATATAATGACTA
1 AATTCTTAAAGTCTGAAAAATATAATGACTA
126244 AATTCT
1 AATTCT
126250 AAATTTATGA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
29 18 0.56
30 7 0.22
31 7 0.22
ACGTcount: A:0.48, C:0.08, G:0.11, T:0.34
Consensus pattern (31 bp):
AATTCTTAAAGTCTGAAAAATATAATGACTA
Found at i:126377 original size:66 final size:66
Alignment explanation
Indices: 126271--126400 Score: 215
Period size: 66 Copynumber: 2.0 Consensus size: 66
126261 GAATATAAAG
* * *
126271 ACTTATAATATAATTTAATCATATTTTTTTAAGGTAAACTAGAAAAGTAATCACCCAACTATTAG
1 ACTTATAATATAATTTAATCATAATTTTTTAAAGTAAACTAGAAAAATAATCACCCAACTATTAG
126336 T
66 T
* *
126337 ACTTATAATATAATTTAATCATAATTTTTTAAAGTAAACTATAAAAATAGTCACCCAACTATTA
1 ACTTATAATATAATTTAATCATAATTTTTTAAAGTAAACTAGAAAAATAATCACCCAACTATTA
126401 CTGTGTTTCT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (66 bp):
ACTTATAATATAATTTAATCATAATTTTTTAAAGTAAACTAGAAAAATAATCACCCAACTATTAG
T
Found at i:127717 original size:2 final size:2
Alignment explanation
Indices: 127712--127746 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
127702 GAGGGAAACA
127712 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
127747 AATGGGGTGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:128057 original size:20 final size:20
Alignment explanation
Indices: 128032--128076 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
128022 ACAACAAAGG
*
128032 TCTAACGC-AATATCAATATT
1 TCTAACGCGAA-ATCAAAATT
128052 TCTAACGCGAAATCAAAATT
1 TCTAACGCGAAATCAAAATT
128072 TCTAA
1 TCTAA
128077 TTTTGTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (20 bp):
TCTAACGCGAAATCAAAATT
Found at i:128163 original size:40 final size:38
Alignment explanation
Indices: 128085--128163 Score: 86
Period size: 40 Copynumber: 2.0 Consensus size: 38
128075 AATTTTGTAT
* * *
128085 TAAAAATATTGGTATGGATTATAAATTTCAATATCCAA
1 TAAAAATATTGGTATGCATTAAAAATTTCAATACCCAA
* * *
128123 TAAAAATATTTTGTATTGCATTAAAAATTTTAGTACCCAA
1 TAAAAATA-TTGGTA-TGCATTAAAAATTTCAATACCCAA
128163 T
1 T
128164 GGAAATTGAG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
38 8 0.24
39 5 0.15
40 20 0.61
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (38 bp):
TAAAAATATTGGTATGCATTAAAAATTTCAATACCCAA
Found at i:129399 original size:59 final size:60
Alignment explanation
Indices: 129336--129468 Score: 142
Period size: 59 Copynumber: 2.2 Consensus size: 60
129326 AAATACAAAT
* * * * *
129336 AAAAAATTATTTTTTTGGTGTCTTTCAAACTATGACCAACATCTCTTTTTT-AGATACCA
1 AAAAAAATATTTTTTCGATGTCTATCAAACTATGACCAACACCTCTTTTTTCAGATACCA
* **** * **
129395 AAAAAAAAAAAAATTCGATGTCTATCAATCTATGACTGACACCTCTTTTTTCAGATACCA
1 AAAAAAATATTTTTTCGATGTCTATCAAACTATGACCAACACCTCTTTTTTCAGATACCA
129455 AAAAAAATATTTTT
1 AAAAAAATATTTTT
129469 GAATGCTTAT
Statistics
Matches: 55, Mismatches: 18, Indels: 1
0.74 0.24 0.01
Matches are distributed among these distances:
59 38 0.69
60 17 0.31
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.37
Consensus pattern (60 bp):
AAAAAAATATTTTTTCGATGTCTATCAAACTATGACCAACACCTCTTTTTTCAGATACCA
Found at i:129672 original size:58 final size:58
Alignment explanation
Indices: 129561--129675 Score: 160
Period size: 58 Copynumber: 2.0 Consensus size: 58
129551 GACACCCACC
* ***
129561 AAAAATACGAATAAAAAAATAATATTTTTTATGTTTGACAAGTAATGGTCGACACCAT
1 AAAAATACGAATAAAAAAATAATATTTTTTATGTTTGACAACTAATAACCGACACCAT
* *
129619 AAAAATACGAATTAAAAAATAA-ATTTTTTGGTGTTTGACAACTAATAACCGACACCA
1 AAAAATACGAATAAAAAAATAATATTTTTT-ATGTTTGACAACTAATAACCGACACCA
129676 ACTTTCCTTC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
57 7 0.14
58 43 0.86
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.30
Consensus pattern (58 bp):
AAAAATACGAATAAAAAAATAATATTTTTTATGTTTGACAACTAATAACCGACACCAT
Found at i:129966 original size:40 final size:38
Alignment explanation
Indices: 129900--129984 Score: 107
Period size: 40 Copynumber: 2.2 Consensus size: 38
129890 AATTTTGTAT
* *
129900 TAAAAATATTGGTATGGATTATAAATTTTAATATCCAA
1 TAAAAATATTGGTATGCATTAAAAATTTTAATATCCAA
* *
129938 TAAAAATATTTTGTATTGCATTAAAAATTTTAGTATCCAA
1 TAAAAATA-TTGGTA-TGCATTAAAAATTTTAATATCCAA
*
129978 TGAAAAT
1 TAAAAAT
129985 TGAGACATGA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 8 0.20
39 5 0.12
40 27 0.68
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.40
Consensus pattern (38 bp):
TAAAAATATTGGTATGCATTAAAAATTTTAATATCCAA
Found at i:129983 original size:20 final size:19
Alignment explanation
Indices: 129922--129985 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
129912 TATGGATTAT
*
129922 AAATTTTAATATCCAATAA
1 AAATTTTAGTATCCAATAA
* * *
129941 AAATATTTTGTATTGCATTAA
1 AAAT-TTTAGTA-TCCAATAA
*
129962 AAATTTTAGTATCCAATGA
1 AAATTTTAGTATCCAATAA
129981 AAATT
1 AAATT
129986 GAGACATGAG
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
19 14 0.40
20 11 0.31
21 10 0.29
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.41
Consensus pattern (19 bp):
AAATTTTAGTATCCAATAA
Found at i:131398 original size:58 final size:58
Alignment explanation
Indices: 131308--131426 Score: 202
Period size: 58 Copynumber: 2.1 Consensus size: 58
131298 TAACTGTATC
* *
131308 TACCTCAAGTAAATAACATACAACAGCAGTATAACCAATGGCTTCCAAGTTCTAATGA
1 TACCTCAAGCAAATAACATACAACAGCAGTATAACCAATGCCTTCCAAGTTCTAATGA
* *
131366 TACCTCGAGCAAATAACATACAACAGCAGTATAACCAATTCCTTCCAAGTTCTAATGA
1 TACCTCAAGCAAATAACATACAACAGCAGTATAACCAATGCCTTCCAAGTTCTAATGA
131424 TAC
1 TAC
131427 TAGGTCAAAG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.40, C:0.24, G:0.11, T:0.24
Consensus pattern (58 bp):
TACCTCAAGCAAATAACATACAACAGCAGTATAACCAATGCCTTCCAAGTTCTAATGA
Found at i:138515 original size:32 final size:31
Alignment explanation
Indices: 138479--138542 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
138469 TAAGGATAGA
138479 TGTAAAAATTATACATAAATTTTAATTTAATG
1 TGTAAAAA-TATACATAAATTTTAATTTAATG
** * *
138511 TGTAATTATATACATGAATTTTAATTTGATG
1 TGTAAAAATATACATAAATTTTAATTTAATG
138542 T
1 T
138543 AATTATACAC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 22 0.79
32 6 0.21
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (31 bp):
TGTAAAAATATACATAAATTTTAATTTAATG
Found at i:138525 original size:31 final size:29
Alignment explanation
Indices: 138488--138549 Score: 88
Period size: 31 Copynumber: 2.1 Consensus size: 29
138478 ATGTAAAAAT
138488 TATACATAAATTTTAATTTAATGTGTAATTA
1 TATACATAAATTTTAATTTAA--TGTAATTA
* *
138519 TATACATGAATTTTAATTTGATGTAATTA
1 TATACATAAATTTTAATTTAATGTAATTA
138548 TA
1 TA
138550 CACGTTAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 10 0.34
31 19 0.66
ACGTcount: A:0.40, C:0.03, G:0.08, T:0.48
Consensus pattern (29 bp):
TATACATAAATTTTAATTTAATGTAATTA
Done.