Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004959.1 Kokia drynarioides strain JFW-HI SEQ_118686, 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: 96131
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:1768 original size:21 final size:20
Alignment explanation
Indices: 1742--1785 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
1732 TGAAAACTAT
1742 TTACAAATAAAATCCCTAAGA
1 TTAC-AATAAAATCCCTAAGA
* *
1763 TTACAATCAAATCTCTAAGA
1 TTACAATAAAATCCCTAAGA
1783 TTA
1 TTA
1786 TAAGAATCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.48, C:0.18, G:0.05, T:0.30
Consensus pattern (20 bp):
TTACAATAAAATCCCTAAGA
Found at i:1816 original size:18 final size:17
Alignment explanation
Indices: 1783--1835 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 17
1773 ATCTCTAAGA
*
1783 TTATAAGAAT-CATATC
1 TTATAAGATTACATATC
*
1799 TTCTAAGATTTACATATC
1 TTATAAGA-TTACATATC
* *
1817 ATATAAGATTGCATATC
1 TTATAAGATTACATATC
1834 TT
1 TT
1836 GATGATTACG
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
16 7 0.24
17 10 0.34
18 12 0.41
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.42
Consensus pattern (17 bp):
TTATAAGATTACATATC
Found at i:1817 original size:23 final size:21
Alignment explanation
Indices: 1757--1820 Score: 67
Period size: 23 Copynumber: 2.9 Consensus size: 21
1747 AATAAAATCC
*
1757 CTAAGA-TTACAATCAAATCT
1 CTAAGATTTACAATCATATCT
*
1777 CTAAGATTATAAGAATCATATCTT
1 CTAAGATT-T-ACAATCATATC-T
1801 CTAAGATTTACATATCATAT
1 CTAAGATTTACA-ATCATAT
1821 AAGATTGCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
20 6 0.17
21 1 0.03
22 3 0.08
23 17 0.47
24 9 0.25
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.36
Consensus pattern (21 bp):
CTAAGATTTACAATCATATCT
Found at i:10887 original size:38 final size:38
Alignment explanation
Indices: 10831--10962 Score: 151
Period size: 38 Copynumber: 3.5 Consensus size: 38
10821 AAAAGAGAAA
* *
10831 TACTGATTATACTGAATGCCTGCTTAAGAGAGCAAATC
1 TACTAATTATACTGAATGCTTGCTTAAGAGAGCAAATC
*
10869 TACTAATTATACTGAATGCTTGCTTAAGCA-AGCGAATC
1 TACTAATTATACTGAATGCTTGCTTAAG-AGAGCAAATC
* * * *
10907 TATTGATTATACTGAATGCTTGCTCAAGCGAG-AGAATC
1 TACTAATTATACTGAATGCTTGCTTAAGAGAGCA-AATC
* *
10945 CACTAATTTTACTGAATG
1 TACTAATTATACTGAATG
10963 TTCGCTCAAA
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
38 78 0.99
39 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Consensus pattern (38 bp):
TACTAATTATACTGAATGCTTGCTTAAGAGAGCAAATC
Found at i:10970 original size:38 final size:38
Alignment explanation
Indices: 10823--10971 Score: 144
Period size: 38 Copynumber: 3.9 Consensus size: 38
10813 TTGAAACGAA
* * * *
10823 AAGAGAA-ATACTGATTATACTGAATGCCTGCTTAAG-
1 AAGAGAATCTACTAATTATACTGAATGCTTGCTCAAGC
*
10859 -AGAGCAAATCTACTAATTATACTGAATGCTTGCTTAAGC
1 AAGAG--AATCTACTAATTATACTGAATGCTTGCTCAAGC
* * *
10898 AAGCGAATCTATTGATTATACTGAATGCTTGCTCAAGC
1 AAGAGAATCTACTAATTATACTGAATGCTTGCTCAAGC
* * *
10936 GAGAGAATCCACTAATTTTACTGAATG-TTCGCTCAA
1 AAGAGAATCTACTAATTATACTGAATGCTT-GCTCAA
10972 ATGAGCAATA
Statistics
Matches: 94, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
35 4 0.04
37 4 0.04
38 83 0.88
40 3 0.03
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (38 bp):
AAGAGAATCTACTAATTATACTGAATGCTTGCTCAAGC
Found at i:15487 original size:30 final size:30
Alignment explanation
Indices: 15453--15564 Score: 102
Period size: 30 Copynumber: 3.8 Consensus size: 30
15443 AAATAAATGC
*
15453 GTAATTTTTGAAAAGTTCGAGGGTTAAAAT
1 GTAATTTTTGAGAAGTTCGAGGGTTAAAAT
* * *
15483 GTAATTTTTGTGAAGTTTGGGGGTTAAAAT
1 GTAATTTTTGAGAAGTTCGAGGGTTAAAAT
* * ** * *
15513 -TTATTTTTTATGAAGTTTAAGGGTCAAATT
1 GTAATTTTTGA-GAAGTTCGAGGGTTAAAAT
*
15543 GTGATTTTTGAGAAGTTC-AGGG
1 GTAATTTTTGAGAAGTTCGAGGG
15565 ACCTTCTGGG
Statistics
Matches: 66, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
29 11 0.17
30 47 0.71
31 8 0.12
ACGTcount: A:0.29, C:0.03, G:0.26, T:0.42
Consensus pattern (30 bp):
GTAATTTTTGAGAAGTTCGAGGGTTAAAAT
Found at i:16497 original size:3 final size:3
Alignment explanation
Indices: 16491--16567 Score: 86
Period size: 3 Copynumber: 25.7 Consensus size: 3
16481 TTCAATTTTT
** *
16491 TTA TTA TCT- TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA TCA TTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
16536 TTA TTA TTA TTA -TA TTTA TTA TTA TCA TTA TT
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TT
16568 GTTAATGTTA
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
2 3 0.05
3 56 0.90
4 3 0.05
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:17226 original size:12 final size:12
Alignment explanation
Indices: 17209--17265 Score: 53
Period size: 12 Copynumber: 4.4 Consensus size: 12
17199 ATTTGTTTTT
17209 TTAAATTTAAAA
1 TTAAATTTAAAA
17221 TTAAATTTAGAATAA
1 TTAAATTT--AA-AA
*
17236 CTTTTAATTTAAAA
1 --TTAAATTTAAAA
17250 -TAAATTTAAAA
1 TTAAATTTAAAA
17261 TTAAA
1 TTAAA
17266 GGTTTGGCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
11 10 0.27
12 12 0.32
14 4 0.11
15 4 0.11
17 7 0.19
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (12 bp):
TTAAATTTAAAA
Found at i:17264 original size:17 final size:17
Alignment explanation
Indices: 17216--17265 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
17206 TTTTTAAATT
* *
17216 TAAAATTAAATTTAGAA
1 TAAATTTAAATTTAAAA
* *
17233 TAACTTTTAATTTAAAA
1 TAAATTTAAATTTAAAA
*
17250 TAAATTTAAAATTAAA
1 TAAATTTAAATTTAAA
17266 GGTTTGGCTT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:17809 original size:48 final size:48
Alignment explanation
Indices: 17737--17849 Score: 174
Period size: 48 Copynumber: 2.4 Consensus size: 48
17727 GATCTGGTTC
*
17737 ACTTCTCTA-TATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCT
1 ACTTCTC-AGTATCTCATCAAGAAGGTAACCGCTTTATTGCTTCGACCT
* *
17785 ACTTCTCAGTATCTTATCAAGAAGGTAACCGCTTTATTGTTTCGACCT
1 ACTTCTCAGTATCTCATCAAGAAGGTAACCGCTTTATTGCTTCGACCT
*
17833 GCTTCTCAGTATCTCAT
1 ACTTCTCAGTATCTCAT
17850 TAGGAAGCTA
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
47 1 0.02
48 58 0.98
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (48 bp):
ACTTCTCAGTATCTCATCAAGAAGGTAACCGCTTTATTGCTTCGACCT
Found at i:18160 original size:209 final size:209
Alignment explanation
Indices: 17788--18356 Score: 789
Period size: 209 Copynumber: 2.7 Consensus size: 209
17778 TCGACCTACT
* * ** * * * *
17788 TCTCAGTATCTTATCAAGAAGGTAACCGCTTTATTGTTTCGACCTGCTTCTCAGTATCTCATTAG
1 TCTCTGTATCTCATCAAGAAGGTAACCATTTTATTGCTTCGACATGCTTCTCAATATCTCATCAG
* * * * *
17853 GAAGCTAGAGTTCGAAGATTTGCTCACTTTGAG-TCTGGTTTCATTGATTTGGTCTACTTCTTAG
66 GAAGCTGGGGTTCGAAGTTTTGCTCACATTGAGCT-TGGTTTCATTGATTTGGTCTACTTCTCAG
* * * *
17917 TATCTCATTAGGAAGATGACCGCATCATTTGTTTTGATCCACTTCTCTGTGTCTCATTAGGAAGA
130 TATCTCATTAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTGTGTCTCATCAAGAAAA
*
17982 CAGATCTGGTTCACA
195 CAGATCTGGTCCACA
* * *
17997 TCTCTGTATCTCATCAAGAAGGTAACCATTTTATTGGTTCGACTTGCTTCTCATTATCTCATCAG
1 TCTCTGTATCTCATCAAGAAGGTAACCATTTTATTGCTTCGACATGCTTCTCAATATCTCATCAG
* *
18062 GATGCTGGGGTTCGAAGTTTTGCTCGCATTGAGCTTGGTTTCATTGATTTGGTCTACTTCTCAGT
66 GAAGCTGGGGTTCGAAGTTTTGCTCACATTGAGCTTGGTTTCATTGATTTGGTCTACTTCTCAGT
* *
18127 ATCTCATTAGGAAGATGACTGCATCACTTGTTTTGATCCACTTCTCTGTGTCTCATCAAGAAAAT
131 ATCTCATTAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTGTGTCTCATCAAGAAAAC
* *
18192 GGATCTGGTCCACT
196 AGATCTGGTCCACA
* *
18206 TCTCTGTATCTCATCAAGAAGCTGACCATTTTATTGCTTCGACATGCTTCTCAATATCTCATCAG
1 TCTCTGTATCTCATCAAGAAGGTAACCATTTTATTGCTTCGACATGCTTCTCAATATCTCATCAG
* * * * *
18271 GAAGCTGGGGTTCGAAGTTTTGCTCACACTGAGCTTTGTTTCATTGAGTTGGTATACTTCTCTGT
66 GAAGCTGGGGTTCGAAGTTTTGCTCACATTGAGCTTGGTTTCATTGATTTGGTCTACTTCTCAGT
* * *
18336 ATGTCATCAAGAAGATGACCG
131 ATCTCATTAGGAAGATGACCG
18357 TCTCGTTGTT
Statistics
Matches: 319, Mismatches: 40, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
209 318 1.00
210 1 0.00
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (209 bp):
TCTCTGTATCTCATCAAGAAGGTAACCATTTTATTGCTTCGACATGCTTCTCAATATCTCATCAG
GAAGCTGGGGTTCGAAGTTTTGCTCACATTGAGCTTGGTTTCATTGATTTGGTCTACTTCTCAGT
ATCTCATTAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTGTGTCTCATCAAGAAAAC
AGATCTGGTCCACA
Found at i:21669 original size:23 final size:23
Alignment explanation
Indices: 21639--21685 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
21629 CAGTCAAATG
21639 TGAAATGAACCGAGCAATGTAAT
1 TGAAATGAACCGAGCAATGTAAT
21662 TGAAATGAACCGAGCAATGTAAT
1 TGAAATGAACCGAGCAATGTAAT
21685 T
1 T
21686 TAGTCTTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.23
Consensus pattern (23 bp):
TGAAATGAACCGAGCAATGTAAT
Found at i:30054 original size:59 final size:58
Alignment explanation
Indices: 29988--30101 Score: 151
Period size: 58 Copynumber: 1.9 Consensus size: 58
29978 GGGAAAATGA
* *
29988 TAATTTTGAACAC-TTCGGTGGCAAAAATGGTAATTTTT-GAATGTTCGAGGGTAAAAGGG
1 TAATTTTGAACACTTTAGG-GGC-AAAATGGTAATTTTTAGAA-GTTCAAGGGTAAAAGGG
* *
30047 TAATTTTGGACACTTTAGGGGCAAAATGGTAATTTTTAGAAGTTTAAGGGTAAAA
1 TAATTTTGAACACTTTAGGGGCAAAATGGTAATTTTTAGAAGTTCAAGGGTAAAA
30102 ATGTGATTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
58 27 0.55
59 18 0.37
60 4 0.08
ACGTcount: A:0.34, C:0.07, G:0.25, T:0.33
Consensus pattern (58 bp):
TAATTTTGAACACTTTAGGGGCAAAATGGTAATTTTTAGAAGTTCAAGGGTAAAAGGG
Found at i:30092 original size:29 final size:29
Alignment explanation
Indices: 30069--30247 Score: 180
Period size: 30 Copynumber: 5.9 Consensus size: 29
30059 CTTTAGGGGC
* *
30069 AAAATGGTAATTTTTAGAAGTTTAAGGGTA
1 AAAAT-GTAATTTTTAGAAGTTTGAGGGTT
* * * **
30099 AAAATGTGATTTTTTTGGAAGTTTAGGGGGAA
1 AAAATGT-A-ATTTTTAGAAGTTT-GAGGGTT
*
30131 AAAATGTAATTTTTGGAAAGTTTGAGGGTT
1 AAAATGTAATTTTTAG-AAGTTTGAGGGTT
*
30161 AAAATGTAATTTTTGTGAAGTTTGAGGGTT
1 AAAATGTAATTTTT-AGAAGTTTGAGGGTT
30191 AAAATGTAATTTTTATGAAGTTTGAGGGTT
1 AAAATGTAATTTTTA-GAAGTTTGAGGGTT
* *
30221 AGAATGTGATTTTTGAGAAGTTT-AGGG
1 AAAATGTAATTTTT-AGAAGTTTGAGGG
30248 ACCTTTTGGG
Statistics
Matches: 129, Mismatches: 13, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
29 6 0.05
30 91 0.71
31 21 0.16
32 11 0.09
ACGTcount: A:0.33, C:0.00, G:0.27, T:0.40
Consensus pattern (29 bp):
AAAATGTAATTTTTAGAAGTTTGAGGGTT
Found at i:30203 original size:60 final size:58
Alignment explanation
Indices: 30010--30248 Score: 209
Period size: 60 Copynumber: 4.0 Consensus size: 58
30000 CTTCGGTGGC
* * * *
30010 AAAAATGGTAATTTTTGAATGTTCGAGGG-TAAAAGGGTAA-TTTTG-GACACTTTAGGGG
1 AAAAATGGTAATTTTTGAA-GTTTGAGGGTTAAAA-TGTAATTTTTGTGA-AGTTTAGGGA
* * * * *
30068 CAAAATGGTAATTTTTAGAAGTTTAAGGGTAAAAATGTGATTTTTTTGGAAGTTTAGGGGGA
1 AAAAATGGTAATTTTT-GAAGTTTGAGGGTTAAAATGTAATTTTTGT-GAAGTTTA--GGGA
*
30130 AAAAAT-GTAATTTTTGGAAAGTTTGAGGGTTAAAATGTAATTTTTGTGAAGTTTGAGGGT
1 AAAAATGGTAATTTTT-G-AAGTTTGAGGGTTAAAATGTAATTTTTGTGAAGTTT-AGGGA
* * * *
30190 TAAAAT-GTAATTTTTATGAAGTTTGAGGGTTAGAATGTGATTTTTGAGAAGTTTAGGGA
1 AAAAATGGTAA-TTTT-TGAAGTTTGAGGGTTAAAATGTAATTTTTGTGAAGTTTAGGGA
30249 CCTTTTGGGT
Statistics
Matches: 149, Mismatches: 21, Indels: 21
0.78 0.11 0.11
Matches are distributed among these distances:
58 25 0.17
59 15 0.10
60 50 0.34
61 24 0.16
62 35 0.23
ACGTcount: A:0.33, C:0.02, G:0.28, T:0.38
Consensus pattern (58 bp):
AAAAATGGTAATTTTTGAAGTTTGAGGGTTAAAATGTAATTTTTGTGAAGTTTAGGGA
Found at i:31324 original size:3 final size:3
Alignment explanation
Indices: 31309--31379 Score: 99
Period size: 3 Copynumber: 23.7 Consensus size: 3
31299 AATTTTGTTT
**
31309 TTA TTA TCT- TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
31354 TTA TTA TTA TTA TTA TTA TCA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
31380 GTTAACATTA
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
2 1 0.02
3 58 0.97
4 1 0.02
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:31388 original size:12 final size:12
Alignment explanation
Indices: 31318--31391 Score: 64
Period size: 12 Copynumber: 6.4 Consensus size: 12
31308 TTTATTATCT
*
31318 TTATTATTAAAA
1 TTATTATTAACA
31330 TTATTATT---A
1 TTATTATTAACA
**
31339 TTATTATTATTA
1 TTATTATTAACA
**
31351 TTATTATTATTA
1 TTATTATTAACA
*
31363 TTATTATTATCA
1 TTATTATTAACA
*
31375 TTATTGTTAACA
1 TTATTATTAACA
31387 TTATT
1 TTATT
31392 TATTCGATGT
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
9 9 0.16
12 47 0.84
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (12 bp):
TTATTATTAACA
Found at i:32068 original size:12 final size:12
Alignment explanation
Indices: 32053--32089 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
32043 GACTTTTTTT
32053 AATTTAAAATTA
1 AATTTAAAATTA
*
32065 AATTTAGAA-TA
1 AATTTAAAATTA
32076 AATTTAAAATTA
1 AATTTAAAATTA
32088 AA
1 AA
32090 GTTTTGGCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (12 bp):
AATTTAAAATTA
Found at i:34172 original size:18 final size:19
Alignment explanation
Indices: 34139--34174 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
34129 AAAATTAGGA
34139 GTTTCAATCTTTTCTTGCT
1 GTTTCAATCTTTTCTTGCT
*
34158 GTTTCAGTC-TTTCTTGC
1 GTTTCAATCTTTTCTTGC
34175 ACAAAACAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.08, C:0.22, G:0.14, T:0.56
Consensus pattern (19 bp):
GTTTCAATCTTTTCTTGCT
Found at i:36128 original size:3 final size:3
Alignment explanation
Indices: 36111--36164 Score: 54
Period size: 3 Copynumber: 16.3 Consensus size: 3
36101 AAACGTTTTT
*
36111 ATA ATAA ATA CATA ATAA ATA ATT ATA ATA ATAA ATAA ATA ATA ATA
1 ATA AT-A ATA -ATA AT-A ATA ATA ATA ATA AT-A AT-A ATA ATA ATA
36158 ATA ATA A
1 ATA ATA A
36165 GAAATGTGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
3 29 0.64
4 16 0.36
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:36147 original size:20 final size:20
Alignment explanation
Indices: 36111--36164 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
36101 AAACGTTTTT
36111 ATAATAAATACAT-AATAAATA
1 ATAAT-AATA-ATAAATAAATA
*
36132 ATTATAATAATAAATAAATA
1 ATAATAATAATAAATAAATA
36152 ATAATAATAATAA
1 ATAATAATAATAA
36165 GAAATGTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 24 0.80
21 4 0.13
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (20 bp):
ATAATAATAATAAATAAATA
Found at i:36148 original size:23 final size:23
Alignment explanation
Indices: 36109--36169 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
36099 CAAAACGTTT
*
36109 TTATAATAAATACAT-AATAAATAA
1 TTATAAT-AATAAATAAAT-AATAA
36133 TTATAATAATAAATAAATAATAA
1 TTATAATAATAAATAAATAATAA
* *
36156 TAATAATAAGAAAT
1 TTATAATAATAAAT
36170 GTGAAGGGTC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 23 0.70
24 10 0.30
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (23 bp):
TTATAATAATAAATAAATAATAA
Found at i:37171 original size:30 final size:30
Alignment explanation
Indices: 37123--37379 Score: 231
Period size: 30 Copynumber: 8.5 Consensus size: 30
37113 TAAAAATCCT
* **
37123 ATTTTGACCCTCTAAACTTCTCTAAAATTGT
1 ATTTTGACCC-CTAAACTTTTCTAAAATTAC
*
37154 ATTTTGACCCATAAACTTTT-TAAAAATTAC
1 ATTTTGACCCCTAAACTTTTCT-AAAATTAC
* *
37184 ATTTTAACCCCTAAACTATTTC-AAAATTCC
1 ATTTTGACCCCTAAACT-TTTCTAAAATTAC
* *
37214 ATTTTAACCCTTAAACTTTTCTAAAATTAC
1 ATTTTGACCCCTAAACTTTTCTAAAATTAC
* *
37244 ATTTTGACCCCCAAATATTTTCTAAAATTAC
1 ATTTTGACCCCTAAA-CTTTTCTAAAATTAC
*
37275 ATTTTAACCCCTTAAACTTTTCTAAAATTAC
1 ATTTTGACCCC-TAAACTTTTCTAAAATTAC
** * * *
37306 ATTTTGACCTTTAAACTTCTCCAAAATTATG
1 ATTTTGACCCCTAAACTTTTCTAAAATTA-C
*
37337 ATTTTG--CCCTCAAA-TATTC-AAAATTACC
1 ATTTTGACCCCT-AAACTTTTCTAAAATTA-C
*
37365 ATTTTG-CCCCCAAAC
1 ATTTTGACCCCTAAAC
37380 ATCCAAAATT
Statistics
Matches: 187, Mismatches: 29, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
28 16 0.09
29 13 0.07
30 90 0.48
31 65 0.35
32 3 0.02
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.39
Consensus pattern (30 bp):
ATTTTGACCCCTAAACTTTTCTAAAATTAC
Found at i:37406 original size:29 final size:28
Alignment explanation
Indices: 37325--37416 Score: 112
Period size: 28 Copynumber: 3.2 Consensus size: 28
37315 TTTAAACTTC
* *
37325 TCCAAAATTATGATTTTGCCCTCAAATA
1 TCCAAAATTATCATTTTGCCCCCAAATA
* * *
37353 TTCAAAATTACCATTTTGCCCCCAAACA
1 TCCAAAATTATCATTTTGCCCCCAAATA
* *
37381 TCCAAAATTTATCATTTTACCCCCAAATT
1 TCCAAAA-TTATCATTTTGCCCCCAAATA
37410 TCCAAAA
1 TCCAAAA
37417 ATCACATTTC
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
28 29 0.55
29 24 0.45
ACGTcount: A:0.37, C:0.27, G:0.03, T:0.33
Consensus pattern (28 bp):
TCCAAAATTATCATTTTGCCCCCAAATA
Found at i:37425 original size:28 final size:29
Alignment explanation
Indices: 37364--37425 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 29
37354 TCAAAATTAC
* * *
37364 CATTTTGCCCCCAAACATCCAAAATTTAT
1 CATTTTACCCCCAAACATCCAAAAATCAT
**
37393 CATTTTACCCCCAAATTTCCAAAAATCA-
1 CATTTTACCCCCAAACATCCAAAAATCAT
37421 CATTT
1 CATTT
37426 CCAAACTCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 5 0.18
29 23 0.82
ACGTcount: A:0.35, C:0.31, G:0.02, T:0.32
Consensus pattern (29 bp):
CATTTTACCCCCAAACATCCAAAAATCAT
Found at i:37427 original size:15 final size:15
Alignment explanation
Indices: 37404--37448 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
37394 ATTTTACCCC
37404 CAAATTTCCAAAAAT
1 CAAATTTCCAAAAAT
* *
37419 CACATTTCC-AAACT
1 CAAATTTCCAAAAAT
37433 CAAATTTTCCAAAAAT
1 CAAA-TTTCCAAAAAT
37449 TTGATTTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 7 0.29
15 13 0.54
16 4 0.17
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (15 bp):
CAAATTTCCAAAAAT
Found at i:41746 original size:17 final size:16
Alignment explanation
Indices: 41718--41749 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
41708 ACTATTTTTG
41718 AAATTATAAAAATATA
1 AAATTATAAAAATATA
41734 AAATTACTAAAAATAT
1 AAATTA-TAAAAATAT
41750 TCAGATACCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATTATAAAAATATA
Found at i:41764 original size:180 final size:184
Alignment explanation
Indices: 41479--41828 Score: 483
Period size: 180 Copynumber: 1.9 Consensus size: 184
41469 AAAAAAAAAA
* * *
41479 GCATAAAATTTTATAAAATGCAAGATTTTATTTTTGAAAAAAAATATTGCTATTATTGAAATTAT
1 GCATAAAATTTTATAAAATACAAGAATTTATTTTTG-AAAAAAATATTACTATTATTGAAATTAT
* * * * **
41544 AAAAAGCATAAAATTGCTAAAAACATTTAGATATCCAGATTTAAATGAATATAGACAATTGTTTG
65 AAAAAGCATAAAATTACTAAAAACATTCAGATACCCAGATTCAAATGAATATAGACAATAATTTG
*
41609 TCTAGGTTCATTAAGAATAAAAAATAAAAGAAATAGATTTTTCCAGGTTCATTAC
130 TCTAAGTTCATTAAGAATAAAAAATAAAAGAAATAGATTTTTCCAGGTTCATTAC
* * *
41664 GCATAACATTTTATAAAATACAATAATTTA-TTTTG-AAAAAA-ATTACTATTTTTGAAATTATA
1 GCATAAAATTTTATAAAATACAAGAATTTATTTTTGAAAAAAATATTACTATTATTGAAATTATA
* * *
41726 AAAA-TATAAAATTACTAAAAATATTCAGATACCCAGATTCAAATGAATATAGACAGTAATTTGT
66 AAAAGCATAAAATTACTAAAAACATTCAGATACCCAGATTCAAATGAATATAGACAATAATTTGT
** * *
41790 CTAAGTTCATTAAGTTTGAAAGATAAAAGAAATAGATTT
131 CTAAGTTCATTAAGAATAAAAAATAAAAGAAATAGATTT
41829 CCTAATTTTT
Statistics
Matches: 145, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
180 85 0.59
181 23 0.16
182 6 0.04
184 5 0.03
185 26 0.18
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.35
Consensus pattern (184 bp):
GCATAAAATTTTATAAAATACAAGAATTTATTTTTGAAAAAAATATTACTATTATTGAAATTATA
AAAAGCATAAAATTACTAAAAACATTCAGATACCCAGATTCAAATGAATATAGACAATAATTTGT
CTAAGTTCATTAAGAATAAAAAATAAAAGAAATAGATTTTTCCAGGTTCATTAC
Found at i:47450 original size:13 final size:14
Alignment explanation
Indices: 47432--47468 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
47422 AGCAGATTAT
47432 TTCTTTT-TTTTTA
1 TTCTTTTCTTTTTA
*
47445 TTCTTTTCTCTTT-
1 TTCTTTTCTTTTTA
47458 TTCTTTTCTTT
1 TTCTTTTCTTT
47469 CTTTTTCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 17 0.81
14 4 0.19
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (14 bp):
TTCTTTTCTTTTTA
Found at i:47458 original size:18 final size:18
Alignment explanation
Indices: 47431--47468 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
47421 AAGCAGATTA
*
47431 TTTCT-TTTTTTTTATTCT
1 TTTCTCTTTTTCTT-TTCT
47449 TTTCTCTTTTTCTTTTCT
1 TTTCTCTTTTTCTTTTCT
47467 TT
1 TT
47469 CTTTTTCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTCTCTTTTTCTTTTCT
Found at i:63708 original size:17 final size:17
Alignment explanation
Indices: 63688--63748 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
63678 CACATTCCCT
* *
63688 TTGTTATTGCATTTTTA
1 TTGTCATTGCATTTTCA
* * *
63705 TTGTCACTGCATCTACA
1 TTGTCATTGCATTTTCA
63722 TTGTCATTGCATTTTCA
1 TTGTCATTGCATTTTCA
63739 TATGTCATTG
1 T-TGTCATTG
63749 TAAATTAAAG
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
17 27 0.77
18 8 0.23
ACGTcount: A:0.20, C:0.16, G:0.13, T:0.51
Consensus pattern (17 bp):
TTGTCATTGCATTTTCA
Found at i:76860 original size:20 final size:20
Alignment explanation
Indices: 76835--76873 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
76825 TTTCAATTCT
76835 TGAATGGAAATGGGAATGCC
1 TGAATGGAAATGGGAATGCC
76855 TGAATGGAAATGGGAATGC
1 TGAATGGAAATGGGAATGC
76874 ATTACGATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.08, G:0.36, T:0.21
Consensus pattern (20 bp):
TGAATGGAAATGGGAATGCC
Found at i:80171 original size:3 final size:3
Alignment explanation
Indices: 80163--80229 Score: 109
Period size: 3 Copynumber: 22.7 Consensus size: 3
80153 ACAGTTTTAA
80163 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
80211 AAT AAT -GT ATT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
80230 ATAGTTTTAA
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
2 1 0.02
3 59 0.98
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:81485 original size:22 final size:23
Alignment explanation
Indices: 81460--81512 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
81450 GAGCATCGAG
81460 GTGCTAAACAGAGAGCACAA-AC
1 GTGCTAAACAGAGAGCACAATAC
* *
81482 GTGCTAATCGGAGAGCACAATAC
1 GTGCTAAACAGAGAGCACAATAC
*
81505 GTTCTAAA
1 GTGCTAAA
81513 TAAATGGAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.40, C:0.21, G:0.23, T:0.17
Consensus pattern (23 bp):
GTGCTAAACAGAGAGCACAATAC
Found at i:90779 original size:18 final size:20
Alignment explanation
Indices: 90750--90800 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
90740 GATTGGTATG
90750 GTTTATATTAAG-TAAAAAAT
1 GTTTA-ATTAAGATAAAAAAT
90770 -TTTAATTAAGATTAAAAAAT
1 GTTTAATTAAGA-TAAAAAAT
*
90790 GATTAATTAAG
1 GTTTAATTAAG
90801 GCTTCATGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 6 0.22
19 4 0.15
20 8 0.30
21 9 0.33
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (20 bp):
GTTTAATTAAGATAAAAAAT
Found at i:90786 original size:19 final size:19
Alignment explanation
Indices: 90751--90789 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
90741 ATTGGTATGG
90751 TTTATATTAAGTAAAAAAT
1 TTTATATTAAGTAAAAAAT
90770 TTTA-ATTAAGATTAAAAAAT
1 TTTATATTAAG--TAAAAAAT
90790 GATTAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 4 0.22
20 8 0.44
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (19 bp):
TTTATATTAAGTAAAAAAT
Found at i:90787 original size:20 final size:21
Alignment explanation
Indices: 90762--90800 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
90752 TTATATTAAG
*
90762 TAAAAAAT-TTTAATTAAGAT
1 TAAAAAATGATTAATTAAGAT
90782 TAAAAAATGATTAATTAAG
1 TAAAAAATGATTAATTAAG
90801 GCTTCATGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (21 bp):
TAAAAAATGATTAATTAAGAT
Found at i:94961 original size:36 final size:36
Alignment explanation
Indices: 94914--94985 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
94904 TCATCATTCA
*
94914 AACATATGCATCACTCTTGTGTTTGCGTATATGTGT
1 AACATATGCATCACTCTTGTGTTTGCATATATGTGT
94950 AACATATGCATCACTCTTGTGTTTGCATATATGTGT
1 AACATATGCATCACTCTTGTGTTTGCATATATGTGT
94986 GCCTGCATCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.24, C:0.17, G:0.18, T:0.42
Consensus pattern (36 bp):
AACATATGCATCACTCTTGTGTTTGCATATATGTGT
Found at i:95908 original size:14 final size:14
Alignment explanation
Indices: 95889--95916 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
95879 TTGGCACCAC
95889 CCTGCAGAACACAT
1 CCTGCAGAACACAT
95903 CCTGCAGAACACAT
1 CCTGCAGAACACAT
95917 TCATTAAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.36, G:0.14, T:0.14
Consensus pattern (14 bp):
CCTGCAGAACACAT
Done.