Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014989.1 Kokia drynarioides strain JFW-HI SEQ_130033, 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: 245740
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 678 characters in sequence are not A, C, G, or T
Found at i:1556 original size:2 final size:2
Alignment explanation
Indices: 1549--1581 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1539 TAAAAACATA
1549 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1582 ATTACACAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8953 original size:13 final size:13
Alignment explanation
Indices: 8935--8961 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
8925 TTTAACATTA
8935 TTTTTAAAAAGTG
1 TTTTTAAAAAGTG
8948 TTTTTAAAAAGTG
1 TTTTTAAAAAGTG
8961 T
1 T
8962 GGTAGAAAAA
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:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (13 bp):
TTTTTAAAAAGTG
Found at i:9206 original size:21 final size:21
Alignment explanation
Indices: 9180--9248 Score: 68
Period size: 24 Copynumber: 3.1 Consensus size: 21
9170 TATTGTTAAT
*
9180 ATTTTAATATATAAAATATTA
1 ATTTTAATATTTAAAATATTA
*
9201 ATTTTAAATATTTCTAAATAATTA
1 ATTTT-AATATTT-AAAAT-ATTA
*
9225 ATATTAATTATTTAAAA-ATTA
1 ATTTTAA-TATTTAAAATATTA
9246 ATT
1 ATT
9249 AGATTATATA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
21 11 0.28
22 6 0.15
23 9 0.23
24 13 0.33
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTTTAATATTTAAAATATTA
Found at i:9213 original size:30 final size:30
Alignment explanation
Indices: 9177--9288 Score: 90
Period size: 30 Copynumber: 3.7 Consensus size: 30
9167 ATTTATTGTT
*
9177 AATATTTTAATATATAAAATATTAATTTTA
1 AATATTTTAATATATATAATATTAATTTTA
9207 AATATTTCTAA-ATA-ATTAATATTAATTATTTA
1 AATATTT-TAATATATA-TAATATTAA-T-TTTA
* *
9239 AAAATTAATTAGAT-TATATAA-ACTAATTTTA
1 AATATT--TTA-ATATATATAATATTAATTTTA
*
9270 AATATTTAAATATA-ATAAT
1 AATATTTTAATATATATAAT
9289 TAAATATTTA
Statistics
Matches: 66, Mismatches: 5, Indels: 23
0.70 0.05 0.24
Matches are distributed among these distances:
28 6 0.09
29 5 0.08
30 18 0.27
31 13 0.20
32 10 0.15
33 6 0.09
34 7 0.11
35 1 0.02
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (30 bp):
AATATTTTAATATATATAATATTAATTTTA
Found at i:9224 original size:24 final size:22
Alignment explanation
Indices: 9180--9298 Score: 67
Period size: 21 Copynumber: 5.6 Consensus size: 22
9170 TATTGTTAAT
*
9180 ATTTT-AATATATAAA-ATATTA
1 ATTTTAAATATTTAAATA-ATTA
9201 ATTTTAAATATTTCTAAATAATTA
1 ATTTTAAATA-TT-TAAATAATTA
* *
9225 ATATTAATTATTTAAA-AATTA
1 ATTTTAAATATTTAAATAATTA
* * * *
9246 A--TTAGAT-TATATA-AACTA
1 ATTTTAAATATTTAAATAATTA
9264 ATTTTAAATATTTAAAT-A-TA
1 ATTTTAAATATTTAAATAATTA
*
9284 ATAATTAAATATTTA
1 AT-TTTAAATATTTA
9299 TATTTAAATA
Statistics
Matches: 77, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
18 9 0.12
19 4 0.05
20 9 0.12
21 27 0.35
22 8 0.10
23 3 0.04
24 16 0.21
25 1 0.01
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (22 bp):
ATTTTAAATATTTAAATAATTA
Found at i:9291 original size:13 final size:13
Alignment explanation
Indices: 9270--9309 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
9260 ACTAATTTTA
9270 AATATTTAAATAT
1 AATATTTAAATAT
*
9283 AATAATTAAATATT
1 AATATTTAAATA-T
*
9297 TATATTTAAATAT
1 AATATTTAAATAT
9310 GAGCACAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
AATATTTAAATAT
Found at i:9307 original size:14 final size:14
Alignment explanation
Indices: 9270--9309 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
9260 ACTAATTTTA
9270 AATATTTAAATA-T
1 AATATTTAAATATT
*
9283 AATAATTAAATATT
1 AATATTTAAATATT
*
9297 TATATTTAAATAT
1 AATATTTAAATAT
9310 GAGCACAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AATATTTAAATATT
Found at i:14174 original size:15 final size:17
Alignment explanation
Indices: 14146--14177 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
14136 GTGATATATT
14146 TTTTTTTATAATTTTGA
1 TTTTTTTATAATTTTGA
14163 TTTTTTT-T-ATTTTGA
1 TTTTTTTATAATTTTGA
14178 GCTAAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (17 bp):
TTTTTTTATAATTTTGA
Found at i:14396 original size:17 final size:19
Alignment explanation
Indices: 14364--14402 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
14354 GTTCAAATTT
14364 AATTAAAAATAAGAAT-CA
1 AATTAAAAATAAGAATACA
*
14382 AATTAATAA-AAGAATACA
1 AATTAAAAATAAGAATACA
14400 AAT
1 AAT
14403 ATTAAAGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.23
Consensus pattern (19 bp):
AATTAAAAATAAGAATACA
Found at i:22316 original size:35 final size:35
Alignment explanation
Indices: 22270--22337 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
22260 AAGCACGATA
22270 AGGGCATAAAGAACATTAACGGCGAAGATTATAAT
1 AGGGCATAAAGAACATTAACGGCGAAGATTATAAT
22305 AGGGCATAAAGAACATTAACGGCGAAGATTATA
1 AGGGCATAAAGAACATTAACGGCGAAGATTATA
22338 TTATATTATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.46, C:0.12, G:0.24, T:0.19
Consensus pattern (35 bp):
AGGGCATAAAGAACATTAACGGCGAAGATTATAAT
Found at i:22368 original size:25 final size:25
Alignment explanation
Indices: 22334--22387 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
22324 CGGCGAAGAT
22334 TATATTATATTATCATTTAAAAT-A
1 TATATTATATTATCATTTAAAATGA
* * *
22358 TATATATATATTTTTATTTAATATGA
1 TATAT-TATATTATCATTTAAAATGA
22384 TATA
1 TATA
22388 GTTTTAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 5 0.20
25 15 0.60
26 5 0.20
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (25 bp):
TATATTATATTATCATTTAAAATGA
Found at i:29376 original size:29 final size:30
Alignment explanation
Indices: 29332--29395 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
29322 TTGACATTAT
*
29332 TTGATTCTTTTTAATAGTACAAGGACTAAA
1 TTGATTCTATTTAATAGTACAAGGACTAAA
* * * *
29362 TTGATTC-ATTTAATATTATAGGGACTAAT
1 TTGATTCTATTTAATAGTACAAGGACTAAA
29391 TTGAT
1 TTGAT
29396 CAGGTTCCTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 22 0.76
30 7 0.24
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (30 bp):
TTGATTCTATTTAATAGTACAAGGACTAAA
Found at i:30264 original size:20 final size:20
Alignment explanation
Indices: 30239--30280 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
30229 TAATTTAAAG
30239 ATGATATGCTTTTTGTCTTT
1 ATGATATGCTTTTTGTCTTT
30259 ATGATATGCTTTTTGTCTTT
1 ATGATATGCTTTTTGTCTTT
30279 AT
1 AT
30281 TGAAGTACTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.17, C:0.10, G:0.14, T:0.60
Consensus pattern (20 bp):
ATGATATGCTTTTTGTCTTT
Found at i:36827 original size:3 final size:3
Alignment explanation
Indices: 36819--36851 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
36809 GTGGGGGACT
36819 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG
36852 ATTCCCTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.33, T:0.33
Consensus pattern (3 bp):
CTG
Found at i:41420 original size:16 final size:16
Alignment explanation
Indices: 41381--41418 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
41371 TATTAAATAA
*
41381 AAAATTTATTATTTTT
1 AAAATTTATTATATTT
41397 AAAATTTATTA-ATTT
1 AAAATTTATTATATTT
41412 AAAATTT
1 AAAATTT
41419 TAAGGGAACG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AAAATTTATTATATTT
Found at i:43788 original size:2 final size:2
Alignment explanation
Indices: 43781--43812 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
43771 AGATATTATC
43781 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
43813 CTCTTTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44864 original size:14 final size:15
Alignment explanation
Indices: 44845--44879 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
44835 AAACAATTTT
44845 TTATCTTAAAA-TAA
1 TTATCTTAAAATTAA
44859 TTATCTTAAAATTAA
1 TTATCTTAAAATTAA
44874 TTATCT
1 TTATCT
44880 AATTACATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.55
15 9 0.45
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (15 bp):
TTATCTTAAAATTAA
Found at i:59181 original size:21 final size:21
Alignment explanation
Indices: 59157--59197 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
59147 AGATTAATTA
*
59157 TATAAATATATCCAACTTTTC
1 TATAAATATATACAACTTTTC
* *
59178 TATAGATATATAGAACTTTT
1 TATAAATATATACAACTTTT
59198 ATCAGTAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.44
Consensus pattern (21 bp):
TATAAATATATACAACTTTTC
Found at i:59229 original size:21 final size:21
Alignment explanation
Indices: 59205--59244 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
59195 TTTATCAGTA
*
59205 ATTCCATTTCATTTATATTAT
1 ATTCCATATCATTTATATTAT
*
59226 ATTCTATATCATTTATATT
1 ATTCCATATCATTTATATT
59245 TTTAAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTCCATATCATTTATATTAT
Found at i:65439 original size:2 final size:2
Alignment explanation
Indices: 65432--65469 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
65422 ATCTTTTTAT
65432 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
65470 AAATCTATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:66437 original size:91 final size:91
Alignment explanation
Indices: 66280--66446 Score: 210
Period size: 91 Copynumber: 1.8 Consensus size: 91
66270 TTCAAATTTG
* * * *
66280 ATTTTTTTCTTAATTTGGTACCTAAACTTTTTCTGATCCAATTTGGTACTCAAACTTGACACTTT
1 ATTTTTTTCTTAAGTTGATACCTAAACTTTTTCGGATCCAATTTGGTACTCAAACTTAACACTTT
*
66345 TTTCTAATTTGGCACCTAAACTTGAC
66 TTCCTAATTTGGCACCTAAACTTGAC
** * * ***
66371 ATTTTTTTCTTAAGTTGATATTTAAACTTTTTGGGATCCAATTTGGTAC-CTGAACTTAATTTTT
1 ATTTTTTTCTTAAGTTGATACCTAAACTTTTTCGGATCCAATTTGGTACTC-AAACTTAACACTT
66435 TTTCCTAATTTG
65 TTTCCTAATTTG
66447 ATACCTAATT
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
90 1 0.02
91 62 0.98
ACGTcount: A:0.25, C:0.16, G:0.11, T:0.49
Consensus pattern (91 bp):
ATTTTTTTCTTAAGTTGATACCTAAACTTTTTCGGATCCAATTTGGTACTCAAACTTAACACTTT
TTCCTAATTTGGCACCTAAACTTGAC
Found at i:71188 original size:30 final size:31
Alignment explanation
Indices: 71131--71190 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
71121 GAATTGGATC
*
71131 AAATCAAAATTTCATGAATAAAGTTGCACAA
1 AAATCAAAAGTTCATGAATAAAGTTGCACAA
*
71162 AAATC-AAAGTTCATGTATACAA-TTGCACA
1 AAATCAAAAGTTCATGAATA-AAGTTGCACA
71191 TTAAACCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 19 0.73
31 7 0.27
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.27
Consensus pattern (31 bp):
AAATCAAAAGTTCATGAATAAAGTTGCACAA
Found at i:83110 original size:4 final size:4
Alignment explanation
Indices: 83101--83175 Score: 87
Period size: 4 Copynumber: 18.8 Consensus size: 4
83091 GAACAATAAT
* * * *
83101 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ATAC ATAC ATAC ACAT ACAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * *
83149 ACAT ACAT ACAC ACAT ACAC ACAC ACA
1 ACAC ACAC ACAC ACAC ACAC ACAC ACA
83176 TACATACATA
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 63 1.00
ACGTcount: A:0.51, C:0.40, G:0.00, T:0.09
Consensus pattern (4 bp):
ACAC
Found at i:83176 original size:12 final size:12
Alignment explanation
Indices: 83103--83203 Score: 103
Period size: 12 Copynumber: 8.2 Consensus size: 12
83093 ACAATAATAC
*
83103 ACACACACACAC
1 ACACACACACAT
*
83115 ACACACACACAC
1 ACACACACACAT
* *
83127 ACATACATACAT
1 ACACACACACAT
83139 ACACATACACACAT
1 ACAC--ACACACAT
*
83153 ACATACACACAT
1 ACACACACACAT
83165 ACACACACACAT
1 ACACACACACAT
* *
83177 ACATACATACAT
1 ACACACACACAT
* *
83189 ACATACATACAT
1 ACACACACACAT
83201 ACA
1 ACA
83204 TACATACATG
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
12 68 0.87
14 10 0.13
ACGTcount: A:0.50, C:0.36, G:0.00, T:0.14
Consensus pattern (12 bp):
ACACACACACAT
Found at i:83180 original size:4 final size:4
Alignment explanation
Indices: 83127--83212 Score: 122
Period size: 4 Copynumber: 22.0 Consensus size: 4
83117 ACACACACAC
* * * *
83127 ACAT ACAT ACAT AC-- ACAT ACAC ACAT ACAT ACAC ACAT ACAC ACAC
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
83173 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
83213 GTGTGTGTAA
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
2 2 0.03
4 72 0.97
ACGTcount: A:0.50, C:0.30, G:0.00, T:0.20
Consensus pattern (4 bp):
ACAT
Found at i:110315 original size:17 final size:19
Alignment explanation
Indices: 110295--110331 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
110285 AGAAAAACGA
110295 AATCG-AAAATT-TATTTG
1 AATCGTAAAATTCTATTTG
*
110312 AATCGTAATATTCTATTTG
1 AATCGTAAAATTCTATTTG
110331 A
1 A
110332 TTCAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 5 0.29
18 5 0.29
19 7 0.41
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (19 bp):
AATCGTAAAATTCTATTTG
Found at i:116152 original size:2 final size:2
Alignment explanation
Indices: 116145--116182 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
116135 AATTATTCAA
116145 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
116183 TAAGGATATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:116227 original size:23 final size:23
Alignment explanation
Indices: 116193--116245 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
116183 TAAGGATATG
116193 TATG-TTTTTTAATAATTTTATA
1 TATGTTTTTTTAATAATTTTATA
116215 TATGTTTTTTTAATAATTTTATA
1 TATGTTTTTTTAATAATTTTATA
*
116238 TATATTTT
1 TATGTTTT
116246 AAAATTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 4 0.14
23 25 0.86
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (23 bp):
TATGTTTTTTTAATAATTTTATA
Found at i:120832 original size:24 final size:26
Alignment explanation
Indices: 120785--120833 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
120775 ACCATTTCAA
*
120785 AGGAACATTTTTCAGTCTACCCAAAAC
1 AGGAACATTATTCAGTCTA-CCAAAAC
120812 AGGAACATTATTCA-TCT-CCAAA
1 AGGAACATTATTCAGTCTACCAAA
120834 TTCAACAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
26 3 0.14
27 13 0.62
ACGTcount: A:0.39, C:0.24, G:0.10, T:0.27
Consensus pattern (26 bp):
AGGAACATTATTCAGTCTACCAAAAC
Found at i:127182 original size:6 final size:6
Alignment explanation
Indices: 127171--127201 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
127161 GAATTTGAGA
127171 CTTTCC CTTTCC CTTTCC CTTTCC CTTTCC C
1 CTTTCC CTTTCC CTTTCC CTTTCC CTTTCC C
127202 CATTTCTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (6 bp):
CTTTCC
Found at i:134032 original size:2 final size:2
Alignment explanation
Indices: 134025--134051 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
134015 CAAATATTCA
134025 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
134052 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:135689 original size:19 final size:19
Alignment explanation
Indices: 135610--135701 Score: 55
Period size: 19 Copynumber: 4.8 Consensus size: 19
135600 ATAAAATTCA
* *
135610 TAAAAATATTATAAAATATA
1 TAAAAA-ATTATAAAAAATG
* * *
135630 TAGAAATTTAGAAAAAA--
1 TAAAAAATTATAAAAAATG
* * *
135647 TAATAAAATTTTATACAATCG
1 TAA-AAAATTATAAAAAAT-G
135668 TAAAAAATTATAAAAAATG
1 TAAAAAATTATAAAAAATG
135687 TAAAGAAA-TATAAAA
1 TAAA-AAATTATAAAA
135702 TTCGTAAAAA
Statistics
Matches: 54, Mismatches: 13, Indels: 11
0.69 0.17 0.14
Matches are distributed among these distances:
17 2 0.04
18 9 0.17
19 20 0.37
20 20 0.37
21 3 0.06
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (19 bp):
TAAAAAATTATAAAAAATG
Found at i:135708 original size:19 final size:19
Alignment explanation
Indices: 135665--135723 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
135655 TTTTATACAA
*
135665 TCGTAAAAAATTATAAAAAA
1 TCGTAAAAAA-TATAAAAAT
135685 T-GTAAAGAAATAT-AAAAT
1 TCGTAAA-AAATATAAAAAT
*
135703 TCGTAAAAAAATATGAAAAT
1 TCGT-AAAAAATATAAAAAT
135723 T
1 T
135724 ATTGTATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 5 0.15
19 16 0.47
20 13 0.38
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.27
Consensus pattern (19 bp):
TCGTAAAAAATATAAAAAT
Found at i:135923 original size:28 final size:27
Alignment explanation
Indices: 135886--135947 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
135876 ACTTTACAAT
* *
135886 TTTTTATAATTTTTAAATGATTTTTATA
1 TTTTTATAATTTTT-AATAAATTTTATA
135914 TATTTT-TAATTTTTAATAAATTTTATA
1 T-TTTTATAATTTTTAATAAATTTTATA
135941 TTTTTAT
1 TTTTTAT
135948 TAAAAATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
26 4 0.13
27 13 0.43
28 9 0.30
29 4 0.13
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (27 bp):
TTTTTATAATTTTTAATAAATTTTATA
Found at i:135927 original size:17 final size:19
Alignment explanation
Indices: 135905--135951 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 19
135895 TTTTTAAATG
*
135905 ATTTTTATAT-ATTTTTA-
1 ATTTTTATATAAATTTTAT
135922 ATTTTTA-ATAAATTTTAT
1 ATTTTTATATAAATTTTAT
135940 ATTTTTAT-TAAA
1 ATTTTTATATAAA
135952 AATTAATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 2 0.08
17 13 0.50
18 11 0.42
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTTTTATATAAATTTTAT
Found at i:135936 original size:18 final size:18
Alignment explanation
Indices: 135917--135951 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
135907 TTTTATATAT
135917 TTTTA-ATTTTTAATAAA
1 TTTTATATTTTTAATAAA
*
135934 TTTTATATTTTTATTAAA
1 TTTTATATTTTTAATAAA
135952 AATTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTATATTTTTAATAAA
Found at i:135950 original size:28 final size:29
Alignment explanation
Indices: 135886--135950 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
135876 ACTTTACAAT
* *
135886 TTTTTA-TAATTTTTAAATGATTTTTATA
1 TTTTTATTAATTTTTAAATAAATTTTATA
*
135914 TATTT-TTAATTTTT-AATAAATTTTATA
1 TTTTTATTAATTTTTAAATAAATTTTATA
135941 TTTTTATTAA
1 TTTTTATTAA
135951 AAATTAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
27 15 0.48
28 16 0.52
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (29 bp):
TTTTTATTAATTTTTAAATAAATTTTATA
Found at i:138691 original size:19 final size:19
Alignment explanation
Indices: 138669--138714 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 19
138659 AAAACTAAAC
138669 AAAAACTATTATTAATGAT
1 AAAAACTATTATTAATGAT
138688 AAAAA-TGATTATTAATGAT
1 AAAAACT-ATTATTAATGAT
138707 AAAAACTA
1 AAAAACTA
138715 AAAGTCAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 1 0.04
19 23 0.92
20 1 0.04
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.33
Consensus pattern (19 bp):
AAAAACTATTATTAATGAT
Found at i:142889 original size:58 final size:58
Alignment explanation
Indices: 142805--142976 Score: 193
Period size: 58 Copynumber: 2.9 Consensus size: 58
142795 TGATTTGAGA
* * *
142805 AAGTTAAGGGGTCAAAATATGATTTTAGAAAAGTTTAGGGGTTAAAATATAATTTTGGAT
1 AAGTTTAGGGGTC-AAATATGATTTTAGAAAAGTTTA-GGGTTAAAATATAATTTTGAAG
* * * * *
142865 AAGTTT-GGGGTCAAATGTGGTTTTAGGAAAGTTTAATGGTTAAAATGTAATTTTGAAG
1 AAGTTTAGGGGTCAAATATGATTTTAGAAAAGTTT-AGGGTTAAAATATAATTTTGAAG
* * * * *
142923 AAGTTTAGGGTTAAAATATAATTTTAAAAAAGTTTAGGGTCAAAATATAATTTT
1 AAGTTTAGGGGTCAAATATGATTTTAGAAAAGTTTAGGGTTAAAATATAATTTT
142977 TAAAGAAAAT
Statistics
Matches: 92, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
58 59 0.64
59 28 0.30
60 5 0.05
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.37
Consensus pattern (58 bp):
AAGTTTAGGGGTCAAATATGATTTTAGAAAAGTTTAGGGTTAAAATATAATTTTGAAG
Found at i:142910 original size:88 final size:86
Alignment explanation
Indices: 142760--142966 Score: 247
Period size: 88 Copynumber: 2.4 Consensus size: 86
142750 NNNNNNNNNA
* *
142760 AAAATATAATTATGGAAAAGTTTGGGATCAAAATGTGATTTGAGAAAGTTAAGGGGTCAAAATAT
1 AAAATATAATTTTGGAAAAGTTTGGGGTC-AAATGTGATTTGAGAAAGTTAAGGGGTCAAAATAT
*
142825 GATTTTAGAA-AAGTTTAGGGGTT
65 AATTTT-GAAGAAGTTTA-GGGTT
* * * * * *
142848 AAAATATAATTTTGGATAAGTTTGGGGTCAAATGTGGTTTTAGGAAAGTTTAA-TGGTTAAAATG
1 AAAATATAATTTTGGAAAAGTTTGGGGTCAAATGTGATTTGA-GAAAG-TTAAGGGGTCAAAATA
142912 TAATTTTGAAGAAGTTTAGGGTT
64 TAATTTTGAAGAAGTTTAGGGTT
** *
142935 AAAATATAATTTTAAAAAAGTTTAGGGTCAAA
1 AAAATATAATTTTGGAAAAGTTTGGGGTCAAA
142967 ATATAATTTT
Statistics
Matches: 103, Mismatches: 13, Indels: 7
0.84 0.11 0.06
Matches are distributed among these distances:
87 47 0.46
88 52 0.50
89 4 0.04
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.35
Consensus pattern (86 bp):
AAAATATAATTTTGGAAAAGTTTGGGGTCAAATGTGATTTGAGAAAGTTAAGGGGTCAAAATATA
ATTTTGAAGAAGTTTAGGGTT
Found at i:142976 original size:29 final size:29
Alignment explanation
Indices: 142760--142976 Score: 167
Period size: 29 Copynumber: 7.4 Consensus size: 29
142750 NNNNNNNNNA
*
142760 AAAATATAATTATGGAAAAGTTT-GGGATC
1 AAAATATAATTTTGGAAAAGTTTAGGG-TC
* * *
142789 AAAATGTGA-TTT-GAGAAAGTTAAGGGGTC
1 AAAATATAATTTTGGA-AAAGTTTA-GGGTC
* * *
142818 AAAATATGATTTTAGAAAAGTTTAGGGGTT
1 AAAATATAATTTTGGAAAAGTTTA-GGGTC
* *
142848 AAAATATAATTTTGGATAAGTTTGGGGTC
1 AAAATATAATTTTGGAAAAGTTTAGGGTC
* ** * *
142877 -AAATGTGGTTTTAGG-AAAGTTTAATGGTT
1 AAAATATAATTTT-GGAAAAGTTT-AGGGTC
* *
142906 AAAATGTAATTTT-GAAGAAGTTTAGGGTT
1 AAAATATAATTTTGGAA-AAGTTTAGGGTC
**
142935 AAAATATAATTTTAAAAAAGTTTAGGGTC
1 AAAATATAATTTTGGAAAAGTTTAGGGTC
142964 AAAATATAATTTT
1 AAAATATAATTTT
142977 TAAAGAAAAT
Statistics
Matches: 152, Mismatches: 25, Indels: 22
0.76 0.13 0.11
Matches are distributed among these distances:
27 2 0.01
28 24 0.16
29 68 0.45
30 56 0.37
31 2 0.01
ACGTcount: A:0.40, C:0.02, G:0.22, T:0.36
Consensus pattern (29 bp):
AAAATATAATTTTGGAAAAGTTTAGGGTC
Found at i:146158 original size:22 final size:22
Alignment explanation
Indices: 146124--146165 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
146114 ATATGACTAG
146124 AAATTTATATTTTAAAAATTAA
1 AAATTTATATTTTAAAAATTAA
*
146146 AAATATTAT-TTTTAATAATT
1 AAAT-TTATATTTTAAAAATT
146166 TGTGGATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AAATTTATATTTTAAAAATTAA
Found at i:147421 original size:20 final size:20
Alignment explanation
Indices: 147384--147421 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
147374 AAATAATTTT
*
147384 TAAAAAATTTAAATATAATA
1 TAAAAAATCTAAATATAATA
147404 TAAAAATATCTAAA-ATAA
1 TAAAAA-ATCTAAATATAA
147422 ATTTTGATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (20 bp):
TAAAAAATCTAAATATAATA
Found at i:160262 original size:54 final size:57
Alignment explanation
Indices: 160204--160313 Score: 140
Period size: 57 Copynumber: 2.0 Consensus size: 57
160194 CTATCTTAAC
* * *
160204 AAAAATTACAAAATAATT-T-AAAATAT-TA-ATAAAA-TTTAAATTTTATATTTTTTA
1 AAAAATTAC-AAA-AATTCTAAAAATATATATAAAAAAGTTAAAATTTTAAATTTTTTA
160258 AAAAATTACAAAAATTCTAAAAATATATATAAAAAAGTTAAAATTTTAAATTTTTT
1 AAAAATTACAAAAATTCTAAAAATATATATAAAAAAGTTAAAATTTTAAATTTTTT
160314 CTAAAATAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
52 4 0.08
53 4 0.08
54 16 0.33
55 2 0.04
56 5 0.10
57 17 0.35
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (57 bp):
AAAAATTACAAAAATTCTAAAAATATATATAAAAAAGTTAAAATTTTAAATTTTTTA
Found at i:161053 original size:18 final size:17
Alignment explanation
Indices: 161007--161054 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
160997 AATTTGTGAT
* *
161007 AATTAGAATT-AATTAT
1 AATTATAATTAAATTAC
161023 AATTATAATTTAAATTAC
1 AATTATAA-TTAAATTAC
161041 AATTATTAATTAAA
1 AATTA-TAATTAAA
161055 AATTGACCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 7 0.26
17 2 0.07
18 15 0.56
19 3 0.11
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
AATTATAATTAAATTAC
Found at i:161290 original size:18 final size:20
Alignment explanation
Indices: 161252--161293 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
161242 TTATGCTAAT
*
161252 TATTGTAAATAAAAATAAAA
1 TATTGTAAAAAAAAATAAAA
161272 TATT-TAAAAAAAAAT-AAA
1 TATTGTAAAAAAAAATAAAA
161290 TATT
1 TATT
161294 AAATATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
19 10 0.48
20 4 0.19
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
TATTGTAAAAAAAAATAAAA
Found at i:161297 original size:25 final size:25
Alignment explanation
Indices: 161258--161305 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
161248 TAATTATTGT
*
161258 AAATAAAAATAAAATATTTAAAAAA
1 AAATAAAAATAAAATATATAAAAAA
* *
161283 AAATAAATATTAAATATATAAAA
1 AAATAAAAATAAAATATATAAAA
161306 TTATATGCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (25 bp):
AAATAAAAATAAAATATATAAAAAA
Found at i:175411 original size:4 final size:4
Alignment explanation
Indices: 175387--175440 Score: 67
Period size: 4 Copynumber: 13.8 Consensus size: 4
175377 GGGGACCAAC
* *
175387 GAAA -AAA GAAG GAAA -AAA GAAA GAAA AAAGA GAAA GAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA
175434 GAAA GAA
1 GAAA GAA
175441 GAAGGGGAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
3 6 0.14
4 34 0.79
5 3 0.07
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:175956 original size:21 final size:19
Alignment explanation
Indices: 175916--175956 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
175906 TTTTTTTAAA
*
175916 TTCGAAAATATAAAAATAT
1 TTCGAAAATAAAAAAATAT
175935 TTCGAAAATAGAAAAAAGTAT
1 TTCGAAAATA-AAAAAA-TAT
175956 T
1 T
175957 ATAAAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
20 5 0.26
21 4 0.21
ACGTcount: A:0.56, C:0.05, G:0.10, T:0.29
Consensus pattern (19 bp):
TTCGAAAATAAAAAAATAT
Found at i:177040 original size:22 final size:22
Alignment explanation
Indices: 177015--177071 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
177005 GAGGTGTTGG
177015 TGAGCTGGAATTTCGGTTTTGC
1 TGAGCTGGAATTTCGGTTTTGC
*
177037 TGAGCTAGAATTTCGGTTTTGC
1 TGAGCTGGAATTTCGGTTTTGC
177059 TGAGCTGGAATTT
1 TGAGCTGGAATTT
177072 GGGTGGTCCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.18, C:0.12, G:0.30, T:0.40
Consensus pattern (22 bp):
TGAGCTGGAATTTCGGTTTTGC
Found at i:177282 original size:84 final size:83
Alignment explanation
Indices: 177164--177964 Score: 1088
Period size: 84 Copynumber: 9.5 Consensus size: 83
177154 TAAATTTAAA
*
177164 ATTTTATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAGTAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAA-TTTTTATTTAAATATTTAAAATTAGTAAATAATGT
*
177229 ATTGTCAAATGAACACATT
65 ATTGTCAAATCAACACATT
* * * * * *
177248 ATTTGACAAAAATTTATAATATGATAATAGTTTTTTATTTAAATA-TGAAAATTTGATAAATAAT
1 ATTTGATAAAAA-TTGTAATATAATAATA-ATTTTTATTTAAATATTTAAAATTAG-TAAATAAT
177312 GTATTGTCAAATCAACACATT
63 GTATTGTCAAATCAACACATT
**
177333 ATTTGATAAAAATTGTAATATAATAATAAATTTTTATTTAAATATTTAATTTTAGTAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAAT-AATTTTTATTTAAATATTTAAAATTAGTAAATAATGT
*
177398 ATTATCAAATCAACACATT
65 ATTGTCAAATCAACACATT
* *
177417 ATTTGATAAAAATTGTAATATAATAATAATTTCTTATTTAAATATTTAAATTTAGTAAATAATGC
1 ATTTGATAAAAATTGTAATATAATAATAATTT-TTATTTAAATATTTAAAATTAGTAAATAATGT
* *
177482 ATTGTCAAATCAATATATT
65 ATTGTCAAATCAACACATT
* *
177501 ATTTGATAAAAATTATAATATAATAATAATTTGTTATTTAAATATTT-AAATTTGATAAATAATG
1 ATTTGATAAAAATTGTAATATAATAATAATTT-TTATTTAAATATTTAAAATTAG-TAAATAATG
*
177565 TATTGTCAAATCAACATATT
64 TATTGTCAAATCAACACATT
* *
177585 ATTTGATAAAAATTGTAATATAATAATAATTTTTATTTAAATATTTAAATTTAGTAAATAATATA
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTATTTAAATATTTAAAATTAGTAAATAATGTA
*
177650 TTATCAAATCAACACATT
66 TTGTCAAATCAACACATT
* * * * *
177668 ATTTAAAAAAAATTATAATATAATAATAATTTTTATTTAAATA-TAAAAATTTGATAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTATTTAAATATTTAAAATTAG-TAAATAATGT
*
177732 CTTGTCAAATCAACACATT
65 ATTGTCAAATCAACACATT
* *
177751 ATTCGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAATTTAGTAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAA-TTTTTATTTAAATATTTAAAATTAGTAAATAATGT
* *
177816 ATTGTTAAATCAACTCATT
65 ATTGTCAAATCAACACATT
* * * * *
177835 ATTTGATAAAAATTATAATATAATAATAATTTGTAATCTAAATA-TGAAAATTTGATAAATAATG
1 ATTTGATAAAAATTGTAATATAATAATAATTT-TTATTTAAATATTTAAAATTAG-TAAATAATG
* *
177899 TATTGTCAAATGAACACAAT
64 TATTGTCAAATCAACACATT
*
177919 ATTTGATATAAATTGTAATATAATAATAATCTCTTTTATTTAAATA
1 ATTTGATAAAAATTGTAATATAATAATAA--T-TTTTATTTAAATA
177965 ATGTTAAATT
Statistics
Matches: 633, Mismatches: 68, Indels: 30
0.87 0.09 0.04
Matches are distributed among these distances:
82 7 0.01
83 151 0.24
84 382 0.60
85 81 0.13
86 10 0.02
87 2 0.00
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.43
Consensus pattern (83 bp):
ATTTGATAAAAATTGTAATATAATAATAATTTTTATTTAAATATTTAAAATTAGTAAATAATGTA
TTGTCAAATCAACACATT
Found at i:177790 original size:334 final size:335
Alignment explanation
Indices: 177164--177974 Score: 1191
Period size: 334 Copynumber: 2.4 Consensus size: 335
177154 TAAATTTAAA
* * * *
177164 ATTTTATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATT-AGTAAATAATG
1 ATTTGATAAAAATTATAATATAATAATAATTTGTTATTTAAATATTTAAATTTGA-TAAATAATG
* * * *
177228 TATTGTCAAATGAACACATTATTTGACAAAAATTTATAATATGATAATAGTTTTTTATTTAAATA
65 TATTGTCAAATGAACACATTATTTGATAAAAA-TTGTAATATAATAATA-ATTTTTATTTAAATA
** * * * * *
177293 TGAAAATTTGATAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATA
128 TTTAAATTTGATAAATAATATATTATCAAATCAACACATTATTTAAAAAAAATTATAATATAATA
** * *
177358 ATAAATTTTTATTTAAATATTTAATTTTAGTAAATAATGTATTATCAAATCAACACATTATTTGA
193 ATAAATTTTTATTTAAATATAAAATTTGAGTAAATAATGTATTATCAAATCAACACATTATTCGA
177423 TAAAAATTGTAATATAATAATAATTTCTTATTTAAATATTTAAATTTAGTAAATAATGCATTGTC
258 TAAAAATTGTAATATAATAATAATTTCTTATTTAAATATTTAAATTTAGTAAATAATGCATTGTC
*
177488 AAATCAA-TATATT
323 AAATCAACT-CATT
177501 ATTTGATAAAAATTATAATATAATAATAATTTGTTATTTAAATATTTAAATTTGATAAATAATGT
1 ATTTGATAAAAATTATAATATAATAATAATTTGTTATTTAAATATTTAAATTTGATAAATAATGT
* *
177566 ATTGTCAAATCAACATATTATTTGATAAAAATTGTAATATAATAATAATTTTTATTTAAATATTT
66 ATTGTCAAATGAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTATTTAAATATTT
177631 AAATTT-AGTAAATAATATATTATCAAATCAACACATTATTTAAAAAAAATTATAATATAATAAT
131 AAATTTGA-TAAATAATATATTATCAAATCAACACATTATTTAAAAAAAATTATAATATAATAAT
* *
177695 -AATTTTTATTTAAATATAAAAATTTGA-TAAATAATGTCTTGTCAAATCAACACATTATTCGAT
195 AAATTTTTATTTAAATAT-AAAATTTGAGTAAATAATGTATTATCAAATCAACACATTATTCGAT
* * *
177758 AAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAATTTAGTAAATAATGTATTGTTA
259 AAAAATTGTAATATAATAATAATTTCTTATTTAAATATTTAAATTTAGTAAATAATGCATTGTCA
177823 AATCAACTCATT
324 AATCAACTCATT
* * **
177835 ATTTGATAAAAATTATAATATAATAATAATTTGTAATCTAAATATGAAAATTTGATAAATAATGT
1 ATTTGATAAAAATTATAATATAATAATAATTTGTTATTTAAATATTTAAATTTGATAAATAATGT
* *
177900 ATTGTCAAATGAACACAATATTTGATATAAATTGTAATATAATAATAATCTCTTTTATTTAAATA
66 ATTGTCAAATGAACACATTATTTGATAAAAATTGTAATATAATAATAA--T-TTTTATTTAAAT-
177965 ATGTTAAATT
127 AT-TTAAATT
177975 CATTTTAAAT
Statistics
Matches: 430, Mismatches: 35, Indels: 16
0.89 0.07 0.03
Matches are distributed among these distances:
334 227 0.53
335 79 0.18
336 15 0.03
337 99 0.23
338 3 0.01
339 7 0.02
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.43
Consensus pattern (335 bp):
ATTTGATAAAAATTATAATATAATAATAATTTGTTATTTAAATATTTAAATTTGATAAATAATGT
ATTGTCAAATGAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTATTTAAATATTT
AAATTTGATAAATAATATATTATCAAATCAACACATTATTTAAAAAAAATTATAATATAATAATA
AATTTTTATTTAAATATAAAATTTGAGTAAATAATGTATTATCAAATCAACACATTATTCGATAA
AAATTGTAATATAATAATAATTTCTTATTTAAATATTTAAATTTAGTAAATAATGCATTGTCAAA
TCAACTCATT
Found at i:178100 original size:11 final size:12
Alignment explanation
Indices: 178078--178126 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
178068 AAACATGTTC
178078 ATTAATTTTCAA
1 ATTAATTTTCAA
*
178090 ATTAATTTCAACTTAA
1 ATTAATTT----TCAA
178106 ATTAATTTTCAA
1 ATTAATTTTCAA
178118 ATTAATTTT
1 ATTAATTTT
178127 TACACAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
12 20 0.65
16 11 0.35
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (12 bp):
ATTAATTTTCAA
Found at i:178124 original size:16 final size:16
Alignment explanation
Indices: 178088--178122 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
178078 ATTAATTTTC
*
178088 AAATTAATTTCAACTT
1 AAATTAATTTCAAATT
178104 AAATTAATTTTCAAATT
1 AAATTAA-TTTCAAATT
178121 AA
1 AA
178123 TTTTTACACA
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:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATTAATTTCAAATT
Found at i:178135 original size:28 final size:28
Alignment explanation
Indices: 178078--178135 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
178068 AAACATGTTC
**
178078 ATTAATTTTCAAATTAATTTCAACTTAA
1 ATTAATTTTCAAATTAATTTCAACACAA
**
178106 ATTAATTTTCAAATTAATTTTTACACAA
1 ATTAATTTTCAAATTAATTTCAACACAA
178134 AT
1 AT
178136 ATTCTTCATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (28 bp):
ATTAATTTTCAAATTAATTTCAACACAA
Found at i:181972 original size:121 final size:119
Alignment explanation
Indices: 181846--182209 Score: 414
Period size: 121 Copynumber: 3.0 Consensus size: 119
181836 AGGAGAAATT
* * * * * * *
181846 GGTGTCGGTCATTACATGACCAACACAAAAAAAATTT-AATTTTTTACCAAATAAAAAGGGGGTG
1 GGTGTCGATCATTGCATGACCAACAC--CAAAAATTTGATTTTTTTATCAGATAAATA-GGGGTG
* ** * *
181910 TCGGCCATAACATGACTAACACCAAAAAAATTTAAAATTTTTTATCT-AAAAAAAGAG
63 TCGACCATTGCATGGCCAACACCAAAAAAATTTAAAATTTTTTATCTGAAAAAAAG-G
* * *
181967 GGTGTCGACCATTGCATAACCAACACCCAAAAATTTGATTTTTTTATCAGATAAATAGGGGTGTT
1 GGTGTCGATCATTGCATGACCAACA-CCAAAAATTTGATTTTTTTATCAGATAAATAGGGGTGTC
* * * *
182032 GATCATTGCATGGCGAACACCAAAAAAATTTGAAATTTTTTTATCTGAAAAAATGG
65 GACCATTGCATGGCCAACACCAAAAAAATTT-AAAATTTTTTATCTGAAAAAAAGG
* * * *
182088 GGTGTCGATTATTGTATGACCAACATCCAAAAATTTGATTTTTTTATTAGATAAATAGAGGTGTC
1 GGTGTCGATCATTGCATGACCAACA-CCAAAAATTTGATTTTTTTATCAGATAAATAGGGGTGTC
*
182153 GACCATTGCATGGCCAACACC-AAAAAA-TT-AAATTTTTTATCTGACAAAAAGG
65 GACCATTGCATGGCCAACACCAAAAAAATTTAAAATTTTTTATCTGAAAAAAAGG
182205 GGTGT
1 GGTGT
182210 TGGCCATGAT
Statistics
Matches: 208, Mismatches: 31, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
117 25 0.12
119 2 0.01
120 46 0.22
121 127 0.61
122 8 0.04
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (119 bp):
GGTGTCGATCATTGCATGACCAACACCAAAAATTTGATTTTTTTATCAGATAAATAGGGGTGTCG
ACCATTGCATGGCCAACACCAAAAAAATTTAAAATTTTTTATCTGAAAAAAAGG
Found at i:182039 original size:59 final size:59
Alignment explanation
Indices: 181846--182209 Score: 279
Period size: 59 Copynumber: 6.1 Consensus size: 59
181836 AGGAGAAATT
** * ** * * *
181846 GGTGTCGGTCATTACATGACCAACACAAAAAAAATTT-AATTTTTTACCAAATAAAAAGGG
1 GGTGTCGACCATTGCATGACCAACAC-CCAAAAATTTGATTTTTTTATCAGATAAAAA-GG
* ** * * * *
181906 GGTGTCGGCCATAACATGACTAACACCAAAAAAATTTAAAATTTTTTATCTA-A-AAAAAGAG
1 GGTGTCGACCATTGCATGACCAACACC-CAAAAATTT-GATTTTTTTATC-AGATAAAAAG-G
* *
181967 GGTGTCGACCATTGCATAACCAACACCCAAAAATTTGATTTTTTTATCAGATAAATAGG
1 GGTGTCGACCATTGCATGACCAACACCCAAAAATTTGATTTTTTTATCAGATAAAAAGG
* * * * * *
182026 GGTGTTGATCATTGCATGGCGAACACCAAAAAAATTTGAAATTTTTTTATCTGA-AAAAATGG
1 GGTGTCGACCATTGCATGACCAACACC-CAAAAATTTG--ATTTTTTTATCAGATAAAAA-GG
** * * * * *
182088 GGTGTCGATTATTGTATGACCAACATCCAAAAATTTGATTTTTTTATTAGATAAATAGA
1 GGTGTCGACCATTGCATGACCAACACCCAAAAATTTGATTTTTTTATCAGATAAAAAGG
* * * * * *
182147 GGTGTCGACCATTGCATGGCCAACA-CCAAAAAATTAAATTTTTTATCTGACAAAAAGG
1 GGTGTCGACCATTGCATGACCAACACCCAAAAATTTGATTTTTTTATCAGATAAAAAGG
182205 GGTGT
1 GGTGT
182210 TGGCCATGAT
Statistics
Matches: 247, Mismatches: 45, Indels: 26
0.78 0.14 0.08
Matches are distributed among these distances:
58 31 0.13
59 68 0.28
60 59 0.24
61 41 0.17
62 47 0.19
63 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (59 bp):
GGTGTCGACCATTGCATGACCAACACCCAAAAATTTGATTTTTTTATCAGATAAAAAGG
Found at i:188394 original size:2 final size:2
Alignment explanation
Indices: 188387--188412 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
188377 GGTTGTTTTC
188387 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
188413 AATTTAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:189822 original size:69 final size:69
Alignment explanation
Indices: 189731--189862 Score: 167
Period size: 69 Copynumber: 1.9 Consensus size: 69
189721 GTCAGTGATG
* * * *
189731 GAACATGATAAAATCACTTGTGATGTAGG-GACCACGGATAAAGTGGGAATTGATTTAATGGGGC
1 GAACATGATAAAACCACTTGTGATAT-GGAGACCACGAATAAAGTAGGAATTGATTTAATGGGGC
189795 AAAAA
65 AAAAA
** * * *
189800 GAACATGATCCAACCACTTGTGATATGGAGGCCACGAATAATGTAGGTATTGATTTAATGGGG
1 GAACATGATAAAACCACTTGTGATATGGAGACCACGAATAAAGTAGGAATTGATTTAATGGGG
189863 AAAGAAGTAT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
68 2 0.04
69 51 0.96
ACGTcount: A:0.36, C:0.12, G:0.27, T:0.25
Consensus pattern (69 bp):
GAACATGATAAAACCACTTGTGATATGGAGACCACGAATAAAGTAGGAATTGATTTAATGGGGCA
AAAA
Found at i:204294 original size:29 final size:31
Alignment explanation
Indices: 204248--204329 Score: 80
Period size: 29 Copynumber: 2.7 Consensus size: 31
204238 AAATTTATAT
*
204248 TGTTGTTTTT-GTGTTTTTTTTTACTGTTTT-
1 TGTTGTTTTTACTG-TTTTTTTTACTGTTTTC
** *
204278 TG-TGTTTTTACTGTTTTGGTTGCTGTTTTC
1 TGTTGTTTTTACTGTTTTTTTTACTGTTTTC
*
204308 GTGTTGTTTTTACTGTTATTTT
1 -TGTTGTTTTTACTGTTTTTTT
204330 CGTTGTTATT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
29 20 0.49
30 4 0.10
31 2 0.05
32 15 0.37
ACGTcount: A:0.05, C:0.06, G:0.20, T:0.70
Consensus pattern (31 bp):
TGTTGTTTTTACTGTTTTTTTTACTGTTTTC
Found at i:204336 original size:12 final size:12
Alignment explanation
Indices: 204321--204383 Score: 74
Period size: 12 Copynumber: 5.3 Consensus size: 12
204311 TTGTTTTTAC
*
204321 TGTTATTTTCGT
1 TGTTATTTTTGT
204333 TGTTATTTTTGT
1 TGTTATTTTTGT
* **
204345 TATTATTTTTAA
1 TGTTATTTTTGT
*
204357 TGTT-GTTTTGT
1 TGTTATTTTTGT
204368 TGTTATTTTTGT
1 TGTTATTTTTGT
204380 TGTT
1 TGTT
204384 TAAATGTTAT
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
11 8 0.20
12 33 0.80
ACGTcount: A:0.11, C:0.02, G:0.16, T:0.71
Consensus pattern (12 bp):
TGTTATTTTTGT
Found at i:206396 original size:23 final size:23
Alignment explanation
Indices: 206327--206396 Score: 97
Period size: 23 Copynumber: 3.1 Consensus size: 23
206317 ACCAATTATT
* *
206327 ATTAT-TTTGTACCTCTCCTACC
1 ATTATGTTTGTAACTCTCCTATC
*
206349 ATTATGTTTGTAACTTTCCTATC
1 ATTATGTTTGTAACTCTCCTATC
*
206372 ATTATGTTTGTAACTCTCCTGTC
1 ATTATGTTTGTAACTCTCCTATC
206395 AT
1 AT
206397 AATATTTTGT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 5 0.12
23 37 0.88
ACGTcount: A:0.20, C:0.23, G:0.09, T:0.49
Consensus pattern (23 bp):
ATTATGTTTGTAACTCTCCTATC
Found at i:209960 original size:23 final size:23
Alignment explanation
Indices: 209925--209984 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
209915 ACCAATTATT
209925 ATTAT-TTTGTAACTCTCCTACC
1 ATTATGTTTGTAACTCTCCTACC
* *
209947 ATTATGTTTGTAACTCTTCTGCC
1 ATTATGTTTGTAACTCTCCTACC
*
209970 ATTATGTTGGTAACT
1 ATTATGTTTGTAACT
209985 ATACTGCCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
22 5 0.15
23 29 0.85
ACGTcount: A:0.22, C:0.20, G:0.12, T:0.47
Consensus pattern (23 bp):
ATTATGTTTGTAACTCTCCTACC
Found at i:209991 original size:23 final size:23
Alignment explanation
Indices: 209945--210000 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
209935 AACTCTCCTA
* * *
209945 CCATTATGTTTGTAACTCTTCTG
1 CCATTATGTTGGTAACTATACTG
209968 CCATTATGTTGGTAACTATACTG
1 CCATTATGTTGGTAACTATACTG
*
209991 CCATAATGTT
1 CCATTATGTT
210001 TTGTTTTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.43
Consensus pattern (23 bp):
CCATTATGTTGGTAACTATACTG
Found at i:210349 original size:13 final size:13
Alignment explanation
Indices: 210331--210357 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
210321 ATTCATCTAC
210331 AAATACTACGTAA
1 AAATACTACGTAA
210344 AAATACTACGTAA
1 AAATACTACGTAA
210357 A
1 A
210358 GTATACTTGT
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:0.56, C:0.15, G:0.07, T:0.22
Consensus pattern (13 bp):
AAATACTACGTAA
Found at i:213932 original size:20 final size:20
Alignment explanation
Indices: 213903--213943 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
213893 TCTTATTTAA
213903 TTTAAATTA-TATTTTTAAAT
1 TTTAAATTATTA-TTTTAAAT
*
213923 TTTAATTTATTATTTTAAAT
1 TTTAAATTATTATTTTAAAT
213943 T
1 T
213944 GATTTATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTAAATTATTATTTTAAAT
Found at i:213948 original size:18 final size:18
Alignment explanation
Indices: 213924--214023 Score: 84
Period size: 18 Copynumber: 5.6 Consensus size: 18
213914 TTTTTAAATT
213924 TTAATTTATTATTTTAAA
1 TTAATTTATTATTTTAAA
*
213942 TTGATTTATTATTCTCTAAA
1 TTAATTTATTATT-T-TAAA
*
213962 -T-ATGTATT-TTGTT-AA
1 TTAATTTATTATT-TTAAA
*
213977 TTAAATTCTATT-TTTTAAT
1 TT-AATT-TATTATTTTAAA
*
213996 TTAATTTATTACTTTAAA
1 TTAATTTATTATTTTAAA
214014 TTAATTTATT
1 TTAATTTATT
214024 CTTTAAATAG
Statistics
Matches: 67, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
15 2 0.03
16 2 0.03
17 7 0.10
18 41 0.61
19 11 0.16
20 4 0.06
ACGTcount: A:0.33, C:0.04, G:0.03, T:0.60
Consensus pattern (18 bp):
TTAATTTATTATTTTAAA
Found at i:219478 original size:27 final size:27
Alignment explanation
Indices: 219427--219478 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
219417 ATGAGTTCAA
*
219427 AATTATTAAAAAATATAAATTATTAAT
1 AATTATTAAAAAATATAAATAATTAAT
219454 AATTATTAAAAAATCATAAA-AATTA
1 AATTATTAAAAAAT-ATAAATAATTA
219479 TATGGAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (27 bp):
AATTATTAAAAAATATAAATAATTAAT
Found at i:226079 original size:18 final size:18
Alignment explanation
Indices: 226056--226093 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
226046 CAAAGTTCTC
*
226056 TTTTTATTTCTCACTCAA
1 TTTTTATTCCTCACTCAA
*
226074 TTTTTATTCCTCTCTCAA
1 TTTTTATTCCTCACTCAA
226092 TT
1 TT
226094 CTCCCTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.18, C:0.24, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTTATTCCTCACTCAA
Found at i:226163 original size:36 final size:36
Alignment explanation
Indices: 226101--226172 Score: 85
Period size: 36 Copynumber: 2.0 Consensus size: 36
226091 ATTCTCCCTT
226101 TTTTTATTAAAATTGTATTAAGA-TTTTCTAAAATTA
1 TTTTTATTAAAATTGTATTAAGATTTTTC-AAAATTA
* **
226137 TTTTTATTATAATT-TATTTCGTATTTTTCAAAATTA
1 TTTTTATTAAAATTGTATTAAG-ATTTTTCAAAATTA
226173 ATAATGAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
35 5 0.16
36 21 0.68
37 5 0.16
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (36 bp):
TTTTTATTAAAATTGTATTAAGATTTTTCAAAATTA
Found at i:228096 original size:24 final size:24
Alignment explanation
Indices: 228067--228115 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
228057 CTCGATTTTC
* *
228067 CAACTGTTCGCCAAACTACTCCAA
1 CAACTGTACACCAAACTACTCCAA
228091 CAACTGTACACCAAACTACTCCAA
1 CAACTGTACACCAAACTACTCCAA
228115 C
1 C
228116 CCAACATGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.39, G:0.06, T:0.18
Consensus pattern (24 bp):
CAACTGTACACCAAACTACTCCAA
Found at i:238538 original size:35 final size:35
Alignment explanation
Indices: 238487--238553 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
238477 ATTTTTTTAA
* * *
238487 CATGAATCTTGAACCCTAAATCTTAAATCTTAAAC
1 CATGAATCTTAAACCCTAAATCTCAAACCTTAAAC
*
238522 CATGTATCTTAAACCCTAAATCTCAAACCTTA
1 CATGAATCTTAAACCCTAAATCTCAAACCTTA
238554 GACCTTAGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.39, C:0.25, G:0.04, T:0.31
Consensus pattern (35 bp):
CATGAATCTTAAACCCTAAATCTCAAACCTTAAAC
Found at i:238733 original size:35 final size:35
Alignment explanation
Indices: 238651--238738 Score: 90
Period size: 35 Copynumber: 2.5 Consensus size: 35
238641 TTCAAAGTTT
* * *
238651 CAAGGTCTAGGGTTTAGGTTTTAAGGTCCAGGGTT
1 CAAGGTCTAGGGTTTAGGATTTAAGGTCCAAGGTC
* * *
238686 CACA-GTCAAGGGTTTCGGATTT-AGAGTCTAAGGTC
1 CA-AGGTCTAGGGTTTAGGATTTAAG-GTCCAAGGTC
238721 CAAGGTCTAGGGTTTAGG
1 CAAGGTCTAGGGTTTAGG
238739 GTTCATAATC
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
34 3 0.07
35 38 0.90
36 1 0.02
ACGTcount: A:0.23, C:0.14, G:0.33, T:0.31
Consensus pattern (35 bp):
CAAGGTCTAGGGTTTAGGATTTAAGGTCCAAGGTC
Found at i:238791 original size:56 final size:56
Alignment explanation
Indices: 238662--238793 Score: 147
Period size: 56 Copynumber: 2.4 Consensus size: 56
238652 AAGGTCTAGG
* ** * * *
238662 GTTTAGGTTTTAAGGTCCAGGGTTCACAGTCAAGGGTTTCGGATTTAGAGTCTAAG
1 GTTTAGGGTTTAAGGTTTAGGGTTCACAATCAAGGGTTTCGGATTTAGAGTCCAAA
** * * * * *
238718 GTCCAAGGTCTAGGGTTTAGGGTTCATAATCAAGGGTTTGGGATTTAGAGTCCAAA
1 GTTTAGGGTTTAAGGTTTAGGGTTCACAATCAAGGGTTTCGGATTTAGAGTCCAAA
238774 GTTTAGGGTTTAAGGTTTAG
1 GTTTAGGGTTTAAGGTTTAG
238794 AATTTGGGGT
Statistics
Matches: 58, Mismatches: 18, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.24, C:0.11, G:0.31, T:0.34
Consensus pattern (56 bp):
GTTTAGGGTTTAAGGTTTAGGGTTCACAATCAAGGGTTTCGGATTTAGAGTCCAAA
Found at i:239898 original size:44 final size:43
Alignment explanation
Indices: 239831--239918 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 43
239821 TAAAAATAAT
* *
239831 AACATCTGAATGTGTTGTTTTTATTAATCTCTTAATTAATTTAA
1 AACATCTGAATGTGTTATATTTATTAATCTC-TAATTAATTTAA
**
239875 AACATCTGAATGTGTTATATTTATTTTTCTCTAATTAATTTAA
1 AACATCTGAATGTGTTATATTTATTAATCTCTAATTAATTTAA
239918 A
1 A
239919 TTAATTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 13 0.32
44 27 0.68
ACGTcount: A:0.33, C:0.09, G:0.08, T:0.50
Consensus pattern (43 bp):
AACATCTGAATGTGTTATATTTATTAATCTCTAATTAATTTAA
Found at i:240703 original size:19 final size:19
Alignment explanation
Indices: 240681--240725 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
240671 TTTTATTAGG
240681 ATTTAATATTTAATATAT-T
1 ATTTAATATTTAA-ATATGT
* *
240700 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
240719 ATTTAAT
1 ATTTAAT
240726 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:240710 original size:26 final size:25
Alignment explanation
Indices: 240664--240716 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 25
240654 TTTATTTTAA
240664 AATATATTTTTATTAGGATTTAATATTT
1 AATATATTTTTATT--GATTTAA-ATTT
240692 AATATATTATTTATT-ATTTAAATTT
1 AATATATT-TTTATTGATTTAAATTT
240717 GTATTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
25 4 0.17
26 6 0.25
28 8 0.33
29 6 0.25
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (25 bp):
AATATATTTTTATTGATTTAAATTT
Found at i:243616 original size:59 final size:60
Alignment explanation
Indices: 243547--243708 Score: 168
Period size: 59 Copynumber: 2.8 Consensus size: 60
243537 ATGCTTTGAA
* * * *
243547 AAAAATGGTAATTTTCGAAAGATTCAATGTTAAAAATGAAATTTTAAGATAT-TAGGGGT
1 AAAAATGGTAATTTTCGAAAGATTCAAGGTCAAAAATGAAATTTTAAGACATCCAGGGGT
* * * * * *
243606 AAAAATGGTAATTTTTGGAAGGTTCAAGGTCAAAAATGGAATTTTTAGACATCCGGGGGT
1 AAAAATGGTAATTTTCGAAAGATTCAAGGTCAAAAATGAAATTTTAAGACATCCAGGGGT
* *** *
243666 -AAAATGGTAATTTTGGAAAG-TTTGGGGTCAAAAATGGAATTTT
1 AAAAATGGTAATTTTCGAAAGATTCAAGGTCAAAAATGAAATTTT
243709 GGAAAATTCG
Statistics
Matches: 87, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
58 20 0.23
59 62 0.71
60 5 0.06
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.33
Consensus pattern (60 bp):
AAAAATGGTAATTTTCGAAAGATTCAAGGTCAAAAATGAAATTTTAAGACATCCAGGGGT
Found at i:243692 original size:29 final size:30
Alignment explanation
Indices: 243598--243981 Score: 221
Period size: 29 Copynumber: 13.0 Consensus size: 30
243588 TTTTAAGATA
*
243598 TTAGGGGTAAAAATGGTAATTTTTGGAAGGT
1 TTAGGGGTAAAAATGGTAA-TTTTGGAAAGT
* * * *
243629 TCA-AGGTCAAAAATGG-AATTTTTAGACA-T
1 TTAGGGGT-AAAAATGGTAA-TTTTGGAAAGT
***
243658 CCGGGGGT-AAAATGGTAATTTTGGAAAGT
1 TTAGGGGTAAAAATGGTAATTTTGGAAAGT
*
243687 TT-GGGGTCAAAAATGG-AATTTTGGAAA-A
1 TTAGGGGT-AAAAATGGTAATTTTGGAAAGT
* * * **
243715 TTCGAGGGTAAAAAT-ATATTTTTTTATAAAGT
1 TTAG-GGGTAAAAATGGTA--ATTTTGGAAAGT
* * * *
243747 TTA-GGGTTAAAATAG-AGTTTTAGAAAGT
1 TTAGGGGTAAAAATGGTAATTTTGGAAAGT
* ** *
243775 TTAGAGGT-AAAATTTTAATTTTTAGAAAGT
1 TTAGGGGTAAAAATGGTAA-TTTTGGAAAGT
*
243805 TTAGGGTTAAAAATGG-AATTTTGGAAAGT
1 TTAGGGGTAAAAATGGTAATTTTGGAAAGT
* *
243834 TCAGGGGTAAAAAT-GTAATTTGTAGAAAGT
1 TTAGGGGTAAAAATGGTAATTT-TGGAAAGT
**
243864 TTAGGATTAAAAATGG-AATTTTGGAAAG-
1 TTAGGGGTAAAAATGGTAATTTTGGAAAGT
* **
243892 TTCGAGGGTAAAAA-AATAATTTTTGGAAAGT
1 TTAG-GGGTAAAAATGGTAA-TTTTGGAAAGT
* *
243923 TCAGGGTTAAAAATGG-AATTTTGGAAAGT
1 TTAGGGGTAAAAATGGTAATTTTGGAAAGT
**
243952 TT-GAGGGTAAAAA-AATAATTTTGGAAAGT
1 TTAG-GGGTAAAAATGGTAATTTTGGAAAGT
243981 T
1 T
243982 AGAGGACCTT
Statistics
Matches: 273, Mismatches: 53, Indels: 56
0.71 0.14 0.15
Matches are distributed among these distances:
28 44 0.16
29 104 0.38
30 98 0.36
31 25 0.09
32 2 0.01
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.34
Consensus pattern (30 bp):
TTAGGGGTAAAAATGGTAATTTTGGAAAGT
Found at i:243729 original size:59 final size:58
Alignment explanation
Indices: 243602--243981 Score: 356
Period size: 59 Copynumber: 6.4 Consensus size: 58
243592 AAGATATTAG
* * * * * * * * *
243602 GGGTAAAAATGGTAATTTTTGGAAGGTTCAAGGTCAAAAATGGAATTTTTAGACA-TCCGG
1 GGGTAAAAAT-ATAA-TTTTGGAAAGTTTAGGGTTAAAAATGGAA-TTTTGGAAAGTTCGA
* * * *
243662 GGGT-AAAATGGTAATTTTGGAAAGTTTGGGGTCAAAAATGGAATTTTGGAAAATTCGA
1 GGGTAAAAAT-ATAATTTTGGAAAGTTTAGGGTTAAAAATGGAATTTTGGAAAGTTCGA
* ** * * * *
243720 GGGTAAAAATATATTTTTTTATAAAGTTTAGGGTT-AAAATAGAGTTTTAGAAAGTT-TA
1 GGGTAAAAATATA--ATTTTGGAAAGTTTAGGGTTAAAAATGGAATTTTGGAAAGTTCGA
* * *
243778 GAGGTAAAATTTTAATTTTTAGAAAGTTTAGGGTTAAAAATGGAATTTTGGAAAGTTC-A
1 G-GGTAAAAATATAA-TTTTGGAAAGTTTAGGGTTAAAAATGGAATTTTGGAAAGTTCGA
* * *
243837 GGGGTAAAAATGTAATTTGTAGAAAGTTTAGGATTAAAAATGGAATTTTGGAAAGTTCGA
1 -GGGTAAAAATATAATTT-TGGAAAGTTTAGGGTTAAAAATGGAATTTTGGAAAGTTCGA
* * *
243897 GGGTAAAAAAATAATTTTTGGAAAGTTCAGGGTTAAAAATGGAATTTTGGAAAGTTTGA
1 GGGTAAAAATATAA-TTTTGGAAAGTTTAGGGTTAAAAATGGAATTTTGGAAAGTTCGA
*
243956 GGGTAAAAAAATAATTTTGGAAAGTT
1 GGGTAAAAATATAATTTTGGAAAGTT
243982 AGAGGACCTT
Statistics
Matches: 273, Mismatches: 35, Indels: 26
0.82 0.10 0.08
Matches are distributed among these distances:
57 7 0.03
58 69 0.25
59 173 0.63
60 24 0.09
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.34
Consensus pattern (58 bp):
GGGTAAAAATATAATTTTGGAAAGTTTAGGGTTAAAAATGGAATTTTGGAAAGTTCGA
Done.