Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015209.1 Kokia drynarioides strain JFW-HI SEQ_130253, 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: 307560
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 274 characters in sequence are not A, C, G, or T
Found at i:3410 original size:3 final size:3
Alignment explanation
Indices: 3404--3433 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3394 ACCACCTTAT
3404 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3434 ACTTCTAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:4547 original size:33 final size:33
Alignment explanation
Indices: 4510--4651 Score: 128
Period size: 33 Copynumber: 4.4 Consensus size: 33
4500 ATCTTATTAT
*
4510 AGGGGCATCATCCCTGCTACTTGGCCTGCTTGA
1 AGGGGCATCATCCCTGCTACTTGGCCTGCTTAA
* * * * *
4543 AGGGGCATCATCCCTACTAATTGGTCGGCTTAT
1 AGGGGCATCATCCCTGCTACTTGGCCTGCTTAA
* ** *
4576 A--GACA-CATCCCTGCTACTTTTCCTGCTCAA
1 AGGGGCATCATCCCTGCTACTTGGCCTGCTTAA
* * * *
4606 AGGAGTATCATCCCAGCTACTTGTCCTGCTTAA
1 AGGGGCATCATCCCTGCTACTTGGCCTGCTTAA
*
4639 AGGAGCATCATCC
1 AGGGGCATCATCC
4652 GTACTAACTG
Statistics
Matches: 84, Mismatches: 22, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
30 18 0.21
31 3 0.04
32 1 0.01
33 62 0.74
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28
Consensus pattern (33 bp):
AGGGGCATCATCCCTGCTACTTGGCCTGCTTAA
Found at i:31181 original size:5 final size:5
Alignment explanation
Indices: 31171--31203 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
31161 AAATAATCAA
*
31171 TTTCT TTTCT TTTCT TTTCT CTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
31204 TGGTGCTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTCT
Found at i:51426 original size:10 final size:9
Alignment explanation
Indices: 51401--51425 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
51391 TTTTTACTAA
51401 TTTAAAATT
1 TTTAAAATT
51410 TTTAAAATT
1 TTTAAAATT
51419 TTTAAAA
1 TTTAAAA
51426 AATCTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
TTTAAAATT
Found at i:57322 original size:60 final size:59
Alignment explanation
Indices: 57224--57367 Score: 173
Period size: 59 Copynumber: 2.4 Consensus size: 59
57214 AACTTAATAT
* * ** ** * *
57224 TTTTTTTTAATTTGGTATCTAAATTTTTTTTTACTCAATTTGATATTTGAATTTGACAC
1 TTTTTCTTAATTTGGTACCTAAATTTTTTTGGACTCAATTTGATACCTAAACTTGACAC
* * *
57283 TTTTTCTTAAATTGGTACCTAAACTTTTTTTGGACTCAATTTGGTACCTAAACTTGACAT
1 TTTTTCTTAATTTGGTACCTAAA-TTTTTTTGGACTCAATTTGATACCTAAACTTGACAC
57343 TTTTTC-TAATTTGGTACCTAAATTT
1 TTTTTCTTAATTTGGTACCTAAATTT
57368 ATTAAATATT
Statistics
Matches: 72, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
58 3 0.04
59 35 0.49
60 34 0.47
ACGTcount: A:0.26, C:0.12, G:0.10, T:0.52
Consensus pattern (59 bp):
TTTTTCTTAATTTGGTACCTAAATTTTTTTGGACTCAATTTGATACCTAAACTTGACAC
Found at i:60120 original size:21 final size:22
Alignment explanation
Indices: 60086--60129 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
60076 TTTAATGCTA
*
60086 TTTAATAATCAAATTAAC-AAT
1 TTTAATAATCAAATGAACTAAT
60107 TTTAATAA-CGAAATGAACTAAT
1 TTTAATAATC-AAATGAACTAAT
60129 T
1 T
60130 AATACAATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 1 0.05
21 15 0.75
22 4 0.20
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.36
Consensus pattern (22 bp):
TTTAATAATCAAATGAACTAAT
Found at i:62004 original size:41 final size:42
Alignment explanation
Indices: 61943--62028 Score: 120
Period size: 41 Copynumber: 2.1 Consensus size: 42
61933 CTTATAATGT
*
61943 TATCTTTAAAATTTAAATTTACATTTTCTCTTAAAAGTGAAA
1 TATCTTTAAAATTTAAATTTAAATTTTCTCTTAAAAGTGAAA
* * * *
61985 TATC-TTAAGATTTAAATTTAAATTTTTTTTTAAAAGTGGAA
1 TATCTTTAAAATTTAAATTTAAATTTTCTCTTAAAAGTGAAA
62026 TAT
1 TAT
62029 ACGTTATTAC
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 35 0.90
42 4 0.10
ACGTcount: A:0.40, C:0.06, G:0.07, T:0.48
Consensus pattern (42 bp):
TATCTTTAAAATTTAAATTTAAATTTTCTCTTAAAAGTGAAA
Found at i:62353 original size:25 final size:24
Alignment explanation
Indices: 62307--62363 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
62297 TTTTTTAAAA
* *
62307 ATATTATCTTTAAAATTTAAATGT
1 ATATTATCTTTAAAAGTGAAATGT
* *
62331 ATATTCTCTCTTAAAAGTGAAATAT
1 ATATTATCT-TTAAAAGTGAAATGT
*
62356 ATCTTATC
1 ATATTATC
62364 ACTACACTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
24 8 0.31
25 18 0.69
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.46
Consensus pattern (24 bp):
ATATTATCTTTAAAAGTGAAATGT
Found at i:63963 original size:36 final size:39
Alignment explanation
Indices: 63923--64017 Score: 94
Period size: 36 Copynumber: 2.5 Consensus size: 39
63913 ATGTAGATAT
*
63923 TAATTTTAAAATAATATATAATAA-ATA-ATAA-ACATA
1 TAATTTTAAAATAATATATAATAATATATAAAATACATA
*
63959 TAA-TTTAAAATTAAT-TAATAATAATATATAAAATACGTA
1 TAATTTTAAAA-TAATAT-ATAATAATATATAAAATACATA
* *
63998 TGATATTAAAATAA-ATATAA
1 TAATTTTAAAATAATATATAA
64018 ATTAATTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
35 8 0.17
36 14 0.29
37 3 0.06
38 7 0.15
39 10 0.21
40 6 0.12
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (39 bp):
TAATTTTAAAATAATATATAATAATATATAAAATACATA
Found at i:73633 original size:165 final size:165
Alignment explanation
Indices: 73361--73695 Score: 661
Period size: 165 Copynumber: 2.0 Consensus size: 165
73351 AGCCATAAAG
73361 GATTAGAAAGCCCCAAATCTGATCTCACAATTTCCTTCTCTTTCTTCATTTCTAGTTTTTTCCTC
1 GATTAGAAAGCCCCAAATCTGATCTCACAATTTCCTTCTCTTTCTTCATTTCTAGTTTTTTCCTC
73426 CACAGCAATCTCTCCATCTTTTTCAGCTCTTCAAGTTAATCATTAAAATTAGAGCCATGATAAAG
66 CACAGCAATCTCTCCATCTTTTTCAGCTCTTCAAGTTAATCATTAAAATTAGAGCCATGATAAAG
73491 CACCATTCTCTCTTTGTTCTTCATTCTTTTCCTAT
131 CACCATTCTCTCTTTGTTCTTCATTCTTTTCCTAT
73526 GATTAGAAAGCCCCAAATCTGATCTCACAATTTCCTTCTCTTTCTTCATTTCTAGTTTTTTCCTC
1 GATTAGAAAGCCCCAAATCTGATCTCACAATTTCCTTCTCTTTCTTCATTTCTAGTTTTTTCCTC
*
73591 TACAGCAATCTCTCCATCTTTTTCAGCTCTTCAAGTTAATCATTAAAATTAGAGCCATGATAAAG
66 CACAGCAATCTCTCCATCTTTTTCAGCTCTTCAAGTTAATCATTAAAATTAGAGCCATGATAAAG
73656 CACCATTCTCTCTTTGTTCTTCATTCTTTTCCTAT
131 CACCATTCTCTCTTTGTTCTTCATTCTTTTCCTAT
73691 GATTA
1 GATTA
73696 CCTTCATTGA
Statistics
Matches: 169, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
165 169 1.00
ACGTcount: A:0.24, C:0.26, G:0.08, T:0.41
Consensus pattern (165 bp):
GATTAGAAAGCCCCAAATCTGATCTCACAATTTCCTTCTCTTTCTTCATTTCTAGTTTTTTCCTC
CACAGCAATCTCTCCATCTTTTTCAGCTCTTCAAGTTAATCATTAAAATTAGAGCCATGATAAAG
CACCATTCTCTCTTTGTTCTTCATTCTTTTCCTAT
Found at i:80441 original size:62 final size:59
Alignment explanation
Indices: 80359--80473 Score: 151
Period size: 63 Copynumber: 1.9 Consensus size: 59
80349 CATTGGCATG
*
80359 ACTTAAAAAAAACTTAATAACACAATGTCTT-AAATAAAAACATTCAAATAGTTAAGTC
1 ACTTAAAAAAAACTTAATAACACAATGACTTAAAATAAAAACATTCAAATAGTTAAGTC
* * *
80417 ACTTAAATAAAAACTCTATAATAACTCAATGACTTAAAATGAAAACCTTCAAATAGT
1 ACTTAAA-AAAAA--CT-TAATAACACAATGACTTAAAATAAAAACATTCAAATAGT
80474 ACAATTATCA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
58 7 0.15
59 5 0.10
61 2 0.04
62 15 0.31
63 19 0.40
ACGTcount: A:0.52, C:0.15, G:0.05, T:0.28
Consensus pattern (59 bp):
ACTTAAAAAAAACTTAATAACACAATGACTTAAAATAAAAACATTCAAATAGTTAAGTC
Found at i:80452 original size:31 final size:31
Alignment explanation
Indices: 80356--80454 Score: 77
Period size: 31 Copynumber: 3.3 Consensus size: 31
80346 ACTCATTGGC
*
80356 ATGACTTAAA-AAAAA--CT-TAATAACACA
1 ATGACTTAAATAAAAACTCTATAATAACTCA
* * *
80383 ATGTCTTAAATAAAAACAT-TCA-AAT-AGTTA
1 ATGACTTAAATAAAAAC-TCT-ATAATAACTCA
*
80413 AGTCACTTAAATAAAAACTCTATAATAACTCA
1 A-TGACTTAAATAAAAACTCTATAATAACTCA
80445 ATGACTTAAA
1 ATGACTTAAA
80455 ATGAAAACCT
Statistics
Matches: 53, Mismatches: 9, Indels: 16
0.68 0.12 0.21
Matches are distributed among these distances:
27 9 0.17
28 5 0.09
30 6 0.11
31 29 0.55
32 4 0.08
ACGTcount: A:0.53, C:0.14, G:0.05, T:0.28
Consensus pattern (31 bp):
ATGACTTAAATAAAAACTCTATAATAACTCA
Found at i:102793 original size:27 final size:29
Alignment explanation
Indices: 102764--102819 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
102754 CATGTATTAA
102764 TTTTT-ATCAATTTGGCCCCTATACTTATT
1 TTTTTAATCAATTTGGCCCCTATACTTA-T
* *
102793 TTTTTAATCAGTTTGGCTCCTATACTT
1 TTTTTAATCAATTTGGCCCCTATACTT
102820 TCATTTTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.20, C:0.20, G:0.09, T:0.52
Consensus pattern (29 bp):
TTTTTAATCAATTTGGCCCCTATACTTAT
Found at i:102826 original size:29 final size:30
Alignment explanation
Indices: 102763--102826 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
102753 ACATGTATTA
* *
102763 ATTTTTATCAATTTGGCCCCTATACTTATT
1 ATTTTAATCAATTTGGCCCCTATACTTATC
* * *
102793 TTTTTAATCAGTTTGGCTCCTATACTT-TC
1 ATTTTAATCAATTTGGCCCCTATACTTATC
102822 ATTTT
1 ATTTT
102827 GTAATCCCCA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
29 5 0.18
30 23 0.82
ACGTcount: A:0.20, C:0.19, G:0.08, T:0.53
Consensus pattern (30 bp):
ATTTTAATCAATTTGGCCCCTATACTTATC
Found at i:107948 original size:36 final size:36
Alignment explanation
Indices: 107899--107968 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
107889 TGTATTTAGA
* * *
107899 AAGGGGCATATCTCCGTGCCCGTATTTGGTTCAAGT
1 AAGGGGCAGATCTCCATGCCCGTATTTGGATCAAGT
107935 AAGGGGCAGATCTCCATGCCCGTATTTGGATCAA
1 AAGGGGCAGATCTCCATGCCCGTATTTGGATCAA
107969 ATATTAATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (36 bp):
AAGGGGCAGATCTCCATGCCCGTATTTGGATCAAGT
Found at i:109040 original size:14 final size:17
Alignment explanation
Indices: 109008--109039 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
108998 CAAAAATCAA
109008 AACAATAAGAAAAACAC
1 AACAATAAGAAAAACAC
109025 AACAA-AAGAAAAACA
1 AACAATAAGAAAAACA
109040 AATATAACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.75, C:0.16, G:0.06, T:0.03
Consensus pattern (17 bp):
AACAATAAGAAAAACAC
Found at i:109732 original size:22 final size:22
Alignment explanation
Indices: 109706--109748 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
109696 AAATCGAAAT
* *
109706 AATTATAGGAATTAATTTTTAG
1 AATTAAAGGAATTAAATTTTAG
*
109728 AATTAAATGAATTAAATTTTA
1 AATTAAAGGAATTAAATTTTA
109749 TATGTGTGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (22 bp):
AATTAAAGGAATTAAATTTTAG
Found at i:113212 original size:19 final size:19
Alignment explanation
Indices: 113190--113239 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
113180 AAGTTAATAC
113190 ATTTTTTAAATTCTAAAA-T
1 ATTTTTTAAATTC-AAAATT
*
113209 ATTTGTTAATATTCAAAATT
1 ATTTTTTAA-ATTCAAAATT
*
113229 ATGTTTTAAAT
1 ATTTTTTAAAT
113240 GATTAATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (19 bp):
ATTTTTTAAATTCAAAATT
Found at i:113237 original size:20 final size:18
Alignment explanation
Indices: 113192--113239 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 18
113182 GTTAATACAT
113192 TTTTTAAATTCTAAAATA
1 TTTTTAAATTCTAAAATA
113210 TTTGTTAATATTC-AAAATTA
1 TTT-TTAA-ATTCTAAAA-TA
113230 TGTTTTAAAT
1 T-TTTTAAAT
113240 GATTAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 3 0.12
19 10 0.38
20 11 0.42
21 2 0.08
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (18 bp):
TTTTTAAATTCTAAAATA
Found at i:125389 original size:31 final size:31
Alignment explanation
Indices: 125352--125430 Score: 108
Period size: 31 Copynumber: 2.5 Consensus size: 31
125342 TTTTGGTCCT
125352 ATTTGGTACTCAAACTTGACA-TTTTTTCTTA
1 ATTTGGTACTCAAACTTGACACTTTTTT-TTA
125383 ATTTGGTAC-CTAAACTTGACACTTTTTTTTA
1 ATTTGGTACTC-AAACTTGACACTTTTTTTTA
* *
125414 AGTTGGTACTTAAACTT
1 ATTTGGTACTCAAACTT
125431 TTTGGGGTCC
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
30 1 0.02
31 36 0.84
32 6 0.14
ACGTcount: A:0.27, C:0.15, G:0.11, T:0.47
Consensus pattern (31 bp):
ATTTGGTACTCAAACTTGACACTTTTTTTTA
Found at i:125673 original size:31 final size:31
Alignment explanation
Indices: 125638--125733 Score: 92
Period size: 31 Copynumber: 3.2 Consensus size: 31
125628 GCTTAGATAT
*
125638 CAAATTAGGAAAAAATGTCAAGTTCAGGTAC
1 CAAATTAGGAAAAAATGTCAAGTTTAGGTAC
* *
125669 CAAATTGGGTCCAAAAA----AAGTTTAGGTAC
1 CAAATTAGG--AAAAAATGTCAAGTTTAGGTAC
* * *
125698 CAAATTAAGAAAAAGTGTCAAGTTTATGTAC
1 CAAATTAGGAAAAAATGTCAAGTTTAGGTAC
125729 CAAAT
1 CAAAT
125734 GTTATATTAA
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
27 4 0.08
29 18 0.35
31 24 0.47
33 5 0.10
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.25
Consensus pattern (31 bp):
CAAATTAGGAAAAAATGTCAAGTTTAGGTAC
Found at i:125710 original size:60 final size:60
Alignment explanation
Indices: 125621--125733 Score: 163
Period size: 60 Copynumber: 1.9 Consensus size: 60
125611 ATTGAATCTT
* *
125621 AAAAAAAGCTTAGATATCAAATTAGGAAAAAATGTCAAGTTCAGGTACCAAATTGGGTCC
1 AAAAAAAGCTTAGATACCAAATTAAGAAAAAATGTCAAGTTCAGGTACCAAATTGGGTCC
* * * * *
125681 AAAAAAAGTTTAGGTACCAAATTAAGAAAAAGTGTCAAGTTTATGTACCAAAT
1 AAAAAAAGCTTAGATACCAAATTAAGAAAAAATGTCAAGTTCAGGTACCAAAT
125734 GTTATATTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.47, C:0.12, G:0.17, T:0.25
Consensus pattern (60 bp):
AAAAAAAGCTTAGATACCAAATTAAGAAAAAATGTCAAGTTCAGGTACCAAATTGGGTCC
Found at i:133201 original size:3 final size:3
Alignment explanation
Indices: 133193--133218 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
133183 CTCTCTCCAC
133193 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
133219 AAATCACCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:133250 original size:14 final size:15
Alignment explanation
Indices: 133231--133267 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
133221 ATCACCCATG
133231 TTTTTTTTCTTTTC-
1 TTTTTTTTCTTTTCA
133245 TTTTTTTT-TTTTCA
1 TTTTTTTTCTTTTCA
*
133259 TGTTTTTTC
1 TTTTTTTTC
133268 CATTGTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.03, C:0.11, G:0.03, T:0.84
Consensus pattern (15 bp):
TTTTTTTTCTTTTCA
Found at i:133977 original size:19 final size:19
Alignment explanation
Indices: 133950--133989 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
133940 TGTATTAACT
*
133950 TTTTGGTGTTTAATTTGAG
1 TTTTAGTGTTTAATTTGAG
*
133969 TTTTAGTGTTTCATTTGAG
1 TTTTAGTGTTTAATTTGAG
133988 TT
1 TT
133990 ATATTATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.15, C:0.03, G:0.23, T:0.60
Consensus pattern (19 bp):
TTTTAGTGTTTAATTTGAG
Found at i:134016 original size:18 final size:18
Alignment explanation
Indices: 133982--134021 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
133972 TAGTGTTTCA
133982 TTTGAGTTATATTATTAT
1 TTTGAGTTATATTATTAT
*
134000 GTTTGAGTT-TTTTATTAT
1 -TTTGAGTTATATTATTAT
134018 TTTG
1 TTTG
134022 TTAATAGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 8 0.40
19 8 0.40
ACGTcount: A:0.20, C:0.00, G:0.15, T:0.65
Consensus pattern (18 bp):
TTTGAGTTATATTATTAT
Found at i:137310 original size:31 final size:31
Alignment explanation
Indices: 137245--137306 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
137235 TTAAAATATT
137245 ATTTTTTAATTACATAAATATTAAATAAATA
1 ATTTTTTAATTACATAAATATTAAATAAATA
* * *
137276 ATTTTTTAATTTCA-AAATATTACATTAATA
1 ATTTTTTAATTACATAAATATTAAATAAATA
137306 A
1 A
137307 ATTTAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 15 0.54
31 13 0.46
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (31 bp):
ATTTTTTAATTACATAAATATTAAATAAATA
Found at i:139985 original size:31 final size:30
Alignment explanation
Indices: 139940--140000 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
139930 AAAAAACGAA
*
139940 AATATTAAAATTATACATTAATTTTAATTT
1 AATATTAAAATTATACATGAATTTTAATTT
* * *
139970 AATATATAATATTATATATGAATTTTCATTT
1 AATAT-TAAAATTATACATGAATTTTAATTT
140001 CGTACAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (30 bp):
AATATTAAAATTATACATGAATTTTAATTT
Found at i:142625 original size:19 final size:20
Alignment explanation
Indices: 142590--142644 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
142580 TTATTTATGT
* *
142590 TAATATTTTATATAAT-ATA
1 TAATATTATATAAAATAATA
142609 TAAT-TTATAATAAAATAAATA
1 TAATATTAT-ATAAAAT-AATA
142630 TAATATTATATAAAA
1 TAATATTATATAAAA
142645 AATGTTAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 3 0.10
19 10 0.33
21 13 0.43
22 4 0.13
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TAATATTATATAAAATAATA
Found at i:142630 original size:23 final size:23
Alignment explanation
Indices: 142601--142647 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
142591 AATATTTTAT
*
142601 ATAATATATAAT-TTATA-ATAAA
1 ATAA-ATATAATATTATATAAAAA
142623 ATAAATATAATATTATATAAAAA
1 ATAAATATAATATTATATAAAAA
142646 AT
1 AT
142648 GTTAAGTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 7 0.32
22 9 0.41
23 6 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
ATAAATATAATATTATATAAAAA
Found at i:142632 original size:21 final size:22
Alignment explanation
Indices: 142601--142644 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
142591 AATATTTTAT
142601 ATAATATATAAT-TTATAATAAA
1 ATAATATATAATATTAT-ATAAA
142623 ATAA-ATATAATATTATATAAA
1 ATAATATATAATATTATATAAA
142644 A
1 A
142645 AATGTTAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
ATAATATATAATATTATATAAA
Found at i:147027 original size:29 final size:28
Alignment explanation
Indices: 146984--147235 Score: 222
Period size: 29 Copynumber: 8.7 Consensus size: 28
146974 TTTTTGAACA
* *
146984 AAAATGTGACTTTTGGAAGTTTGGGGGT
1 AAAATGTAATTTTTGGAAGTTTGGGGGT
*
147012 AAAATGATAATTTTTGGAAGTTCGGGGGT
1 AAAATG-TAATTTTTGGAAGTTTGGGGGT
* * **
147041 AAAAATGTGATTTTTTGGAAGTATGGGGCA
1 -AAAATGT-AATTTTTGGAAGTTTGGGGGT
*
147071 AAAATGTGACTTTTTGGAAGTTT-GGGGT
1 AAAATGT-AATTTTTGGAAGTTTGGGGGT
*
147099 AAAATGGTAATTTTTGGAAGTTTAGGGGT
1 AAAAT-GTAATTTTTGGAAGTTTGGGGGT
* * *
147128 AAAAATGTGATTTTTGGAAAGTTTAGAGGT
1 -AAAATGTAATTTTTGG-AAGTTTGGGGGT
* *
147158 AAAATGGTAATTTTTGGAAG-TT-CGGGA
1 AAAAT-GTAATTTTTGGAAGTTTGGGGGT
* *
147185 AAAATTGTAATTTTTGAGAAATTTGAGGGT
1 AAAA-TGTAATTTTTG-GAAGTTTGGGGGT
*
147215 CAAAATATAATTTTTGAGAAG
1 -AAAATGTAATTTTTG-GAAG
147236 CTCGAGAGCC
Statistics
Matches: 187, Mismatches: 24, Indels: 24
0.80 0.10 0.10
Matches are distributed among these distances:
27 16 0.09
28 34 0.18
29 68 0.36
30 65 0.35
31 4 0.02
ACGTcount: A:0.33, C:0.02, G:0.29, T:0.36
Consensus pattern (28 bp):
AAAATGTAATTTTTGGAAGTTTGGGGGT
Found at i:147128 original size:87 final size:86
Alignment explanation
Indices: 146982--147146 Score: 278
Period size: 87 Copynumber: 1.9 Consensus size: 86
146972 AATTTTTGAA
*
146982 CAAAAATGTGACTTTTGGAAGTTTGGGGGTAAAATGATAATTTTTGGAAGTTCGGGGGTAAAAAT
1 CAAAAATGTGACTTTTGGAAGTTTGGGGGTAAAATGATAATTTTTGGAAGTTCAGGGGTAAAAAT
147047 GTGATTTTTTGGAAGTATGGGG
66 GTGA-TTTTTGGAAGTATGGGG
* *
147069 CAAAAATGTGACTTTTTGGAAGTTT-GGGGTAAAATGGTAATTTTTGGAAGTTTAGGGGTAAAAA
1 CAAAAATGTGAC-TTTTGGAAGTTTGGGGGTAAAATGATAATTTTTGGAAGTTCAGGGGTAAAAA
147133 TGTGATTTTTGGAA
65 TGTGATTTTTGGAA
147147 AGTTTAGAGG
Statistics
Matches: 74, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
86 9 0.12
87 53 0.72
88 12 0.16
ACGTcount: A:0.31, C:0.03, G:0.30, T:0.36
Consensus pattern (86 bp):
CAAAAATGTGACTTTTGGAAGTTTGGGGGTAAAATGATAATTTTTGGAAGTTCAGGGGTAAAAAT
GTGATTTTTGGAAGTATGGGG
Found at i:147162 original size:87 final size:87
Alignment explanation
Indices: 146982--147200 Score: 277
Period size: 87 Copynumber: 2.5 Consensus size: 87
146972 AATTTTTGAA
* *
146982 CAAAAATGTGAC-TTTTGGAAGTTTGGGGGTAAAATGATAATTTTTGGAAGTTCGGGGGTAAAAA
1 CAAAAATGTGACTTTTTGGAAGTTT-GGGGTAAAATGGTAATTTTTGGAAGTTCAGGGGTAAAAA
*
147046 TGTGATTTTTTGGAAGTATGGGG
65 TGTGATTTTTTGGAAGTATGAGG
*
147069 CAAAAATGTGACTTTTTGGAAGTTTGGGGTAAAATGGTAATTTTTGGAAGTTTAGGGGTAAAAAT
1 CAAAAATGTGACTTTTTGGAAGTTTGGGGTAAAATGGTAATTTTTGGAAGTTCAGGGGTAAAAAT
*
147134 GTGA-TTTTTGGAAAGTTTAGAGG
66 GTGATTTTTTGG-AAGTAT-GAGG
* * * * *
147157 -TAAAATG-GTAATTTTTGGAAG-TTCGGGAAAAATTGTAATTTTTG
1 CAAAAATGTG-ACTTTTTGGAAGTTTGGGGTAAAATGGTAATTTTTG
147201 AGAAATTTGA
Statistics
Matches: 118, Mismatches: 10, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
86 28 0.24
87 75 0.64
88 15 0.13
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.37
Consensus pattern (87 bp):
CAAAAATGTGACTTTTTGGAAGTTTGGGGTAAAATGGTAATTTTTGGAAGTTCAGGGGTAAAAAT
GTGATTTTTTGGAAGTATGAGG
Found at i:147174 original size:59 final size:56
Alignment explanation
Indices: 146994--147267 Score: 234
Period size: 59 Copynumber: 4.7 Consensus size: 56
146984 AAAATGTGAC
* * *
146994 TTTTGGAAGTTTGGGGGT-AAAATGATAATTTTTGGAAGTTCGGGGGTAAAAAT-GTGATT
1 TTTTGGAAGTTT-GGGGTAAAAATG-TGATTTTTGGAAGTT-TGGGGT-AAAATGGT-AAT
* *
147053 TTTTGGAAGTATGGGGCAAAAATGTGACTTTTTGGAAGTTTGGGGTAAAATGGTAAT
1 TTTTGGAAGTTTGGGGTAAAAATGTGA-TTTTTGGAAGTTTGGGGTAAAATGGTAAT
*
147110 TTTTGGAAGTTTAGGGGTAAAAATGTGATTTTTGGAAAGTTTAGAGGTAAAATGGTAAT
1 TTTTGGAAGTTT-GGGGTAAAAATGTGATTTTTGG-AAGTTT-GGGGTAAAATGGTAAT
* * * *
147169 TTTTGGAAG-TTCGGG-AAAAATTGTAATTTTTGAGAAATTTGAGGGTCAAAAT-ATAAT
1 TTTTGGAAGTTTGGGGTAAAAA-TGTGATTTTTG-GAAGTTTG-GGGT-AAAATGGTAAT
* * * **
147226 TTTTGAGAAGCTCGAGAGCCAAAATGTGATTTTTGGACAGTT
1 TTTTG-GAAGTTTG-GGGTAAAAATGTGATTTTTGGA-AGTT
147268 CAGGGACCTT
Statistics
Matches: 181, Mismatches: 19, Indels: 29
0.79 0.08 0.13
Matches are distributed among these distances:
56 6 0.03
57 55 0.30
58 45 0.25
59 56 0.31
60 15 0.08
61 4 0.02
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.36
Consensus pattern (56 bp):
TTTTGGAAGTTTGGGGTAAAAATGTGATTTTTGGAAGTTTGGGGTAAAATGGTAAT
Found at i:147249 original size:30 final size:30
Alignment explanation
Indices: 147192--147260 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
147182 GGAAAAATTG
* * * *
147192 TAATTTTTGAGAAATTTGAGGGTCAAAATA
1 TAATTTTTGAGAAACTCGAGAGCCAAAATA
* *
147222 TAATTTTTGAGAAGCTCGAGAGCCAAAATG
1 TAATTTTTGAGAAACTCGAGAGCCAAAATA
*
147252 TGATTTTTG
1 TAATTTTTG
147261 GACAGTTCAG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.35, C:0.07, G:0.22, T:0.36
Consensus pattern (30 bp):
TAATTTTTGAGAAACTCGAGAGCCAAAATA
Found at i:147258 original size:87 final size:85
Alignment explanation
Indices: 146984--147273 Score: 219
Period size: 87 Copynumber: 3.3 Consensus size: 85
146974 TTTTTGAACA
* * * * * ** *
146984 AAAATGTGACTTTTGGAAGTTTGGGGGTAAAATGATAATTTTTGGAAGTTCGGGGGTAAAAATGT
1 AAAATGTGATTTTTGGAAG-TT-CGGGAAAAATGGTAATTTTTGGAAATTTAGGGGTAAAAATAT
* * * *
147049 GATTTTTTGG-AAGTATG-GGGCA
64 -AATTTTTGGAAAGT-CGAGAGCC
* * * *
147071 AAAATGTGACTTTTTGGAAGTTTGGGGTAAAATGGTAATTTTTGGAAGTTTAGGGGTAAAAATGT
1 AAAATGTGA-TTTTTGGAAG-TTCGGGAAAAATGGTAATTTTTGGAAATTTAGGGGTAAAAATAT
* ** **
147136 GATTTTTGGAAAGTTTAGAGGT
64 AATTTTTGGAAAGTCGAGAGCC
* * *
147158 AAAATGGTAATTTTTGGAAGTTCGGGAAAAATTGTAATTTTTGAGAAATTT-GAGGGTCAAAATA
1 AAAAT-GTGATTTTTGGAAGTTCGGGAAAAATGGTAATTTTTG-GAAATTTAG-GGGTAAAAATA
147222 TAATTTTT-GAGAAGCTCGAGAGCC
63 TAATTTTTGGA-AAG-TCGAGAGCC
147246 AAAATGTGATTTTTGGACAGTTCAGGGA
1 AAAATGTGATTTTTGGA-AGTTC-GGGA
147274 CCTTTTGGGT
Statistics
Matches: 170, Mismatches: 23, Indels: 18
0.81 0.11 0.09
Matches are distributed among these distances:
86 31 0.18
87 105 0.62
88 30 0.18
89 4 0.02
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (85 bp):
AAAATGTGATTTTTGGAAGTTCGGGAAAAATGGTAATTTTTGGAAATTTAGGGGTAAAAATATAA
TTTTTGGAAAGTCGAGAGCC
Found at i:149055 original size:6 final size:6
Alignment explanation
Indices: 149046--149115 Score: 60
Period size: 6 Copynumber: 12.0 Consensus size: 6
149036 TTTGGATTTT
* *
149046 TTTAAA TTTAGAA --TAAT TTTTAAA TTTAAA CTTAAA -TTAAA TTTAAA
1 TTTAAA TTTA-AA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA
149093 TTTAAA TTTACAA --TAAA TTTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA
149116 AAGTGAGTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
4 3 0.06
5 9 0.17
6 32 0.60
7 9 0.17
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:149080 original size:12 final size:12
Alignment explanation
Indices: 149065--149098 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
149055 AGAATAATTT
149065 TTAAATTTAAAC
1 TTAAATTTAAAC
*
149077 TTAAA-TTAAAT
1 TTAAATTTAAAC
149088 TTAAATTTAAA
1 TTAAATTTAAA
149099 TTTACAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (12 bp):
TTAAATTTAAAC
Found at i:149087 original size:17 final size:17
Alignment explanation
Indices: 149065--149100 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
149055 AGAATAATTT
149065 TTAAATTTAAACTTAAA
1 TTAAATTTAAACTTAAA
*
149082 TTAAATTTAAATTTAAA
1 TTAAATTTAAACTTAAA
149099 TT
1 TT
149101 TACAATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAAATTTAAACTTAAA
Found at i:149092 original size:23 final size:23
Alignment explanation
Indices: 149046--149115 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
149036 TTTGGATTTT
* * *
149046 TTTAAATTTAGAATAATTTTTAAA
1 TTTAAACTTACAATAA-ATTTAAA
149070 TTTAAACTTA-AATTAAATTTAAA
1 TTTAAACTTACAA-TAAATTTAAA
*
149093 TTTAAATTTACAATAAATTTAAA
1 TTTAAACTTACAATAAATTTAAA
149116 AAGTGAGTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
23 27 0.66
24 14 0.34
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (23 bp):
TTTAAACTTACAATAAATTTAAA
Found at i:153234 original size:20 final size:20
Alignment explanation
Indices: 153190--153238 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 20
153180 TTATACTGTA
153190 TAAAAATAAATATAATTTAT
1 TAAAAATAAATATAATTTAT
*
153210 T--AAATAATTATATATTT-T
1 TAAAAATAAATATA-ATTTAT
153228 TAAAAATAAAT
1 TAAAAATAAAT
153239 TTAAAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
18 12 0.50
19 4 0.17
20 8 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAAAATAAATATAATTTAT
Found at i:157286 original size:11 final size:10
Alignment explanation
Indices: 157270--157294 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
157260 NNNNNNCCCC
157270 AAAAAAAAAG
1 AAAAAAAAAG
157280 AAAAAAAAAG
1 AAAAAAAAAG
157290 AAAAA
1 AAAAA
157295 GTGGTTTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:160795 original size:31 final size:31
Alignment explanation
Indices: 160760--160819 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
160750 CAACCTAACA
* *
160760 ACTTAAATAAAAACTTTTAAATAGTTCAAAG
1 ACTTAAATAAAAACATTCAAATAGTTCAAAG
*
160791 ACTTAAATGAAAACATTCAAATAGTTCAA
1 ACTTAAATAAAAACATTCAAATAGTTCAA
160820 TGATCATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.52, C:0.12, G:0.07, T:0.30
Consensus pattern (31 bp):
ACTTAAATAAAAACATTCAAATAGTTCAAAG
Found at i:165570 original size:16 final size:16
Alignment explanation
Indices: 165551--165601 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
165541 ACATAATATC
165551 TTAAATACAGAAGTCA
1 TTAAATACAGAAGTCA
**
165567 TTAAA-ATTGATA-TC-
1 TTAAATACAGA-AGTCA
165581 TTAAATACAGAAGTCA
1 TTAAATACAGAAGTCA
165597 TTAAA
1 TTAAA
165602 ATTGATAGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
14 6 0.22
15 10 0.37
16 11 0.41
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.31
Consensus pattern (16 bp):
TTAAATACAGAAGTCA
Found at i:165582 original size:30 final size:30
Alignment explanation
Indices: 165546--165608 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
165536 ACTTTACATA
165546 ATATCTTAAATACAGAAGTCATTAAAATTG
1 ATATCTTAAATACAGAAGTCATTAAAATTG
165576 ATATCTTAAATACAGAAGTCATTAAAATTG
1 ATATCTTAAATACAGAAGTCATTAAAATTG
165606 ATA
1 ATA
165609 GTAAGTTTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.33
Consensus pattern (30 bp):
ATATCTTAAATACAGAAGTCATTAAAATTG
Found at i:169871 original size:26 final size:27
Alignment explanation
Indices: 169836--169886 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
169826 TTTGATCGAT
169836 TTTAGGCTCTGTACTTTTC-AAATTGG
1 TTTAGGCTCTGTACTTTTCGAAATTGG
*
169862 TTTAGTCTCTGTACTTTTCGAAATT
1 TTTAGGCTCTGTACTTTTCGAAATT
169887 TGAAATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.49
Consensus pattern (27 bp):
TTTAGGCTCTGTACTTTTCGAAATTGG
Found at i:188188 original size:111 final size:109
Alignment explanation
Indices: 187970--188219 Score: 306
Period size: 111 Copynumber: 2.3 Consensus size: 109
187960 ATCTGGTTTT
* * * * *
187970 ACTTGGTTATGTTTTTGTGTCCATGCTTCTTACGCTTTTGTGCCTTCTTGATTTCACTCGAAAAT
1 ACTTGGTTATG-TTCTGTTTCCATGCTTCTAACGCTTTTGAGCCTTCTTGAATTCACTCGAAAAT
188035 TTGAAGTTAGGGTTAGATTAACAGCTAGATTGACAGGACGGAACG
65 TTGAAGTTAGGGTTAGATTAACAGCTAGATTGACAGGACGGAACG
* * * *
188080 ACTTGGTTATGTTCTGTTTCCATGCTTCTAACGCTTTTGAGCCTTCTTTAATTCTGC-CAGATAT
1 ACTTGGTTATGTTCTGTTTCCATGCTTCTAACGCTTTTGAGCCTTCTTGAATTC-ACTC-GAAAA
** * *
188144 TTTGAAGTTTAGGGTTAGATTAATGGCTAGATTTAC-GGATCGGAATG
64 TTTGAAG-TTAGGGTTAGATTAACAGCTAGATTGACAGGA-CGGAACG
*
188191 ACTTGGTTATGTTCTGTTCCCATGACTTC
1 ACTTGGTTATGTTCTGTTTCCATG-CTTC
188220 GATGATTCAA
Statistics
Matches: 121, Mismatches: 14, Indels: 8
0.85 0.10 0.06
Matches are distributed among these distances:
109 38 0.31
110 25 0.21
111 54 0.45
112 4 0.03
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (109 bp):
ACTTGGTTATGTTCTGTTTCCATGCTTCTAACGCTTTTGAGCCTTCTTGAATTCACTCGAAAATT
TGAAGTTAGGGTTAGATTAACAGCTAGATTGACAGGACGGAACG
Found at i:188671 original size:157 final size:157
Alignment explanation
Indices: 188482--188809 Score: 557
Period size: 157 Copynumber: 2.1 Consensus size: 157
188472 CGATCTTTGG
*
188482 TAATCATGCTACTCATCCAACTTTGTGAATGAGATCTAGGTTTTCATAGATGACAAGTTGTTTTC
1 TAATTATGCTACTCATCCAACTTTGTGAATGAGATCTAGGTTTTCATAGATGACAAGTTGTTTTC
*
188547 CCCTATAATTTGAGCAATCCCACATGTTGCCTTTGTTTATTATGTAACAGCATAAAAGTACTCTT
66 CCCTATAATTTGAGCAATCCCACATGTTGCCTTTGTTTATTATGTAACAGCATAAAAGAACTCTT
* *
188612 CCTTTACTCATCAAAGCCGGTCCTTCC
131 CCCTCACTCATCAAAGCCGGTCCTTCC
* *
188639 TAATTATGCTACTCATCCAACTTTGTGAATGAGATCTGGGTTTTCATAGATGACAAGTTGTTTTT
1 TAATTATGCTACTCATCCAACTTTGTGAATGAGATCTAGGTTTTCATAGATGACAAGTTGTTTTC
* * *
188704 CTCTATAATTTGAGCACTCCCACATGTTGCCTTTGTTTTTTATGTAACAGCATAAAAGAACTCTT
66 CCCTATAATTTGAGCAATCCCACATGTTGCCTTTGTTTATTATGTAACAGCATAAAAGAACTCTT
188769 CCCTCACTCATCAAAGCCGGTCCTTCC
131 CCCTCACTCATCAAAGCCGGTCCTTCC
* *
188796 TAATTGTGATACTC
1 TAATTATGCTACTC
188810 GTCCTGCCTT
Statistics
Matches: 160, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
157 160 1.00
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (157 bp):
TAATTATGCTACTCATCCAACTTTGTGAATGAGATCTAGGTTTTCATAGATGACAAGTTGTTTTC
CCCTATAATTTGAGCAATCCCACATGTTGCCTTTGTTTATTATGTAACAGCATAAAAGAACTCTT
CCCTCACTCATCAAAGCCGGTCCTTCC
Found at i:194012 original size:3 final size:3
Alignment explanation
Indices: 194006--194041 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
193996 TTTGCATCAC
194006 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
194042 TGGCAACTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:194874 original size:17 final size:17
Alignment explanation
Indices: 194852--194884 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
194842 TAGAATTGGG
*
194852 TTGAAAAAATTATTAAA
1 TTGAAAAAAATATTAAA
194869 TTGAAAAAAATATTAA
1 TTGAAAAAAATATTAA
194885 GATGTTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (17 bp):
TTGAAAAAAATATTAAA
Found at i:196154 original size:19 final size:20
Alignment explanation
Indices: 196116--196159 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
196106 TTCAAAAAGG
196116 TAATTAAGAGTTATTTTTTT
1 TAATTAAGAGTTATTTTTTT
196136 TAATTAAGAGTTA-TTTTTT
1 TAATTAAGAGTTATTTTTTT
196155 TAATT
1 TAATT
196160 TCATGTATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (20 bp):
TAATTAAGAGTTATTTTTTT
Found at i:196447 original size:21 final size:23
Alignment explanation
Indices: 196423--196467 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
196413 TTTTAATAAC
*
196423 TAAAA-GAAAAATTAT-TAAATA
1 TAAAATGAAAAATGATATAAATA
*
196444 TAAAATTAAAAATGATATAAATA
1 TAAAATGAAAAATGATATAAATA
196467 T
1 T
196468 TTTTTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 8 0.40
23 7 0.35
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.31
Consensus pattern (23 bp):
TAAAATGAAAAATGATATAAATA
Found at i:210502 original size:13 final size:15
Alignment explanation
Indices: 210474--210511 Score: 55
Period size: 13 Copynumber: 2.7 Consensus size: 15
210464 GGAAAATTTT
210474 AAAGAGAGAGAGAAG
1 AAAGAGAGAGAGAAG
210489 AAAGA-AGA-AGAAG
1 AAAGAGAGAGAGAAG
210502 AAA-AGAGAGA
1 AAAGAGAGAGA
210512 TAATGTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 1 0.05
13 11 0.52
14 4 0.19
15 5 0.24
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (15 bp):
AAAGAGAGAGAGAAG
Found at i:213220 original size:7 final size:8
Alignment explanation
Indices: 213206--213230 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
213196 GATTTAATAA
213206 ATTTTTTT
1 ATTTTTTT
213214 ATTTTTTT
1 ATTTTTTT
213222 ATTTTTTT
1 ATTTTTTT
213230 A
1 A
213231 AATTTTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (8 bp):
ATTTTTTT
Found at i:219497 original size:6 final size:6
Alignment explanation
Indices: 219486--219512 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
219476 CAGTGAACAC
219486 GCATGT GCATGT GCATGT GCATGT GCA
1 GCATGT GCATGT GCATGT GCATGT GCA
219513 AAGGTTTCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.33, T:0.30
Consensus pattern (6 bp):
GCATGT
Found at i:225895 original size:3 final size:3
Alignment explanation
Indices: 225887--225920 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
225877 AGCGAGAGAG
225887 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
225921 ATTTACAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:248160 original size:24 final size:24
Alignment explanation
Indices: 248133--248180 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
248123 TACAAATCGA
*
248133 TTAAATCGA-ATTTTTTATAATTTT
1 TTAAATAGATATTTTTTA-AATTTT
*
248157 TTAAATATATATTTTTTAAATTTT
1 TTAAATAGATATTTTTTAAATTTT
248181 ATATAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (24 bp):
TTAAATAGATATTTTTTAAATTTT
Found at i:248185 original size:18 final size:18
Alignment explanation
Indices: 248145--248194 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 18
248135 AAATCGAATT
248145 TTTTATA-ATTTTTTAAA
1 TTTTATATATTTTTTAAA
248162 ---TATATATTTTTTAAA
1 TTTTATATATTTTTTAAA
248177 TTTTATATAATTTTTTAA
1 TTTTATAT-ATTTTTTAA
248195 TCAAACCTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
14 4 0.14
15 10 0.36
18 5 0.18
19 9 0.32
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTATATATTTTTTAAA
Found at i:248559 original size:31 final size:29
Alignment explanation
Indices: 248503--248568 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 29
248493 GAAAATATAA
* *
248503 AATTTTAAAAAATTAAATTAAAATTTTAT
1 AATTTTAAAAAATCAAAATAAAATTTTAT
*
248532 AATTTTAAGAGAAATCAAAATATAATTTTAT
1 AATTTTAA-A-AAATCAAAATAAAATTTTAT
*
248563 CATTTT
1 AATTTT
248569 TTAACTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 8 0.26
30 1 0.03
31 22 0.71
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (29 bp):
AATTTTAAAAAATCAAAATAAAATTTTAT
Found at i:248593 original size:54 final size:51
Alignment explanation
Indices: 248515--248617 Score: 120
Period size: 54 Copynumber: 2.0 Consensus size: 51
248505 TTTTAAAAAA
*
248515 TTAAATTAAAATTTTATAATTTTAAGAGAAATC-AAAATATAATTTTATCATTTT
1 TTAAATTAAAATTTTATAAATTTAA-A-AAATCAAAAATAT-ATTTT-TCATTTT
* *
248569 TTAACTTAAAA-TTTATAAAATTTAAAAGATCAAAAATATATTTTTCATT
1 TTAAATTAAAATTTTAT-AAATTTAAAAAATCAAAAATATATTTTTCATT
248618 ATAGGGGCCG
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
51 5 0.11
52 9 0.20
53 13 0.30
54 17 0.39
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.45
Consensus pattern (51 bp):
TTAAATTAAAATTTTATAAATTTAAAAAATCAAAAATATATTTTTCATTTT
Found at i:258032 original size:29 final size:29
Alignment explanation
Indices: 257987--258421 Score: 319
Period size: 29 Copynumber: 14.9 Consensus size: 29
257977 CCCTAAGCTG
**
257987 TCCAAAAATTTTATTTTTACCCCCGAACT
1 TCCAAAAATTCCATTTTTACCCCCGAACT
* * *
258016 TCTAAAAA-TCCTATTTTTAACCTCGAAACT
1 TCCAAAAATTCC-ATTTTTACCCCCG-AACT
*
258046 TCCAAAAATTCCATTTTTACCCTCGAACT
1 TCCAAAAATTCCATTTTTACCCCCGAACT
* * * *
258075 TCCTAAAATCCCATTTTTATCCCCAAACT
1 TCCAAAAATTCCATTTTTACCCCCGAACT
* *
258104 TCCAAAAATTCCATTTTTAACCTCGAAACT
1 TCCAAAAATTCCATTTTTACCCCCG-AACT
* *
258134 TCCAAAAATTCCATTTCTACCCTCGAACT
1 TCCAAAAATTCCATTTTTACCCCCGAACT
* *
258163 TCCAAAAATTCCATTTTTGCCCCTCAAACT
1 TCCAAAAATTCCATTTTTACCCC-CGAACT
** **
258193 TCCAAAAACCCCATTTTTTACCCCAAAACT
1 TCCAAAAATTCCA-TTTTTACCCCCGAACT
* *
258223 TCCAAAAATTCCATTTCTACCCTCGAACT
1 TCCAAAAATTCCATTTTTACCCCCGAACT
* **
258252 TCCAAAAATTCCATTTTTGA-CCCCAAAAG
1 TCCAAAAATTCCATTTTT-ACCCCCGAACT
* * * * *
258281 TCCTAAAATTTCAATTTTACTCCCGGA-T
1 TCCAAAAATTCCATTTTTACCCCCGAACT
* * * * *
258309 GTCTAAAAACTCTATTTTCGA-CCTCGATAC-
1 -TCCAAAAATTCCATTTT-TACCCCCGA-ACT
* *
258339 TCCAAAAATTCCATTTTTACTCTCGAA-T
1 TCCAAAAATTCCATTTTTACCCCCGAACT
* * * *
258367 GT-CTAAAATTCCATTTTTAACCCCAAATTT
1 -TCCAAAAATTCCATTTTTACCCCCGAA-CT
* *
258397 TCCCAAAATTATCA-TTTTACCCCCG
1 TCCAAAAATT-CCATTTTTACCCCCG
258422 GGTATCCAAA
Statistics
Matches: 318, Mismatches: 69, Indels: 37
0.75 0.16 0.09
Matches are distributed among these distances:
28 24 0.08
29 178 0.56
30 102 0.32
31 14 0.04
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.34
Consensus pattern (29 bp):
TCCAAAAATTCCATTTTTACCCCCGAACT
Found at i:258053 original size:30 final size:30
Alignment explanation
Indices: 257987--258274 Score: 342
Period size: 29 Copynumber: 9.7 Consensus size: 30
257977 CCCTAAGCTG
** *
257987 TCCAAAAATTTTATTTTTACCCCCG-AACT
1 TCCAAAAATTCCATTTTTACCCTCGAAACT
* *
258016 TCTAAAAA-TCCTATTTTTAACCTCGAAACT
1 TCCAAAAATTCC-ATTTTTACCCTCGAAACT
258046 TCCAAAAATTCCATTTTTACCCTCG-AACT
1 TCCAAAAATTCCATTTTTACCCTCGAAACT
* *
258075 TCCTAAAATCCCATTTTTATCCC-C-AAACT
1 TCCAAAAATTCCATTTTTA-CCCTCGAAACT
*
258104 TCCAAAAATTCCATTTTTAACCTCGAAACT
1 TCCAAAAATTCCATTTTTACCCTCGAAACT
*
258134 TCCAAAAATTCCATTTCTACCCTCG-AACT
1 TCCAAAAATTCCATTTTTACCCTCGAAACT
*
258163 TCCAAAAATTCCATTTTTGCCCCTC-AAACT
1 TCCAAAAATTCCATTTTT-ACCCTCGAAACT
** *
258193 TCCAAAAACCCCATTTTTTACCC-CAAAACT
1 TCCAAAAATTCCA-TTTTTACCCTCGAAACT
*
258223 TCCAAAAATTCCATTTCTACCCTCG-AACT
1 TCCAAAAATTCCATTTTTACCCTCGAAACT
258252 TCCAAAAATTCCATTTTTGACCC
1 TCCAAAAATTCCATTTTT-ACCC
258275 CAAAAGTCCT
Statistics
Matches: 222, Mismatches: 24, Indels: 25
0.82 0.09 0.09
Matches are distributed among these distances:
28 3 0.01
29 113 0.51
30 98 0.44
31 8 0.04
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.33
Consensus pattern (30 bp):
TCCAAAAATTCCATTTTTACCCTCGAAACT
Found at i:258083 original size:59 final size:58
Alignment explanation
Indices: 257987--258388 Score: 329
Period size: 59 Copynumber: 6.9 Consensus size: 58
257977 CCCTAAGCTG
** *
257987 TCCAAAAATTTTATTTTTACCCCCGAACTT-CTAAAAATCCTATTTTTAACCTCGAAACT
1 TCCAAAAATTCCATTTTTACCCTCGAACTTCCT-AAAATCC-ATTTTTAACCTCGAAACT
* *
258046 TCCAAAAATTCCATTTTTACCCTCGAACTTCCTAAAATCCCATTTTTATCC-CCAAACT
1 TCCAAAAATTCCATTTTTACCCTCGAACTTCCTAAAAT-CCATTTTTAACCTCGAAACT
* * * *
258104 TCCAAAAATTCCATTTTTAACCTCGAAACTTCCAAAAATTCCATTTCTACCCTCG-AACT
1 TCCAAAAATTCCATTTTTACCCTCG-AACTTCCTAAAA-TCCATTTTTAACCTCGAAACT
* * * * * * *
258163 TCCAAAAATTCCATTTTTGCCCCTCAAACTTCCAAAAACCCCATTTTTTACCCCAAAACT
1 TCCAAAAATTCCATTTTT-ACCCTCGAACTTCCTAAAA-TCCATTTTTAACCTCGAAACT
* * * * **
258223 TCCAAAAATTCCATTTCTACCCTCGAACTTCCAAAAATTCCATTTTTGACC-CCAAAAG
1 TCCAAAAATTCCATTTTTACCCTCGAACTTCCTAAAA-TCCATTTTTAACCTCGAAACT
* * * * * ** *
258281 TCCTAAAATTTCAATTTTACTCC-CGGA-TGT-CTAAAAACTCTATTTTCGACCTCGATAC-
1 TCCAAAAATTCCATTTTTAC-CCTCGAACT-TCCT-AAAA-TCCATTTTTAACCTCGAAACT
*
258339 TCCAAAAATTCCATTTTTACTCTCGAA-TGT-CTAAAATTCCATTTTTAACC
1 TCCAAAAATTCCATTTTTACCCTCGAACT-TCCTAAAA-TCCATTTTTAACC
258389 CCAAATTTTC
Statistics
Matches: 281, Mismatches: 50, Indels: 26
0.79 0.14 0.07
Matches are distributed among these distances:
57 17 0.06
58 94 0.33
59 139 0.49
60 31 0.11
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (58 bp):
TCCAAAAATTCCATTTTTACCCTCGAACTTCCTAAAATCCATTTTTAACCTCGAAACT
Found at i:258741 original size:97 final size:96
Alignment explanation
Indices: 258637--258829 Score: 234
Period size: 97 Copynumber: 2.0 Consensus size: 96
258627 AAAACTTTAA
* *
258637 AATCGAGGCAATA-TTCTTTTAT-TTCGAGTT-TCGAAA-ATTTGTGCCTTAACTCACTAGGTGC
1 AATCGAGGCAATATTTC-CTTATCTTCGA-TTCT-GAAATA-TTGCGCCTTAACTCACTAGGTGC
* *
258698 AATTTTTTCTTCAAATCGA-ATTAATCAAATACCCTT
62 AA-CTTTTCTTCAAATCGAGA-TAATCAAATAACCTT
* *
258734 AATCGAGGCAATGTTTCCTTATCTTCGATTCTGAAATATTGCGCCTTAACTTACTAGGTGCAACT
1 AATCGAGGCAATATTTCCTTATCTTCGATTCTGAAATATTGCGCCTTAACTCACTAGGTGCAACT
*
258799 TTTCTTCAAATCGAGATAATCGAATAACCTT
66 TTTCTTCAAATCGAGATAATCAAATAACCTT
258830 TTCGTAAAAA
Statistics
Matches: 84, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
96 28 0.33
97 46 0.55
98 10 0.12
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (96 bp):
AATCGAGGCAATATTTCCTTATCTTCGATTCTGAAATATTGCGCCTTAACTCACTAGGTGCAACT
TTTCTTCAAATCGAGATAATCAAATAACCTT
Found at i:265070 original size:9 final size:9
Alignment explanation
Indices: 265056--265100 Score: 63
Period size: 9 Copynumber: 4.9 Consensus size: 9
265046 TCATCACTTG
265056 AAAATTTTA
1 AAAATTTTA
265065 AAAATTTTA
1 AAAATTTTA
265074 AAAACTTTTA
1 AAAA-TTTTA
* *
265084 TAATTTTTA
1 AAAATTTTA
265093 AAAATTTT
1 AAAATTTT
265101 CAAGAGTGCC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
9 24 0.77
10 7 0.23
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (9 bp):
AAAATTTTA
Found at i:265091 original size:19 final size:18
Alignment explanation
Indices: 265056--265100 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
265046 TCATCACTTG
265056 AAAATTTTAAAAATTTTA
1 AAAATTTTAAAAATTTTA
* *
265074 AAAACTTTTATAATTTTTA
1 AAAA-TTTTAAAAATTTTA
265093 AAAATTTT
1 AAAATTTT
265101 CAAGAGTGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (18 bp):
AAAATTTTAAAAATTTTA
Found at i:274562 original size:13 final size:13
Alignment explanation
Indices: 274544--274570 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
274534 ATAGCATCAC
274544 TGTGGTCCCCCAT
1 TGTGGTCCCCCAT
274557 TGTGGTCCCCCAT
1 TGTGGTCCCCCAT
274570 T
1 T
274571 ATAATAACCA
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:0.07, C:0.37, G:0.22, T:0.33
Consensus pattern (13 bp):
TGTGGTCCCCCAT
Found at i:277038 original size:63 final size:63
Alignment explanation
Indices: 276934--277062 Score: 231
Period size: 63 Copynumber: 2.0 Consensus size: 63
276924 CAGTTTGGGG
* *
276934 AATAGTTGTTGATCGTCGGTAAAAACGACAGCACCGGCAAGGGACATTACCTCCGAGTCTCAA
1 AATAGTTGTTGATCGTCGGTAAAAACGACAACACCGACAAGGGACATTACCTCCGAGTCTCAA
*
276997 AATAGTTGTTGATCGTCGGTAGAAACGACAACACCGACAAGGGACATTACCTCCGAGTCTCAA
1 AATAGTTGTTGATCGTCGGTAAAAACGACAACACCGACAAGGGACATTACCTCCGAGTCTCAA
277060 AAT
1 AAT
277063 TGGAAATAAT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.21
Consensus pattern (63 bp):
AATAGTTGTTGATCGTCGGTAAAAACGACAACACCGACAAGGGACATTACCTCCGAGTCTCAA
Found at i:282554 original size:137 final size:137
Alignment explanation
Indices: 282308--282579 Score: 517
Period size: 137 Copynumber: 2.0 Consensus size: 137
282298 AAGGGTTGAG
282308 GACAGACTATGAATACTTTTAAGCATTGTATTAAAAAAAATTAGATCTATGCTCGAATTGATTAA
1 GACAGACTATGAATACTTTTAAGCATTGTATTAAAAAAAATTAGATCTATGCTCGAATTGATTAA
*
282373 ACTAATAGTTCTCGATTCAATTAATTTGATTCTCAATCTAAAAATAATTAAATTAAAATTTTCAT
66 ACTAATAGTTCTCGATGCAATTAATTTGATTCTCAATCTAAAAATAATTAAATTAAAATTTTCAT
282438 AAACAAA
131 AAACAAA
* *
282445 GACAGACTATGAATATTTTTAAGCATTGTATTAAAAAAATTTAGATCTATGCTCGAATTGATTAA
1 GACAGACTATGAATACTTTTAAGCATTGTATTAAAAAAAATTAGATCTATGCTCGAATTGATTAA
282510 ACTAATAGTTCTCGATGCAATTAATTTGATTCTCAATCTAAAAATAATTAAATTAAAATTTTCAT
66 ACTAATAGTTCTCGATGCAATTAATTTGATTCTCAATCTAAAAATAATTAAATTAAAATTTTCAT
282575 AAACA
131 AAACA
282580 CATATTTCAA
Statistics
Matches: 132, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
137 132 1.00
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.36
Consensus pattern (137 bp):
GACAGACTATGAATACTTTTAAGCATTGTATTAAAAAAAATTAGATCTATGCTCGAATTGATTAA
ACTAATAGTTCTCGATGCAATTAATTTGATTCTCAATCTAAAAATAATTAAATTAAAATTTTCAT
AAACAAA
Found at i:287098 original size:16 final size:17
Alignment explanation
Indices: 287065--287099 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
287055 ATTAAAGCAT
287065 TTTAAAATTTAGGAGTAA
1 TTTAAAATTTA-GAGTAA
287083 TTTAAAATTT-GAGTAA
1 TTTAAAATTTAGAGTAA
287099 T
1 T
287100 AATTGAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
18 10 0.59
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (17 bp):
TTTAAAATTTAGAGTAA
Found at i:287102 original size:19 final size:18
Alignment explanation
Indices: 287065--287103 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
287055 ATTAAAGCAT
*
287065 TTTAAAATTTAGGAGTAA
1 TTTAAAATTTAGGAATAA
*
287083 TTTAAAATTTGAGTAATAA
1 TTTAAAATTT-AGGAATAA
287102 TT
1 TT
287104 GAAGAACATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.44
Consensus pattern (18 bp):
TTTAAAATTTAGGAATAA
Found at i:288936 original size:37 final size:36
Alignment explanation
Indices: 288838--288937 Score: 119
Period size: 36 Copynumber: 2.8 Consensus size: 36
288828 TTTGACAAAT
* * * *
288838 AATCATTACTATTTATCTCTATCTTTTCTTTGTAGA
1 AATCATTACTGTTTATCTCCATCTTTTCTTTGGAAA
* * *
288874 AATCATTACTGTTCATCTTCGTCTTTTCTTTGCGAAA
1 AATCATTACTGTTTATCTCCATCTTTTCTTTG-GAAA
*
288911 AATCATTATTGTTTATCTCCATCTTTT
1 AATCATTACTGTTTATCTCCATCTTTT
288938 TGTCATTCCG
Statistics
Matches: 52, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
36 27 0.52
37 25 0.48
ACGTcount: A:0.23, C:0.19, G:0.07, T:0.51
Consensus pattern (36 bp):
AATCATTACTGTTTATCTCCATCTTTTCTTTGGAAA
Found at i:291673 original size:18 final size:19
Alignment explanation
Indices: 291635--291675 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
291625 AATTTTTGGG
* *
291635 TTTCGGTCTCGAGTTTAAT
1 TTTCGATCTCGAGTCTAAT
291654 TTTCGATCTCGA-TCTAAT
1 TTTCGATCTCGAGTCTAAT
291672 TTTC
1 TTTC
291676 AAGTTCAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.17, C:0.20, G:0.15, T:0.49
Consensus pattern (19 bp):
TTTCGATCTCGAGTCTAAT
Found at i:291923 original size:27 final size:27
Alignment explanation
Indices: 291892--291962 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 27
291882 TTGAAAAATA
*
291892 AAAAATAATTATTTT-ATATTAAAAGGT
1 AAAAATAA-AATTTTAATATTAAAAGGT
291919 AAAAATAAAATTTTAGATATTAAAAGAGT
1 AAAAATAAAATTTTA-ATATTAAAAG-GT
* *
291948 TAAATTAAAATTTTA
1 AAAAATAAAATTTTA
291963 TAAAATTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
26 5 0.13
27 8 0.21
28 10 0.26
29 15 0.39
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (27 bp):
AAAAATAAAATTTTAATATTAAAAGGT
Found at i:291957 original size:29 final size:28
Alignment explanation
Indices: 291907--291962 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
291897 TAATTATTTT
291907 ATATTAAAAGGTAAAAATAAAATTTTAG
1 ATATTAAAAGGTAAAAATAAAATTTTAG
* *
291935 ATATTAAAAGAGTTAAATTAAAATTTTA
1 ATATTAAAAG-GTAAAAATAAAATTTTA
291963 TAAAATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 10 0.40
29 15 0.60
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (28 bp):
ATATTAAAAGGTAAAAATAAAATTTTAG
Found at i:296930 original size:17 final size:18
Alignment explanation
Indices: 296906--296949 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
296896 AAAAAAAATA
296906 TAATTTTAAT-T-TTTTT
1 TAATTTTAATGTATTTTT
296922 TAGATTTT-ATGTATTTTT
1 TA-ATTTTAATGTATTTTT
296940 TAATTTTAAT
1 TAATTTTAAT
296950 ATTTAGGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
16 4 0.17
17 11 0.46
18 9 0.38
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (18 bp):
TAATTTTAATGTATTTTT
Found at i:297440 original size:31 final size:31
Alignment explanation
Indices: 297373--297440 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 31
297363 AACTTAACAA
*
297373 CTCAATAACTTAAATAAAAACTTTCGAATTG
1 CTCAATAACTTAAATAAAAACTTTCGAATAG
* * * * **
297404 TTCAATGACTTAAATTAAAATTTTTTAATAG
1 CTCAATAACTTAAATAAAAACTTTCGAATAG
297435 CTCAAT
1 CTCAAT
297441 TATAAATTTG
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.43, C:0.13, G:0.06, T:0.38
Consensus pattern (31 bp):
CTCAATAACTTAAATAAAAACTTTCGAATAG
Found at i:300024 original size:2 final size:2
Alignment explanation
Indices: 300017--300045 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
300007 CAACATCTTA
300017 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
300046 AATGAAACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:306033 original size:18 final size:18
Alignment explanation
Indices: 306012--306049 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
306002 AATTCAAAGG
306012 AATATATAAAA-ATACATA
1 AATATATAAAAGA-ACATA
*
306030 AATATTTAAAAGAACATA
1 AATATATAAAAGAACATA
306048 AA
1 AA
306050 AATGGATGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (18 bp):
AATATATAAAAGAACATA
Found at i:307465 original size:21 final size:22
Alignment explanation
Indices: 307436--307526 Score: 94
Period size: 23 Copynumber: 4.1 Consensus size: 22
307426 ATACGGAACA
*
307436 AACAAAGAGTAC-CAAAGTACT
1 AACAGAGAGTACACAAAGTACT
* * *
307457 AACAGAGAGCACACACAGTGCT
1 AACAGAGAGTACACAAAGTACT
307479 GAACAGAGAGTACACAAAGTACT
1 -AACAGAGAGTACACAAAGTACT
* * *
307502 AATCAGAGAGCACACACAGTGCT
1 AA-CAGAGAGTACACAAAGTACT
307525 AA
1 AA
307527 TAACAGAGAG
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
21 10 0.18
22 9 0.16
23 38 0.67
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (22 bp):
AACAGAGAGTACACAAAGTACT
Found at i:307515 original size:46 final size:44
Alignment explanation
Indices: 307436--307524 Score: 151
Period size: 46 Copynumber: 2.0 Consensus size: 44
307426 ATACGGAACA
307436 AACAAAGAGTACCAAAGTACTAACAGAGAGCACACACAGTGCTG
1 AACAAAGAGTACCAAAGTACTAACAGAGAGCACACACAGTGCTG
*
307480 AACAGAGAGTACACAAAGTACTAATCAGAGAGCACACACAGTGCT
1 AACAAAGAGTAC-CAAAGTACTAA-CAGAGAGCACACACAGTGCT
307525 AATAACAGAG
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
44 11 0.26
45 11 0.26
46 20 0.48
ACGTcount: A:0.45, C:0.22, G:0.20, T:0.12
Consensus pattern (44 bp):
AACAAAGAGTACCAAAGTACTAACAGAGAGCACACACAGTGCTG
Found at i:307533 original size:25 final size:24
Alignment explanation
Indices: 307456--307560 Score: 110
Period size: 23 Copynumber: 4.5 Consensus size: 24
307446 ACCAAAGTAC
307456 TAACAGAGAGCACACACAGTGCT-
1 TAACAGAGAGCACACACAGTGCTA
* * * *
307479 GAACAGAGAGTACACAAAGTACTA
1 TAACAGAGAGCACACACAGTGCTA
*
307503 -ATCAGAGAGCACACACAGTGCTAA
1 TAACAGAGAGCACACACAGTGCT-A
*
307527 TAACAGAGAGCACGAGAC-GTGCTA
1 TAACAGAGAGCAC-ACACAGTGCTA
307551 -AACAGAGAGC
1 TAACAGAGAGC
Statistics
Matches: 68, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
23 47 0.69
24 2 0.03
25 16 0.24
26 3 0.04
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.11
Consensus pattern (24 bp):
TAACAGAGAGCACACACAGTGCTA
Found at i:307557 original size:48 final size:45
Alignment explanation
Indices: 307448--307560 Score: 131
Period size: 46 Copynumber: 2.4 Consensus size: 45
307438 CAAAGAGTAC
307448 CAAAGTACT-AACAGAGAGCACACACAGTGCTGAACAGAGAGTACA
1 CAAAGTACTAAACAGAGAGCACACACAGTGCTGAACAGAGAG-ACA
* *
307493 CAAAGTACTAATCAGAGAGCACACACAGTGCTAATAACAGAGAG-CA
1 CAAAGTACTAAACAGAGAGCACACACAGTGCT--GAACAGAGAGACA
* *
307539 CGAGACGTGCTAAACAGAGAGC
1 C-A-AAGTACTAAACAGAGAGC
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
45 9 0.16
46 24 0.41
47 1 0.02
48 24 0.41
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (45 bp):
CAAAGTACTAAACAGAGAGCACACACAGTGCTGAACAGAGAGACA
Done.