Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014915.1 Kokia drynarioides strain JFW-HI SEQ_129958, 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: 192502
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 298 characters in sequence are not A, C, G, or T
Found at i:2016 original size:99 final size:100
Alignment explanation
Indices: 1844--2044 Score: 323
Period size: 99 Copynumber: 2.0 Consensus size: 100
1834 ATTAAATTAA
* * * *
1844 TTCATTTAATAATAAAAAACGCTAATTCCATGCACTTTCACCTTCTATATTAAGGCTTAGATTAT
1 TTCATTTAATAATAAAAAACACTAATTCCATGCACTTTCACCTTCTAGATTAAGGCTTAGACTAC
*
1909 GACATCTTTACATTTATTTTTGGGTTAATGATTTT
66 GACATCTTTACATTTATTTTTGGGTTAATGACTTT
* *
1944 TTCATTTAATAGTAAAAAA-ACTAATTCCATGCACTTTCACCTTCTAGATTAAGGCTTCGACTAC
1 TTCATTTAATAATAAAAAACACTAATTCCATGCACTTTCACCTTCTAGATTAAGGCTTAGACTAC
*
2008 GACATCTTTACGTTTATTTTTGGGTTAATGACTTT
66 GACATCTTTACATTTATTTTTGGGTTAATGACTTT
2043 TT
1 TT
2045 GAAGGGTAAT
Statistics
Matches: 93, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
99 75 0.81
100 18 0.19
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (100 bp):
TTCATTTAATAATAAAAAACACTAATTCCATGCACTTTCACCTTCTAGATTAAGGCTTAGACTAC
GACATCTTTACATTTATTTTTGGGTTAATGACTTT
Found at i:3247 original size:24 final size:26
Alignment explanation
Indices: 3200--3247 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
3190 TATTATTATT
3200 ATTTATATTTAGTTGTTTATTTTGAC
1 ATTTATATTTAGTTGTTTATTTTGAC
3226 ATTTA-ATTTA-TTGATTT-TTTTG
1 ATTTATATTTAGTTG-TTTATTTTG
3248 TTTATTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 8 0.38
26 5 0.24
ACGTcount: A:0.23, C:0.02, G:0.10, T:0.65
Consensus pattern (26 bp):
ATTTATATTTAGTTGTTTATTTTGAC
Found at i:4337 original size:111 final size:111
Alignment explanation
Indices: 4143--4363 Score: 361
Period size: 111 Copynumber: 2.0 Consensus size: 111
4133 ATCGAGATGG
* * **
4143 TGCATTTGGCCGGATACAACGAAGAAAAGCTCTTGACCGTTCTTATGATGTGATTCCGATCACAT
1 TGCATTTGACCAGATACAACGAAGAAAAGCTCCCGACCGTTCTTATGATGTGATTCCGATCACAT
*
4208 CATATTATGATGCATTTCACAAATGTTCAGATTGGCCCAAACGAGT
66 CATATTATGATGCATTTCACAAATGTTCAGATTAGCCCAAACGAGT
* *
4254 TGCATTTGACCAGATACGACGAAGAAAAGCTCCCGATCGTTCTTATGATGTGATTCCGATCACAT
1 TGCATTTGACCAGATACAACGAAGAAAAGCTCCCGACCGTTCTTATGATGTGATTCCGATCACAT
* *
4319 CATATTATGATGCATTTCAGAAATGTTTAGATTAGCCCAAACGAG
66 CATATTATGATGCATTTCACAAATGTTCAGATTAGCCCAAACGAG
4364 AAGAGGCCAA
Statistics
Matches: 101, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
111 101 1.00
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.29
Consensus pattern (111 bp):
TGCATTTGACCAGATACAACGAAGAAAAGCTCCCGACCGTTCTTATGATGTGATTCCGATCACAT
CATATTATGATGCATTTCACAAATGTTCAGATTAGCCCAAACGAGT
Found at i:4653 original size:49 final size:49
Alignment explanation
Indices: 4565--4712 Score: 138
Period size: 49 Copynumber: 3.0 Consensus size: 49
4555 GCATTAAAAA
* ** *
4565 TGTGTTTTAATTATGTCATGCATTACATAGCTCAT-ATGTTATTAAAGTC
1 TGTGTTTTAATTATGACATGCATTATGTAACTC-TCATGTTATTAAAGTC
* * * *
4614 TGTGTTTTAATTATGCCATGCGTTATGTAACTCTCATGTTATTTAAGTT
1 TGTGTTTTAATTATGACATGCATTATGTAACTCTCATGTTATTAAAGTC
* * * *
4663 TGTATAATAAATTATGACATGTATTATGTAACT-TCAATGTTAGTTAAAGT
1 TGTGT-TTTAATTATGACATGCATTATGTAACTCTC-ATGTTA-TTAAAGT
4713 TTGCATTATT
Statistics
Matches: 81, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
48 1 0.01
49 46 0.57
50 28 0.35
51 6 0.07
ACGTcount: A:0.30, C:0.10, G:0.15, T:0.45
Consensus pattern (49 bp):
TGTGTTTTAATTATGACATGCATTATGTAACTCTCATGTTATTAAAGTC
Found at i:7908 original size:91 final size:91
Alignment explanation
Indices: 7751--7929 Score: 340
Period size: 91 Copynumber: 2.0 Consensus size: 91
7741 TAAAAATGCC
*
7751 TTTATGAGAAAATTAGGTACCATCATTAATGTGATTGTGAGGCAAGACATCACGTGCTTCTTTTT
1 TTTATGAGAAAATTAGGTACCATCATTAATGTGATTGTGAGGCAAGACATCACGTGCTTCTCTTT
7816 TAGTAATTAATTACCTACGTAAGGCG
66 TAGTAATTAATTACCTACGTAAGGCG
*
7842 TTTATGAGAAAATTAGGTACCATCATTAATGTGATTGTGAGGCAGGACATCACGTGCTTCTCTTT
1 TTTATGAGAAAATTAGGTACCATCATTAATGTGATTGTGAGGCAAGACATCACGTGCTTCTCTTT
7907 TAGTAATTAATTACCTACGTAAG
66 TAGTAATTAATTACCTACGTAAG
7930 ATTCTGTGAT
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 86 1.00
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.35
Consensus pattern (91 bp):
TTTATGAGAAAATTAGGTACCATCATTAATGTGATTGTGAGGCAAGACATCACGTGCTTCTCTTT
TAGTAATTAATTACCTACGTAAGGCG
Found at i:19988 original size:25 final size:25
Alignment explanation
Indices: 19960--20012 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
19950 GTTAGGTATT
19960 TTTCTTTGGCACAATATGATAAAAA
1 TTTCTTTGGCACAATATGATAAAAA
*
19985 TTTCTTTGGCACGATATGATAAAAA
1 TTTCTTTGGCACAATATGATAAAAA
20010 TTT
1 TTT
20013 GTTGTAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (25 bp):
TTTCTTTGGCACAATATGATAAAAA
Found at i:22448 original size:25 final size:25
Alignment explanation
Indices: 22395--22440 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
22385 GTTTGATCCA
22395 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAATTCTAAAAAGATAATTTG
*
22420 AATTAAA-TCTAAACA-ATAATT
1 AATTAAATTCTAAAAAGATAATT
22441 CCTTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (25 bp):
AATTAAATTCTAAAAAGATAATTTG
Found at i:23837 original size:23 final size:23
Alignment explanation
Indices: 23810--23862 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
23800 ATCACACTTC
*
23810 TTATAAATAATATAATTTTTTTG
1 TTATAAATAATAGAATTTTTTTG
** *
23833 TTAT-AATTTTAGAATTTTTTTT
1 TTATAAATAATAGAATTTTTTTG
23855 TTATAAAT
1 TTATAAAT
23863 TAGATATATC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 18 0.72
23 7 0.28
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (23 bp):
TTATAAATAATAGAATTTTTTTG
Found at i:25801 original size:60 final size:60
Alignment explanation
Indices: 25680--25801 Score: 138
Period size: 60 Copynumber: 2.0 Consensus size: 60
25670 GAGGAGCCGT
* * * ** *
25680 GGAGGTCAGACAAGGAAGGAGCAACTGGGGACAGAAGGGTACCAGGAGCTGGGAAGCAAA
1 GGAGGTCAGACAAGAAAGGAGCAACTAGGAACAGAAGGGTACCAGGAAATGGGAAGAAAA
** **
25740 GGAGGTCAGACAAGAAAGGAGCAGA-TAGGAAGTGAAGGGTACCAGGAAATGGGGCGAAAA
1 GGAGGTCAGACAAGAAAGGAGCA-ACTAGGAACAGAAGGGTACCAGGAAATGGGAAGAAAA
25800 GG
1 GG
25802 TGGACTGAGT
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
60 50 0.98
61 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.42, T:0.07
Consensus pattern (60 bp):
GGAGGTCAGACAAGAAAGGAGCAACTAGGAACAGAAGGGTACCAGGAAATGGGAAGAAAA
Found at i:26980 original size:40 final size:40
Alignment explanation
Indices: 26922--27053 Score: 117
Period size: 40 Copynumber: 3.3 Consensus size: 40
26912 CTTTATATTT
* * *
26922 TTTTGGTAAATAGGTAGATATATTGGTAATTCATTTGAAA
1 TTTTGATAAATAGTTAGATATATTGATAATTCATTTGAAA
* *
26962 TTTTGATAAATTGTTAGATATATTTATAAATT--TTT-ATATA
1 TTTTGATAAATAGTTAGATATATTGAT-AATTCATTTGA-A-A
* * * * * *
27002 TTTTGGTAAATCGTAAGATATATTGATTAGTCATTAGAAA
1 TTTTGATAAATAGTTAGATATATTGATAATTCATTTGAAA
27042 TTTTGATAAATA
1 TTTTGATAAATA
27054 TTTAAAATTT
Statistics
Matches: 72, Mismatches: 14, Indels: 12
0.73 0.14 0.12
Matches are distributed among these distances:
38 1 0.01
39 6 0.08
40 57 0.79
41 7 0.10
42 1 0.01
ACGTcount: A:0.37, C:0.02, G:0.14, T:0.46
Consensus pattern (40 bp):
TTTTGATAAATAGTTAGATATATTGATAATTCATTTGAAA
Found at i:26992 original size:20 final size:21
Alignment explanation
Indices: 26963--27025 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 21
26953 CATTTGAAAT
26963 TTTGATAAATTGTTAGATATA
1 TTTGATAAATTGTTAGATATA
* *
26984 TTT-ATAAATTTTTATATAT-
1 TTTGATAAATTGTTAGATATA
* * *
27003 TTTGGTAAATCGTAAGATATA
1 TTTGATAAATTGTTAGATATA
27024 TT
1 TT
27026 GATTAGTCAT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
19 3 0.09
20 25 0.76
21 5 0.15
ACGTcount: A:0.37, C:0.02, G:0.11, T:0.51
Consensus pattern (21 bp):
TTTGATAAATTGTTAGATATA
Found at i:27036 original size:80 final size:81
Alignment explanation
Indices: 26878--27052 Score: 210
Period size: 80 Copynumber: 2.2 Consensus size: 81
26868 TAAATTGTTA
* * * * * *
26878 AAATTTTGGTAAATCGTTAGCTATGCTTATTAATCTTTATATTTTTTTGGTAAATAGGTAGATAT
1 AAATTTTGATAAATCGTTAGATATACTTATAAATCTTTATATTATTTTGGTAAATACGTAGATAT
* * *
26943 ATTGGTAATTCATTTG
66 ATTGATAAGTCATTAG
* * *
26959 AAATTTTGATAAATTGTTAGATATATTTATAAATTTTTATA-TATTTTGGTAAAT-CGTAAGATA
1 AAATTTTGATAAATCGTTAGATATACTTATAAATCTTTATATTATTTTGGTAAATACGT-AGATA
*
27022 TATTGATTAGTCATTAG
65 TATTGATAAGTCATTAG
27039 AAATTTTGATAAAT
1 AAATTTTGATAAAT
27053 ATTTAAAATT
Statistics
Matches: 80, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
79 2 0.03
80 44 0.55
81 34 0.43
ACGTcount: A:0.35, C:0.04, G:0.14, T:0.47
Consensus pattern (81 bp):
AAATTTTGATAAATCGTTAGATATACTTATAAATCTTTATATTATTTTGGTAAATACGTAGATAT
ATTGATAAGTCATTAG
Found at i:27065 original size:20 final size:21
Alignment explanation
Indices: 27042--27082 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
27032 TCATTAGAAA
27042 TTTTGATAAATATTT-AAAAT
1 TTTTGATAAATATTTGAAAAT
* *
27062 TTTTGGTAAATCTTTGAAAAT
1 TTTTGATAAATATTTGAAAAT
27083 ATTGGTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.39, C:0.02, G:0.10, T:0.49
Consensus pattern (21 bp):
TTTTGATAAATATTTGAAAAT
Found at i:28441 original size:20 final size:20
Alignment explanation
Indices: 28393--28431 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
28383 ACTTACTATT
*
28393 TTGATAAACTCTTATAAATA
1 TTGATAAATTCTTATAAATA
28413 TTGATAAATTCTTATAAAT
1 TTGATAAATTCTTATAAAT
28432 TTTAGTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.44
Consensus pattern (20 bp):
TTGATAAATTCTTATAAATA
Found at i:28672 original size:20 final size:20
Alignment explanation
Indices: 28649--28704 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
28639 GGCAAAACAA
28649 TAGAAATTTTGATAAA-TCGT
1 TAGAAATTTTGATAAATTC-T
* *
28669 TAGATATTTTTATAAATTCT
1 TAGAAATTTTGATAAATTCT
* *
28689 TAAAAATATTGATAAA
1 TAGAAATTTTGATAAA
28705 ACATTGGATA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
20 27 0.93
21 2 0.07
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.43
Consensus pattern (20 bp):
TAGAAATTTTGATAAATTCT
Found at i:28701 original size:40 final size:40
Alignment explanation
Indices: 28652--28738 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 40
28642 AAAACAATAG
* * * *
28652 AAATTTTGATAAATCGTTAGATATTTTTA-TAAATTCTTAA
1 AAATATTGATAAAACATTAGATA-TATTAGTAAATTCTTAA
* *
28692 AAATATTGATAAAACATTGGATATATTAGTAAATTTTTAA
1 AAATATTGATAAAACATTAGATATATTAGTAAATTCTTAA
28732 AAATATT
1 AAATATT
28739 AGTAAAATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
39 4 0.10
40 36 0.90
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (40 bp):
AAATATTGATAAAACATTAGATATATTAGTAAATTCTTAA
Found at i:29029 original size:20 final size:20
Alignment explanation
Indices: 29006--29070 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
28996 TAAATATTAG
* *
29006 TAAATTGTTAGATATATTGA
1 TAAATCGTTAAATATATTGA
* *
29026 TAAATCCTTAAAAATATTGA
1 TAAATCGTTAAATATATTGA
* *
29046 TAAATCGTTAAATATTTTCA
1 TAAATCGTTAAATATATTGA
29066 TAAAT
1 TAAAT
29071 TTTTAAAAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.42
Consensus pattern (20 bp):
TAAATCGTTAAATATATTGA
Found at i:29069 original size:40 final size:40
Alignment explanation
Indices: 28997--29080 Score: 98
Period size: 40 Copynumber: 2.1 Consensus size: 40
28987 AGTTTCCAAT
* * *
28997 AAATATTAGTAAATTGTTAGATATATTGATAAATCCTTAA
1 AAATATTAGTAAATCGTTAAATATATTCATAAATCCTTAA
* **
29037 AAATATT-GATAAATCGTTAAATATTTTCATAAATTTTTAA
1 AAATATTAG-TAAATCGTTAAATATATTCATAAATCCTTAA
29077 AAAT
1 AAAT
29081 TATGGTTAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
39 1 0.03
40 36 0.97
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (40 bp):
AAATATTAGTAAATCGTTAAATATATTCATAAATCCTTAA
Found at i:29119 original size:20 final size:20
Alignment explanation
Indices: 29096--29171 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
29086 TTAATGATTT
29096 GATAATTTGGTAAATCATTA
1 GATAATTTGGTAAATCATTA
* * *
29116 GATATTTTAGTAAATCTTTA
1 GATAATTTGGTAAATCATTA
* * *
29136 GAGATTTTGGTAAATCCTTA
1 GATAATTTGGTAAATCATTA
*
29156 GATTCA-TTGGTAAATC
1 GA-TAATTTGGTAAATC
29172 CTTATAAATA
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.34, C:0.08, G:0.16, T:0.42
Consensus pattern (20 bp):
GATAATTTGGTAAATCATTA
Found at i:29184 original size:20 final size:20
Alignment explanation
Indices: 29142--29184 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
29132 TTTAGAGATT
* *
29142 TTGGTAAATCCTTAGATTCA
1 TTGGTAAATCCTTAAAATCA
29162 TTGGTAAATCCTTATAAAT-A
1 TTGGTAAATCCTTA-AAATCA
29182 TTG
1 TTG
29185 ATAATCGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.42
Consensus pattern (20 bp):
TTGGTAAATCCTTAAAATCA
Found at i:29327 original size:20 final size:20
Alignment explanation
Indices: 29277--29327 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
29267 TTTGATAATT
*
29277 CGTTAGATATATTAATAAAT
1 CGTTAGATATATTAATAAAC
* **
29297 CTTTA-ATTATATTGGTAAAC
1 CGTTAGA-TATATTAATAAAC
29317 CGTTAGATATA
1 CGTTAGATATA
29328 ATTCGGTGAT
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
19 1 0.04
20 22 0.92
21 1 0.04
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.41
Consensus pattern (20 bp):
CGTTAGATATATTAATAAAC
Found at i:33312 original size:24 final size:24
Alignment explanation
Indices: 33285--33348 Score: 119
Period size: 24 Copynumber: 2.7 Consensus size: 24
33275 TTATTAACAT
33285 TGTTCGTGAACATGTTTAAGTATA
1 TGTTCGTGAACATGTTTAAGTATA
33309 TGTTCGTGAACATGTTTAAGTATA
1 TGTTCGTGAACATGTTTAAGTATA
*
33333 TGTTCATGAACATGTT
1 TGTTCGTGAACATGTT
33349 CAATTAAGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.42
Consensus pattern (24 bp):
TGTTCGTGAACATGTTTAAGTATA
Found at i:33383 original size:23 final size:23
Alignment explanation
Indices: 33338--33384 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
33328 GTATATGTTC
* *
33338 ATGAACATGTTCAATTAAGTTAA
1 ATGAACATGTTCAATGAAATTAA
33361 ATGAACATGTTC-ATGAACATTAA
1 ATGAACATGTTCAATGAA-ATTAA
33384 A
1 A
33385 CAAACGAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.32
Consensus pattern (23 bp):
ATGAACATGTTCAATGAAATTAA
Found at i:33400 original size:14 final size:14
Alignment explanation
Indices: 33381--33432 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
33371 TCATGAACAT
33381 TAAACAAACGAATA
1 TAAACAAACGAATA
* *
33395 TAAACACACGTAATTT
1 TAAACAAACG-AA-TA
*
33411 TAAATAAACGAATA
1 TAAACAAACGAATA
33425 TAAACAAA
1 TAAACAAA
33433 ACATTTGAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
14 17 0.57
15 4 0.13
16 9 0.30
ACGTcount: A:0.60, C:0.13, G:0.06, T:0.21
Consensus pattern (14 bp):
TAAACAAACGAATA
Found at i:50424 original size:3 final size:3
Alignment explanation
Indices: 50411--50508 Score: 85
Period size: 3 Copynumber: 32.3 Consensus size: 3
50401 TTAATAACAC
* * *
50411 AAT AA- AAT AAT AAT TAT AGT ATT AAAT AA- AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT
* * *
50454 AAT AAT AAT AAT AAT AAT AAT AAT AAT GAC AAT AAAT ATT AATT AATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AA-T AA-T
50502 AAT AAT A
1 AAT AAT A
50509 TAAACAACAA
Statistics
Matches: 78, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
2 6 0.08
3 60 0.77
4 12 0.15
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:50447 original size:32 final size:32
Alignment explanation
Indices: 50411--50479 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
50401 TTAATAACAC
* * *
50411 AATAAAATAATAATTATAGTATTAAATAA-AAT
1 AATAAAATAATAATAATAATAAT-AATAATAAT
*
50443 AATAATATAATAATAATAATAATAATAATAAT
1 AATAAAATAATAATAATAATAATAATAATAAT
50475 AATAA
1 AATAA
50480 TGACAATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 5 0.16
32 27 0.84
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (32 bp):
AATAAAATAATAATAATAATAATAATAATAAT
Found at i:50743 original size:19 final size:20
Alignment explanation
Indices: 50721--50769 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 20
50711 AAATTTAATG
*
50721 ATAAATAAA-TAAATAAATA
1 ATAAATAAATTAAAGAAATA
50740 ATAAATGTAAATTAAAGAAATA
1 ATAAA--TAAATTAAAGAAATA
50762 AT-AATAAA
1 ATAAATAAA
50770 ATAGATAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 9 0.35
21 6 0.23
22 11 0.42
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (20 bp):
ATAAATAAATTAAAGAAATA
Found at i:50771 original size:26 final size:26
Alignment explanation
Indices: 50717--50769 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
50707 TATAAAATTT
*
50717 AATGATAAATAAATAAATAAATAATA
1 AATGATAAATAAAGAAATAAATAATA
50743 AATG-TAAATTAAAGAAAT-AATAATA
1 AATGATAAA-TAAAGAAATAAATAATA
50768 AA
1 AA
50770 ATAGATAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (26 bp):
AATGATAAATAAAGAAATAAATAATA
Found at i:50821 original size:20 final size:19
Alignment explanation
Indices: 50798--50845 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
50788 GCATGAAAAT
* *
50798 AAAAAAAACAATTAGATAA
1 AAAAAAAAAAATTAAATAA
50817 AAAAATAAAAAATTAAATAA
1 AAAAA-AAAAAATTAAATAA
50837 AAATAAAAA
1 AAA-AAAAA
50846 TAAAAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 5 0.20
20 18 0.72
21 2 0.08
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (19 bp):
AAAAAAAAAAATTAAATAA
Found at i:50840 original size:6 final size:6
Alignment explanation
Indices: 50817--50894 Score: 59
Period size: 6 Copynumber: 12.3 Consensus size: 6
50807 AATTAGATAA
* ** *
50817 AAAAAT AAAAA- ATTAAAT AAAAAT AAAAAT AAAAATT AAATGT TAAAAT
1 AAAAAT AAAAAT A-AAAAT AAAAAT AAAAAT AAAAA-T AAAAAT AAAAAT
*
50866 AAACAAAT AAATAT AAAAAAT AAAAAT AA
1 -AA-AAAT AAAAAT -AAAAAT AAAAAT AA
50895 TTGAGATTAT
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
5 1 0.02
6 38 0.68
7 13 0.23
8 4 0.07
ACGTcount: A:0.76, C:0.01, G:0.01, T:0.22
Consensus pattern (6 bp):
AAAAAT
Found at i:50844 original size:23 final size:21
Alignment explanation
Indices: 50793--50891 Score: 78
Period size: 21 Copynumber: 4.5 Consensus size: 21
50783 AAATGGCATG
*
50793 AAAATAAAAAAAACAATTAGAT
1 AAAATAAAAAAAA-AATTAAAT
*
50815 AAAA-AAATAAAAAATTAAAT
1 AAAATAAAAAAAAAATTAAAT
50835 AAAAATAAAAATAAAAATTAAATGTT
1 -AAAATAAAAA-AAAAATTAAA---T
*
50861 AAAATAAACAAATAAA-TATAA-
1 AAAATAAA-AAAAAAATTA-AAT
50882 AAAATAAAAA
1 AAAATAAAAA
50892 TAATTGAGAT
Statistics
Matches: 65, Mismatches: 4, Indels: 18
0.75 0.05 0.21
Matches are distributed among these distances:
20 9 0.14
21 19 0.29
22 8 0.12
23 10 0.15
24 2 0.03
25 14 0.22
26 3 0.05
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (21 bp):
AAAATAAAAAAAAAATTAAAT
Found at i:50857 original size:17 final size:17
Alignment explanation
Indices: 50794--50846 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 17
50784 AATGGCATGA
50794 AAATAAAAA-AAACAATT
1 AAATAAAAATAAA-AATT
*
50811 AGATAAAAAAATAAAAAATT
1 A-A-ATAAAAAT-AAAAATT
50831 AAATAAAAATAAAAAT
1 AAATAAAAATAAAAAT
50847 AAAAATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
17 7 0.23
18 8 0.27
19 7 0.23
20 5 0.17
21 3 0.10
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (17 bp):
AAATAAAAATAAAAATT
Found at i:62488 original size:11 final size:12
Alignment explanation
Indices: 62461--62486 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
62451 TCTTTTAATC
62461 TTTAAATTTTTT
1 TTTAAATTTTTT
62473 TTTAAATTTTTT
1 TTTAAATTTTTT
62485 TT
1 TT
62487 AAGAGTAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTAAATTTTTT
Found at i:78016 original size:17 final size:18
Alignment explanation
Indices: 77984--78017 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
77974 ACTATATGTT
77984 AACCCTTAAAAAATTAAC
1 AACCCTTAAAAAATTAAC
*
78002 AACCC-TAATAAATTAA
1 AACCCTTAAAAAATTAA
78018 GGCAACGTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.56, C:0.21, G:0.00, T:0.24
Consensus pattern (18 bp):
AACCCTTAAAAAATTAAC
Found at i:78715 original size:21 final size:21
Alignment explanation
Indices: 78671--78716 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
78661 ATCATAATAT
*
78671 AAATTTTCATATAATGTTTCA
1 AAATTTTCATATAATATTTCA
*
78692 AAATTTT-ATATAACTATTTGA
1 AAATTTTCATATAA-TATTTCA
78713 AAAT
1 AAAT
78717 ATGAAACAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (21 bp):
AAATTTTCATATAATATTTCA
Found at i:89513 original size:109 final size:108
Alignment explanation
Indices: 89384--89588 Score: 265
Period size: 109 Copynumber: 1.9 Consensus size: 108
89374 GAAAAAGGAC
* *
89384 ATTTATCGATTTAAAATAGGATATTCAAATACTT-AGGTTCGAA-GAAAAATCATACCTAGTACG
1 ATTTATCAATTTAAAATAGGATATTCAAATACTTAAGG-TC-AACGAAAAATCATACCTA--ACA
*
89447 T-TT-GAGCACAATTTCTCGAGTTCGCTAGAATAAAAGAATATTGAAT
62 TATTAGAGCACAATTTCTCGAGTTCCCTA-AATAAAAGAATATTGAAT
* * * *
89493 ATTTATCAATTTTAAATAGGATATTTAATTATTTAAGGTCAACGAAAAATCATACCTAACATATT
1 ATTTATCAATTTAAAATAGGATATTCAAATACTTAAGGTCAACGAAAAATCATACCTAACATATT
*
89558 AGGGCACAATTTCTCGAGTTCCCTAAATAAA
66 AGAGCACAATTTCTCGAGTTCCCTAAATAAA
89589 TAAACATTGT
Statistics
Matches: 84, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
107 3 0.04
108 10 0.12
109 68 0.81
110 3 0.04
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (108 bp):
ATTTATCAATTTAAAATAGGATATTCAAATACTTAAGGTCAACGAAAAATCATACCTAACATATT
AGAGCACAATTTCTCGAGTTCCCTAAATAAAAGAATATTGAAT
Found at i:93022 original size:23 final size:23
Alignment explanation
Indices: 92962--93031 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
92952 GCACGTCTCG
*
92962 TGCTCTCTGTTATTAGCACTGTGTA
1 TGCTCTCTG--ATTAGCACTTTGTA
* * *
92987 TGTTGTCTAATTAGCACTTTGTA
1 TGCTCTCTGATTAGCACTTTGTA
*
93010 TGCTCTCTGATTAGTACTTTGT
1 TGCTCTCTGATTAGCACTTTGT
93032 GTATTCTCTA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
23 31 0.84
25 6 0.16
ACGTcount: A:0.17, C:0.17, G:0.19, T:0.47
Consensus pattern (23 bp):
TGCTCTCTGATTAGCACTTTGTA
Found at i:95955 original size:2 final size:2
Alignment explanation
Indices: 95950--95993 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
95940 CAATAAACAA
95950 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
95992 TC
1 TC
95994 ATAACTAGTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:100062 original size:21 final size:20
Alignment explanation
Indices: 100038--100076 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
100028 TTTTTGCCTA
*
100038 ATTAACTCGAATTTCAATTTG
1 ATTAAATCGAATTT-AATTTG
*
100059 ATTAAATCTAATTTAATT
1 ATTAAATCGAATTTAATT
100077 ACAAAAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.46
Consensus pattern (20 bp):
ATTAAATCGAATTTAATTTG
Found at i:100643 original size:29 final size:29
Alignment explanation
Indices: 100579--100644 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
100569 TTTAATAGTT
* *
100579 TATATTTTTATAAATTTAAAAGATTAAAT
1 TATATTTTTATAAATTTAAAAGATCAAAG
* ** *
100608 TAAATTTTTATATTTTTAAAAGGTCAAAG
1 TATATTTTTATAAATTTAAAAGATCAAAG
100637 TATATTTT
1 TATATTTT
100645 ACTTTTAATT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (29 bp):
TATATTTTTATAAATTTAAAAGATCAAAG
Found at i:103407 original size:22 final size:21
Alignment explanation
Indices: 103382--103423 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
103372 TTTTTTTAGA
*
103382 TTTAATGAGAATTTTCAAAACT
1 TTTAAT-AGAACTTTCAAAACT
*
103404 TTTAGTAGAACTTTCAAAAC
1 TTTAATAGAACTTTCAAAAC
103424 AAATTGGAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (21 bp):
TTTAATAGAACTTTCAAAACT
Found at i:113339 original size:9 final size:9
Alignment explanation
Indices: 113325--113393 Score: 57
Period size: 10 Copynumber: 7.1 Consensus size: 9
113315 TTAATTTTTT
113325 AAAATTAAA
1 AAAATTAAA
113334 AAAATTATAA
1 AAAATTA-AA
113344 AAAATTATAA
1 AAAATTA-AA
**
113354 AATTAATTTTA
1 AA--AATTAAA
113365 AAAATTAAA
1 AAAATTAAA
*
113374 AATCATTAAA
1 AA-AATTAAA
*
113384 AATATTAAA
1 AAAATTAAA
113393 A
1 A
113394 GTATAATAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
9 21 0.42
10 22 0.44
11 3 0.06
12 4 0.08
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (9 bp):
AAAATTAAA
Found at i:113347 original size:19 final size:20
Alignment explanation
Indices: 113325--113393 Score: 72
Period size: 19 Copynumber: 3.5 Consensus size: 20
113315 TTAATTTTTT
113325 AAAATTAAAAA-AATTATAA
1 AAAATTAAAAATAATTATAA
*
113344 AAAATTATAAAATTAATT-TTA
1 AAAATTA-AAAA-TAATTATAA
*
113365 AAAATTAAAAATCATTA-AA
1 AAAATTAAAAATAATTATAA
*
113384 AATATTAAAA
1 AAAATTAAAA
113394 GTATAATAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
19 21 0.50
20 8 0.19
21 9 0.21
22 4 0.10
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAATTAAAAATAATTATAA
Found at i:120708 original size:31 final size:32
Alignment explanation
Indices: 120649--120708 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
120639 TAATTTTCGT
*
120649 AAAATTTTAATTGTGATTTTAATTTATATTTG
1 AAAATTTTAATTGTGATTTTAATATATATTTG
*
120681 AAAA-TTTAATTTTGA-TTTAATCATATAT
1 AAAATTTTAATTGTGATTTTAAT-ATATAT
120709 ATTTAAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 6 0.24
31 15 0.60
32 4 0.16
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (32 bp):
AAAATTTTAATTGTGATTTTAATATATATTTG
Found at i:120988 original size:2 final size:2
Alignment explanation
Indices: 120969--121027 Score: 91
Period size: 2 Copynumber: 29.5 Consensus size: 2
120959 ATTATTAAAA
* * *
120969 AT AT AC AT AT AT AC AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
121011 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
121028 AAAGACATGT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:130884 original size:20 final size:19
Alignment explanation
Indices: 130859--130905 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
130849 AAATTACAAA
130859 AAAAAAATCCAAAATAATTT
1 AAAAAAATCC-AAATAATTT
* *
130879 AAAAAAATTCAAATTATTT
1 AAAAAAATCCAAATAATTT
*
130898 ATAAAAAT
1 AAAAAAAT
130906 TTCAAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAAAAATCCAAATAATTT
Found at i:130909 original size:20 final size:19
Alignment explanation
Indices: 130859--130911 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
130849 AAATTACAAA
*
130859 AAAAAAATCCAAAATAATTT
1 AAAAAAATTC-AAATAATTT
*
130879 AAAAAAATTCAAATTATTT
1 AAAAAAATTCAAATAATTT
*
130898 ATAAAAATTTCAAA
1 A-AAAAAATTCAAA
130912 ATTTATATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 9 0.31
20 20 0.69
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAAAAATTCAAATAATTT
Found at i:138325 original size:21 final size:21
Alignment explanation
Indices: 138261--138339 Score: 56
Period size: 21 Copynumber: 3.9 Consensus size: 21
138251 TCAAAGGCGA
138261 AATTAA-TTTTTT-TTTTAAT
1 AATTAATTTTTTTATTTTAAT
* * ** *
138280 TA-TAATTTTTATGATAGTAAA
1 AATTAATTTTT-TTATTTTAAT
138301 AATTAATTTTTTTATTTTAAT
1 AATTAATTTTTTTATTTTAAT
* * *
138322 AATTTATATTTTAATTTT
1 AATTAATTTTTTTATTTT
138340 TAAAAATTTA
Statistics
Matches: 43, Mismatches: 13, Indels: 6
0.69 0.21 0.10
Matches are distributed among these distances:
18 3 0.07
19 5 0.12
20 1 0.02
21 26 0.60
22 8 0.19
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (21 bp):
AATTAATTTTTTTATTTTAAT
Found at i:138358 original size:21 final size:22
Alignment explanation
Indices: 138315--138362 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
138305 AATTTTTTTA
* * *
138315 TTTTAATAATTTATATTTTAAT
1 TTTTAAAAATTTATAATTAAAT
138337 TTTTAAAAATTTA-AATTAAAT
1 TTTTAAAAATTTATAATTAAAT
138358 TTTTA
1 TTTTA
138363 TATTTTTAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTTAAAAATTTATAATTAAAT
Found at i:142651 original size:20 final size:19
Alignment explanation
Indices: 142626--142667 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
142616 TGCTCTCTCT
*
142626 TTTACTCTCTTTTTTTTTTA
1 TTTACTCTC-TGTTTTTTTA
142646 TTTACTCTCTGTTTTTTTA
1 TTTACTCTCTGTTTTTTTA
142665 TTT
1 TTT
142668 TATAACATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.10, C:0.14, G:0.02, T:0.74
Consensus pattern (19 bp):
TTTACTCTCTGTTTTTTTA
Found at i:142669 original size:20 final size:19
Alignment explanation
Indices: 142625--142669 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
142615 ATGCTCTCTC
*
142625 TTTTACTCTCTTTTTTTTT
1 TTTTACTCTCTTTTTTTTA
142644 TATTTACTCTCTGTTTTTTTA
1 T-TTTACTCTCT-TTTTTTTA
142665 TTTTA
1 TTTTA
142670 TAACATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 14 0.61
21 8 0.35
ACGTcount: A:0.11, C:0.13, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTTACTCTCTTTTTTTTA
Found at i:143971 original size:8 final size:9
Alignment explanation
Indices: 143936--143970 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
143926 CAAAATTTAT
*
143936 ATTAAAAAA
1 ATTATAAAA
143945 ATTATAAAA
1 ATTATAAAA
143954 ATT-TAAAA
1 ATTATAAAA
143962 ATTATAAAA
1 ATTATAAAA
143971 TATATATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
ATTATAAAA
Found at i:153806 original size:18 final size:20
Alignment explanation
Indices: 153769--153807 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
153759 ACGGAAGCTT
*
153769 ATTTTAATATTCTTTTATGC
1 ATTTTAATATTCTATTATGC
153789 ATTTTAAT-TT-TATTATGC
1 ATTTTAATATTCTATTATGC
153807 A
1 A
153808 CATTTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 2 0.11
20 8 0.44
ACGTcount: A:0.28, C:0.08, G:0.05, T:0.59
Consensus pattern (20 bp):
ATTTTAATATTCTATTATGC
Found at i:155892 original size:28 final size:29
Alignment explanation
Indices: 155838--155893 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
155828 GCCCTTTGTG
*
155838 ATTTTTAAAAATTTTAATTAACTCCCAAA
1 ATTTTTAAAAATTTTAATTAACGCCCAAA
155867 ATTTTT-AAAATTTCTAATTAA-GCCCAA
1 ATTTTTAAAAATTT-TAATTAACGCCCAA
155894 CAAAAATCAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 12 0.48
29 13 0.52
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.41
Consensus pattern (29 bp):
ATTTTTAAAAATTTTAATTAACGCCCAAA
Found at i:157776 original size:26 final size:23
Alignment explanation
Indices: 157746--157796 Score: 57
Period size: 26 Copynumber: 2.1 Consensus size: 23
157736 AATTATCAAG
*
157746 TTCAAAGATTAATGTTGACAAAAAAA
1 TTCAAAGATCAA-GTT-A-AAAAAAA
*
157772 TTCAAGGATCAAGTTAAAAAAAA
1 TTCAAAGATCAAGTTAAAAAAAA
157795 TT
1 TT
157797 GACAAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 9 0.39
24 1 0.04
25 3 0.13
26 10 0.43
ACGTcount: A:0.53, C:0.08, G:0.12, T:0.27
Consensus pattern (23 bp):
TTCAAAGATCAAGTTAAAAAAAA
Found at i:158270 original size:24 final size:24
Alignment explanation
Indices: 158211--158271 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
158201 GACTAATAAT
* *
158211 AGTTTAACTCAAACAAATAAACGA
1 AGTTTAACTGAAACAAATAAACAA
* *
158235 AGTTTAATTGAAACAATTAAACAA
1 AGTTTAACTGAAACAAATAAACAA
158259 AGTTTAACTGAAA
1 AGTTTAACTGAAA
158272 GATTATTTCT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.52, C:0.11, G:0.10, T:0.26
Consensus pattern (24 bp):
AGTTTAACTGAAACAAATAAACAA
Found at i:160242 original size:24 final size:24
Alignment explanation
Indices: 160214--160299 Score: 127
Period size: 24 Copynumber: 3.6 Consensus size: 24
160204 AGACTAATAT
*
160214 GAGTTTAACTCAAACAAATAAACA
1 GAGTTTAACTGAAACAAATAAACA
* *
160238 TAGTTTAATTGAAACAAATAAACA
1 GAGTTTAACTGAAACAAATAAACA
* *
160262 GAGTTTAATTGAAACAAATAAATA
1 GAGTTTAACTGAAACAAATAAACA
160286 GAGTTTAACTGAAA
1 GAGTTTAACTGAAA
160300 GATTATTTAT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.52, C:0.09, G:0.12, T:0.27
Consensus pattern (24 bp):
GAGTTTAACTGAAACAAATAAACA
Found at i:160868 original size:52 final size:52
Alignment explanation
Indices: 160776--160880 Score: 140
Period size: 52 Copynumber: 2.0 Consensus size: 52
160766 TTACAAATAG
* ** **
160776 TAAGAAATTATTATTTAATTATTTAATTTTAATCCGTTAATTATTATGATGT
1 TAAGAAAATATTATCAAATTATTTAATTTTAATCAATTAATTATTATGATGT
*
160828 TAAGAAAATATTATCAAATTATTTAATTTTAAAT-AATTAATTATTATGTTGT
1 TAAGAAAATATTATCAAATTATTTAATTTT-AATCAATTAATTATTATGATGT
160880 T
1 T
160881 CAAATTAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
52 43 0.93
53 3 0.07
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (52 bp):
TAAGAAAATATTATCAAATTATTTAATTTTAATCAATTAATTATTATGATGT
Found at i:165640 original size:81 final size:81
Alignment explanation
Indices: 165505--165667 Score: 281
Period size: 81 Copynumber: 2.0 Consensus size: 81
165495 AAAAGAAAGA
* * * *
165505 AAGCAAGTGCAATGACAAGCAAAGATACCTACAAGTCACAGGGAGCTAAGTACAGCACCTGTCCT
1 AAGCAAGTGCAATGACAAGCAAAGATACCTAAAAGTCACAAGGAACTAAGTACAGCACCTGTCCC
*
165570 GGATAATGTTAATGCT
66 GAATAATGTTAATGCT
165586 AAGCAAGTGCAATGACAAGCAAAGATACCTAAAAGTCACAAGGAACTAAGTACAGCACCTGTCCC
1 AAGCAAGTGCAATGACAAGCAAAGATACCTAAAAGTCACAAGGAACTAAGTACAGCACCTGTCCC
165651 GAATAATGTTAATGCT
66 GAATAATGTTAATGCT
165667 A
1 A
165668 TGGATGCCAC
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 77 1.00
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.19
Consensus pattern (81 bp):
AAGCAAGTGCAATGACAAGCAAAGATACCTAAAAGTCACAAGGAACTAAGTACAGCACCTGTCCC
GAATAATGTTAATGCT
Found at i:171182 original size:22 final size:22
Alignment explanation
Indices: 171142--171200 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 22
171132 CAAAAAACGC
* *
171142 AAAAAAAATCA-AAATATTTAT
1 AAAAAAAATTATAAAAATTTAT
*
171163 AAAAAAAATTATAAAAATTTCT
1 AAAAAAAATTATAAAAATTTAT
* *
171185 AAGAAATA-TATAAAAA
1 AAAAAAAATTATAAAAA
171201 AGTTAAGATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 18 0.56
22 14 0.44
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.27
Consensus pattern (22 bp):
AAAAAAAATTATAAAAATTTAT
Found at i:174047 original size:17 final size:16
Alignment explanation
Indices: 174026--174064 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
174016 TTCTATTATA
174026 AAAATTAAAAAAAAAT
1 AAAATTAAAAAAAAAT
* *
174042 ATAAATTTAATAAAAAT
1 A-AAATTAAAAAAAAAT
174059 AAAATT
1 AAAATT
174065 CAATTTTATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAATTAAAAAAAAAT
Found at i:174684 original size:17 final size:17
Alignment explanation
Indices: 174654--174687 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
174644 AATTCTCTCT
* *
174654 TTCTTTTTTTTTTTACC
1 TTCTTCTTTCTTTTACC
174671 TTCTTCTTTCTTTTACC
1 TTCTTCTTTCTTTTACC
174688 ATGGCTCAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.24, G:0.00, T:0.71
Consensus pattern (17 bp):
TTCTTCTTTCTTTTACC
Found at i:174853 original size:15 final size:17
Alignment explanation
Indices: 174822--174855 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
174812 CATACATGGA
174822 TTCATGTTTTTCTCTCT
1 TTCATGTTTTTCTCTCT
174839 TTCAT-TTTTTC-CTCT
1 TTCATGTTTTTCTCTCT
174854 TT
1 TT
174856 GATGATGTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 6 0.35
17 5 0.29
ACGTcount: A:0.06, C:0.24, G:0.03, T:0.68
Consensus pattern (17 bp):
TTCATGTTTTTCTCTCT
Found at i:178537 original size:16 final size:18
Alignment explanation
Indices: 178498--178531 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
178488 TAAATTTATA
178498 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
178515 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
178532 AATTTAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:183242 original size:89 final size:89
Alignment explanation
Indices: 183091--183271 Score: 344
Period size: 89 Copynumber: 2.0 Consensus size: 89
183081 CCTCATTGCT
* *
183091 TCTTTGGCTCTGCATGTGGTTATGTTCTATATACCTATCTATAGCAGAACATTCCAAATGATATA
1 TCTTTGGCTCTGCATGTGGTTATGTTCTATATACCTATCTACAGCAAAACATTCCAAATGATATA
183156 ATCTCAAGTTTAATACCTTGTTTA
66 ATCTCAAGTTTAATACCTTGTTTA
183180 TCTTTGGCTCTGCATGTGGTTATGTTCTATATACCTATCTACAGCAAAACATTCCAAATGATATA
1 TCTTTGGCTCTGCATGTGGTTATGTTCTATATACCTATCTACAGCAAAACATTCCAAATGATATA
183245 ATCTCAAGTTTAATACCTTGTTTA
66 ATCTCAAGTTTAATACCTTGTTTA
183269 TCT
1 TCT
183272 ATGCAGGAAT
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 90 1.00
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (89 bp):
TCTTTGGCTCTGCATGTGGTTATGTTCTATATACCTATCTACAGCAAAACATTCCAAATGATATA
ATCTCAAGTTTAATACCTTGTTTA
Found at i:183869 original size:58 final size:58
Alignment explanation
Indices: 183793--183934 Score: 171
Period size: 58 Copynumber: 2.4 Consensus size: 58
183783 TCCATTCAAC
* * * * * *
183793 TAATAATAATTGTATTAAAAATGTTATTAAATTATATATTA-TTTTATTAAATTGTATT
1 TAATAATAATTATATT-AAAATATAATTAAATCATATATTATTTTTATTAAATTATATA
* *
183851 TAATAATAATTATGTTAAAATATAATTAAATCATTTATTATTTTTATTAAATTATATA
1 TAATAATAATTATATTAAAATATAATTAAATCATATATTATTTTTATTAAATTATATA
*
183909 TAATAATAATCT-TATTAAAATTTAAT
1 TAATAATAAT-TATATTAAAATATAAT
183935 AAGAATAATC
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
57 20 0.28
58 51 0.71
59 1 0.01
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (58 bp):
TAATAATAATTATATTAAAATATAATTAAATCATATATTATTTTTATTAAATTATATA
Found at i:183941 original size:25 final size:26
Alignment explanation
Indices: 183894--183944 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
183884 TTTATTATTT
*
183894 TTATTAAATTATATATAATAATAATC
1 TTATTAAATTATATATAAGAATAATC
183920 TTATTAAAATT-TA-ATAAGAATAATC
1 TTATT-AAATTATATATAAGAATAATC
183945 ATCTACCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 11 0.48
26 7 0.30
27 5 0.22
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (26 bp):
TTATTAAATTATATATAAGAATAATC
Found at i:192386 original size:31 final size:31
Alignment explanation
Indices: 192329--192407 Score: 87
Period size: 31 Copynumber: 2.7 Consensus size: 31
192319 TTGACAAAAA
*
192329 ATAATAATATATAAA-A-TTT--AAAAATAT
1 ATAATAATAAATAAAGATTTTGAAAAAATAT
*
192356 ATCAA-AATAAATAAATATTTTGAAAAAATAT
1 AT-AATAATAAATAAAGATTTTGAAAAAATAT
*
192387 ATAATAATAAATTAAGATTTT
1 ATAATAATAAATAAAGATTTT
192408 ATATTAATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
27 11 0.26
28 3 0.07
29 3 0.07
30 2 0.05
31 24 0.56
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (31 bp):
ATAATAATAAATAAAGATTTTGAAAAAATAT
Done.