Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023747.1 Corchorus olitorius cultivar O-4 contig23780, 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: 107474
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:3088 original size:32 final size:31
Alignment explanation
Indices: 2982--3089 Score: 78
Period size: 32 Copynumber: 3.4 Consensus size: 31
2972 AAAGAGGTCT
*
2982 TCAACTTTGATTTGGACTCTTAAGAAGCAAAGA
1 TCAAATTTGATTT-GACTCTT-AGAAGCAAAGA
* * * *
3015 TCAAATTTGATATG--TTTTAGTCAAAG-AGATA
1 TCAAATTTGATTTGACTCTTAG---AAGCAAAGA
*
3046 TTCAACTTTGATTTGAACTCTTAGAAGCAAAGA
1 -TCAAATTTGATTTG-ACTCTTAGAAGCAAAGA
3079 TCAAATTTGAT
1 TCAAATTTGAT
3090 ACATCCCACA
Statistics
Matches: 56, Mismatches: 11, Indels: 17
0.67 0.13 0.20
Matches are distributed among these distances:
29 2 0.04
30 3 0.05
31 3 0.05
32 29 0.52
33 14 0.25
35 5 0.09
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (31 bp):
TCAAATTTGATTTGACTCTTAGAAGCAAAGA
Found at i:10628 original size:12 final size:13
Alignment explanation
Indices: 10606--10633 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
10596 AAGGTTTGTC
10606 TTTTTCTTTTTTT
1 TTTTTCTTTTTTT
10619 TTTTTCTTTTTTT
1 TTTTTCTTTTTTT
10632 TT
1 TT
10634 AATTTGTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (13 bp):
TTTTTCTTTTTTT
Found at i:21799 original size:21 final size:21
Alignment explanation
Indices: 21773--21812 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
21763 GAACCATCTG
21773 CTCCTTAAG-TGAGTCATTAGT
1 CTCCTTAAGTTG-GTCATTAGT
21794 CTCCTTAAGTTGGTCATTA
1 CTCCTTAAGTTGGTCATTA
21813 AATTTGTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (21 bp):
CTCCTTAAGTTGGTCATTAGT
Found at i:26167 original size:81 final size:81
Alignment explanation
Indices: 26036--26214 Score: 216
Period size: 81 Copynumber: 2.2 Consensus size: 81
26026 TAAATAATTT
* * * *
26036 AAATCAAGGGCCAAATTGCATCAAACAATAAATAGCAACTTAAATTAGGGACCAAACTGAATCAA
1 AAAT-AAGGACCAAATTGAATCAAACAATAAATAGCAACCTAAATCAGGGACCAAACTGAATCAA
26101 ATCACACAAATAAAGAA
65 ATCACACAAATAAAGAA
* * * * * *
26118 AAATAAGGACCAAATTGAATCAAATAGTAACTAG-AATCCTAAATCAGGGACGAAATTGAATGAA
1 AAATAAGGACCAAATTGAATCAAACAATAAATAGCAA-CCTAAATCAGGGACCAAACTGAATCAA
* * *
26182 ATCACACATATCAAGAC
65 ATCACACAAATAAAGAA
26199 AAATAAGGACCAAATT
1 AAATAAGGACCAAATT
26215 AAACTTTCTA
Statistics
Matches: 83, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
80 2 0.02
81 77 0.93
82 4 0.05
ACGTcount: A:0.51, C:0.17, G:0.13, T:0.18
Consensus pattern (81 bp):
AAATAAGGACCAAATTGAATCAAACAATAAATAGCAACCTAAATCAGGGACCAAACTGAATCAAA
TCACACAAATAAAGAA
Found at i:29707 original size:27 final size:27
Alignment explanation
Indices: 29664--29736 Score: 85
Period size: 26 Copynumber: 2.7 Consensus size: 27
29654 TAATGGACTT
** *
29664 AAAATGACCAACGTGCCCCTGAATAAG
1 AAAATGACCAAAATGCCCCTGAATAAA
* * *
29691 CAAATGACCAAAATG-CCCTTAGTAAA
1 AAAATGACCAAAATGCCCCTGAATAAA
29717 AAAATGACCAAAATGCCCCT
1 AAAATGACCAAAATGCCCCT
29737 AAGTGACCCT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
26 22 0.58
27 16 0.42
ACGTcount: A:0.44, C:0.26, G:0.14, T:0.16
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGAATAAA
Found at i:35068 original size:33 final size:33
Alignment explanation
Indices: 34998--35074 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 33
34988 GAAACTATGG
* * *
34998 ATTTTGAACTTTGAGTTTTGATATGATATCCAG
1 ATTTTGAACTTTGAATTTTGAAATGATATCCAA
* *
35031 ATTTTTAACTTTGAATTTTGAAATGCA-ATGCAA
1 ATTTTGAACTTTGAATTTTGAAATG-ATATCCAA
35064 ATTTTGAACTT
1 ATTTTGAACTT
35075 CTTAATTAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
33 36 0.97
34 1 0.03
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.45
Consensus pattern (33 bp):
ATTTTGAACTTTGAATTTTGAAATGATATCCAA
Found at i:35186 original size:55 final size:54
Alignment explanation
Indices: 35112--35260 Score: 190
Period size: 54 Copynumber: 2.7 Consensus size: 54
35102 AATTCAACCT
* * * *
35112 TGATCATGGAAACCTTTCTTGGAACGATCGCACTGGATCAATTTAGAGATCAACTC
1 TGATCATCGAAAAC-TTCTTGGAACGACCACACTGGATCAA-TTAGAGATCAACTC
* ** *
35168 TGATCATCGTAAACTTCTTGGAATTACCACACTGGATCAATTGGAGATCAACTC
1 TGATCATCGAAAACTTCTTGGAACGACCACACTGGATCAATTAGAGATCAACTC
* *
35222 TGATCATCGAAAACTTCTTGGAACGACAACATTGGATCA
1 TGATCATCGAAAACTTCTTGGAACGACCACACTGGATCA
35261 TTAAAAACTT
Statistics
Matches: 80, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
54 47 0.59
55 22 0.28
56 11 0.14
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.28
Consensus pattern (54 bp):
TGATCATCGAAAACTTCTTGGAACGACCACACTGGATCAATTAGAGATCAACTC
Found at i:35260 original size:33 final size:33
Alignment explanation
Indices: 35223--35295 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
35213 GATCAACTCT
* *
35223 GATCATCGAAAACTTCTTGGAACGACAACATTG
1 GATCATCAAAAACTTCTTGGAACGACAACACTG
* * **
35256 GATCATTAAAAACTTCTTGGAATGACCGCACTG
1 GATCATCAAAAACTTCTTGGAACGACAACACTG
35289 GATCATC
1 GATCATC
35296 TGGGATCAAC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (33 bp):
GATCATCAAAAACTTCTTGGAACGACAACACTG
Found at i:35346 original size:86 final size:87
Alignment explanation
Indices: 35178--35348 Score: 229
Period size: 86 Copynumber: 2.0 Consensus size: 87
35168 TGATCATCGT
* *
35178 AAACTTCTTGGAATTACCACACTGGATCAATTGGAGATCAACTCTGATCATCGAAAACTTCTTGG
1 AAACTTCTTGGAATGACCACACTGGATCAATTGGAGATCAACTCTGATCATCGAAAACTTCTTGA
*
35243 AACGACAACATTGGATCATTAA
66 AACGACAACACTGGATCATTAA
* * * *
35265 AAACTTCTTGGAATGACCGCACTGGATC-ATCTGG-GATCAACTTTGATCCTCGAAAACTTTTTG
1 AAACTTCTTGGAATGACCACACTGGATCAAT-TGGAGATCAACTCTGATCATCGAAAACTTCTTG
* **
35328 AAATGACCGCACTGGATCATT
65 AAACGACAACACTGGATCATT
35349 TTAAGATAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
86 44 0.60
87 29 0.40
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.29
Consensus pattern (87 bp):
AAACTTCTTGGAATGACCACACTGGATCAATTGGAGATCAACTCTGATCATCGAAAACTTCTTGA
AACGACAACACTGGATCATTAA
Found at i:35434 original size:54 final size:54
Alignment explanation
Indices: 35264--36106 Score: 1119
Period size: 54 Copynumber: 15.7 Consensus size: 54
35254 TGGATCATTA
* ** *
35264 AAAACTTCT-TGGAATGACCGCACTGGATCATC-TGGGATCAACTTTGATC-CTCG
1 AAAACTTCTATGGAA-GACCGCACTGGGTCATCTTAAGATCAACTTAGATCTCT-G
* * * * *** *
35317 AAAACTT-TTTGAAATGACCGCACTGGATCATTTTAAGAT-AAAAAAAATCTCTG
1 AAAACTTCTATGGAA-GACCGCACTGGGTCATCTTAAGATCAACTTAGATCTCTG
* *
35370 AAAACCTCTATGGAAGACCGCACTGGGTCATCTGAAGATCAACTTAGATCTCTG
1 AAAACTTCTATGGAAGACCGCACTGGGTCATCTTAAGATCAACTTAGATCTCTG
*
35424 AAAACTTCTATGGAAGACCGCACTGGGTCATCTTAAGATCAACTTAGATCTTTG
1 AAAACTTCTATGGAAGACCGCACTGGGTCATCTTAAGATCAACTTAGATCTCTG
35478 AAAACTTCTATGGAAGACCGCACTGGGTCATCTTAAGATCAACTTAGATCTCTG
1 AAAACTTCTATGGAAGACCGCACTGGGTCATCTTAAGATCAACTTAGATCTCTG
* *
35532 AAAACCTCTATGGAAGACCGCACTGGGTCAT-TTGAAGATCAACTTAGATCTTTG
1 AAAACTTCTATGGAAGACCGCACTGGGTCATCTT-AAGATCAACTTAGATCTCTG
*
35586 AAAACTTCTATGGAAGACCACACTGGGTCATCTTAAGATCAACTTAGATCTCTG
1 AAAACTTCTATGGAAGACCGCACTGGGTCATCTTAAGATCAACTTAGATCTCTG
* *
35640 AAAACTTCTATGGAAGACCGCACTTGGTCATCTTAAGATCAACTTAGATTTCTG
1 AAAACTTCTATGGAAGACCGCACTGGGTCATCTTAAGATCAACTTAGATCTCTG
* * * * *
35694 AAAACTTATATGGAAGACCACACTGGGTCATCTGAAAATCAACTTAGAACTCTG
1 AAAACTTCTATGGAAGACCGCACTGGGTCATCTTAAGATCAACTTAGATCTCTG
* * *
35748 AAAACTTCTATGAAAGACCGCA-TTGGTTATCTTAAGATCAACTTAGATCTCTG
1 AAAACTTCTATGGAAGACCGCACTGGGTCATCTTAAGATCAACTTAGATCTCTG
* * *
35801 AAAACTTCTATGAAAGACCGCATTGGGTCATCTTAAGATCAACTTAGATCTTTG
1 AAAACTTCTATGGAAGACCGCACTGGGTCATCTTAAGATCAACTTAGATCTCTG
* **
35855 AAAACTTCTATGGATGACCGCACTGGGTCATCTTAAGATCAACTTAGATCTCAAA
1 AAAACTTCTATGGAAGACCGCACTGGGTCATCTTAAGATCAACTTAGATCTC-TG
* * * * * *
35910 AAAACTTCTATGGAAGACCGCACTAGGTTATCTGAAGATCAATTTAGATTTCTA
1 AAAACTTCTATGGAAGACCGCACTGGGTCATCTTAAGATCAACTTAGATCTCTG
*
35964 AAAACTTCTA-GGAAAGACCACACT-GGTCATCTTAAGATCAACTTAGATCTCTG
1 AAAACTTCTATGG-AAGACCGCACTGGGTCATCTTAAGATCAACTTAGATCTCTG
* * ** * * *
36017 AAAACTTCTGTGAAATCCCGCATTGTGTCATCTTAAGATCAACTTAGATCTCTA
1 AAAACTTCTATGGAAGACCGCACTGGGTCATCTTAAGATCAACTTAGATCTCTG
* *
36071 AAAACTTCTATGGAAGACTGCGCTGGGTCATCTTAA
1 AAAACTTCTATGGAAGACCGCACTGGGTCATCTTAA
36107 ACACCTAAAC
Statistics
Matches: 694, Mismatches: 84, Indels: 23
0.87 0.10 0.03
Matches are distributed among these distances:
52 1 0.00
53 153 0.22
54 492 0.71
55 48 0.07
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (54 bp):
AAAACTTCTATGGAAGACCGCACTGGGTCATCTTAAGATCAACTTAGATCTCTG
Found at i:36175 original size:37 final size:37
Alignment explanation
Indices: 36107--36478 Score: 347
Period size: 37 Copynumber: 10.1 Consensus size: 37
36097 GTCATCTTAA
* ** * * * *
36107 ACACCTAAACAGGAATTTTGAACAAGAATTTGACAAG
1 ACACCTAAACAGGGACCTTAAATAAGGATTTGATAAG
* * *
36144 AAACCTAAACATGCACCTTAAATAAGGATTTGATAAG
1 ACACCTAAACAGGGACCTTAAATAAGGATTTGATAAG
* * * * *
36181 AAACCTAAACAGGAACCTTGAACAA-GATTTTGATGAG
1 ACACCTAAACAGGGACCTTAAATAAGGA-TTTGATAAG
*
36218 ACACCTAAACAGGGACCTTAAATAAGGATTTAATAAG
1 ACACCTAAACAGGGACCTTAAATAAGGATTTGATAAG
* * * * * *
36255 AAACCTAAACAGGAATCTTGAACAA-GATTTTGATGAG
1 ACACCTAAACAGGGACCTTAAATAAGGA-TTTGATAAG
* * * *
36292 ACACTTAAATAGAGACCTTAAATAAGGGTTTGATAAG
1 ACACCTAAACAGGGACCTTAAATAAGGATTTGATAAG
36329 ACACCTAAACAGGGACCTTAAATAAGGATTTGATAAG
1 ACACCTAAACAGGGACCTTAAATAAGGATTTGATAAG
* * * * *
36366 ACACCTAAACAGGAATCTTGAACAA-GATTTTAATGAA-
1 ACACCTAAACAGGGACCTTAAATAAGGA-TTTGAT-AAG
36403 ACACCTAAACAGGGACCTTAAATAAGGATTTGATAAG
1 ACACCTAAACAGGGACCTTAAATAAGGATTTGATAAG
** * * * *
36440 ACACCTAAACAGAAATCTTGAATAAGGTTTTGATGAG
1 ACACCTAAACAGGGACCTTAAATAAGGATTTGATAAG
36477 AC
1 AC
36479 TGAATTTTGT
Statistics
Matches: 270, Mismatches: 57, Indels: 16
0.79 0.17 0.05
Matches are distributed among these distances:
36 8 0.03
37 255 0.94
38 7 0.03
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.23
Consensus pattern (37 bp):
ACACCTAAACAGGGACCTTAAATAAGGATTTGATAAG
Found at i:36464 original size:111 final size:111
Alignment explanation
Indices: 36107--36473 Score: 409
Period size: 111 Copynumber: 3.3 Consensus size: 111
36097 GTCATCTTAA
** * * * * * * * * *
36107 ACACCTAAACAGGAATTTTGAACAAGAATTTGACAAGAAACCTAAACATGCACCTTAAATAAGGA
1 ACACCTAAACAGGAACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGAATCTTGAACAA-GA
* * * *
36172 TTTGATAA-G-AA-ACCTAAACAGGAACCTTGAACAA-GATTTTGATGAG
65 TTT--TAATGAAACACCTAAACAGGGACCTTAAATAAGGA-TTTGATAAG
* *
36218 ACACCTAAACAGGGACCTTAAATAAGGATTTAATAAGAAACCTAAACAGGAATCTTGAACAAGAT
1 ACACCTAAACAGGAACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGAATCTTGAACAAGAT
* * * * * *
36283 TTTGATGAGACACTTAAATAGAGACCTTAAATAAGGGTTTGATAAG
66 TTTAATGAAACACCTAAACAGGGACCTTAAATAAGGATTTGATAAG
* *
36329 ACACCTAAACAGGGACCTTAAATAAGGATTTGATAAGACACCTAAACAGGAATCTTGAACAAGAT
1 ACACCTAAACAGGAACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGAATCTTGAACAAGAT
36394 TTTAATGAAACACCTAAACAGGGACCTTAAATAAGGATTTGATAAG
66 TTTAATGAAACACCTAAACAGGGACCTTAAATAAGGATTTGATAAG
* * * *
36440 ACACCTAAACAGAAATCTTGAATAAGGTTTTGAT
1 ACACCTAAACAGGAACCTTAAATAAGGATTTGAT
36474 GAGACTGAAT
Statistics
Matches: 216, Mismatches: 36, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
108 2 0.01
109 1 0.00
110 6 0.03
111 206 0.95
112 1 0.00
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.24
Consensus pattern (111 bp):
ACACCTAAACAGGAACCTTAAATAAGGATTTGATAAGAAACCTAAACAGGAATCTTGAACAAGAT
TTTAATGAAACACCTAAACAGGGACCTTAAATAAGGATTTGATAAG
Found at i:37454 original size:7 final size:6
Alignment explanation
Indices: 37444--37503 Score: 52
Period size: 6 Copynumber: 10.0 Consensus size: 6
37434 TTTTTCATTC
** *
37444 TTTTCGT TTTTCT TTTTCT TTTTC- TTTGGT TTCTCTT TTTTCT TTTTC-
1 TTTTC-T TTTTCT TTTTCT TTTTCT TTTTCT TTTTC-T TTTTCT TTTTCT
*
37492 TTTGCT TTTTCT
1 TTTTCT TTTTCT
37504 CTCTCTCTCT
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
5 7 0.17
6 25 0.60
7 10 0.24
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.77
Consensus pattern (6 bp):
TTTTCT
Found at i:37458 original size:12 final size:11
Alignment explanation
Indices: 37441--37503 Score: 54
Period size: 11 Copynumber: 5.4 Consensus size: 11
37431 TGATTTTTCA
37441 TTCTTTTCGTTT
1 TTCTTTTC-TTT
37453 TTCTTTTTCTTT
1 TTC-TTTTCTTT
**
37465 TTCTTTGGTTT
1 TTCTTTTCTTT
*
37476 CTCTTTTTTCTTT
1 -T-TCTTTTCTTT
*
37489 TTCTTTGCTTT
1 TTCTTTTCTTT
37500 TTCT
1 TTCT
37504 CTCTCTCTCT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
11 18 0.44
12 11 0.27
13 12 0.29
ACGTcount: A:0.00, C:0.17, G:0.06, T:0.76
Consensus pattern (11 bp):
TTCTTTTCTTT
Found at i:37509 original size:30 final size:30
Alignment explanation
Indices: 37450--37533 Score: 75
Period size: 30 Copynumber: 2.8 Consensus size: 30
37440 ATTCTTTTCG
* *
37450 TTTTTCTTTTTCTTTTTCTTTGGTTTCTCT
1 TTTTTCTTTTTCTTTTTCTTTGCTCTCTCT
37480 TTTTTCTTTTTCTTTGCTT-TTT-CTCTCTCT
1 TTTTTCTTTTTCTTT--TTCTTTGCTCTCTCT
* * *
37510 CTCTCTCTCTTTCTTTTT-TTTGCT
1 -TTTTTCTTTTTCTTTTTCTTTGCT
37534 TCACCAGGCA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
29 5 0.11
30 23 0.51
31 15 0.33
32 2 0.04
ACGTcount: A:0.00, C:0.23, G:0.05, T:0.73
Consensus pattern (30 bp):
TTTTTCTTTTTCTTTTTCTTTGCTCTCTCT
Found at i:38206 original size:13 final size:13
Alignment explanation
Indices: 38143--38207 Score: 67
Period size: 14 Copynumber: 4.8 Consensus size: 13
38133 ACTCAAAACC
38143 TTTTTGAAAACTCA
1 TTTTTGAAAA-TCA
38157 TTTTTGAAAATCGA
1 TTTTTGAAAATC-A
* * *
38171 TTCTTGAAAACCG
1 TTTTTGAAAATCA
*
38184 TTTCTTGAAATTCA
1 TTT-TTGAAAATCA
38198 TTTTTGAAAA
1 TTTTTGAAAA
38208 ATGTTCTTTA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
13 10 0.24
14 31 0.76
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (13 bp):
TTTTTGAAAATCA
Found at i:38208 original size:28 final size:28
Alignment explanation
Indices: 38143--38207 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
38133 ACTCAAAACC
38143 TTTTTGAAAACTCATTTTTGAAAATCGA
1 TTTTTGAAAACTCATTTTTGAAAATCGA
* * *
38171 TTCTTGAAAAC-CGTTTCTTGAAATTC-A
1 TTTTTGAAAACTCATTT-TTGAAAATCGA
38198 TTTTTGAAAA
1 TTTTTGAAAA
38208 ATGTTCTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 14 0.44
28 18 0.56
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (28 bp):
TTTTTGAAAACTCATTTTTGAAAATCGA
Found at i:39463 original size:22 final size:23
Alignment explanation
Indices: 39425--39469 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
39415 AAAATAAATT
39425 TTAAGGATTTTAATTAAT-TTTA
1 TTAAGGATTTTAATTAATGTTTA
**
39447 TTAAGGATTTTGGTTAATGTTTA
1 TTAAGGATTTTAATTAATGTTTA
39470 ATTGTTCATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (23 bp):
TTAAGGATTTTAATTAATGTTTA
Found at i:39668 original size:19 final size:19
Alignment explanation
Indices: 39632--39669 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
39622 ATTTTAATGT
*
39632 GTTCTTAATATTGAATTAA
1 GTTCTTAATAATGAATTAA
39651 GTTCATTAATAATG-ATTAA
1 GTTC-TTAATAATGAATTAA
39670 ACATTGATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (19 bp):
GTTCTTAATAATGAATTAA
Found at i:43851 original size:27 final size:26
Alignment explanation
Indices: 43785--43851 Score: 64
Period size: 26 Copynumber: 2.5 Consensus size: 26
43775 GCATATCCAG
* ** * *
43785 GGGCATTTTAGTCATTTTTACACTAA
1 GGGCATTTGAGTCATTTGCACATTCA
43811 GGGCATTTTG-GTCATTTGCACATTCA
1 GGGCA-TTTGAGTCATTTGCACATTCA
43837 GAGGCATTTGAGTCA
1 G-GGCATTTGAGTCA
43852 ATTCTCAATC
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
26 22 0.67
27 11 0.33
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.37
Consensus pattern (26 bp):
GGGCATTTGAGTCATTTGCACATTCA
Found at i:46388 original size:14 final size:15
Alignment explanation
Indices: 46371--46400 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
46361 ATTGTACAAG
46371 GAGGAAGAAG-AGGA
1 GAGGAAGAAGAAGGA
46385 GAGGAAGAAGAAGGA
1 GAGGAAGAAGAAGGA
46400 G
1 G
46401 GAAAGGGGCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (15 bp):
GAGGAAGAAGAAGGA
Found at i:46389 original size:17 final size:18
Alignment explanation
Indices: 46369--46402 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
46359 GAATTGTACA
*
46369 AGGAGGAAGAA-GAGGAG
1 AGGAAGAAGAAGGAGGAG
46386 AGGAAGAAGAAGGAGGA
1 AGGAAGAAGAAGGAGGA
46403 AAGGGGCGCG
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:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (18 bp):
AGGAAGAAGAAGGAGGAG
Found at i:49529 original size:2 final size:2
Alignment explanation
Indices: 49522--49546 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
49512 AGACCCAATC
49522 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
49547 AAGGCCCAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52453 original size:30 final size:30
Alignment explanation
Indices: 52380--52456 Score: 102
Period size: 30 Copynumber: 2.5 Consensus size: 30
52370 GAGAATGACG
* *
52380 AGGAGGAAGATTCCGATCTCTTTGTTTGTGA
1 AGGA-GAAGATTCTGATCTCTTTATTTGTGA
52411 AGGAGAAGATTCTGATCTCTTTATTTGTGA
1 AGGAGAAGATTCTGATCTCTTTATTTGTGA
*
52441 ATGAG-AGAATTCTGAT
1 AGGAGAAG-ATTCTGAT
52457 TTTGTCATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
29 2 0.05
30 36 0.86
31 4 0.10
ACGTcount: A:0.27, C:0.10, G:0.26, T:0.36
Consensus pattern (30 bp):
AGGAGAAGATTCTGATCTCTTTATTTGTGA
Found at i:55348 original size:24 final size:23
Alignment explanation
Indices: 55319--55388 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 23
55309 TTTATGGTTT
*
55319 TTTCCTAGAAGGAGTAGGTTTTAC
1 TTTCCTACAAGGA-TAGGTTTTAC
* *
55343 TTTCCTACCA-GAAAGGTTTTAC
1 TTTCCTACAAGGATAGGTTTTAC
*
55365 TATTCCTACAAGGATTAGGATTTA
1 T-TTCCTACAAGGA-TAGGTTTTA
55389 GGTTAAGTGT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
22 10 0.27
23 10 0.27
24 10 0.27
25 7 0.19
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.37
Consensus pattern (23 bp):
TTTCCTACAAGGATAGGTTTTAC
Found at i:58146 original size:13 final size:13
Alignment explanation
Indices: 58128--58162 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
58118 TTATTTTAAG
*
58128 AATTAATTATATT
1 AATTAATTATATA
58141 AATTAATTATATA
1 AATTAATTATATA
58154 AATATAATT
1 AAT-TAATT
58163 GTAAATATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
AATTAATTATATA
Found at i:59022 original size:25 final size:25
Alignment explanation
Indices: 58993--59078 Score: 172
Period size: 25 Copynumber: 3.4 Consensus size: 25
58983 TTAATCAAAT
58993 TATAATTTTTTAAAATTTATTTTTA
1 TATAATTTTTTAAAATTTATTTTTA
59018 TATAATTTTTTAAAATTTATTTTTA
1 TATAATTTTTTAAAATTTATTTTTA
59043 TATAATTTTTTAAAATTTATTTTTA
1 TATAATTTTTTAAAATTTATTTTTA
59068 TATAATTTTTT
1 TATAATTTTTT
59079 TTATAATTAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 61 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (25 bp):
TATAATTTTTTAAAATTTATTTTTA
Found at i:59024 original size:15 final size:15
Alignment explanation
Indices: 58997--59083 Score: 81
Period size: 14 Copynumber: 6.6 Consensus size: 15
58987 TCAAATTATA
*
58997 ATTTTT-TAAAATTT
1 ATTTTTATATAATTT
59011 ATTTTTATATAA--T
1 ATTTTTATATAATTT
59024 -TTTTTA-A-AATTT
1 ATTTTTATATAATTT
59036 ATTTTTATATAA--T
1 ATTTTTATATAATTT
59049 -TTTTTA-A-AATTT
1 ATTTTTATATAATTT
59061 ATTTTTATATAATTT
1 ATTTTTATATAATTT
59076 -TTTTTATA
1 ATTTTTATA
59084 ATTATAGGTC
Statistics
Matches: 61, Mismatches: 1, Indels: 22
0.73 0.01 0.26
Matches are distributed among these distances:
10 4 0.07
11 2 0.03
12 14 0.23
13 14 0.23
14 16 0.26
15 11 0.18
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
ATTTTTATATAATTT
Found at i:59027 original size:12 final size:12
Alignment explanation
Indices: 59012--59086 Score: 59
Period size: 12 Copynumber: 6.1 Consensus size: 12
59002 TTAAAATTTA
59012 TTTTTATATAAT
1 TTTTTATATAAT
59024 TTTTTA-A-AATTT
1 TTTTTATATAA--T
59036 ATTTTTATATAAT
1 -TTTTTATATAAT
59049 TTTTTA-A-AATTT
1 TTTTTATATAA--T
59061 ATTTTTATATAAT
1 -TTTTTATATAAT
*
59074 TTTTTTTATAAT
1 TTTTTATATAAT
59086 T
1 T
59087 ATAGGTCAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 20
0.71 0.01 0.27
Matches are distributed among these distances:
10 4 0.08
11 2 0.04
12 26 0.50
13 14 0.27
14 2 0.04
15 4 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTTTATATAAT
Found at i:60028 original size:29 final size:31
Alignment explanation
Indices: 59986--60083 Score: 103
Period size: 31 Copynumber: 3.2 Consensus size: 31
59976 AAATCTTAAC
* * *
59986 TTAGTAGTAAACTTT-TTAAGTT-GCTCAAT
1 TTAGTACTAAACTTTATCAAATTGGCTCAAT
*
60015 TTAGTACTAAACTTTATCAAATTGGTTCAAT
1 TTAGTACTAAACTTTATCAAATTGGCTCAAT
* *
60046 TT-GATACTAAACTTTATCATATTGGTTCAAT
1 TTAG-TACTAAACTTTATCAAATTGGCTCAAT
*
60077 ATAGTAC
1 TTAGTAC
60084 CTTTTCGGAT
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
29 14 0.24
30 6 0.10
31 38 0.64
32 1 0.02
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (31 bp):
TTAGTACTAAACTTTATCAAATTGGCTCAAT
Found at i:60054 original size:31 final size:31
Alignment explanation
Indices: 60010--60083 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
60000 TTTAAGTTGC
60010 TCAATTTAGTACTAAACTTTATCAAATTGGT
1 TCAATTTAGTACTAAACTTTATCAAATTGGT
*
60041 TCAATTT-GATACTAAACTTTATCATATTGGT
1 TCAATTTAG-TACTAAACTTTATCAAATTGGT
*
60072 TCAATATAGTAC
1 TCAATTTAGTAC
60084 CTTTTCGGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
30 1 0.03
31 37 0.95
32 1 0.03
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (31 bp):
TCAATTTAGTACTAAACTTTATCAAATTGGT
Found at i:63204 original size:13 final size:13
Alignment explanation
Indices: 63186--63210 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
63176 TTTAATGTTC
63186 TAAATATTATTTA
1 TAAATATTATTTA
63199 TAAATATTATTT
1 TAAATATTATTT
63211 GGAATTCTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATATTATTTA
Found at i:70447 original size:54 final size:55
Alignment explanation
Indices: 70359--70464 Score: 187
Period size: 54 Copynumber: 1.9 Consensus size: 55
70349 CATTCCCTGT
70359 AAAAAAAATGACACAAAGGGGGGGATTAGTTTCGGGTTAGGAGAAGTTTGCAAAC
1 AAAAAAAATGACACAAAGGGGGGGATTAGTTTCGGGTTAGGAGAAGTTTGCAAAC
* *
70414 AAAAGAAATGACATAAA-GGGGGGATTAGTTTCGGGTTAGGAGAAGTTTGCA
1 AAAAAAAATGACACAAAGGGGGGGATTAGTTTCGGGTTAGGAGAAGTTTGCA
70465 GTTAGTAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
54 34 0.69
55 15 0.31
ACGTcount: A:0.39, C:0.08, G:0.32, T:0.22
Consensus pattern (55 bp):
AAAAAAAATGACACAAAGGGGGGGATTAGTTTCGGGTTAGGAGAAGTTTGCAAAC
Found at i:80030 original size:29 final size:30
Alignment explanation
Indices: 79998--80061 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 30
79988 GGACGGTTTA
* *
79998 CCCCCTAAACTTCAATTTT-GGATATTTTG
1 CCCCCTAAACTACAATTTTGGGACATTTTG
* *
80027 -CCCCTGAACTACAATTTTGGGACGTTTTG
1 CCCCCTAAACTACAATTTTGGGACATTTTG
80056 CCCCCT
1 CCCCCT
80062 CAACCTAACG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 16 0.55
29 8 0.28
30 5 0.17
ACGTcount: A:0.20, C:0.30, G:0.14, T:0.36
Consensus pattern (30 bp):
CCCCCTAAACTACAATTTTGGGACATTTTG
Found at i:88405 original size:31 final size:31
Alignment explanation
Indices: 88367--88426 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
88357 TGACTATGAG
88367 GTCCTGGATTCAAATCTCACGGAAAATGATA
1 GTCCTGGATTCAAATCTCACGGAAAATGATA
88398 GTCCTGGATTCAAATCTCACGGAAAATGA
1 GTCCTGGATTCAAATCTCACGGAAAATGA
88427 ATTCAGTGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (31 bp):
GTCCTGGATTCAAATCTCACGGAAAATGATA
Found at i:88452 original size:39 final size:39
Alignment explanation
Indices: 88398--88472 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
88388 GAAAATGATA
*
88398 GTCCTGGATTCAAATCTCACGGAAAATGAATTCAGTGAG
1 GTCCTGAATTCAAATCTCACGGAAAATGAATTCAGTGAG
*
88437 GTCCTGAATTCAAATCTCACGGAAAATGAGTTCAGT
1 GTCCTGAATTCAAATCTCACGGAAAATGAATTCAGT
88473 TTGTAATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (39 bp):
GTCCTGAATTCAAATCTCACGGAAAATGAATTCAGTGAG
Found at i:88829 original size:29 final size:29
Alignment explanation
Indices: 88778--88834 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
88768 TATATTGACT
*
88778 ATCACTTTGCACCCAATTTTTTTATTTTG
1 ATCACTTTGCACCCAATTGTTTTATTTTG
*
88807 ATCACTTTGCACCCTGA-TGTTTTATTTT
1 ATCACTTTGCACCC-AATTGTTTTATTTT
88835 TGTTCCATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 24 0.96
30 1 0.04
ACGTcount: A:0.19, C:0.21, G:0.09, T:0.51
Consensus pattern (29 bp):
ATCACTTTGCACCCAATTGTTTTATTTTG
Found at i:89848 original size:31 final size:31
Alignment explanation
Indices: 89813--89880 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
89803 CAAAAAGCGA
*
89813 TCAATTTATTCCCCGTACTCACAAGATTAGG
1 TCAATTTACTCCCCGTACTCACAAGATTAGG
* * * *
89844 TCAATTTACTCTCTGTACTCGCAAGATTGGG
1 TCAATTTACTCCCCGTACTCACAAGATTAGG
89875 TCAATT
1 TCAATT
89881 GAGTCCAATC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (31 bp):
TCAATTTACTCCCCGTACTCACAAGATTAGG
Found at i:90024 original size:293 final size:293
Alignment explanation
Indices: 89497--90083 Score: 1030
Period size: 293 Copynumber: 2.0 Consensus size: 293
89487 ATATTCACTT
* *
89497 TTGTCCATGTATTCAAAAAGCGATCAATTTATTTCCCGTACTCATAAGATTAGCTCAATTTACTC
1 TTGTCCATGTATTCAAAAAGCGATCAATTTATTCCCCGTACTCACAAGATTAGCTCAATTTACTC
* * *
89562 TCTGTACTCGTAAGATTGGGTTAATTGAGTCCAATCGATAAAGGTGTGCACTTAATTGACCTAAT
66 TCTGTACTCGCAAGATTGGGTCAATTGAGTCCAATCAATAAAGGTGTGCACTTAATTGACCTAAT
*
89627 ATTGTGAGTATAGAGACTAGATTCACCCAATCTTATGAGTATATTGACTAAATTGATCGTTTTTT
131 ATTGTGAGTATAGAGACTAGATTCACCAAATCTTATGAGTATATTGACTAAATTGATCGTTTTTT
* * *
89692 AGTACATGGACAGAATTGAACATTTTTGTACAGTACAGGGACCTCCTAGGCATTTTCACCCCTCT
196 AGTACATAGACAAAATTGAACATTTTTGTACAATACAGGGACCTCCTAGGCATTTTCACCCCTCT
*
89757 ACCCAAATCTTGTTTTAAATAATGAATTTCAAG
261 ACCCAAATCTTCTTTTAAATAATGAATTTCAAG
*
89790 TTGTCCATGTATTCAAAAAGCGATCAATTTATTCCCCGTACTCACAAGATTAGGTCAATTTACTC
1 TTGTCCATGTATTCAAAAAGCGATCAATTTATTCCCCGTACTCACAAGATTAGCTCAATTTACTC
*
89855 TCTGTACTCGCAAGATTGGGTCAATTGAGTCCAATCAATAAAGGTGTGGACTTAATTGACCTAAT
66 TCTGTACTCGCAAGATTGGGTCAATTGAGTCCAATCAATAAAGGTGTGCACTTAATTGACCTAAT
*
89920 ATTGTGAGTATAGGGACTAGATTCACCAAATCTTATGAGTATATTGACTAAATTGATCGTTTTTT
131 ATTGTGAGTATAGAGACTAGATTCACCAAATCTTATGAGTATATTGACTAAATTGATCGTTTTTT
*
89985 AGTACATAGACAAAATTGAACATTTTTGTACAATACAGGGACCTCCTAGGTATTTTCACCCCTCT
196 AGTACATAGACAAAATTGAACATTTTTGTACAATACAGGGACCTCCTAGGCATTTTCACCCCTCT
* *
90050 GCCCATATCTTCTTTTAAATAATGAATTTCAAG
261 ACCCAAATCTTCTTTTAAATAATGAATTTCAAG
90083 T
1 T
90084 ATTATATATT
Statistics
Matches: 278, Mismatches: 16, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
293 278 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (293 bp):
TTGTCCATGTATTCAAAAAGCGATCAATTTATTCCCCGTACTCACAAGATTAGCTCAATTTACTC
TCTGTACTCGCAAGATTGGGTCAATTGAGTCCAATCAATAAAGGTGTGCACTTAATTGACCTAAT
ATTGTGAGTATAGAGACTAGATTCACCAAATCTTATGAGTATATTGACTAAATTGATCGTTTTTT
AGTACATAGACAAAATTGAACATTTTTGTACAATACAGGGACCTCCTAGGCATTTTCACCCCTCT
ACCCAAATCTTCTTTTAAATAATGAATTTCAAG
Found at i:90381 original size:21 final size:20
Alignment explanation
Indices: 90313--90433 Score: 91
Period size: 22 Copynumber: 5.7 Consensus size: 20
90303 TATTTTTATG
90313 AAATTTTGATAACTACCCTACT
1 AAATTTTGATAACTA-CCTA-T
*
90335 AAATTTTGATAACCACGCTAT
1 AAATTTTGATAACTAC-CTAT
*
90356 GAAATTTTGATAATTACCTAT
1 -AAATTTTGATAACTACCTAT
* * *
90377 AAAATTGTGATAAACTTCATAT
1 -AAATTTTGAT-AACTACCTAT
* *
90399 GAAACTTTGATAACCTAACTAT
1 -AAATTTTGATAA-CTACCTAT
90421 GAAATTTT-ATAAC
1 -AAATTTTGATAAC
90434 CTTCATATGA
Statistics
Matches: 80, Mismatches: 15, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
20 1 0.01
21 21 0.26
22 58 0.73
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.36
Consensus pattern (20 bp):
AAATTTTGATAACTACCTAT
Found at i:90400 original size:43 final size:41
Alignment explanation
Indices: 90309--90454 Score: 127
Period size: 43 Copynumber: 3.4 Consensus size: 41
90299 TTAATATTTT
*
90309 TATGAAATTTTGATAACTACCCTACTAAATTTTGATAACCAC-GC-
1 TATGAAATTTTGATAACTA-CCTA-TAAA-TTTGATAA--ACTTCA
*
90353 TATGAAATTTTGATAATTACCTATAAAATTGTGATAAACTTCA
1 TATGAAATTTTGATAACTACCTAT-AAATT-TGATAAACTTCA
* * * *
90396 TATGAAACTTTGATAACCTAACTATGAAATTTTATAACCTTCA
1 TATGAAATTTTGATAA-CTACCTAT-AAATTTGATAAACTTCA
*
90439 TATG-ATTTTTGATAAC
1 TATGAAATTTTGATAAC
90455 CTCCCTATGT
Statistics
Matches: 87, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
41 3 0.03
42 13 0.15
43 42 0.48
44 29 0.33
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.38
Consensus pattern (41 bp):
TATGAAATTTTGATAACTACCTATAAATTTGATAAACTTCA
Found at i:90442 original size:21 final size:21
Alignment explanation
Indices: 90386--90456 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
90376 TAAAATTGTG
* *
90386 ATAAACTTCATATGAAACTTTG
1 ATAACCTTCATATGAAA-TTTT
*
90408 ATAACC-TAACTATGAAATTTT
1 ATAACCTTCA-TATGAAATTTT
*
90429 ATAACCTTCATATG-ATTTTT
1 ATAACCTTCATATGAAATTTT
90449 GATAACCT
1 -ATAACCT
90457 CCCTATGTGA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
20 5 0.12
21 22 0.54
22 14 0.34
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.39
Consensus pattern (21 bp):
ATAACCTTCATATGAAATTTT
Found at i:90463 original size:21 final size:21
Alignment explanation
Indices: 90404--90496 Score: 64
Period size: 22 Copynumber: 4.3 Consensus size: 21
90394 CATATGAAAC
** *
90404 TTTGATAACCTAACTATGAAAT
1 TTTGATAACCTCCCTATG-ATT
* *
90426 TTT-ATAACCTTCATATGATT
1 TTTGATAACCTCCCTATGATT
90446 TTTGATAACCTCCCTATG-TGAT
1 TTTGATAACCTCCCTATGAT--T
* * *
90468 TTTGTTAATCTCCCTATAATTT
1 TTTGATAACCTCCCTATGA-TT
90490 TTTGATA
1 TTTGATA
90497 TTATAGTATG
Statistics
Matches: 56, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
20 6 0.11
21 23 0.41
22 26 0.46
24 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.09, T:0.46
Consensus pattern (21 bp):
TTTGATAACCTCCCTATGATT
Found at i:91914 original size:107 final size:106
Alignment explanation
Indices: 91791--92004 Score: 410
Period size: 107 Copynumber: 2.0 Consensus size: 106
91781 TTTTTTAATA
*
91791 AGAACAAAAGCAAACAATCATCAAAATTCGTACATACGTTTAAAAATTCAACTCCTTTGCGTTTT
1 AGAACAAAAACAAACAATCATCAAAATTCGTACATACGTTTAAAAATTCAACTCCTTTGCGTTTT
91856 AAAAAATCATCAAACATAGTATTGCAAAAAAATGAAGAAAAT
66 AAAAAATCATCAAACATAGTATTG-AAAAAAATGAAGAAAAT
91898 AGAACAAAAACAAACAATCATCAAAATTCGTACATACGTTTAAAAATTCAACTCCTTTGCGTTTT
1 AGAACAAAAACAAACAATCATCAAAATTCGTACATACGTTTAAAAATTCAACTCCTTTGCGTTTT
91963 AAAAAATCATCAAACATAGTATTGAAAAAAATGAAGAAAAT
66 AAAAAATCATCAAACATAGTATTGAAAAAAATGAAGAAAAT
92004 A
1 A
92005 ATTTACTCTT
Statistics
Matches: 106, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
106 18 0.17
107 88 0.83
ACGTcount: A:0.50, C:0.15, G:0.09, T:0.25
Consensus pattern (106 bp):
AGAACAAAAACAAACAATCATCAAAATTCGTACATACGTTTAAAAATTCAACTCCTTTGCGTTTT
AAAAAATCATCAAACATAGTATTGAAAAAAATGAAGAAAAT
Found at i:92221 original size:15 final size:15
Alignment explanation
Indices: 92201--92232 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
92191 GACAAGAAGT
92201 TATCAATACCATACC
1 TATCAATACCATACC
92216 TATCAATACCATACC
1 TATCAATACCATACC
92231 TA
1 TA
92233 GACAGTAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.31, G:0.00, T:0.28
Consensus pattern (15 bp):
TATCAATACCATACC
Found at i:93256 original size:26 final size:26
Alignment explanation
Indices: 93227--93322 Score: 147
Period size: 26 Copynumber: 3.7 Consensus size: 26
93217 GGTCATCCAG
93227 GGGCATTTTGGTCATTTTTACACTAA
1 GGGCATTTTGGTCATTTTTACACTAA
* * * *
93253 GGGCATTTTGGTCATTTTCATATCCAG
1 GGGCATTTTGGTCATTTTTACA-CTAA
93280 GGGCATTTTGGTCATTTTTACACTAA
1 GGGCATTTTGGTCATTTTTACACTAA
93306 GGGCATTTTGGTCATTT
1 GGGCATTTTGGTCATTT
93323 GCATATTCAG
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
26 39 0.64
27 22 0.36
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.43
Consensus pattern (26 bp):
GGGCATTTTGGTCATTTTTACACTAA
Found at i:93286 original size:53 final size:53
Alignment explanation
Indices: 93221--93350 Score: 233
Period size: 53 Copynumber: 2.5 Consensus size: 53
93211 CTTTAGGGTC
*
93221 ATCCAGGGGCATTTTGGTCATTTTTACACTAAGGGCATTTTGGTCATTTTCAT
1 ATCCAGGGGCATTTTGGTCATTTTTACACTAAGGGCATTTTGGTCATTTGCAT
93274 ATCCAGGGGCATTTTGGTCATTTTTACACTAAGGGCATTTTGGTCATTTGCAT
1 ATCCAGGGGCATTTTGGTCATTTTTACACTAAGGGCATTTTGGTCATTTGCAT
* *
93327 ATTCAGGGGCATGTTGGTCATTTT
1 ATCCAGGGGCATTTTGGTCATTTT
93351 AAGTCCACCC
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 74 1.00
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (53 bp):
ATCCAGGGGCATTTTGGTCATTTTTACACTAAGGGCATTTTGGTCATTTGCAT
Found at i:93334 original size:26 final size:27
Alignment explanation
Indices: 93225--93350 Score: 141
Period size: 26 Copynumber: 4.7 Consensus size: 27
93215 AGGGTCATCC
*
93225 AGGGGCATTTTGGTCATTTTTACACTA
1 AGGGGCATTTTGGTCATTTTCACACTA
* *
93252 A-GGGCATTTTGGTCATTTTCATA-TCC
1 AGGGGCATTTTGGTCATTTTCACACT-A
*
93278 AGGGGCATTTTGGTCATTTTTACACTA
1 AGGGGCATTTTGGTCATTTTCACACTA
* * * *
93305 A-GGGCATTTTGGTCATTTGCATATTC
1 AGGGGCATTTTGGTCATTTTCACACTA
*
93331 AGGGGCATGTTGGTCATTTT
1 AGGGGCATTTTGGTCATTTT
93351 AAGTCCACCC
Statistics
Matches: 82, Mismatches: 13, Indels: 8
0.80 0.13 0.08
Matches are distributed among these distances:
25 1 0.01
26 42 0.51
27 38 0.46
28 1 0.01
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.41
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTTCACACTA
Found at i:96201 original size:43 final size:43
Alignment explanation
Indices: 96154--96241 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
96144 GTTCGTAAAT
96154 TAGGGTTTGTTCACTTTAAATATGCTCATTTTAAGTTCTTACA
1 TAGGGTTTGTTCACTTTAAATATGCTCATTTTAAGTTCTTACA
96197 TAGGGTTTGTTCACTTTAAATATGCTCATTTTAAGTTCTTACA
1 TAGGGTTTGTTCACTTTAAATATGCTCATTTTAAGTTCTTACA
96240 TA
1 TA
96242 AGGAATTTAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.47
Consensus pattern (43 bp):
TAGGGTTTGTTCACTTTAAATATGCTCATTTTAAGTTCTTACA
Found at i:103998 original size:51 final size:52
Alignment explanation
Indices: 103934--104033 Score: 141
Period size: 51 Copynumber: 1.9 Consensus size: 52
103924 TTCCCCGAAA
* * *
103934 CCCAAAATCAAAACTGTCATTTTCTTCTTTTTCGAA-ACCC-AAATCAAACGT
1 CCCAAAATCAAAACTGCCATTTTATTCTTCTTC-AATACCCAAAATCAAACGT
*
103985 CCCAAAATTAAAACTGCCATTTTATTCTTCTTCAATACCCAAAATCAAA
1 CCCAAAATCAAAACTGCCATTTTATTCTTCTTCAATACCCAAAATCAAA
104034 TCAAACCCCA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
50 2 0.05
51 33 0.77
52 8 0.19
ACGTcount: A:0.38, C:0.27, G:0.04, T:0.31
Consensus pattern (52 bp):
CCCAAAATCAAAACTGCCATTTTATTCTTCTTCAATACCCAAAATCAAACGT
Found at i:106339 original size:22 final size:20
Alignment explanation
Indices: 106311--106367 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 20
106301 GGAGCAAGTT
* *
106311 TGTAGCTGTAGAAGCTTGTG
1 TGTAGCTGTTGAAGCGTGTG
*
106331 CATGTAGCTGTTCAAGCGTGTG
1 --TGTAGCTGTTGAAGCGTGTG
106353 TGTAGCTGTTGAAGC
1 TGTAGCTGTTGAAGC
106368 CTTGGGATTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 14 0.45
22 17 0.55
ACGTcount: A:0.19, C:0.14, G:0.33, T:0.33
Consensus pattern (20 bp):
TGTAGCTGTTGAAGCGTGTG
Done.