Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009779.1 Corchorus capsularis cultivar CVL-1 contig09800, 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: 95165
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:312 original size:21 final size:21
Alignment explanation
Indices: 284--332 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
274 GGAAAAAAAC
*
284 TTTATATATATA-TA-ATTTT
1 TTTATATATATACAACATTTT
303 TTTATATATATACAACATTTT
1 TTTATATATATACAACATTTT
*
324 TTTGTATAT
1 TTTATATAT
333 TCTTCGTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 12 0.46
20 1 0.04
21 13 0.50
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTATATATATACAACATTTT
Found at i:323 original size:19 final size:19
Alignment explanation
Indices: 284--324 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
274 GGAAAAAAAC
* **
284 TTTATATATATATAATTTT
1 TTTATATATATACAACATT
303 TTTATATATATACAACATT
1 TTTATATATATACAACATT
322 TTT
1 TTT
325 TTGTATATTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTATATATATACAACATT
Found at i:462 original size:22 final size:22
Alignment explanation
Indices: 437--487 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
427 GAATTGTTTC
*
437 CTTTTATAATTGGAATGAATAT
1 CTTTCATAATTGGAATGAATAT
459 CTTTCATAATTGGAATGAATAT
1 CTTTCATAATTGGAATGAATAT
481 CTTTCAT
1 CTTTCAT
488 TTTCAGACGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (22 bp):
CTTTCATAATTGGAATGAATAT
Found at i:1820 original size:15 final size:15
Alignment explanation
Indices: 1800--1835 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
1790 CACAAATTTA
1800 CAATTGTCAATAACT
1 CAATTGTCAATAACT
1815 CAATTGTCAATAACT
1 CAATTGTCAATAACT
1830 CAATTG
1 CAATTG
1836 AAAAGTAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.33
Consensus pattern (15 bp):
CAATTGTCAATAACT
Found at i:2037 original size:57 final size:59
Alignment explanation
Indices: 1965--2077 Score: 176
Period size: 57 Copynumber: 1.9 Consensus size: 59
1955 GAGAGAAAAA
* *
1965 TAAATGCAAGGAAGAACAACTAAGAAAAC-GAAAAAAAAAAG-AAAAAGAAACTTATGG
1 TAAATACAAGGAAGAACAACTAAGAAAACGGAAAAAAAAAAGCAAAAAAAAACTTATGG
* *
2022 TAAATACAGGGAAGAACAACTAAGAAAACGGGAAAAAAAAAGCAAAAAAAAACTTA
1 TAAATACAAGGAAGAACAACTAAGAAAACGGAAAAAAAAAAGCAAAAAAAAACTTA
2078 CGGGTTTAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
57 27 0.54
58 11 0.22
59 12 0.24
ACGTcount: A:0.64, C:0.10, G:0.17, T:0.10
Consensus pattern (59 bp):
TAAATACAAGGAAGAACAACTAAGAAAACGGAAAAAAAAAAGCAAAAAAAAACTTATGG
Found at i:2128 original size:2 final size:2
Alignment explanation
Indices: 2121--2151 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2111 TAGGAAAGCT
2121 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2152 TATTAAGTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3675 original size:18 final size:18
Alignment explanation
Indices: 3652--3688 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3642 AATCTCCTTT
3652 TCACCATTATTCCATCCA
1 TCACCATTATTCCATCCA
3670 TCACCATTATTCCATCCA
1 TCACCATTATTCCATCCA
3688 T
1 T
3689 TTTTAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.38, G:0.00, T:0.35
Consensus pattern (18 bp):
TCACCATTATTCCATCCA
Found at i:6515 original size:44 final size:44
Alignment explanation
Indices: 6452--6539 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
6442 AATCAGCTTC
6452 GTTGGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAAG
1 GTTGGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAAG
6496 GTTGGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAAG
1 GTTGGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAAG
6540 ACAATTCAGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.39
Consensus pattern (44 bp):
GTTGGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAAG
Found at i:7083 original size:17 final size:17
Alignment explanation
Indices: 7058--7094 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
7048 GTTATCCAGC
7058 ACCTAATGCTACCTAGT
1 ACCTAATGCTACCTAGT
* *
7075 ACCTCATGCTACCTGGT
1 ACCTAATGCTACCTAGT
7092 ACC
1 ACC
7095 ATGAGAGGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.24, C:0.35, G:0.14, T:0.27
Consensus pattern (17 bp):
ACCTAATGCTACCTAGT
Found at i:12085 original size:40 final size:40
Alignment explanation
Indices: 12040--12230 Score: 118
Period size: 40 Copynumber: 5.2 Consensus size: 40
12030 AATTCAGGGT
* *
12040 AATTAAGAAAAGAAAGTATAGTCAAGGTCCTAAGTTGGGC
1 AATTAAGAAAAGAAAGTATAGTCAAGGTCCTAATTTGGGA
* *
12080 AATTAAG--AAG--AG--TA---AA-GTCTTAATTTAGGGT
1 AATTAAGAAAAGAAAGTATAGTCAAGGTCCTAATTT-GGGA
*
12111 AATTAAGAAGAGAAAGTATAGTCAAGGTCCTAATTTGGGA
1 AATTAAGAAAAGAAAGTATAGTCAAGGTCCTAATTTGGGA
* * * *
12151 AATTAAG--AAG---G----GT-AAAGTCTTAATTCAGGGT
1 AATTAAGAAAAGAAAGTATAGTCAAGGTCCTAATT-TGGGA
*
12182 AATTAAGAAAAGAAAGTATAGTCAAGGTCCTAAGTT-GGA
1 AATTAAGAAAAGAAAGTATAGTCAAGGTCCTAATTTGGGA
12221 CAATTAAGAA
1 -AATTAAGAA
12231 GAGTAAGAGA
Statistics
Matches: 112, Mismatches: 16, Indels: 46
0.64 0.09 0.26
Matches are distributed among these distances:
30 18 0.16
31 24 0.21
33 5 0.04
34 2 0.02
35 3 0.03
36 3 0.03
37 2 0.02
38 5 0.04
39 2 0.02
40 30 0.27
41 18 0.16
ACGTcount: A:0.43, C:0.07, G:0.24, T:0.26
Consensus pattern (40 bp):
AATTAAGAAAAGAAAGTATAGTCAAGGTCCTAATTTGGGA
Found at i:12111 original size:71 final size:71
Alignment explanation
Indices: 12027--12267 Score: 376
Period size: 71 Copynumber: 3.4 Consensus size: 71
12017 AGTTCAAGGA
12027 CTTAATTCAGGGTAATTAAGAAAAGAAAGTATAGTCAAGGTCCTAAGTTGGGCAATTAAGAAGAG
1 CTTAATTCAGGGTAATTAAGAAAAGAAAGTATAGTCAAGGTCCTAAGTTGGGCAATTAAGAAGAG
12092 TAAAGT
66 TAAAGT
* * * * *
12098 CTTAATTTAGGGTAATTAAGAAGAGAAAGTATAGTCAAGGTCCTAATTTGGGAAATTAAGAAGGG
1 CTTAATTCAGGGTAATTAAGAAAAGAAAGTATAGTCAAGGTCCTAAGTTGGGCAATTAAGAAGAG
12163 TAAAGT
66 TAAAGT
*
12169 CTTAATTCAGGGTAATTAAGAAAAGAAAGTATAGTCAAGGTCCTAAGTTGGACAATTAAGAAGAG
1 CTTAATTCAGGGTAATTAAGAAAAGAAAGTATAGTCAAGGTCCTAAGTTGGGCAATTAAGAAGAG
12234 TAAGAGAAT
66 TAA-AG--T
*
12243 -TTAATTCTGGGTAATTAAGTAAAAG
1 CTTAATTCAGGGTAATTAAG-AAAAG
12268 CAGGTAAAGA
Statistics
Matches: 154, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
71 128 0.83
72 2 0.01
73 18 0.12
74 6 0.04
ACGTcount: A:0.42, C:0.07, G:0.24, T:0.27
Consensus pattern (71 bp):
CTTAATTCAGGGTAATTAAGAAAAGAAAGTATAGTCAAGGTCCTAAGTTGGGCAATTAAGAAGAG
TAAAGT
Found at i:12286 original size:37 final size:36
Alignment explanation
Indices: 12232--12612 Score: 295
Period size: 37 Copynumber: 10.1 Consensus size: 36
12222 AATTAAGAAG
* *
12232 AGTAAGAGAATTTAATTCTGGGTAATTAAGTAAAAGC
1 AGTAA-AGAACTTAATTCAGGGTAATTAAGTAAAAGC
* *
12269 AGGTAAAGAACTTAATTCAGGGTAGTTAAGTGAAGGAGC
1 A-GTAAAGAACTTAATTCAGGGTAATTAAGT-AA-AAGC
* * * *
12308 AGTTAAGAACTTAATTCATGGCAATTAAGTAAAAAC
1 AGTAAAGAACTTAATTCAGGGTAATTAAGTAAAAGC
* *
12344 AGTCAAA-ATCTTAATTCAGGGCAATTAAGAAAAGTAAACATAGTC
1 AGT-AAAGAACTTAATTCAGGGTAATT-----AAGT-AA-A-AG-C
* * * *
12389 AGTCAAA-ATCTTCATTCAAGG-AAATAAGGTAAAAGC
1 AGT-AAAGAACTTAATTCAGGGTAATTAA-GTAAAAGC
* *
12425 AGTCAAAGGAGCTTAATTCAGGGAAATTAAGT-AAA-C
1 AGT-AAA-GAACTTAATTCAGGGTAATTAAGTAAAAGC
*
12461 ATGGTCAAAGAACTTAATTCAGGATAATTAAGTAAAAAGC
1 A--GT-AAAGAACTTAATTCAGGGTAATTAAGT-AAAAGC
* * **
12501 AGTTAAGAACTTAGTTCAGGACAATTAAGTAAAAGC
1 AGTAAAGAACTTAATTCAGGGTAATTAAGTAAAAGC
* *
12537 AGTTAAGAACTTAATTTAGGGTAATTAAGTAAAAGC
1 AGTAAAGAACTTAATTCAGGGTAATTAAGTAAAAGC
* *
12573 AGTTGAAGAACTTAATTCAGGGTAATTAAGTAAAAAC
1 AG-TAAAGAACTTAATTCAGGGTAATTAAGTAAAAGC
12610 AGT
1 AGT
12613 TAAAAGGTAA
Statistics
Matches: 287, Mismatches: 34, Indels: 47
0.78 0.09 0.13
Matches are distributed among these distances:
36 73 0.25
37 110 0.38
38 53 0.18
39 16 0.06
40 4 0.01
41 4 0.01
42 2 0.01
43 1 0.00
44 4 0.01
45 20 0.07
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.26
Consensus pattern (36 bp):
AGTAAAGAACTTAATTCAGGGTAATTAAGTAAAAGC
Found at i:12562 original size:73 final size:73
Alignment explanation
Indices: 12238--12615 Score: 259
Period size: 73 Copynumber: 5.0 Consensus size: 73
12228 GAAGAGTAAG
* * * * * ** *
12238 AGAATTTAATTCTGGGTAATTAAGTAAAAGCAGGTAAAGAACTTAATTCAGGGTAGTTAAGTGAA
1 AGAACTTAATTCAGGATAATTAAGTAAAAGCAGTTGAAGAACTTAATTCAGGACAATTAAGT-AA
* *
12303 GGAGCAGTTA
65 -AAACAGTTA
* * * *
12313 AGAACTTAATTCATGG-CAATTAAGTAAAAACAG-TCAA-AATCTTAATTCAGGGCAATTAAGAA
1 AGAACTTAATTCA-GGATAATTAAGTAAAAGCAGTTGAAGAA-CTTAATTCAGGACAATT-----
*
12375 AAGTAAACATAGTCAGTCA
59 AAGTAAA-A-A--CAGTTA
* ** *
12394 A-AATCTTCATTCAAGGA-AA-TAAGGTAAAAGCAGTCAAAGGAGCTTAATTCAGGGA-AATTAA
1 AGAA-CTTAATTC-AGGATAATTAA-GTAAAAGCAGTTGAA-GAACTTAATTCA-GGACAATTAA
* ** *
12455 GTAAACATGGTCAA
61 GTAAAAACAGT-TA
*
12469 AGAACTTAATTCAGGATAATTAAGTAAAAAGCAGTT-AAGAACTTAGTTCAGGACAATTAAGTAA
1 AGAACTTAATTCAGGATAATTAAGT-AAAAGCAGTTGAAGAACTTAATTCAGGACAATTAAGTAA
*
12533 AAGCAGTTA
65 AAACAGTTA
* * **
12542 AGAACTTAATTTAGGGTAATTAAGTAAAAGCAGTTGAAGAACTTAATTCAGGGTAATTAAGTAAA
1 AGAACTTAATTCAGGATAATTAAGTAAAAGCAGTTGAAGAACTTAATTCAGGACAATTAAGTAAA
12607 AACAGTTA
66 AACAGTTA
12615 A
1 A
12616 AAGGTAAGGA
Statistics
Matches: 242, Mismatches: 35, Indels: 54
0.73 0.11 0.16
Matches are distributed among these distances:
72 10 0.04
73 63 0.26
74 47 0.19
75 41 0.17
76 17 0.07
78 10 0.04
79 4 0.02
80 5 0.02
81 26 0.11
82 3 0.01
83 13 0.05
84 3 0.01
ACGTcount: A:0.45, C:0.10, G:0.19, T:0.26
Consensus pattern (73 bp):
AGAACTTAATTCAGGATAATTAAGTAAAAGCAGTTGAAGAACTTAATTCAGGACAATTAAGTAAA
AACAGTTA
Found at i:12662 original size:41 final size:40
Alignment explanation
Indices: 12629--12956 Score: 364
Period size: 41 Copynumber: 8.5 Consensus size: 40
12619 GTAAGGATAG
12629 GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAA
1 GCACAGACTTAATTTC-AGGAAGGAAATTAGGTAAAGACAA
* * * * *
12670 GTATAGACTTAA-TTCA-G--GGTAATTAAGTAAAG-TAA
1 GCACAGACTTAATTTCAGGAAGGAAATTAGGTAAAGACAA
12705 GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAA
1 GCACAGACTTAATTTC-AGGAAGGAAATTAGGTAAAGACAA
* * * *
12746 GCATAGACTTAA-TTCA-G--GGTAATTAAGTAAAG-TAA
1 GCACAGACTTAATTTCAGGAAGGAAATTAGGTAAAGACAA
12781 GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAA
1 GCACAGACTTAATTTC-AGGAAGGAAATTAGGTAAAGACAA
* * * *
12822 GCATAGACTTAA-TTCA-G--GGTAATTAAGTAAAG-TAA
1 GCACAGACTTAATTTCAGGAAGGAAATTAGGTAAAGACAA
12857 GCACAGACTTAATTTCAGTGAAGGAAATTAGGTAAAGACAA
1 GCACAGACTTAATTTCAG-GAAGGAAATTAGGTAAAGACAA
*
12898 GCATAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAA
1 GCACAGACTTAATTTC-AGGAAGGAAATTAGGTAAAGACAA
*
12939 GCACATACTTAA-TTCAGG
1 GCACAGACTTAATTTCAGG
12957 GTAATTAAGT
Statistics
Matches: 239, Mismatches: 29, Indels: 40
0.78 0.09 0.13
Matches are distributed among these distances:
35 38 0.16
36 49 0.21
37 2 0.01
38 6 0.03
39 6 0.03
40 51 0.21
41 85 0.36
42 2 0.01
ACGTcount: A:0.44, C:0.11, G:0.21, T:0.24
Consensus pattern (40 bp):
GCACAGACTTAATTTCAGGAAGGAAATTAGGTAAAGACAA
Found at i:12721 original size:76 final size:76
Alignment explanation
Indices: 12629--12911 Score: 541
Period size: 76 Copynumber: 3.7 Consensus size: 76
12619 GTAAGGATAG
*
12629 GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGTATAGACTTAATTCAGGGTAATT
1 GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTCAGGGTAATT
12694 AAGTAAAGTAA
66 AAGTAAAGTAA
12705 GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTCAGGGTAATT
1 GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTCAGGGTAATT
12770 AAGTAAAGTAA
66 AAGTAAAGTAA
12781 GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTCAGGGTAATT
1 GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTCAGGGTAATT
12846 AAGTAAAGTAA
66 AAGTAAAGTAA
12857 GCACAGACTTAATTTC-AGTGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATT
1 GCACAGACTTAATTTCAAG-GAAGGAAATTAGGTAAAGACAAGCATAGACTTAATT
12912 TCAAGGAAGG
Statistics
Matches: 205, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
75 2 0.01
76 203 0.99
ACGTcount: A:0.44, C:0.11, G:0.21, T:0.24
Consensus pattern (76 bp):
GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTCAGGGTAATT
AAGTAAAGTAA
Found at i:12953 original size:117 final size:116
Alignment explanation
Indices: 12629--12989 Score: 422
Period size: 117 Copynumber: 3.1 Consensus size: 116
12619 GTAAGGATAG
*
12629 GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGTATAGACTTAA-TTC-A-G--GG
1 GCACAGACTTAATTTC-AGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTTCAAGGAAGG
* * * * * *
12689 TAATTAAGTAAAG-TAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAA
65 AAATTAGGTAAAGACAAGCACAGACTTAA-TTC-A-G--GGTAATTAAGTAAAG-TAA
* * * * *
12746 GCATAGACTTAA-TTCA-G--GGTAATTAAGTAAAG-TAAGCACAGACTTAATTTCAAGGAAGGA
1 GCACAGACTTAATTTCAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTTCAAGGAAGGA
*
12806 AATTAGGTAAAGACAAGCATAGACTTAATTCAGGGTAATTAAGTAAAGTAA
66 AATTAGGTAAAGACAAGCACAGACTTAATTCAGGGTAATTAAGTAAAGTAA
12857 GCACAGACTTAATTTCAGTGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTTCAAGGAAGG
1 GCACAGACTTAATTTCAG-GAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTTCAAGGAAGG
* *
12922 AAATTAGGTAAAGACAAGCACATACTTAATTCAGGGTAATTAAGTAAA-TTA
65 AAATTAGGTAAAGACAAGCACAGACTTAATTCAGGGTAATTAAGTAAAGTAA
*
12973 GCAAAGACTTAATTTCA
1 GCACAGACTTAATTTCA
12990 TAAGAATTAA
Statistics
Matches: 210, Mismatches: 22, Indels: 25
0.82 0.09 0.10
Matches are distributed among these distances:
111 25 0.12
112 33 0.16
113 1 0.00
114 4 0.02
115 2 0.01
116 50 0.24
117 95 0.45
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.25
Consensus pattern (116 bp):
GCACAGACTTAATTTCAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTTCAAGGAAGGA
AATTAGGTAAAGACAAGCACAGACTTAATTCAGGGTAATTAAGTAAAGTAA
Found at i:13021 original size:152 final size:151
Alignment explanation
Indices: 12629--13004 Score: 453
Period size: 152 Copynumber: 2.5 Consensus size: 151
12619 GTAAGGATAG
* * * **
12629 GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGTATAGACTTAATTCAGGGTAATT
1 GCACAGACTTAATTTCAAGG-AGGAAATTAAGTAAAGACAAGCAAAGACTTAATTCAAAGTAATT
12694 AAGTAAAGTAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAAT
65 AAGTAAAGTAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAAT
* *
12759 TCAGGGTAATTAAGTAAAGTAA
130 TCAGGGAAATTAAGTAAAGCAA
* * **
12781 GCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATTCAGGGTAATT
1 GCACAGACTTAATTTCAAGG-AGGAAATTAAGTAAAGACAAGCAAAGACTTAATTCAAAGTAATT
12846 AAGTAAAGTAAGCACAGACTTAATTTC-AGTGAAGGAAATTAGGTAAAGACAAGCATAGACTTAA
65 AAGTAAAGTAAGCACAGACTTAATTTCAAG-GAAGGAAATTAGGTAAAGACAAGCATAGACTTAA
*
12910 TTTCAAGGAAGGAAATTAGGTAAAGACAA
129 -TTC-A-G--GGAAATTAAGTAAAG-CAA
* * **
12939 GCACATACTTAA-TTC-A-G-GGTAATTAAGT-AA-ATTAGCAAAGACTTAATTTCATAAG-AAT
1 GCACAGACTTAATTTCAAGGAGGAAATTAAGTAAAGACAAGCAAAGACTTAA-TTCA-AAGTAAT
12997 TAAGTAAA
64 TAAGTAAA
13005 ATCATCAAAG
Statistics
Matches: 203, Mismatches: 12, Indels: 18
0.87 0.05 0.08
Matches are distributed among these distances:
151 15 0.07
152 142 0.70
153 13 0.06
154 1 0.00
155 2 0.01
156 1 0.00
157 16 0.08
158 13 0.06
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (151 bp):
GCACAGACTTAATTTCAAGGAGGAAATTAAGTAAAGACAAGCAAAGACTTAATTCAAAGTAATTA
AGTAAAGTAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCATAGACTTAATT
CAGGGAAATTAAGTAAAGCAA
Found at i:13035 original size:36 final size:36
Alignment explanation
Indices: 12959--13057 Score: 105
Period size: 36 Copynumber: 2.8 Consensus size: 36
12949 AATTCAGGGT
* *
12959 AATTAAGT-AAATTAGCAAAGACTTAATTTCATAAG
1 AATTAAGTAAAATCAGCAAAGACTTAATTCCATAAG
*
12994 AATTAAGTAAAATCATCAAAGACTTAA-TCCA-AAG
1 AATTAAGTAAAATCAGCAAAGACTTAATTCCATAAG
* *
13028 ATGATTAAGTAAGATCAGACAAAAACTTAA
1 A--ATTAAGTAAAATCAG-CAAAGACTTAA
13058 CCTCCGGGGA
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
34 4 0.07
35 11 0.20
36 29 0.54
37 10 0.19
ACGTcount: A:0.52, C:0.11, G:0.11, T:0.26
Consensus pattern (36 bp):
AATTAAGTAAAATCAGCAAAGACTTAATTCCATAAG
Found at i:13194 original size:111 final size:111
Alignment explanation
Indices: 13067--13332 Score: 390
Period size: 111 Copynumber: 2.4 Consensus size: 111
13057 ACCTCCGGGG
* * * *
13067 ATTAAGTAAAGAAAAGGACTTGGTTCCAAGGAAGGGAATTAAGTAGAGCAATAGACTTGATTCCA
1 ATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGCAAGAGACTTGATTCCA
13132 AAGAAGGGAATTAAGTA-GAGCAAAGGACTTGATTCCAAGGAAGGGA
66 AAGAAGGGAATTAAGTATG-GCAAAGGACTTGATTCCAAGGAAGGGA
* * *
13178 ATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGAGAATTAAGTAGAGTAAGGGACTTGATTCCA
1 ATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGCAAGAGACTTGATTCCA
* * *
13243 AGGAAGGGAATTAAGTATGGTAGAGGACTTGATTCCAAGGAAGGGA
66 AAGAAGGGAATTAAGTATGGCAAAGGACTTGATTCCAAGGAAGGGA
* * * *
13289 ATTAAGTAGAGTTAAGGACTTAATTTCAAGGAAGGAAATTAAGT
1 ATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGGGAATTAAGT
13333 CAAGTTAGGG
Statistics
Matches: 139, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
111 138 0.99
112 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.28, T:0.23
Consensus pattern (111 bp):
ATTAAGTAGAGTAAAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGCAAGAGACTTGATTCCA
AAGAAGGGAATTAAGTATGGCAAAGGACTTGATTCCAAGGAAGGGA
Found at i:13339 original size:37 final size:37
Alignment explanation
Indices: 13080--13351 Score: 347
Period size: 37 Copynumber: 7.4 Consensus size: 37
13070 AAGTAAAGAA
* *
13080 AAGGACTTGGTTCCAAGGAAGGGAATTAAGTAGAG-C
1 AAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGTT
* * **
13116 AATAGACTTGATTCCAAAGAAGGGAATTAAGTAGAGCA
1 AA-GGACTTGATTCCAAGGAAGGGAATTAAGTAGAGTT
*
13154 AAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGTA
1 AAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGTT
*
13191 AAGGACTTGATTCCAAGGAAGAGAATTAAGTAGAG-T
1 AAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGTT
13227 AAGGGACTTGATTCCAAGGAAGGGAATTAAGTATG-G-T
1 AA-GGACTTGATTCCAAGGAAGGGAATTAAGTA-GAGTT
13264 AGAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGTT
1 A-AGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGTT
* * *
13302 AAGGACTTAATTTCAAGGAAGGAAATTAAGTCA-AGTT
1 AAGGACTTGATTCCAAGGAAGGGAATTAAGT-AGAGTT
* *
13339 AGGGACTTAATTC
1 AAGGACTTGATTC
13352 GGGGTAATTA
Statistics
Matches: 213, Mismatches: 15, Indels: 15
0.88 0.06 0.06
Matches are distributed among these distances:
36 5 0.02
37 201 0.94
38 7 0.03
ACGTcount: A:0.39, C:0.09, G:0.28, T:0.23
Consensus pattern (37 bp):
AAGGACTTGATTCCAAGGAAGGGAATTAAGTAGAGTT
Found at i:13387 original size:36 final size:36
Alignment explanation
Indices: 13344--13457 Score: 167
Period size: 36 Copynumber: 3.2 Consensus size: 36
13334 AAGTTAGGGA
*
13344 CTTAATTCGGGGTAATTAAGTAGCGTCAATAAAAGG
1 CTTAATTCAGGGTAATTAAGTAGCGTCAATAAAAGG
*
13380 CTTAATTCAGGGTAATTAAGTAACGTCAATAAAAGG
1 CTTAATTCAGGGTAATTAAGTAGCGTCAATAAAAGG
* * *
13416 CTTAATTTAGGGTAATTAAGTGGAGTCAAT-AAAGAG
1 CTTAATTCAGGGTAATTAAGTAGCGTCAATAAAAG-G
13452 CTTAAT
1 CTTAAT
13458 CTAAGAAGAG
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
35 4 0.06
36 67 0.94
ACGTcount: A:0.39, C:0.10, G:0.22, T:0.30
Consensus pattern (36 bp):
CTTAATTCAGGGTAATTAAGTAGCGTCAATAAAAGG
Found at i:14125 original size:14 final size:14
Alignment explanation
Indices: 14108--14134 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
14098 TTTTCACTTT
14108 TTTAAATTTAAATA
1 TTTAAATTTAAATA
14122 TTTAAATTTAAAT
1 TTTAAATTTAAAT
14135 TATAATAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTAAATTTAAATA
Found at i:14719 original size:28 final size:28
Alignment explanation
Indices: 14678--14764 Score: 104
Period size: 28 Copynumber: 3.1 Consensus size: 28
14668 AGACGTTTGT
*
14678 CATGCTAGTTTATACTCAATTACTG-AGTC
1 CATG-TAGTTTATACTCAATCAC-GAAGTC
*
14707 CATGTAGTTTATACTCAATCGCGAAGTC
1 CATGTAGTTTATACTCAATCACGAAGTC
* * *
14735 CTTGTAGTTTATACTCAATCGCGGAGTC
1 CATGTAGTTTATACTCAATCACGAAGTC
14763 CA
1 CA
14765 AATGTGCATC
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
27 1 0.02
28 47 0.90
29 4 0.08
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.34
Consensus pattern (28 bp):
CATGTAGTTTATACTCAATCACGAAGTC
Found at i:26373 original size:98 final size:96
Alignment explanation
Indices: 26206--26400 Score: 372
Period size: 98 Copynumber: 2.0 Consensus size: 96
26196 TAAGTTAATA
26206 TTGCATATTGATTGCTCTTATTTAATTGTATGCCACTATGTGGGTGTTTGAGGAAACAATAACTC
1 TTGCATATTGATTGCTCTTATTTAATTGTATGCCACTATGTGGGTGTTTGAGGAAACAATAACTC
26271 ATGATTCTGTAACAGGGTATTTAATTCAACT
66 ATGATTCTGTAACAGGGTATTTAATTCAACT
26302 TTGCATATTGATTGCTCTTATTTAATTTTGTATGCCACTATGTGGGTGTTTGAGGAAACAATAAC
1 TTGCATATTGATTGCTCTTATTTAA--TTGTATGCCACTATGTGGGTGTTTGAGGAAACAATAAC
26367 TCATGATTCTGTAACAGGGTATTTAATTCAACT
64 TCATGATTCTGTAACAGGGTATTTAATTCAACT
26400 T
1 T
26401 AGATGATTAG
Statistics
Matches: 97, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
96 25 0.26
98 72 0.74
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (96 bp):
TTGCATATTGATTGCTCTTATTTAATTGTATGCCACTATGTGGGTGTTTGAGGAAACAATAACTC
ATGATTCTGTAACAGGGTATTTAATTCAACT
Found at i:37368 original size:21 final size:21
Alignment explanation
Indices: 37327--37369 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
37317 AGAATAATAG
*
37327 AATCATAAAGATAAAATATGA
1 AATCATAAAGATAAAAGATGA
*
37348 AATCATAAA-ATATCAAGATGA
1 AATCATAAAGATA-AAAGATGA
37369 A
1 A
37370 TAATCAGGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.60, C:0.07, G:0.09, T:0.23
Consensus pattern (21 bp):
AATCATAAAGATAAAAGATGA
Found at i:40298 original size:2 final size:2
Alignment explanation
Indices: 40293--40318 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40283 TTTTTCCGGA
40293 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
40319 CCGAGGAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48492 original size:2 final size:2
Alignment explanation
Indices: 48485--48509 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
48475 AAAAATGTAC
48485 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
48510 AGAAATTAGA
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:51236 original size:19 final size:19
Alignment explanation
Indices: 51183--51239 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
51173 CGCCCATGCC
51183 TTTAAGTGTTTGAATTTTT
1 TTTAAGTGTTTGAATTTTT
**** *
51202 TTTGAACAAATAGAATTTTT
1 TTT-AAGTGTTTGAATTTTT
51222 TTTAAGTGTTTGAATTTT
1 TTTAAGTGTTTGAATTTT
51240 ACAAATGGAA
Statistics
Matches: 27, Mismatches: 10, Indels: 2
0.69 0.26 0.05
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.28, C:0.02, G:0.14, T:0.56
Consensus pattern (19 bp):
TTTAAGTGTTTGAATTTTT
Found at i:53513 original size:31 final size:31
Alignment explanation
Indices: 53414--53580 Score: 134
Period size: 31 Copynumber: 5.5 Consensus size: 31
53404 GCCGGCTAAT
*
53414 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAATGTTTGCCAAAA
* * ** * * **
53445 TACTTAAATAA-GGCCCGATCTTT--TAATT
1 TGCTCAAATAAGGGCCTAATGTTTGCCAAAA
53473 TGGC-CAAATAAGGGCCTAATGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAATGTTTGCCAAAA
* **
53504 TGCTCAAATAAGGGCC-ACATCTTTG--AATT
1 TGCTCAAATAAGGGCCTA-ATGTTTGCCAAAA
*
53533 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAATGTTTGCCAAAA
53564 TGCTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
53581 GTCTCACGCG
Statistics
Matches: 101, Mismatches: 24, Indels: 22
0.69 0.16 0.15
Matches are distributed among these distances:
28 9 0.09
29 30 0.30
30 16 0.16
31 46 0.46
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAATGTTTGCCAAAA
Found at i:53548 original size:29 final size:29
Alignment explanation
Indices: 53450--53548 Score: 89
Period size: 29 Copynumber: 3.4 Consensus size: 29
53440 CAAAATACTT
*
53450 AAATAA-GGCC-CGATCTTTTAATTTGGCC
1 AAATAAGGGCCAC-ATCTTTGAATTTGGCC
* **
53478 AAATAAGGGCCTA-ATGTTTGCCAAAAT-GCTC
1 AAATAAGGGCC-ACATCTTTG--AATTTGGC-C
53509 AAATAAGGGCCACATCTTTGAATTTGGCC
1 AAATAAGGGCCACATCTTTGAATTTGGCC
53538 AAATAAGGGCC
1 AAATAAGGGCC
53549 TAACGTTTGC
Statistics
Matches: 56, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
28 6 0.11
29 24 0.43
30 5 0.09
31 21 0.38
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.26
Consensus pattern (29 bp):
AAATAAGGGCCACATCTTTGAATTTGGCC
Found at i:53550 original size:60 final size:60
Alignment explanation
Indices: 53418--53579 Score: 265
Period size: 60 Copynumber: 2.7 Consensus size: 60
53408 GCTAATTGCT
* * *
53418 CAAATAAGGGCCTAACGTTTGCCAAAATACTTAAATAA-GGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGGC
*
53477 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGCCAC-ATCTTTGAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCC-CGATCTTTGAATTTGGC
53537 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
53580 TGTCTCACGC
Statistics
Matches: 96, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
59 35 0.36
60 60 0.62
61 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGGC
Found at i:53646 original size:31 final size:29
Alignment explanation
Indices: 53608--53775 Score: 92
Period size: 31 Copynumber: 5.6 Consensus size: 29
53598 AATTGACATC
53608 AGGCCCTTATTTGAGCATTTTCGATAACGTT
1 AGGCCCTTATTTGAGCATTTT-GA-AACGTT
** * *
53639 AGGCCCTTATTTG-GCCAAATT-AAAAGATC
1 AGGCCCTTATTTGAG-CATTTTGAAACG-TT
* *
53668 GGGCCCTTATTTGAACATTTTCGATAACGTT
1 AGGCCCTTATTTGAGCATTTT-GA-AACGTT
** ** * *
53699 AGATCCTTATTTG-GCCAAATT-AAAAGAT
1 AGGCCCTTATTTGAG-CATTTTGAAACGTT
*
53727 CGGACCCTTATTTGAGCATTTTGGCAAACGTT
1 AGG-CCCTTATTTGAGCATTTT-G-AAACGTT
*
53759 AGACCCTTATTTGAGCA
1 AGGCCCTTATTTGAGCA
53776 ATTAGCCTAT
Statistics
Matches: 98, Mismatches: 27, Indels: 24
0.66 0.18 0.16
Matches are distributed among these distances:
28 8 0.08
29 32 0.33
30 2 0.02
31 47 0.48
32 9 0.09
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (29 bp):
AGGCCCTTATTTGAGCATTTTGAAACGTT
Found at i:53687 original size:60 final size:60
Alignment explanation
Indices: 53609--53771 Score: 265
Period size: 60 Copynumber: 2.7 Consensus size: 60
53599 ATTGACATCA
*
53609 GGCCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCG
* *
53669 GGCCCTTATTTGAACATTTTCGATAACGTTAGATCCTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCG
* *
53729 GACCCTTATTTGAGCATTTTGGCA-AACGTTAGACCCTTATTTG
1 GGCCCTTATTTGAGCATTTTCG-ATAACGTTAGACCCTTATTTG
53772 AGCAATTAGC
Statistics
Matches: 95, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
60 94 0.99
61 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (60 bp):
GGCCCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCG
Found at i:53740 original size:29 final size:29
Alignment explanation
Indices: 53642--53740 Score: 83
Period size: 29 Copynumber: 3.3 Consensus size: 29
53632 TAACGTTAGG
*
53642 CCCTTATTTGGCCAAATTAAAAGATCGGG
1 CCCTTATTTGGCCAAATTAAAAGATCGGA
** ** * **
53671 CCCTTATTTGAACATTTTCGATAACG-TTAGA
1 CCCTTATTTGGCCAAATT--A-AAAGATCGGA
*
53702 TCCTTATTTGGCCAAATTAAAAGATCGGA
1 CCCTTATTTGGCCAAATTAAAAGATCGGA
53731 CCCTTATTTG
1 CCCTTATTTG
53741 AGCATTTTGG
Statistics
Matches: 49, Mismatches: 17, Indels: 8
0.66 0.23 0.11
Matches are distributed among these distances:
28 3 0.06
29 27 0.55
31 16 0.33
32 3 0.06
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.34
Consensus pattern (29 bp):
CCCTTATTTGGCCAAATTAAAAGATCGGA
Found at i:53847 original size:39 final size:39
Alignment explanation
Indices: 53793--53870 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
53783 TATTTTGCCT
53793 CTAATTTTCTCTAATCTTTTCCACCACACGTTAGTCAAA
1 CTAATTTTCTCTAATCTTTTCCACCACACGTTAGTCAAA
*
53832 CTAATTTTCTCTAATCTTTTCCAGCACACGTTAGTCAAA
1 CTAATTTTCTCTAATCTTTTCCACCACACGTTAGTCAAA
53871 GAGAGAGGGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.28, C:0.27, G:0.06, T:0.38
Consensus pattern (39 bp):
CTAATTTTCTCTAATCTTTTCCACCACACGTTAGTCAAA
Found at i:63302 original size:37 final size:36
Alignment explanation
Indices: 63169--63324 Score: 197
Period size: 36 Copynumber: 4.3 Consensus size: 36
63159 CTCTTCTTAG
* * *
63169 ATTAAGCTCTTTATTGAC-TCCACTTAATTATCCTGA
1 ATTAAGCCCTTTATTGACGT-TACTTAATTACCCTGA
**
63205 ATTAAGCATTTTATTGACGTTACTTAATTACCCTGA
1 ATTAAGCCCTTTATTGACGTTACTTAATTACCCTGA
*
63241 ATTAAGCCTTTTATTGACGTTACTTAATTACCCTGA
1 ATTAAGCCCTTTATTGACGTTACTTAATTACCCTGA
* * *
63277 ATTAAGCCCCTTTATCGACGCTACTTAATTACCCCGA
1 ATTAAG-CCCTTTATTGACGTTACTTAATTACCCTGA
63314 ATTAAGTCCCT
1 ATTAAG-CCCT
63325 AACTTGACTT
Statistics
Matches: 108, Mismatches: 10, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
36 71 0.66
37 37 0.34
ACGTcount: A:0.28, C:0.23, G:0.10, T:0.38
Consensus pattern (36 bp):
ATTAAGCCCTTTATTGACGTTACTTAATTACCCTGA
Found at i:63354 original size:37 final size:37
Alignment explanation
Indices: 63313--63422 Score: 152
Period size: 37 Copynumber: 3.0 Consensus size: 37
63303 AATTACCCCG
*
63313 AATTAAGTCCCTAACT-TGACTTAATTTCCTTCCTTGA
1 AATTAAGTCCCTAACTCT-ACTTAATTCCCTTCCTTGA
* *
63350 AATTAAGTCCTTAACTCTACTTAATTCCCTTCCTTGG
1 AATTAAGTCCCTAACTCTACTTAATTCCCTTCCTTGA
*
63387 AATCAAGTCCTCT-ACTCTACTTAATTCCCTTCCTTG
1 AATTAAGTCC-CTAACTCTACTTAATTCCCTTCCTTG
63423 GAACCAAGTC
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
37 64 0.97
38 2 0.03
ACGTcount: A:0.25, C:0.28, G:0.07, T:0.40
Consensus pattern (37 bp):
AATTAAGTCCCTAACTCTACTTAATTCCCTTCCTTGA
Found at i:63423 original size:37 final size:36
Alignment explanation
Indices: 63331--63452 Score: 156
Period size: 37 Copynumber: 3.3 Consensus size: 36
63321 CCCTAACTTG
* * *
63331 ACTTAATTTCCTTCCTTGAAATTAAGTCCTTAACTCT
1 ACTTAATTCCCTTCCTTGGAATCAAGTCCTT-ACTCT
63368 ACTTAATTCCCTTCCTTGGAATCAAGTCCTCTACTCT
1 ACTTAATTCCCTTCCTTGGAATCAAGTCCT-TACTCT
* * *
63405 ACTTAATTCCCTTCCTTGGAACCAAGTCCTTTTCTTT
1 ACTTAATTCCCTTCCTTGGAATCAAGTCC-TTACTCT
63442 ACTTAA-TCCCT
1 ACTTAATTCCCT
63453 AGAGGTTAAG
Statistics
Matches: 77, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
36 5 0.06
37 70 0.91
38 2 0.03
ACGTcount: A:0.23, C:0.30, G:0.07, T:0.41
Consensus pattern (36 bp):
ACTTAATTCCCTTCCTTGGAATCAAGTCCTTACTCT
Found at i:63677 original size:117 final size:115
Alignment explanation
Indices: 63525--63748 Score: 367
Period size: 117 Copynumber: 1.9 Consensus size: 115
63515 TTAATTCTAA
* *
63525 TGAAATTAAGTCTTTGCTAATTTACTTAATTACCCTGAATTAAGTATGTGCTTGTCTTTACCTAA
1 TGAAATTAAGTCTGTGCTAATTTACTTAATTACCCTGAATTAAGTATATGCTTGTCTTTACCTAA
*
63590 TTTCCTTCCTTGAAATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCAC
66 TTTCCTTCCTTGAAATTAAGTCTATGCTT-ACTTTACCTAATTTCCTTCAC
* *
63641 TGAAATTAAGTCTGTGCTTACTTTACTTAATTACCCTGAATTAAGTCTATGCTTGTCTTTACCTA
1 TGAAATTAAGTCTGTGC-TAATTTACTTAATTACCCTGAATTAAGTATATGCTTGTCTTTACCTA
* *
63706 ATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACTTAATT
65 ATTTCCTTCCTTGAAATTAAGTCTATGCTTACTTTACCTAATT
63749 ACCCTGAATT
Statistics
Matches: 100, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
116 27 0.27
117 73 0.73
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.45
Consensus pattern (115 bp):
TGAAATTAAGTCTGTGCTAATTTACTTAATTACCCTGAATTAAGTATATGCTTGTCTTTACCTAA
TTTCCTTCCTTGAAATTAAGTCTATGCTTACTTTACCTAATTTCCTTCAC
Found at i:63694 original size:76 final size:76
Alignment explanation
Indices: 63603--63809 Score: 398
Period size: 76 Copynumber: 2.7 Consensus size: 76
63593 CCTTCCTTGA
63603 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCAC-TGAAATTAAGTCTGTGCTTACTTTAC
1 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTC-CTTGAAATTAAGTCTGTGCTTACTTTAC
63667 TTAATTACCCTG
65 TTAATTACCCTG
63679 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACT
1 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACT
63744 TAATTACCCTG
66 TAATTACCCTG
63755 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGC
1 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGC
63810 CTATCCTTAC
Statistics
Matches: 130, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
75 1 0.01
76 129 0.99
ACGTcount: A:0.24, C:0.21, G:0.11, T:0.44
Consensus pattern (76 bp):
AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACT
TAATTACCCTG
Found at i:63821 original size:41 final size:40
Alignment explanation
Indices: 63558--63809 Score: 301
Period size: 41 Copynumber: 6.5 Consensus size: 40
63548 ACTTAATTAC
*
63558 CCTG-AATTAAGTATGTGCTTGTCTTTACCTAATTTCCTT
1 CCTGAAATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTT
*
63597 CCTTGAAATTAAGTCTATGCTTGTCTTTACCTAATTTCCTT
1 CC-TGAAATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTT
* * *
63638 CACTGAAATTAAGTCTGTGCTT-ACTTTACTTAA-TTAC--
1 C-CTGAAATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTT
*
63675 CCTG-AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTT
1 CCTGAAATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTT
* * *
63714 CCTTGAAATTAAGTCTGTGCTT-ACTTTACTTAA-TTAC--
1 CC-TGAAATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTT
*
63751 CCTG-AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTT
1 CCTGAAATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTT
63790 CCTTGAAATTAAGTCTGTGC
1 CC-TGAAATTAAGTCTGTGC
63810 CTATCCTTAC
Statistics
Matches: 179, Mismatches: 19, Indels: 28
0.79 0.08 0.12
Matches are distributed among these distances:
35 30 0.17
36 23 0.13
37 9 0.05
39 12 0.07
40 24 0.13
41 80 0.45
42 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.12, T:0.44
Consensus pattern (40 bp):
CCTGAAATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTT
Found at i:63821 original size:117 final size:116
Alignment explanation
Indices: 63525--63784 Score: 352
Period size: 117 Copynumber: 2.3 Consensus size: 116
63515 TTAATTCTAA
* * * *
63525 TGAAATTAAGTCTTTGC-TAATTTACTTAATTACCCTGAATTAAGTATGTGCTTGTCTTTACCTA
1 TGAAATTAAGTCTATGCTTACTTTACCTAATTACCCTGAATTAAGTCTGTGCTTGTCTTTACCTA
* *
63589 ATTTCCTTCCTTGAAATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCAC
66 ATTTCCTTCCTTGAAATTAAGTCTATGCTTGACTTTACCTAATTTAC-TCAC
* * *
63641 TGAAATTAAGTCTGTGCTTACTTTACTTAATTACCCTGAATTAAGTCTATGCTTGTCTTTACCTA
1 TGAAATTAAGTCTATGCTTACTTTACCTAATTACCCTGAATTAAGTCTGTGCTTGTCTTTACCTA
* *
63706 ATTTCCTTCCTTGAAATTAAGTCTGTGCTT-ACTTTACTTAA-TTAC-C-C
66 ATTTCCTTCCTTGAAATTAAGTCTATGCTTGACTTTACCTAATTTACTCAC
*
63753 TG-AATTAAGTCTATGCTTGTCTTTACCTAATT
1 TGAAATTAAGTCTATGCTT-ACTTTACCTAATT
63785 TCCTTCCTTG
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
111 15 0.11
112 14 0.11
113 1 0.01
115 3 0.02
116 25 0.19
117 73 0.56
ACGTcount: A:0.25, C:0.20, G:0.11, T:0.45
Consensus pattern (116 bp):
TGAAATTAAGTCTATGCTTACTTTACCTAATTACCCTGAATTAAGTCTGTGCTTGTCTTTACCTA
ATTTCCTTCCTTGAAATTAAGTCTATGCTTGACTTTACCTAATTTACTCAC
Found at i:63875 original size:38 final size:38
Alignment explanation
Indices: 63822--64128 Score: 211
Period size: 38 Copynumber: 8.0 Consensus size: 38
63812 ATCCTTACCT
*
63822 TTTAACTG-TTTTTACTTAATTACCCTGAATTAAGTCC
1 TTTAACTGCTTTTTACTTAATTACCCTGAATTAAGTTC
* * *
63859 TTCAACTGCTTTTTACTTAATTATCCTGAATTAAGTTA
1 TTTAACTGCTTTTTACTTAATTACCCTGAATTAAGTTC
* * * * *
63897 TTTGAC--CATGTTTACTTAATTTCCCTTAATTAAGCTCC
1 TTTAACTGC-TTTTTACTTAATTACCCTGAATTAAG-TTC
* * * * *
63935 TTTGACTGC-TTTTACCTT-ATTTCCTTGAATGAAGAT-
1 TTTAACTGCTTTTTA-CTTAATTACCCTGAATTAAGTTC
* * *
63971 TTTGACTGACTATGTTTACTTTTCTTAATTGCCCTGAATTAAGAT-
1 TTTAACTG-CT-T-TTTA-----CTTAATTACCCTGAATTAAGTTC
* *
64016 TTTGACTG-TTTTTACTTAATTGCCCTGAATTAAGTTC
1 TTTAACTGCTTTTTACTTAATTACCCTGAATTAAGTTC
* * * *
64053 -TCAACTGCTCCTTCACTTAACTACCCTGAATTAAGTTC
1 TTTAACTGCT-TTTTACTTAATTACCCTGAATTAAGTTC
* *
64091 TTTACCTGC-TTTTACTTAATTACCCAGAATTAAGTTC
1 TTTAACTGCTTTTTACTTAATTACCCTGAATTAAGTTC
64128 T
1 T
64129 CTTACTCTTC
Statistics
Matches: 216, Mismatches: 35, Indels: 38
0.75 0.12 0.13
Matches are distributed among these distances:
36 35 0.16
37 56 0.26
38 78 0.36
39 10 0.05
40 5 0.02
41 4 0.02
42 1 0.00
43 1 0.00
44 3 0.01
45 23 0.11
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.45
Consensus pattern (38 bp):
TTTAACTGCTTTTTACTTAATTACCCTGAATTAAGTTC
Found at i:64225 original size:71 final size:71
Alignment explanation
Indices: 64099--64326 Score: 375
Period size: 71 Copynumber: 3.2 Consensus size: 71
64089 TCTTTACCTG
* * *
64099 CTTTTACTTAATTACCCAGAATTAAGTTCTCTTACTCTTCTTAATTGTCCAACTTAGGACCTTGA
1 CTTTT-CTTAATTACCCTGAATTAAG-ACT-TTACTCTTCTTAATTGCCCAACTTAGGACCTTGA
64164 CTATACTTT
63 CTATACTTT
*
64173 CTTTTCTTAATTACCCTGAATTAAGACTTTACCCTTCTTAATTGCCCAACTTAGGACCTTGACTA
1 CTTTTCTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTGCCCAACTTAGGACCTTGACTA
64238 TACTTT
66 TACTTT
*
64244 CTTTTCTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTGCCCAACTTAGGACCTTGACTG
1 CTTTTCTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTGCCCAACTTAGGACCTTGACTA
64309 TACTTT
66 TACTTT
*
64315 CTTTTGTTAATT
1 CTTTTCTTAATT
64327 CTTTTTAATC
Statistics
Matches: 147, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
71 121 0.82
72 2 0.01
73 19 0.13
74 5 0.03
ACGTcount: A:0.25, C:0.23, G:0.09, T:0.43
Consensus pattern (71 bp):
CTTTTCTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTGCCCAACTTAGGACCTTGACTA
TACTTT
Found at i:64254 original size:40 final size:40
Alignment explanation
Indices: 64207--64326 Score: 109
Period size: 40 Copynumber: 3.2 Consensus size: 40
64197 GACTTTACCC
64207 TTCTTAATTGCCCAACTTAGGACCTTGACTATACTTTCTT
1 TTCTTAATTGCCCAACTTAGGACCTTGACTATACTTTCTT
* *
64247 TTCTTAATTACCCTGAA-TTA--A----GACTTTAC--TC--
1 TTCTTAATTGCCC--AACTTAGGACCTTGACTATACTTTCTT
*
64278 TTCTTAATTGCCCAACTTAGGACCTTGACTGTACTTTCTT
1 TTCTTAATTGCCCAACTTAGGACCTTGACTATACTTTCTT
*
64318 TTGTTAATT
1 TTCTTAATT
64327 CTTTTTAATC
Statistics
Matches: 62, Mismatches: 5, Indels: 26
0.67 0.05 0.28
Matches are distributed among these distances:
29 2 0.03
30 3 0.05
31 12 0.19
32 1 0.02
33 2 0.03
35 7 0.11
36 7 0.11
38 2 0.03
39 1 0.02
40 20 0.32
41 3 0.05
42 2 0.03
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.44
Consensus pattern (40 bp):
TTCTTAATTGCCCAACTTAGGACCTTGACTATACTTTCTT
Found at i:69066 original size:17 final size:18
Alignment explanation
Indices: 69031--69066 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
69021 GAGAATTGAG
69031 AGAACAAGAATATGGAGA
1 AGAACAAGAATATGGAGA
69049 AGAA-AAGAATATGGAGA
1 AGAACAAGAATATGGAGA
69066 A
1 A
69067 TGGGAGAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.58, C:0.03, G:0.28, T:0.11
Consensus pattern (18 bp):
AGAACAAGAATATGGAGA
Found at i:69621 original size:68 final size:69
Alignment explanation
Indices: 69510--69653 Score: 254
Period size: 68 Copynumber: 2.1 Consensus size: 69
69500 ATCATTCAAG
69510 ATCTTTGAGTCTACTGACTCCAATATGTTAAATAAACTTTGTAAAATATCTAACCTTGGCTTGAT
1 ATCTTTGAGTCTAC-GACTCCAATATGTTAAATAAACTTTGTAAAATATCTAACCTTGGCTTGAT
*
69575 GGTTA
65 GATTA
*
69580 ATCTTTGAGTCTAC-AGTCCAATATGTTAAATAAACTTTGTAAAATATCTAACCTTGGCTTGATG
1 ATCTTTGAGTCTACGACTCCAATATGTTAAATAAACTTTGTAAAATATCTAACCTTGGCTTGATG
69644 ATTA
66 ATTA
69648 ATCTTT
1 ATCTTT
69654 CAATCTCGAT
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
68 58 0.81
70 14 0.19
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (69 bp):
ATCTTTGAGTCTACGACTCCAATATGTTAAATAAACTTTGTAAAATATCTAACCTTGGCTTGATG
ATTA
Found at i:91693 original size:19 final size:19
Alignment explanation
Indices: 91666--91704 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
91656 ATGGTGACGA
*
91666 AAAAATAAAGGCAAGATTG
1 AAAAATAAAGACAAGATTG
* *
91685 AAAAGTAAAGACAAGGTTG
1 AAAAATAAAGACAAGATTG
91704 A
1 A
91705 TTAAACAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (19 bp):
AAAAATAAAGACAAGATTG
Found at i:93328 original size:16 final size:16
Alignment explanation
Indices: 93296--93359 Score: 67
Period size: 16 Copynumber: 4.0 Consensus size: 16
93286 GTATGTTTGG
*
93296 TAGGGAGGAAA-GAAA
1 TAGGAAGGAAAGGAAA
93311 TAGGAAGGAAAGGAAA
1 TAGGAAGGAAAGGAAA
* *
93327 TAGCAAGAAAAAGGAAA
1 TAGGAAG-GAAAGGAAA
* *
93344 TAGGGAGGAAGGGAAA
1 TAGGAAGGAAAGGAAA
93360 GGAAGTCACA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
15 10 0.25
16 17 0.43
17 13 0.32
ACGTcount: A:0.55, C:0.02, G:0.38, T:0.06
Consensus pattern (16 bp):
TAGGAAGGAAAGGAAA
Found at i:94141 original size:91 final size:91
Alignment explanation
Indices: 93903--94310 Score: 317
Period size: 91 Copynumber: 4.5 Consensus size: 91
93893 AAGTAAAGTT
* * * * * * *
93903 CAAAAAT-AAACCTTTGAATCTAAAG-GTCAATTTTCAAATCAAAATTAACTCAAGAATGAAAAT
1 CAAAAATCAAATCTTTGAATC-AAAGACTTAATTTTCAAATTAAGATTAACTCAA-AA--AGATT
* * * *
93966 CATAAATCAATTTTTAAGTTAATCTTAATT
62 CAAAAATCAATTTCTAAGTTAATTTTAATC
* * * * *
93996 CAAAAA-CAAACCCTTAAATCAAAG-TTTAAATTTTCAAATTAACATTAACTCAAAAAGATTCAA
1 CAAAAATCAAATCTTTGAATCAAAGACTT-AATTTTCAAATTAAGATTAACTCAAAAAGATTCAA
*
94059 AAATCAATTTCCAAGTTAATTTTAATC
65 AAATCAATTTCTAAGTTAATTTTAATC
* * * *
94086 CAAAAATCAAATCTTTGAATCAAAGACTTGATTTTCAAATTAAGATTAACCCAAAAAGATTTAAT
1 CAAAAATCAAATCTTTGAATCAAAGACTTAATTTTCAAATTAAGATTAACTCAAAAAGATTCAAA
* *
94151 GATCAAGTTCTAAGTTAATTTTAATC
66 AATCAATTTCTAAGTTAATTTTAATC
* * * * * * * *
94177 CAAAAACCAAGT-TTTGAATTCAAAGAGTCCATTTTTTAAATCAAGATTAACTTAAAAAGATTCA
1 CAAAAATCAAATCTTTGAA-TCAAAGACT-TAATTTTCAAATTAAGATTAACTCAAAAAGATTCA
* * * * * *
94241 CAAGTCATTTTCTAAGTCAATTTCAATT
64 AAAATCAATTTCTAAGTTAATTTTAATC
* * * **
94269 CAGAAATC-AACCCTT-AAGTCAAAGTTTTAATTTTCAAATTAA
1 CAAAAATCAAATCTTTGAA-TCAAAGACTTAATTTTCAAATTAA
94311 AACTAACATA
Statistics
Matches: 251, Mismatches: 57, Indels: 17
0.77 0.18 0.05
Matches are distributed among these distances:
90 51 0.20
91 97 0.39
92 63 0.25
93 40 0.16
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (91 bp):
CAAAAATCAAATCTTTGAATCAAAGACTTAATTTTCAAATTAAGATTAACTCAAAAAGATTCAAA
AATCAATTTCTAAGTTAATTTTAATC
Done.