Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019349.1 Corchorus olitorius cultivar O-4 contig19382, 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: 146902
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:7042 original size:21 final size:21
Alignment explanation
Indices: 7005--7058 Score: 90
Period size: 21 Copynumber: 2.5 Consensus size: 21
6995 ATAAAGCAAT
7005 AAAACAACAGCATATCCCTAATA
1 AAAACAACA--ATATCCCTAATA
7028 AAAACAACAATATCCCTAATA
1 AAAACAACAATATCCCTAATA
7049 AAAACAACAA
1 AAAACAACAA
7059 AATTAGACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 22 0.71
23 9 0.29
ACGTcount: A:0.59, C:0.24, G:0.02, T:0.15
Consensus pattern (21 bp):
AAAACAACAATATCCCTAATA
Found at i:28365 original size:2 final size:2
Alignment explanation
Indices: 28358--28386 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
28348 GACATCTGAA
28358 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28387 GACCAATTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33286 original size:19 final size:19
Alignment explanation
Indices: 33262--33300 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
33252 GTCTGCCAGG
33262 GACAAAGCTGCTTTAGGTT
1 GACAAAGCTGCTTTAGGTT
33281 GACAAAGCTGCTTTAGGTT
1 GACAAAGCTGCTTTAGGTT
33300 G
1 G
33301 GTGAGACGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (19 bp):
GACAAAGCTGCTTTAGGTT
Found at i:43300 original size:285 final size:285
Alignment explanation
Indices: 42790--43417 Score: 1220
Period size: 285 Copynumber: 2.2 Consensus size: 285
42780 ACTTTTAACA
42790 CATATTCACAACGAAACAGGCTTTCTTCATTCTGGTTTTTGCGCATGTTTGAAAGAGTGATGTAC
1 CATATTCACAACGAAACAGGCTTTCTTCATTCTGGTTTTTGCGCATGTTTGAAAGAGTGATGTAC
42855 AGTTGAAAAAGGGCATGCGCAGACACAACATATTTCAAACAGTTAACAAAACCGAAAAGAGTGCC
66 AGTTGAAAAAGGGCATGCGCAGACACAACATATTTCAAACAGTTAACAAAACCGAAAAGAGTGCC
*
42920 ACAATTATAGGAAAGGAAATTTTCCAGGGAAAGCTTAAGTAATGCCATAATAAACAAACATGTCA
131 ACAATTATAGGAAAGGAAATTTTCCAGGGAAAGCTTAAGTAATGCCATAAAAAACAAACATGTCA
42985 AAATGGAGATAAAAGTGAAAGCAAATAACCAATCATGACCAGAAAACATGGGCAAAATTCAATTA
196 AAATGGAGATAAAAGTGAAAGCAAATAACCAATCATGACCAGAAAACATGGGCAAAATTCAATTA
43050 ACAACCATGGGAAGGCCCGACCTTT
261 ACAACCATGGGAAGGCCCGACCTTT
43075 CATATTCACAACGAAACAGGCTTTCTTCATTCTGGTTTTTGCGCATGTTTGAAAGAGTGATGTAC
1 CATATTCACAACGAAACAGGCTTTCTTCATTCTGGTTTTTGCGCATGTTTGAAAGAGTGATGTAC
**
43140 AGTTGACCAAGGGCATGCGCAGACACAACATATTTCAAACAGTTAACAAAACCGAAAAGAGTGCC
66 AGTTGAAAAAGGGCATGCGCAGACACAACATATTTCAAACAGTTAACAAAACCGAAAAGAGTGCC
43205 ACAATTATAGGAAAGGAAATTTTCCAGGGAAAGCTTAAGTAATGCCATAAAAAACAAACATGTCA
131 ACAATTATAGGAAAGGAAATTTTCCAGGGAAAGCTTAAGTAATGCCATAAAAAACAAACATGTCA
*
43270 AAATGGAGATAAAAGTGAAAGCAAATAACCAATCATGACCAGCAAACATGGGCAAAATTCAATTA
196 AAATGGAGATAAAAGTGAAAGCAAATAACCAATCATGACCAGAAAACATGGGCAAAATTCAATTA
43335 ACAACCATGGGAAGGCCCGACCTTT
261 ACAACCATGGGAAGGCCCGACCTTT
43360 CATATTCACAACGAAACAGGCTTTCTTCATTCTGGTTTTTGCGCATGTTTGAAAGAGT
1 CATATTCACAACGAAACAGGCTTTCTTCATTCTGGTTTTTGCGCATGTTTGAAAGAGT
43418 AGTCCCCACT
Statistics
Matches: 339, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
285 339 1.00
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.23
Consensus pattern (285 bp):
CATATTCACAACGAAACAGGCTTTCTTCATTCTGGTTTTTGCGCATGTTTGAAAGAGTGATGTAC
AGTTGAAAAAGGGCATGCGCAGACACAACATATTTCAAACAGTTAACAAAACCGAAAAGAGTGCC
ACAATTATAGGAAAGGAAATTTTCCAGGGAAAGCTTAAGTAATGCCATAAAAAACAAACATGTCA
AAATGGAGATAAAAGTGAAAGCAAATAACCAATCATGACCAGAAAACATGGGCAAAATTCAATTA
ACAACCATGGGAAGGCCCGACCTTT
Found at i:44474 original size:3 final size:3
Alignment explanation
Indices: 44468--44497 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
44458 TAATAATGAT
44468 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
44498 TATGAACACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:57499 original size:33 final size:30
Alignment explanation
Indices: 57418--57515 Score: 160
Period size: 30 Copynumber: 3.2 Consensus size: 30
57408 TTGCAGGTGG
57418 AGATTTCAACTTCCTTCTTTTAGAACTTGA
1 AGATTTCAACTTCCTTCTTTTAGAACTTGA
57448 AGATTTCAACTTCCTTCTTTTAGAACTTGA
1 AGATTTCAACTTCCTTCTTTTAGAACTTGA
*
57478 AGATTTCAAGTGCTTCCTTCTTTTAGACCTTGA
1 AGATTTCAA---CTTCCTTCTTTTAGAACTTGA
57511 AGATT
1 AGATT
57516 CCTGATTTTC
Statistics
Matches: 64, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
30 39 0.61
33 25 0.39
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.43
Consensus pattern (30 bp):
AGATTTCAACTTCCTTCTTTTAGAACTTGA
Found at i:59894 original size:42 final size:43
Alignment explanation
Indices: 59839--59933 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 43
59829 AGTGCATTAT
*
59839 CTAA-ATTATA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTATACCTCCATCTCTAGATAATTCATCAAAATAAAG
*
59880 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTATA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
59925 CTAATATTA
1 CTAATATTA
59934 ATTGTTGCTT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
41 4 0.09
42 5 0.11
45 38 0.81
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.34
Consensus pattern (43 bp):
CTAATATTATACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:60924 original size:12 final size:12
Alignment explanation
Indices: 60895--60930 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
60885 AATTTTTTAA
60895 AAAAAATTATTT
1 AAAAAATTATTT
60907 ---AAATTATTT
1 AAAAAATTATTT
60916 AAAAAATTATTT
1 AAAAAATTATTT
60928 AAA
1 AAA
60931 TTTGAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
9 9 0.43
12 12 0.57
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
AAAAAATTATTT
Found at i:68270 original size:41 final size:41
Alignment explanation
Indices: 68213--68292 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 41
68203 AAACATCCTT
68213 CTTTTTCGGTAATTGAAGTTATTAGGAT-TCGTGTTAGGTCA
1 CTTTTTCGGTAATTGAAGTTATTAGGATCT-GTGTTAGGTCA
68254 CTTTTTCGGTAATTGAAGTTATTAGGATCTGTGTTAGGT
1 CTTTTTCGGTAATTGAAGTTATTAGGATCTGTGTTAGGT
68293 AACTGAAACT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
41 37 0.97
42 1 0.03
ACGTcount: A:0.21, C:0.09, G:0.25, T:0.45
Consensus pattern (41 bp):
CTTTTTCGGTAATTGAAGTTATTAGGATCTGTGTTAGGTCA
Found at i:69653 original size:5 final size:5
Alignment explanation
Indices: 69643--69670 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
69633 AGACAAAAAT
69643 CTAAA CTAAA CTAAA CTAAA CTAAA CTA
1 CTAAA CTAAA CTAAA CTAAA CTAAA CTA
69671 TCCAAAGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.57, C:0.21, G:0.00, T:0.21
Consensus pattern (5 bp):
CTAAA
Found at i:76857 original size:13 final size:13
Alignment explanation
Indices: 76839--76872 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
76829 TCCCTAGCAG
76839 CATTGGATATTTT
1 CATTGGATATTTT
76852 CATTGGATATTTT
1 CATTGGATATTTT
*
76865 CAATGGAT
1 CATTGGAT
76873 GCTTAACAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.26, C:0.09, G:0.18, T:0.47
Consensus pattern (13 bp):
CATTGGATATTTT
Found at i:87176 original size:21 final size:19
Alignment explanation
Indices: 87151--87208 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
87141 GCTGCTCTAA
*
87151 TAATCTCATCTGTATAGTACC
1 TAATCTCATCTGTACAGT--C
* *
87172 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAGTC
87191 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
87209 TGTTAAACAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:87502 original size:17 final size:17
Alignment explanation
Indices: 87480--87523 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
87470 ATTTAATTTA
87480 TGACTTTCAATATCTAG
1 TGACTTTCAATATCTAG
87497 TGACTTTCAATATCTAG
1 TGACTTTCAATATCTAG
87514 TGACTTTCAA
1 TGACTTTCAA
87524 CATAATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.41
Consensus pattern (17 bp):
TGACTTTCAATATCTAG
Found at i:91194 original size:22 final size:22
Alignment explanation
Indices: 91139--91288 Score: 94
Period size: 22 Copynumber: 6.9 Consensus size: 22
91129 TTGACTATTT
*
91139 TTATGAAATTTTGATAACTACC
1 TTATGAAATTTTGATAACCACC
* * **
91161 CTAT-TAATTTTGATAACCATG
1 TTATGAAATTTTGATAACCACC
**
91182 TTATGAAATTTTGATAATTTA-C
1 TTATGAAATTTTGATAA-CCACC
* * *
91204 TTATGAAATTGTGATAAACTCC
1 TTATGAAATTTTGATAACCACC
* * *
91226 ATATGAAACTTTGATAACCTA-A
1 TTATGAAATTTTGATAACC-ACC
* *
91248 TTATGAAATTTTAATAAACCTTCC
1 TTATGAAATTTTGAT-AACC-ACC
91272 -TATGAAATTTTG-TAACC
1 TTATGAAATTTTGATAACC
91289 TTCCTATGAT
Statistics
Matches: 96, Mismatches: 26, Indels: 13
0.71 0.19 0.10
Matches are distributed among these distances:
21 20 0.21
22 59 0.61
23 17 0.18
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (22 bp):
TTATGAAATTTTGATAACCACC
Found at i:91239 original size:44 final size:45
Alignment explanation
Indices: 91183--91289 Score: 130
Period size: 44 Copynumber: 2.4 Consensus size: 45
91173 ATAACCATGT
** * *
91183 TATGAAATTTTGATAATTTACTTATGAAATTGTGATAAA-C-TCC
1 TATGAAATTTTGATAACCTAATTATGAAATTGTAATAAACCTTCC
* *
91226 ATATGAAACTTTGATAACCTAATTATGAAATTTTAATAAACCTTCC
1 -TATGAAATTTTGATAACCTAATTATGAAATTGTAATAAACCTTCC
91272 TATGAAATTTTG-TAACCT
1 TATGAAATTTTGATAACCT
91290 TCCTATGATT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
44 39 0.72
45 12 0.22
46 3 0.06
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.40
Consensus pattern (45 bp):
TATGAAATTTTGATAACCTAATTATGAAATTGTAATAAACCTTCC
Found at i:91253 original size:66 final size:65
Alignment explanation
Indices: 91139--91264 Score: 157
Period size: 66 Copynumber: 1.9 Consensus size: 65
91129 TTGACTATTT
* * * * * *
91139 TTATGAAATTTTGATAACTACCCTATTAATTTTGATAACCATGTTATGAAATTTTGATAATTTAC
1 TTATGAAATTGTGATAACTACCATATAAACTTTGATAACCATATTATGAAATTTTAATAATTTAC
91204 TTATGAAATTGTGATAAACT-CCATATGAAACTTTGATAACC-TAATTATGAAATTTTAATAA
1 TTATGAAATTGTGAT-AACTACCATAT-AAACTTTGATAACCAT-ATTATGAAATTTTAATAA
91265 ACCTTCCTAT
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
65 20 0.38
66 32 0.62
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (65 bp):
TTATGAAATTGTGATAACTACCATATAAACTTTGATAACCATATTATGAAATTTTAATAATTTAC
Found at i:91308 original size:21 final size:21
Alignment explanation
Indices: 91140--91310 Score: 73
Period size: 22 Copynumber: 7.9 Consensus size: 21
91130 TGACTATTTT
*
91140 TATGAAATTTTGATAA-CTACCC
1 TATGAAATTTT-ATAACCT-TCC
* * **
91162 TAT-TAATTTTGATAACCATGT
1 TATGAAATTTT-ATAACCTTCC
* *
91183 TATGAAATTTTGATAA-TTTACT
1 TATGAAATTTT-ATAACCTT-CC
* *
91205 TATGAAATTGTGATAAAC-TCC
1 TATGAAATT-TTATAACCTTCC
* ***
91226 ATATGAAACTTTGATAACCTAAT
1 -TATGAAA-TTTTATAACCTTCC
91249 TATGAAATTTTAATAAACCTTCC
1 TATGAAATTTT-AT-AACCTTCC
*
91272 TATGAAATTTTGTAACCTTCC
1 TATGAAATTTTATAACCTTCC
*
91293 TATG-ATTTGTTATAACCT
1 TATGAAATT-TTATAACCT
91311 CTTTGTGAGA
Statistics
Matches: 115, Mismatches: 23, Indels: 23
0.71 0.14 0.14
Matches are distributed among these distances:
20 3 0.03
21 39 0.34
22 54 0.47
23 19 0.17
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (21 bp):
TATGAAATTTTATAACCTTCC
Found at i:108688 original size:27 final size:27
Alignment explanation
Indices: 108650--108707 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
108640 TTTGCTACTC
* * * **
108650 AACTTTTCCTACTTCTTTACATTACCA
1 AACTGTTCCTACTCCTTAACAACACCA
108677 AACTGTTCCTACTCCTTAACAACACCA
1 AACTGTTCCTACTCCTTAACAACACCA
108704 AACT
1 AACT
108708 ACATGAAACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.33, G:0.02, T:0.34
Consensus pattern (27 bp):
AACTGTTCCTACTCCTTAACAACACCA
Found at i:115111 original size:42 final size:44
Alignment explanation
Indices: 115060--115153 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 44
115050 AGTGCATTAT
*
115060 CTAA-ATTCTACT-CT-ATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCCTCATCTCTAGATAATTCATCAAAATAAAG
*
115101 CTGATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTACTCCT-CATCTCTAGATAATTCATCAAAATAAAG
115146 CTAATATT
1 CTAATATT
115154 AATTGTTGCT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 3 0.07
42 8 0.17
43 2 0.04
45 33 0.72
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.35
Consensus pattern (44 bp):
CTAATATTCTACTCCTCATCTCTAGATAATTCATCAAAATAAAG
Found at i:116756 original size:31 final size:31
Alignment explanation
Indices: 116699--116757 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
116689 CAATTGAAAA
*
116699 TTTTACAAGTTCAAGGGCAAATTTGTCTCTT
1 TTTTACAAGTTCAAAGGCAAATTTGTCTCTT
* *
116730 TTTTACAATTTCAAATGCTAAA-TTGTCT
1 TTTTACAAGTTCAAAGGC-AAATTTGTCT
116758 ATTAAGCCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 21 0.88
32 3 0.12
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (31 bp):
TTTTACAAGTTCAAAGGCAAATTTGTCTCTT
Found at i:138320 original size:42 final size:42
Alignment explanation
Indices: 138264--138354 Score: 157
Period size: 42 Copynumber: 2.2 Consensus size: 42
138254 AGTGCATTAT
*
138264 CTAA-ATTCTACTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCCATCTCTAGATAATTCATCAAAATAAAG
*
138305 CTAATATTCTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTACTCCATCTCTAGATAATTCATCAAAATAAAG
138347 CTAATATT
1 CTAATATT
138355 AATTGTTGCT
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 4 0.09
42 43 0.91
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (42 bp):
CTAATATTCTACTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:139131 original size:18 final size:17
Alignment explanation
Indices: 139108--139156 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
139098 AAATAATATA
*
139108 TAGTATATATATTAGTAG
1 TAGTAT-TATATTAGCAG
139126 TAGTATTACTATTAGCAG
1 TAGTATTA-TATTAGCAG
*
139144 TATTATTATATTA
1 TAGTATTATATTA
139157 ATATTATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 7 0.25
18 21 0.75
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.47
Consensus pattern (17 bp):
TAGTATTATATTAGCAG
Found at i:144499 original size:14 final size:14
Alignment explanation
Indices: 144480--144509 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
144470 AAACGCAGTG
144480 ACTTCTATTTATGA
1 ACTTCTATTTATGA
144494 ACTTCTATTTATGA
1 ACTTCTATTTATGA
144508 AC
1 AC
144510 GGTGTATGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.17, G:0.07, T:0.47
Consensus pattern (14 bp):
ACTTCTATTTATGA
Found at i:144855 original size:105 final size:103
Alignment explanation
Indices: 144668--144883 Score: 405
Period size: 105 Copynumber: 2.1 Consensus size: 103
144658 GATATATATA
*
144668 CATTATTTAGCCTTCTTTTCCATGTTATTATATTGCTGACTTATTCTTCATGAACCATAAGGTTG
1 CATTTTTTAGCCTTCTTTTCCATGTTATTATATTGCTGACTTATTCTTCATGAACCATAAGGTTG
144733 GGTTGCTATCATTTTTTTTTTTGGATAAATGGGTTGCTAT
66 GGTTGCTATCA--TTTTTTTTTGGATAAATGGGTTGCTAT
144773 CATTTTTTAGCCTTCTTTTCCATGTTATTATATTGCTGACTTATTCTTCATGAACCATAAGGTTG
1 CATTTTTTAGCCTTCTTTTCCATGTTATTATATTGCTGACTTATTCTTCATGAACCATAAGGTTG
144838 GGTTGCTATCATTTTTTTTTGGATAAATGGGTTGCTAT
66 GGTTGCTATCATTTTTTTTTGGATAAATGGGTTGCTAT
144876 CATTTTTT
1 CATTTTTT
144884 GTTTTTAATT
Statistics
Matches: 110, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
103 35 0.32
105 75 0.68
ACGTcount: A:0.20, C:0.14, G:0.16, T:0.50
Consensus pattern (103 bp):
CATTTTTTAGCCTTCTTTTCCATGTTATTATATTGCTGACTTATTCTTCATGAACCATAAGGTTG
GGTTGCTATCATTTTTTTTTGGATAAATGGGTTGCTAT
Found at i:145502 original size:62 final size:62
Alignment explanation
Indices: 145427--145553 Score: 245
Period size: 62 Copynumber: 2.0 Consensus size: 62
145417 AACACACTTA
*
145427 ATCATAAATATAAAAATAGTAAATCACAAAAAAGGCAGCAGGAAAAGTAAGGGAGAAAATTC
1 ATCATAAATATAAAAATAGTAAATCACAAAAAAGGCAGCAGGAAAAGTAAAGGAGAAAATTC
145489 ATCATAAATATAAAAATAGTAAATCACAAAAAAGGCAGCAGGAAAAGTAAAGGAGAAAATTC
1 ATCATAAATATAAAAATAGTAAATCACAAAAAAGGCAGCAGGAAAAGTAAAGGAGAAAATTC
145551 ATC
1 ATC
145554 GAGGGCCTTT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.57, C:0.10, G:0.17, T:0.17
Consensus pattern (62 bp):
ATCATAAATATAAAAATAGTAAATCACAAAAAAGGCAGCAGGAAAAGTAAAGGAGAAAATTC
Found at i:145969 original size:292 final size:293
Alignment explanation
Indices: 145492--146240 Score: 1136
Period size: 292 Copynumber: 2.5 Consensus size: 293
145482 AAAATTCATC
*
145492 ATAAATATAAAAATAGTAAATCACAAAAAA-GGCAGCAGGAAAAGTAAAGGAGAAAATTCATCGA
1 ATAAATATAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGT--A--AGAAAATTCATCGA
* * * * *
145556 GGGCCTTTTTAGTCACCTGAAAAGTCAGAAAAGACAAAGACAAAAAAGTCAAAAGGAAGCACCAC
62 AGGCCTTTTTAGTCACCCGAAAAGTGAGAAAAGACAAA-AAAAAAAAGCCAAAAGGAAGCACCAC
*
145621 ATTAATCCTCAATTTGGCCTTTTAGGTAATTTCCATAGCAATTGTTAAATTAATGAACTCGGGTA
126 ATTAATCCTCAATTTGGCCTTTTAGGTAATTTCCAAAGCAATTGTTAAATTAATGAACTCGGGTA
* *
145686 GATACATTTATAGCACCAATCCTTTTGAATTCCGGCAGAGGAGTTGAACCGGTAAATCCTAATAT
191 GATACATTTATAGCACCAATCCTTTGGAATTCCGGCAAAGGAGTTGAACCGGTAAATCCTAATAT
145751 CCACACACAATCAATATC-TAATTAAAACACACTTAATA
256 CCACACACAATCAATA-CATAATTAAAACACACTTAATA
**
145789 ATATCTATAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGT-AGAAAATTCATCGAAGGC
1 ATAAATATAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGTAAGAAAATTCATCGAAGGC
* *
145853 CTTTTTAGTCACCCAAAAAGTGAGAAAAGACAAAAAAAAAAAGGCAAAAGGAAGCACCACATTAA
66 CTTTTTAGTCACCCGAAAAGTGAGAAAAGACAAAAAAAAAAAGCCAAAAGGAAGCACCACATTAA
*
145918 TTCTCAATTTGGCCTTTTAGGTAATTTCCAAAGCAATTGTTAAATTAATGAACTCGGGTAGATAC
131 TCCTCAATTTGGCCTTTTAGGTAATTTCCAAAGCAATTGTTAAATTAATGAACTCGGGTAGATAC
*
145983 ATTTATAGCACCAATCCTTTGGAATTCCGGCAAAGGAGTTGAATCGGTAAATCCTAATATCCACA
196 ATTTATAGCACCAATCCTTTGGAATTCCGGCAAAGGAGTTGAACCGGTAAATCCTAATATCCACA
* *
146048 CACAATTAATACATAATTAAAACACACTTAATC
261 CACAATCAATACATAATTAAAACACACTTAATA
* * *
146081 ATAAATACAAAAATAGTAAATTACAAAAAAGGGCAGGAGGAAAAGTAAGGGAGGAAATTTATC-A
1 ATAAATATAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGTAA--GA--AAATTCATCGA
* *
146145 AGGGCCTTTTTAGTCACCCGAAAAGTGAGAAAAGAC---CAAAAAAAGCCAAAAGGAGGCACCAC
62 A-GGCCTTTTTAGTCACCCGAAAAGTGAGAAAAGACAAAAAAAAAAAGCCAAAAGGAAGCACCAC
*
146207 ATTAATCCTCAATTTGGCC-TTTAAGTAATTTCCA
126 ATTAATCCTCAATTTGGCCTTTTAGGTAATTTCCA
146241 TAGTCACTAA
Statistics
Matches: 417, Mismatches: 27, Indels: 20
0.90 0.06 0.04
Matches are distributed among these distances:
291 1 0.00
292 225 0.54
293 63 0.15
294 41 0.10
295 2 0.00
296 2 0.00
297 68 0.16
298 15 0.04
ACGTcount: A:0.44, C:0.17, G:0.16, T:0.23
Consensus pattern (293 bp):
ATAAATATAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGTAAGAAAATTCATCGAAGGC
CTTTTTAGTCACCCGAAAAGTGAGAAAAGACAAAAAAAAAAAGCCAAAAGGAAGCACCACATTAA
TCCTCAATTTGGCCTTTTAGGTAATTTCCAAAGCAATTGTTAAATTAATGAACTCGGGTAGATAC
ATTTATAGCACCAATCCTTTGGAATTCCGGCAAAGGAGTTGAACCGGTAAATCCTAATATCCACA
CACAATCAATACATAATTAAAACACACTTAATA
Found at i:146428 original size:19 final size:18
Alignment explanation
Indices: 146395--146430 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
146385 TTGAAATTAT
*
146395 TCTTCAATGGTCTTCAAA
1 TCTTCAATAGTCTTCAAA
146413 TCTTCAAATAGTCTTCAA
1 TCTTC-AATAGTCTTCAA
146431 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (18 bp):
TCTTCAATAGTCTTCAAA
Done.