Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold764
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: 64012
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Found at i:820 original size:32 final size:32
Alignment explanation
Indices: 784--850 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
774 AATAGCTACG
784 AACTACTTTGATATGATAGAAAGCTAAAATCA
1 AACTACTTTGATATGATAGAAAGCTAAAATCA
816 AACTACTTTGATATGATAGAAAGCTAAAATCA
1 AACTACTTTGATATGATAGAAAGCTAAAATCA
848 AAC
1 AAC
851 GATGAAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.48, C:0.13, G:0.12, T:0.27
Consensus pattern (32 bp):
AACTACTTTGATATGATAGAAAGCTAAAATCA
Found at i:1427 original size:20 final size:20
Alignment explanation
Indices: 1384--1427 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1374 TTTAAATTTT
* * * *
1384 TTAAAAACAAATAACAGATT
1 TTAAAAACAAAGAAAAAATA
1404 TTAAAAACAAAGAAAAAATA
1 TTAAAAACAAAGAAAAAATA
1424 TTAA
1 TTAA
1428 CTAAACAGAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.66, C:0.07, G:0.05, T:0.23
Consensus pattern (20 bp):
TTAAAAACAAAGAAAAAATA
Found at i:4938 original size:12 final size:13
Alignment explanation
Indices: 4921--4955 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
4911 CTTTGTTCCA
4921 TTTCTTTTTTT-T
1 TTTCTTTTTTTCT
4933 TTTCTTTTTTTCT
1 TTTCTTTTTTTCT
*
4946 TTTATTTTTT
1 TTTCTTTTTT
4956 ACCAAAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.89
Consensus pattern (13 bp):
TTTCTTTTTTTCT
Found at i:6600 original size:94 final size:94
Alignment explanation
Indices: 6391--6604 Score: 234
Period size: 94 Copynumber: 2.3 Consensus size: 94
6381 TGTAGTATTA
* * * * * *
6391 TCAAACGCATGCGACGGGATTTACATCAAAGTATAATCTAATAAATAAGTGATTTTTTTTTATGA
1 TCAAACGCATGCGACGGGATTTACATCAAAATATAATCCAACAAATAAGTAACTTTTTTTAATGA
* * * *
6456 ATTTTTTGAAAAACAATGATTGTATTTTG
66 ATTTCTTGAAAAAAAATGATGGTAATTTG
** * * * * *
6485 TCAAATACGTGTGACGAGATTTATATTAAAATATAATCCAACAAATAAGTAACTTTTTTTAATGA
1 TCAAACGCATGCGACGGGATTTACATCAAAATATAATCCAACAAATAAGTAACTTTTTTTAATGA
6550 ATTTCTT-AAAAAAAAT-ATGGGTGAATTTG
66 ATTTCTTGAAAAAAAATGAT-GGT-AATTTG
*
6579 TCAAACGCATGCGGCGGGATTTACAT
1 TCAAACGCATGCGACGGGATTTACAT
6605 AAGACTTCTT
Statistics
Matches: 94, Mismatches: 24, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
92 2 0.02
93 10 0.11
94 82 0.87
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (94 bp):
TCAAACGCATGCGACGGGATTTACATCAAAATATAATCCAACAAATAAGTAACTTTTTTTAATGA
ATTTCTTGAAAAAAAATGATGGTAATTTG
Found at i:7019 original size:52 final size:52
Alignment explanation
Indices: 6963--7061 Score: 189
Period size: 52 Copynumber: 1.9 Consensus size: 52
6953 AAAATAAAAA
6963 ATATTTTTCATATTATGGATATTAATAGACATAAATTATATAATAGATTAAT
1 ATATTTTTCATATTATGGATATTAATAGACATAAATTATATAATAGATTAAT
*
7015 ATATTTTTCATATTATGGATATTAATAGACATAAGTTATATAATAGA
1 ATATTTTTCATATTATGGATATTAATAGACATAAATTATATAATAGA
7062 ATATAAATAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.43
Consensus pattern (52 bp):
ATATTTTTCATATTATGGATATTAATAGACATAAATTATATAATAGATTAAT
Found at i:8392 original size:13 final size:14
Alignment explanation
Indices: 8374--8404 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
8364 CAACAATTTT
8374 AATAAA-ATGTATA
1 AATAAAGATGTATA
8387 AATAAAGATGTATA
1 AATAAAGATGTATA
8401 AATA
1 AATA
8405 TATAGACCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (14 bp):
AATAAAGATGTATA
Found at i:9325 original size:2 final size:2
Alignment explanation
Indices: 9313--9352 Score: 57
Period size: 2 Copynumber: 20.5 Consensus size: 2
9303 ATTAAAAATA
9313 AT AT A- AT AT AT AT A- AGT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A
9353 AGAAAACCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 2 0.06
2 32 0.91
3 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:10188 original size:191 final size:190
Alignment explanation
Indices: 9839--10394 Score: 708
Period size: 191 Copynumber: 2.9 Consensus size: 190
9829 TGCGATAAGC
* * *
9839 TTTATATTAAAATATAATTTAATAAATAAGTGATCATTTTTAATGAAATTTTGAAAAAAATAATA
1 TTTATATTAAAGTATAATTCAATAAATGAGTGATCATTTTTAATGAAATTTTG-AAAAAA-AATA
** * * * * *
9904 TAATTACTTTTTATCGAACATATGAAGTGAGGTTTATATTAAAGTATAATTTAAT-AATAAGT-G
64 TGGTTACCTTTTATCAAACGTATGAGGTGGGGTTTATATTAAAGTATAATTTAATAAATAAGTAG
* * * *
9967 ATCCTTTTTAATGAAATTTTAAAAAAAAATATGACTGCCTTTTATCAGATGTGTACGGCAAGT
129 -TCCTTTTTAATGAAATTTTGAAAAAAAATATGACTGCCTTTTATCAGACGCGTACGACAAGT
* *
10030 TTTATATTAAAGTATAATTCAATAAATGAGTGATCATTTTTAATAAAATTTTGAAAAACAATATG
1 TTTATATTAAAGTATAATTCAATAAATGAGTGATCATTTTTAATGAAATTTTGAAAAAAAATATG
*
10095 GTTACCTTTTATCAAACGTATGAGGTGGGGTTTATATTAAAGTATAATTTAATAAATGAGTAGT-
66 GTTACCTTTTATCAAACGTATGAGGTGGGGTTTATATTAAAGTATAATTTAATAAATAAGTAGTC
* * * **
10159 CTTTTCTAATGAAATTTTGGAAGAAAAATAT-AGCTGTCTTTTATTAGACGCGTGTGACAAGT
131 CTTTT-TAATGAAATTTT-GAAAAAAAATATGA-CTGCCTTTTATCAGACGCGTACGACAAGT
* *
10221 TTTATAATAAAGTATAATTCAATAAATGAGTGATCATTTTTAATGAAATTTTAAAAAAAAATATG
1 TTTATATTAAAGTATAATTCAATAAATGAGTGATCATTTTTAATGAAATTTTGAAAAAAAATATG
* ** * * * * *
10286 GATGTCTTTTATGAAACGTATGAGATGGGGTTTATATTAAAATATAATTTAATAAATAAATAATC
66 GTTACCTTTTATCAAACGTATGAGGTGGGGTTTATATTAAAGTATAATTTAATAAATAAGTAGTC
* *
10351 CTTTTTAATG-AACTTTGAAAAAAAATTATGACTACCTTTTATCA
131 CTTTTTAATGAAATTTTGAAAAAAAA-TATGACTGCCTTTTATCA
10395 AAGATATGAG
Statistics
Matches: 317, Mismatches: 40, Indels: 17
0.85 0.11 0.05
Matches are distributed among these distances:
189 65 0.21
190 43 0.14
191 204 0.64
192 5 0.02
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (190 bp):
TTTATATTAAAGTATAATTCAATAAATGAGTGATCATTTTTAATGAAATTTTGAAAAAAAATATG
GTTACCTTTTATCAAACGTATGAGGTGGGGTTTATATTAAAGTATAATTTAATAAATAAGTAGTC
CTTTTTAATGAAATTTTGAAAAAAAATATGACTGCCTTTTATCAGACGCGTACGACAAGT
Found at i:10403 original size:95 final size:95
Alignment explanation
Indices: 9839--10449 Score: 498
Period size: 95 Copynumber: 6.4 Consensus size: 95
9829 TGCGATAAGC
* *
9839 TTTATATTAAAATATAATTTAATAAATAAGTGATCATTTTTAATGAAATTTTGAAAAAAATAATA
1 TTTATATTAAAGTATAATTTAATAAATAAGTGATCCTTTTTAATG-AATTTTGAAAAAAA-AATA
* * * * * *
9904 TAATTACTTTTTATCGAACATATGA-AGTGAGG
64 TGACTACCTTTTATCAAAGATATGAGA-TGGGG
9936 TTTATATTAAAGTATAATTTAAT-AATAAGTGATCCTTTTTAATGAAATTTT-AAAAAAAAATAT
1 TTTATATTAAAGTATAATTTAATAAATAAGTGATCCTTTTTAATG-AATTTTGAAAAAAAAATAT
* * * * *
9999 GACTGCCTTTTATC--AGATGTG-TACGGCAAGT
65 GACTACCTTTTATCAAAGATATGAGATGG---GG
* * * * *
10030 TTTATATTAAAGTATAATTCAATAAATGAGTGATCATTTTTAATAAAATTTTG-AAAAACAATAT
1 TTTATATTAAAGTATAATTTAATAAATAAGTGATCCTTTTTAAT-GAATTTTGAAAAAAAAATAT
** *
10094 GGTTACCTTTTATCAAACG-TATGAGGTGGGG
65 GACTACCTTTTATCAAA-GATATGAGATGGGG
* * *
10125 TTTATATTAAAGTATAATTTAATAAATGAGT-AGT-CTTTTCTAATGAAATTTTGGAAGAAAAAT
1 TTTATATTAAAGTATAATTTAATAAATAAGTGA-TCCTTTT-TAATG-AATTTTGAAAAAAAAAT
** * * * * * * *
10188 AT-AGCTGTCTTTTATTAGACGCGTGTGACA--AGT
63 ATGA-CTACCTTTTATCA-AAG-ATATGAGATGGGG
* * * *
10221 TTTATAATAAAGTATAATTCAATAAATGAGTGATCATTTTTAATGAAATTTT-AAAAAAAAATAT
1 TTTATATTAAAGTATAATTTAATAAATAAGTGATCCTTTTTAATG-AATTTTGAAAAAAAAATAT
** *
10285 GGA-TGTCTTTTATGAAACG-TATGAGATGGGG
65 -GACTACCTTTTATCAAA-GATATGAGATGGGG
* * * * *
10316 TTTATATTAAAATATAATTTAATAAATAAATAATCCTTTTTAATGAACTTTGAAAAAAAATTATG
1 TTTATATTAAAGTATAATTTAATAAATAAGTGATCCTTTTTAATGAATTTTGAAAAAAAAATATG
* *
10381 ACTACCTTTTATCAAAGATATGAGGTGGGA
66 ACTACCTTTTATCAAAGATATGAGATGGGG
* * *
10411 TTTATATTAAAATATAATTTAAAAAATAAGTTATCCTTT
1 TTTATATTAAAGTATAATTTAATAAATAAGTGATCCTTT
10450 CTAACGAAAC
Statistics
Matches: 417, Mismatches: 68, Indels: 60
0.77 0.12 0.11
Matches are distributed among these distances:
91 1 0.00
92 6 0.01
93 5 0.01
94 52 0.12
95 224 0.54
96 89 0.21
97 33 0.08
98 7 0.02
ACGTcount: A:0.41, C:0.06, G:0.13, T:0.39
Consensus pattern (95 bp):
TTTATATTAAAGTATAATTTAATAAATAAGTGATCCTTTTTAATGAATTTTGAAAAAAAAATATG
ACTACCTTTTATCAAAGATATGAGATGGGG
Found at i:10453 original size:286 final size:285
Alignment explanation
Indices: 9936--10458 Score: 678
Period size: 286 Copynumber: 1.8 Consensus size: 285
9926 TGAAGTGAGG
* * *
9936 TTTATATTAAAGTATAATTTAATAATAAGTGATCCTTTTTAATGAAATTTTAAAAAAAAATATGA
1 TTTATAATAAAGTATAATTCAATAATAAGTGATCATTTTTAATGAAATTTTAAAAAAAAATATGA
* * * * * * * * *
10001 CTGCCTTTTATCAGATGTGTACGGCAAGTTTTATATTAAAGTATAATTCAATAAATGAGTGATCA
66 CTGCCTTTTATCAAACGTATACGACAAGGTTTATATTAAAATATAATTCAATAAATAAATAATCA
* * ** *
10066 TTTTTAATAAAATTTTGAAAAACAATATGGTTACCTTTTATCAAACGTATGAGGTGGGGTTTATA
131 TTTTTAATAAAACTTTGAAAAAAAATATGACTACCTTTTATCAAACGTATGAGGTGGGATTTATA
* * * * *
10131 TTAAAGTATAATTTAATAAATGAGTAGTCTTTTCTAATGAAATTTTGGAAGAAAAATATAGCTGT
196 TTAAAATATAATTTAAAAAATAAGTAGTCCTTTCTAACGAAATTTTGGAAGAAAAATATAGCTGT
10196 CTTTTATTAGACGCGTGTGACAAGT
261 CTTTTATTAGACGCGTGTGACAAGT
*
10221 TTTATAATAAAGTATAATTCAATAAATGAGTGATCATTTTTAATGAAATTTTAAAAAAAAATATG
1 TTTATAATAAAGTATAATTCAAT-AATAAGTGATCATTTTTAATGAAATTTTAAAAAAAAATAT-
* * *** *
10286 GA-TGTCTTTTATGAAACGTATGA-GATGGGGTTTATATTAAAATATAATTTAATAAATAAATAA
64 GACTGCCTTTTATCAAACGTAT-ACGACAAGGTTTATATTAAAATATAATTCAATAAATAAATAA
* *
10349 TCCTTTTTAAT-GAACTTTGAAAAAAAATTATGACTACCTTTTATCAAA-GATATGAGGTGGGAT
128 TCATTTTTAATAAAACTTTGAAAAAAAA-TATGACTACCTTTTATCAAACG-TATGAGGTGGGAT
10412 TTATATTAAAATATAATTTAAAAAATAAGTTA-TCCTTTCTAACGAAA
191 TTATATTAAAATATAATTTAAAAAATAAG-TAGTCCTTTCTAACGAAA
10459 CTAAATTTAT
Statistics
Matches: 201, Mismatches: 31, Indels: 11
0.83 0.13 0.05
Matches are distributed among these distances:
285 35 0.17
286 161 0.80
287 5 0.02
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (285 bp):
TTTATAATAAAGTATAATTCAATAATAAGTGATCATTTTTAATGAAATTTTAAAAAAAAATATGA
CTGCCTTTTATCAAACGTATACGACAAGGTTTATATTAAAATATAATTCAATAAATAAATAATCA
TTTTTAATAAAACTTTGAAAAAAAATATGACTACCTTTTATCAAACGTATGAGGTGGGATTTATA
TTAAAATATAATTTAAAAAATAAGTAGTCCTTTCTAACGAAATTTTGGAAGAAAAATATAGCTGT
CTTTTATTAGACGCGTGTGACAAGT
Found at i:10946 original size:36 final size:37
Alignment explanation
Indices: 10876--10946 Score: 85
Period size: 38 Copynumber: 1.9 Consensus size: 37
10866 AGTTTTGATT
*
10876 TATAAAATATAAAAATACTAAATAATTAATAATTTAAA
1 TATAAAATATAAAAATAC-AAATAATTAAAAATTTAAA
10914 TATAAAATA-AATAAATA-AAACTAA-TAAAAATTT
1 TATAAAATATAA-AAATACAAA-TAATTAAAAATTT
10947 TAAAAATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
36 11 0.37
37 5 0.17
38 14 0.47
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (37 bp):
TATAAAATATAAAAATACAAATAATTAAAAATTTAAA
Found at i:15293 original size:12 final size:12
Alignment explanation
Indices: 15278--15317 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
15268 AAACTTTTTT
15278 AAAAAATAATTG
1 AAAAAATAATTG
*
15290 AAAAAATAAAT-
1 AAAAAATAATTG
15301 -AAAAATAATTG
1 AAAAAATAATTG
15312 AAAAAA
1 AAAAAA
15318 AGGAACAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
10 9 0.38
12 15 0.62
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (12 bp):
AAAAAATAATTG
Found at i:16998 original size:26 final size:25
Alignment explanation
Indices: 16961--17009 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
16951 ATAAAAAAAT
*
16961 TAAAAAATAAAAATAATTCAAATTC
1 TAAAAAATAAAAATAATTAAAATTC
*
16986 TAAAAATTAAAAAATAATTAAAAT
1 TAAAAAAT-AAAAATAATTAAAAT
17010 ATATATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (25 bp):
TAAAAAATAAAAATAATTAAAATTC
Found at i:20138 original size:28 final size:28
Alignment explanation
Indices: 20098--20155 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
20088 ACAGTTAAGT
20098 TTTTCAGTCAAATCTTGTTGATGATTAC
1 TTTTCAGTCAAATCTTGTTGATGATTAC
20126 TTTTCAGTCAAATCTTGTTGATGATTAC
1 TTTTCAGTCAAATCTTGTTGATGATTAC
20154 TT
1 TT
20156 ATAAAATCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.48
Consensus pattern (28 bp):
TTTTCAGTCAAATCTTGTTGATGATTAC
Found at i:21214 original size:29 final size:28
Alignment explanation
Indices: 21182--21448 Score: 160
Period size: 29 Copynumber: 9.3 Consensus size: 28
21172 CATTAATCAT
* * *
21182 TAAACTTTTTAAAATTATACTTTGACTCC
1 TAAACTTTTCAAAATTACACATTGAC-CC
*
21211 TAAACTCTTCAAAATTACACATTGACCC
1 TAAACTTTTCAAAATTACACATTGACCC
* * * **
21239 TTAACATTTCAAAATTCCGGATT-AGCCC
1 TAAACTTTTCAAAATTACACATTGA-CCC
* *
21267 TTAAACTTCTCAAAATTACACTTTGACCC
1 -TAAACTTTTCAAAATTACACATTGACCC
* * *
21296 TTAAACTTTTCATAATTACATATTGATCTC
1 -TAAACTTTTCAAAATTACACATTGA-CCC
*
21326 AAAACTTTTCAAAATTACACATT-ACCCC
1 TAAACTTTTCAAAATTACACATTGA-CCC
* * ****
21354 TAAATTTTTTAAAATTATGGGTTGACCC
1 TAAACTTTTCAAAATTACACATTGACCC
** ** * *
21382 TTAAACTTTAAAAAATTACGTATTAATCTC
1 -TAAACTTTTCAAAATTACACATTGA-CCC
* * *
21412 TAAACTTTTTAAAATTATAGATTGACCCC
1 TAAACTTTTCAAAATTACACATTGA-CCC
*
21441 AAAACTTT
1 TAAACTTT
21449 AAAATGGTTA
Statistics
Matches: 180, Mismatches: 51, Indels: 14
0.73 0.21 0.06
Matches are distributed among these distances:
27 1 0.01
28 44 0.24
29 130 0.72
30 5 0.03
ACGTcount: A:0.37, C:0.20, G:0.05, T:0.37
Consensus pattern (28 bp):
TAAACTTTTCAAAATTACACATTGACCC
Found at i:21340 original size:58 final size:58
Alignment explanation
Indices: 21212--21370 Score: 162
Period size: 57 Copynumber: 2.8 Consensus size: 58
21202 TTTGACTCCT
* * * * *
21212 AAACTCTTCAAAATTACACATTGACCCTT-AACATTTCAAAATTCCGGATTAGCCCTT
1 AAACTTTTCAAAATTACACATTGACCCTTAAACTTTTCAAAATTACAGATTAGCCCTA
* * * * **
21269 AAACTTCTCAAAATTACACTTTGACCCTTAAACTTTTCATAATTACATATT-GATCTCA
1 AAACTTTTCAAAATTACACATTGACCCTTAAACTTTTCAAAATTACAGATTAGCCCT-A
* * *
21327 AAACTTTTCAAAATTACACATT-ACCCCTAAATTTTTTAAAATTA
1 AAACTTTTCAAAATTACACATTGACCCTTAAACTTTTCAAAATTA
21371 TGGGTTGACC
Statistics
Matches: 83, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
57 47 0.57
58 36 0.43
ACGTcount: A:0.38, C:0.23, G:0.04, T:0.36
Consensus pattern (58 bp):
AAACTTTTCAAAATTACACATTGACCCTTAAACTTTTCAAAATTACAGATTAGCCCTA
Found at i:21368 original size:86 final size:87
Alignment explanation
Indices: 21182--21428 Score: 257
Period size: 86 Copynumber: 2.9 Consensus size: 87
21172 CATTAATCAT
* * * * *
21182 TAAACTTTTTAAAATTATACTTTGACTCC-TAAACTCTTCAAAATTACACATTGA-CCCTTAACA
1 TAAACTTTTTAAAATTATACTTTGAC-CCTTAAACTTTTCAAAATTACATATTGATCTCTAAACT
* ** *
21245 TTTCAAAATTCCGGATTAGCCCT
65 TTTCAAAATTACACATTAGCCCC
* * * * *
21268 TAAACTTCTCAAAATTACACTTTGACCCTTAAACTTTTCATAATTACATATTGATCTCAAAACTT
1 TAAACTTTTTAAAATTATACTTTGACCCTTAAACTTTTCAAAATTACATATTGATCTCTAAACTT
21333 TTCAAAATTACACATTA-CCCC
66 TTCAAAATTACACATTAGCCCC
* *** ** * *
21354 TAAATTTTTTAAAATTATGGGTTGACCCTTAAACTTTAAAAAATTACGTATTAATCTCTAAACTT
1 TAAACTTTTTAAAATTATACTTTGACCCTTAAACTTTTCAAAATTACATATTGATCTCTAAACTT
*
21419 TTTAAAATTA
66 TTCAAAATTA
21429 TAGATTGACC
Statistics
Matches: 131, Mismatches: 28, Indels: 4
0.80 0.17 0.02
Matches are distributed among these distances:
85 2 0.02
86 109 0.83
87 20 0.15
ACGTcount: A:0.37, C:0.20, G:0.05, T:0.38
Consensus pattern (87 bp):
TAAACTTTTTAAAATTATACTTTGACCCTTAAACTTTTCAAAATTACATATTGATCTCTAAACTT
TTCAAAATTACACATTAGCCCC
Found at i:22893 original size:5 final size:5
Alignment explanation
Indices: 22880--22915 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
22870 CTAAATATCG
* *
22880 AATAA AATAG AATAA AATAA AATAA AATAA AGTAA A
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA A
22916 TTTAAAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:22923 original size:16 final size:17
Alignment explanation
Indices: 22902--22943 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
22892 TAAAATAAAA
*
22902 TAAAATAAAG-TAAATT
1 TAAAATAAAGAAAAATT
*
22918 TAAAATTAAGAAAAATT
1 TAAAATAAAGAAAAATT
*
22935 AAAAATAAA
1 TAAAATAAA
22944 ATCAATTCTC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (17 bp):
TAAAATAAAGAAAAATT
Found at i:23533 original size:155 final size:156
Alignment explanation
Indices: 23234--23548 Score: 402
Period size: 155 Copynumber: 2.0 Consensus size: 156
23224 TGAAAAACTT
* * *
23234 ATGAAAATAAATAAATTTTTTAAAATTTATTTAATATGAATTAAATAATAATATTTTATGAATTT
1 ATGAAAATAAATAAATTTTTGAAAAATAATTTAATATGAATTAAATAATAATATTTTATGAATTT
* * * *
23299 TAAAAATTAAAAACCAAGAAAAATCCCCCCGAAAACATTTACAGAACAGAAAACTCTGTTATTCG
66 CAAAAATTAAAAACCAAGAAAAATCCCCCCAAAAACATTTACAGAACAGAAAACACCGTTATTCG
* * *
23364 AAAATAAGGAAATTTTAA-TAAAAAA
131 AAAACAAGGAAATTTCAAGGAAAAAA
* *
23389 ATGAAAATGAATGAATTTTTGAAAAATAATTTAATATGAATTAAATAATAATATTTTATGAATTT
1 ATGAAAATAAATAAATTTTTGAAAAATAATTTAATATGAATTAAATAATAATATTTTATGAATTT
** * * * * ** *
23454 CAAAAATTATGAACTAAGAAAAATCCTCCCAAAAATATTTACGGAGTAGAAAACACCGTTTTTC-
66 CAAAAATTAAAAACCAAGAAAAATCCCCCCAAAAACATTTACAGAACAGAAAACACCGTTATTCG
23518 AAAAGCAA-GAGAATTTCAAGGAAAAAA
131 AAAA-CAAGGA-AATTTCAAGGAAAAAA
23545 ATGA
1 ATGA
23549 GAAACTTATA
Statistics
Matches: 136, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
154 6 0.04
155 120 0.88
156 10 0.07
ACGTcount: A:0.51, C:0.09, G:0.10, T:0.30
Consensus pattern (156 bp):
ATGAAAATAAATAAATTTTTGAAAAATAATTTAATATGAATTAAATAATAATATTTTATGAATTT
CAAAAATTAAAAACCAAGAAAAATCCCCCCAAAAACATTTACAGAACAGAAAACACCGTTATTCG
AAAACAAGGAAATTTCAAGGAAAAAA
Found at i:25305 original size:21 final size:19
Alignment explanation
Indices: 25269--25307 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
25259 TATTATTAAT
*
25269 ATTTTTTATTTTTAATAAG
1 ATTTTTTATTTATAATAAG
25288 ATTTATTTAATTTATAATAA
1 ATTT-TTT-ATTTATAATAA
25308 AAATTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 3 0.18
21 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
ATTTTTTATTTATAATAAG
Found at i:26900 original size:19 final size:20
Alignment explanation
Indices: 26861--26903 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
26851 AATTTAGTTA
26861 ATTTATAATATGAATTAATT
1 ATTTATAATATGAATTAATT
26881 ATTTATAATATGAA-TAATT
1 ATTTATAATATGAATTAATT
26900 ATTT
1 ATTT
26904 TGAAGAATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (20 bp):
ATTTATAATATGAATTAATT
Found at i:31287 original size:27 final size:27
Alignment explanation
Indices: 31255--31327 Score: 110
Period size: 27 Copynumber: 2.7 Consensus size: 27
31245 AGCCACCCTT
31255 TGTTTGTCAAAAATGGTGGTTACTTTG
1 TGTTTGTCAAAAATGGTGGTTACTTTG
* * *
31282 TGTTTGTAAAAAATGGTGGTTTCTTTT
1 TGTTTGTCAAAAATGGTGGTTACTTTG
*
31309 TATTTGTCAAAAATGGTGG
1 TGTTTGTCAAAAATGGTGG
31328 CATGTTGTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.25, C:0.05, G:0.25, T:0.45
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTACTTTG
Found at i:31360 original size:51 final size:54
Alignment explanation
Indices: 31257--31363 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 54
31247 CCACCCTTTG
* * * **
31257 TTTGTCAAAAATGGTGGTTACTTTGTGTTTGTAAAAAATGGTGGTTTCTTTTTA
1 TTTGTCAAAAATGGTGGTCACTGTGTGTTTGTAAAAAATGGTGGCTAATTTTTA
* *
31311 TTTGTCAAAAATGGTGG-CA-TGT-TGTTTGTAAAAATTTGTGGCTAATTTTTA
1 TTTGTCAAAAATGGTGGTCACTGTGTGTTTGTAAAAAATGGTGGCTAATTTTTA
31362 TT
1 TT
31364 ACAAAATGGG
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
51 26 0.57
52 2 0.04
53 1 0.02
54 17 0.37
ACGTcount: A:0.25, C:0.06, G:0.21, T:0.48
Consensus pattern (54 bp):
TTTGTCAAAAATGGTGGTCACTGTGTGTTTGTAAAAAATGGTGGCTAATTTTTA
Found at i:31448 original size:13 final size:13
Alignment explanation
Indices: 31406--31452 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
31396 AGGCTCCCTC
*
31406 ATCCCTCTCAAAT
1 ATCCCTCTCAAGT
*
31419 ATCCCTCTCAAGC
1 ATCCCTCTCAAGT
**
31432 ATCCCTCTCTTGT
1 ATCCCTCTCAAGT
31445 ATCCCTCT
1 ATCCCTCT
31453 TCAATTCATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.19, C:0.43, G:0.04, T:0.34
Consensus pattern (13 bp):
ATCCCTCTCAAGT
Found at i:39907 original size:2 final size:2
Alignment explanation
Indices: 39900--39930 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
39890 AGGTTTCAAA
39900 AT 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 AT A
39931 CACATATTAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41579 original size:2 final size:2
Alignment explanation
Indices: 41572--41608 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
41562 GAGATTTCCT
41572 TA TA TA 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 TA TA TA T
41609 GAGCAATGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:42433 original size:13 final size:13
Alignment explanation
Indices: 42414--42448 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
42404 AGCTTTTTTT
42414 TTAAAAAAAA-AA
1 TTAAAAAAAAGAA
42426 TCTAAAAAAAAGAA
1 T-TAAAAAAAAGAA
42440 TTAAAAAAA
1 TTAAAAAAA
42449 TCAACAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 1 0.05
13 17 0.81
14 3 0.14
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.17
Consensus pattern (13 bp):
TTAAAAAAAAGAA
Found at i:44822 original size:3 final size:3
Alignment explanation
Indices: 44814--44858 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
44804 ATATATACTT
44814 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
44859 ATTGTTTATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:46068 original size:20 final size:20
Alignment explanation
Indices: 46027--46068 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
46017 AAAATTGGAA
***
46027 AATGATTTTCAAAATGTTAC
1 AATGATTTTCAAAATAAAAC
46047 AATGATTTTCAAAATAAAAC
1 AATGATTTTCAAAATAAAAC
46067 AA
1 AA
46069 ATGCTTGATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (20 bp):
AATGATTTTCAAAATAAAAC
Found at i:49896 original size:2 final size:2
Alignment explanation
Indices: 49889--49919 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
49879 ACACAGTAAC
49889 AT 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 AT A
49920 AACCTAGTTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54476 original size:24 final size:24
Alignment explanation
Indices: 54428--54477 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
54418 TCTTGAAAAT
*
54428 TTTTATTTATTAAATCTTAATTAA
1 TTTTATTTATTAAATCTTAAATAA
54452 TTTTATTT-TTAAAGT-TATAAATAA
1 TTTTATTTATTAAA-TCT-TAAATAA
54476 TT
1 TT
54478 AATCATACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (24 bp):
TTTTATTTATTAAATCTTAAATAA
Found at i:55482 original size:32 final size:32
Alignment explanation
Indices: 55446--55512 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
55436 AATAGCTACG
55446 AACTACTTTGATATGATAGAAAGCTAAAATCA
1 AACTACTTTGATATGATAGAAAGCTAAAATCA
55478 AACTACTTTGATATGATAGAAAGCTAAAATCA
1 AACTACTTTGATATGATAGAAAGCTAAAATCA
55510 AAC
1 AAC
55513 GATGAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.48, C:0.13, G:0.12, T:0.27
Consensus pattern (32 bp):
AACTACTTTGATATGATAGAAAGCTAAAATCA
Found at i:56092 original size:20 final size:20
Alignment explanation
Indices: 56049--56092 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
56039 TTTATATTTT
* * * *
56049 TTAAAAACAAATAACAGATT
1 TTAAAAACAAAGAAAAAATA
56069 TTAAAAACAAAGAAAAAATA
1 TTAAAAACAAAGAAAAAATA
56089 TTAA
1 TTAA
56093 CTAAACAGAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.66, C:0.07, G:0.05, T:0.23
Consensus pattern (20 bp):
TTAAAAACAAAGAAAAAATA
Found at i:59618 original size:12 final size:12
Alignment explanation
Indices: 59587--59636 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
59577 ATTTTAATTA
*
59587 TTCTTTACTTTT
1 TTCTTTTCTTTT
* *
59599 TCCATTTCTTTT
1 TTCTTTTCTTTT
*
59611 TTTTTTTCTTTT
1 TTCTTTTCTTTT
*
59623 TTCTTTTATTTT
1 TTCTTTTCTTTT
59635 TT
1 TT
59637 ACCAAAGAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (12 bp):
TTCTTTTCTTTT
Found at i:61697 original size:52 final size:52
Alignment explanation
Indices: 61640--61738 Score: 189
Period size: 52 Copynumber: 1.9 Consensus size: 52
61630 AAAAATAAAA
61640 ATATTTTTCATATTATGGATATTAATAGACATAAATTATATAATAGATTAAT
1 ATATTTTTCATATTATGGATATTAATAGACATAAATTATATAATAGATTAAT
*
61692 ATATTTTTCATATTATGGATATTAATAGACATAAGTTATATAATAGA
1 ATATTTTTCATATTATGGATATTAATAGACATAAATTATATAATAGA
61739 ATATAAATAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.43
Consensus pattern (52 bp):
ATATTTTTCATATTATGGATATTAATAGACATAAATTATATAATAGATTAAT
Found at i:63059 original size:13 final size:13
Alignment explanation
Indices: 63037--63066 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
63027 CAACAATTTT
63037 AATAAAATGTATA
1 AATAAAATGTATA
*
63050 AATAAGATGTATA
1 AATAAAATGTATA
63063 AATA
1 AATA
63067 TATAGACCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30
Consensus pattern (13 bp):
AATAAAATGTATA
Found at i:63990 original size:2 final size:2
Alignment explanation
Indices: 63971--64008 Score: 53
Period size: 2 Copynumber: 19.5 Consensus size: 2
63961 AATTAAAATA
63971 AT AT A- AT AT AT A- AGT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A
64009 AGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 2 0.06
2 30 0.91
3 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Done.