Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_2268
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: 24387
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.31
Found at i:5817 original size:69 final size:70
Alignment explanation
Indices: 5697--5870 Score: 203
Period size: 69 Copynumber: 2.5 Consensus size: 70
5687 CTTTCCAAGG
**
5697 AAAATCAACTCATATTGCGAG-AGATGAGTTGAGCCTCAAGACACGTTGAGGTA-TTTTAATTT-
1 AAAATCAACTCATATTGCGAGAAG-TGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTA
*
5759 TTTTTT
65 TGTTTT
** * *
5765 CAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTA
1 -AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTA
5830 TGTTTT
65 TGTTTT
** * *
5836 -AAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
5871 TTTAATTTTT
Statistics
Matches: 91, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
69 76 0.84
70 10 0.11
71 5 0.05
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (70 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCCGAGGTATTTTTAATTTAT
GTTTT
Found at i:5990 original size:74 final size:71
Alignment explanation
Indices: 5874--6216 Score: 507
Period size: 74 Copynumber: 4.8 Consensus size: 71
5864 TAAGCCTTTT
* * **
5874 AATTTTTGTTTTTC-AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
1 AATTTCTG-TTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACG-TGAG
*
5938 GTAATTTT
64 GTAATTTC
*
5946 AATTTCTGTTGTTAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGA
1 AATTTCTGTT-TT-CAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACG-TGA
6011 GGTAATTTC
63 GGTAATTTC
* *
6020 AATTTCTGTTTTCAAAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAGGACACGTGAGGT
1 AATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGTGAGGT
*
6085 ATTTTC
66 AATTTC
6091 AATTTCTGCTTTTC-AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC--GACACGTGAGG
1 AATTTCTG-TTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGTGAGG
6153 TAATTTC
65 TAATTTC
*
6160 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCA-GACAC
1 AATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACAC
6217 ACGTGGTATT
Statistics
Matches: 251, Mismatches: 14, Indels: 14
0.90 0.05 0.05
Matches are distributed among these distances:
68 5 0.02
69 61 0.24
70 5 0.02
71 56 0.22
72 58 0.23
73 2 0.01
74 64 0.25
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (71 bp):
AATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGTGAGGT
AATTTC
Found at i:6189 original size:140 final size:144
Alignment explanation
Indices: 5874--6216 Score: 531
Period size: 140 Copynumber: 2.4 Consensus size: 144
5864 TAAGCCTTTT
* * **
5874 AATTTTTGTTTTTCAAAA-TCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
1 AATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAG
5938 GTAATTTTAATTTCTGTTGTTAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGA
65 GTAATTTTAATTTCTGTTGTT-AAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCA-GA
6003 CACGCTGAGGTAATTTC
128 CACGCTGAGGTAATTTC
*
6020 AATTTCTGTTTTCAAAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAGGACACG-TGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGG
*
6084 T-ATTTTCAATTTCTGCTT-TT-CAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC-GAC
66 TAATTTT-AATTTCTG-TTGTTAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGAC
6145 ACG-TGAGGTAATTTC
129 ACGCTGAGGTAATTTC
6160 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCA-GACAC
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACAC
6217 ACGTGGTATT
Statistics
Matches: 187, Mismatches: 7, Indels: 13
0.90 0.03 0.06
Matches are distributed among these distances:
139 5 0.03
140 63 0.34
141 6 0.03
143 37 0.20
144 5 0.03
145 25 0.13
146 46 0.25
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (144 bp):
AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGG
TAATTTTAATTTCTGTTGTTAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGACAC
GCTGAGGTAATTTC
Found at i:6330 original size:122 final size:122
Alignment explanation
Indices: 6109--6339 Score: 437
Period size: 122 Copynumber: 1.9 Consensus size: 122
6099 CTTTTCAAAA
6109 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCGACACGTGAGGTAATTTCAATTTCTGTTTTCA
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCGACACGTGAGGTAATTTCAATTTCTGTTTTCA
6174 AAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTC-AGACACACGTGGTATTTTT
66 AAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACACGTGGTATTTTT
*
6230 TCAATTCATATTGCGAGAAATGAGTTGAGCCTCAGACACGTGAGGTAATTTCAATTTCTGTTTTC
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTC-GACACGTGAGGTAATTTCAATTTCTGTTTTC
6295 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAC
65 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAC
6340 GTTGAGGTAA
Statistics
Matches: 107, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
121 32 0.30
122 69 0.64
123 6 0.06
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Consensus pattern (122 bp):
TCAACTCATATTGCGAGAAATGAGTTGAGCCTCGACACGTGAGGTAATTTCAATTTCTGTTTTCA
AAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACACGTGGTATTTTT
Found at i:6450 original size:71 final size:71
Alignment explanation
Indices: 6229--6470 Score: 443
Period size: 72 Copynumber: 3.4 Consensus size: 71
6219 GTGGTATTTT
*
6229 TTCAATTCATATTGCGAGAAATGAGTTGAGCCTCAGACACG-TGAGGTAATTTCAATTTCTGTTT
1 TTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGACACGTTGAGGTAATTTCAATTTCTGTTT
6293 TCAAAA
66 TCAAAA
6299 TTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTT
1 TTCAACTCATATTGCGAGAAATGAGTTGAGCCTC-AGACACGTTGAGGTAATTTCAATTTCTGTT
6364 TTCAAAA
65 TTCAAAA
6371 TTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGACACGTTGAGGTAATTTCAATTTCTGTTT
1 TTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGACACGTTGAGGTAATTTCAATTTCTGTTT
6436 TCAAAA
66 TCAAAA
*
6442 TTCAACTCATATTGCGAG-AGTGAGTTGAG
1 TTCAACTCATATTGCGAGAAATGAGTTGAG
6471 AACCTTTAAT
Statistics
Matches: 168, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
70 43 0.26
71 62 0.37
72 63 0.38
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33
Consensus pattern (71 bp):
TTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGACACGTTGAGGTAATTTCAATTTCTGTTT
TCAAAA
Found at i:7198 original size:71 final size:71
Alignment explanation
Indices: 6483--7373 Score: 1494
Period size: 70 Copynumber: 12.9 Consensus size: 71
6473 CCTTTAATTT
6483 TTTCT-TTTTCAAAA-TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTGAGGT-A
1 TTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTGAGGTAA
6545 TTTCAA
66 TTTCAA
6551 TTT-TGTTTT-AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTC-AGACACGTGAGGTAA
1 TTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTGAGGTAA
6613 TTTCAA
66 TTTCAA
6619 TTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTC-AGACAC-TGAGGTAA
1 TTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTGAGGTAA
6682 TTTCAA
66 TTTCAA
**
6688 TTTCTGTTTTCAAAATTCAACTCATATTGCGAG--ATGAG-TGAG--TTGAGACACGCTGAGGTA
1 TTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACG-TGAGGTA
6748 ATTTCAA
65 ATTTCAA
6755 TTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGT-
1 TTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACG-TGAGGTA
*
6819 ATTTTAA
65 ATTTCAA
6826 TTTCTGTTTTCAAAA-TCAACTCATATTGCGAG--A-GAGTTGAGCCTCAAGACACGTGAGGTAA
1 TTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTGAGGTAA
6887 TTTCAA
66 TTTCAA
6893 TTTCTGTTTT-AAAATTCAACTCATATTGCGAG-AATGAGTTGAGCCTCAAGACACGTGAGGTAA
1 TTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTGAGGTAA
6956 TTTCAA
66 TTTCAA
6962 TTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTC-AGACACGTGAGGTAA
1 TTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTGAGGTAA
7026 TTTCAA
66 TTTCAA
7032 TTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTA
1 TTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACG-TGAGGTA
*
7097 TTTTCAA
65 ATTTCAA
7104 TTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTC-AGACACGCTGAGGTA
1 TTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACG-TGAGGTA
7168 ATTTCAA
65 ATTTCAA
* *
7175 TTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACA-TTGAGGTAT
1 TTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTGAGGTAA
7239 TTTCAA
66 TTTCAA
7245 TTT-TGTTTTCAAAA-TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTA
1 TTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACG-TGAGGTA
7308 ATTTCAA
65 ATTTCAA
7315 TTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAG-CTCAA-ACACGTGAG
1 TTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTGAG
7374 TATTTTTTTC
Statistics
Matches: 784, Mismatches: 13, Indels: 51
0.92 0.02 0.06
Matches are distributed among these distances:
64 1 0.00
65 6 0.01
66 14 0.02
67 123 0.16
68 91 0.12
69 117 0.15
70 194 0.25
71 128 0.16
72 110 0.14
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (71 bp):
TTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTGAGGTAA
TTTCAA
Found at i:7562 original size:121 final size:124
Alignment explanation
Indices: 7110--7600 Score: 469
Period size: 140 Copynumber: 3.8 Consensus size: 124
7100 TCAATTTCTG
** *
7110 TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGACACGCTGAGGTAATTTCAA
1 TTTTCAAAA-TC-ACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACACGATGAGGTAATTTCAA
** * * *
7175 TTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATTGAGGTATT
64 TTTCTG-TTTCAAAA-TCAACTCATATTGCGAGAGGTGAGTTGA-ACTCAA-ACACTGA-CTA--
7240 TTCAATTTT
122 -TC-----T
** *
7249 GTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCA
1 -TTTTCAAAATC-ACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGACACGATGAGGTAATTTCA
** * * *
7314 ATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCTCAAACACGTGAGTATTT
63 ATTTCTG-TTTCAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAACTCAAACAC-TGACTATCT
*
7379 TTTTCAAAAT---TCATATTGCGAGAGGTGAGTTGAGCCTCAGACACGATGAGGTAATTGCAATT
1 TTTTCAAAATCACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACACGATGAGGTAATTTCAATT
* *** **
7441 TCTGTTTCAAAATCAACTCATATTACGAGAGGTG-GTTGAACTTTTA-A-TTTCTA-CT
66 TCTGTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAACTCAAACACTGACTATCT
* *
7496 TTTTCAAAATTCACTCATATTGCGAAGAGGTGAGTTGAGCCTC-GACACGCTGAGGTATTTTCAA
1 TTTTCAAAA-TCACTCATATTGCG-AGAGGTGAGTTGAGCCTCAGACACGATGAGGTAATTTCAA
* *
7560 TTTCTGTTT-TAATTCAACTCATATTGCGAGAGGTGAGTTGA
64 TTTCTGTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGA
7601 GCCTCAGGCA
Statistics
Matches: 318, Mismatches: 25, Indels: 35
0.84 0.07 0.09
Matches are distributed among these distances:
117 10 0.03
118 4 0.01
120 24 0.08
121 50 0.16
122 37 0.12
123 8 0.03
124 26 0.08
125 26 0.08
129 10 0.03
130 1 0.00
135 1 0.00
138 6 0.02
139 41 0.13
140 74 0.23
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (124 bp):
TTTTCAAAATCACTCATATTGCGAGAGGTGAGTTGAGCCTCAGACACGATGAGGTAATTTCAATT
TCTGTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAACTCAAACACTGACTATCT
Found at i:7599 original size:67 final size:68
Alignment explanation
Indices: 7503--7630 Score: 224
Period size: 68 Copynumber: 1.9 Consensus size: 68
7493 ACTTTTTCAA
7503 AATTCACTCATATTGCGAAGAGGTGAGTTGAGCCTC-GACACGCTGAGGTATTTTCAATTTCTGT
1 AATTCACTCATATTGCGAAGAGGTGAGTTGAGCCTCAGACACGCTGAGGTATTTTCAATTTCTGT
7567 TTT
66 TTT
*
7570 AATTCAACTCATATTGCG-AGAGGTGAGTTGAGCCTCAGGCACGCTGAGGTATTTTCAATTT
1 AATTC-ACTCATATTGCGAAGAGGTGAGTTGAGCCTCAGACACGCTGAGGTATTTTCAATTT
7631 TCGTTTTTTT
Statistics
Matches: 58, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
67 23 0.40
68 35 0.60
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (68 bp):
AATTCACTCATATTGCGAAGAGGTGAGTTGAGCCTCAGACACGCTGAGGTATTTTCAATTTCTGT
TTT
Found at i:7857 original size:13 final size:14
Alignment explanation
Indices: 7839--7867 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
7829 ACGCTGAGTA
7839 TTTCAA-TTCTGTT
1 TTTCAATTTCTGTT
7852 TTTCAATTTCTGTT
1 TTTCAATTTCTGTT
7866 TT
1 TT
7868 CAAAATCGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.66
Consensus pattern (14 bp):
TTTCAATTTCTGTT
Found at i:8008 original size:13 final size:13
Alignment explanation
Indices: 7990--8015 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7980 TGGAGGTCTT
7990 TTCATTTCTGTTC
1 TTCATTTCTGTTC
8003 TTCATTTCTGTTC
1 TTCATTTCTGTTC
8016 GAAAAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.23, G:0.08, T:0.62
Consensus pattern (13 bp):
TTCATTTCTGTTC
Found at i:8137 original size:151 final size:151
Alignment explanation
Indices: 7882--8153 Score: 365
Period size: 151 Copynumber: 1.8 Consensus size: 151
7872 ATCGACTCAT
* *
7882 ATTGCGAGAGGTGAGTTGAGCCTGGGAACGCTGAGGTATTTTCAATTTCTGTTTGTCAAAAATAA
1 ATTGCGAGAGGTGAGTTGAGCCTAGGAACGCTGAGGTAATTTCAATTTCTGTTTGTCAAAAATAA
** * *
7947 CTCATATTGCGAGAGGTGGTTGACCTCGCCACATGGAGGTCTTTTC-ATTTCTGTTCTTCATTTC
66 CTCATATTGCGAGAAATGGTTGACCTCGACACATGGAGGTATTTTCAATTTCTGTTCTTCATTTC
8011 TGTTCGAAAAAAAATCAACTA
131 TGTTCGAAAAAAAATCAACTA
* *
8032 ATTGCGAGA-GTGGGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTT-TCAAAATT
1 ATTGCGAGAGGTGAGTTGAGCCT-AGGA-ACGCTGAGGTAATTTCAATTTCTGTTTGTCAAAAAT
* * *
8095 CAACTTATATTGCGAGAAATGGTT-AGCCTC-ATACAGTTGAGGTATTTTCAATTTCTGTT
64 -AACTCATATTGCGAGAAATGGTTGA-CCTCGACACA-TGGAGGTATTTTCAATTTCTGTT
8154 TCAAAAAAAA
Statistics
Matches: 105, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
149 12 0.11
150 23 0.22
151 61 0.58
152 9 0.09
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (151 bp):
ATTGCGAGAGGTGAGTTGAGCCTAGGAACGCTGAGGTAATTTCAATTTCTGTTTGTCAAAAATAA
CTCATATTGCGAGAAATGGTTGACCTCGACACATGGAGGTATTTTCAATTTCTGTTCTTCATTTC
TGTTCGAAAAAAAATCAACTA
Found at i:8600 original size:87 final size:87
Alignment explanation
Indices: 8415--8741 Score: 382
Period size: 87 Copynumber: 3.8 Consensus size: 87
8405 TACTTTTTCA
*
8415 AATCAGCTCATATTGCGAGAGGTGAGTTG-G-CTCAGGTCACGCCGAGGTA--TTCAATTTCTGT
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCCGAGGTATTTTCAATTTCTGT
8476 CTTCATTATTATGTTTTTGAAAG
66 -TTCATTATTATGTTTTTGAAAG
* * *
8499 AATCAGCTCATATTGCAAGAGGTGAGTTGAGCCTCAGGTCACGCCGAGGTATTTTCAATCTCTGT
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCCGAGGTATTTTCAATTTCTGT
8564 TTCATTATTATGTTTTTGAAAG
66 TTCATTATTATGTTTTTGAAAG
* * * *
8586 AATCAACTCGTATTGCGAGAGGCCGAGTT-AGCCTCAGGTCACACGTCAAGGTATTTTCAATTTC
1 AATCAACTCATATTGCGAGAGG-TGAGTTGAGCCTCAGGT--CACGCCGAGGTATTTTCAATTTC
* * ** *
8650 CGTTT--TTCAATTCCTGTCTTTCAAAAA
63 TGTTTCATT--ATT-ATGT-TTTTGAAAG
* * *
8677 AATCAACTCATA-TGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGT
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCCGAGGTATTTTCAATTTCTGT
8741 T
66 T
8742 GTCAAAAAAA
Statistics
Matches: 209, Mismatches: 22, Indels: 20
0.83 0.09 0.08
Matches are distributed among these distances:
84 28 0.13
85 1 0.00
86 19 0.09
87 53 0.25
88 38 0.18
89 32 0.15
90 21 0.10
91 17 0.08
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.34
Consensus pattern (87 bp):
AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCCGAGGTATTTTCAATTTCTGT
TTCATTATTATGTTTTTGAAAG
Found at i:8703 original size:89 final size:87
Alignment explanation
Indices: 8414--8875 Score: 366
Period size: 87 Copynumber: 5.4 Consensus size: 87
8404 CTACTTTTTC
*
8414 AAATCAGCTCATATTGCGAGAGGTGAGTTG-G-CTCAGGT-CACGCCGAGGTA--TTCAATTT-C
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTACACG-CGAGGTATTTTCAATTTCC
**
8473 TGTCTTCATTATTATGTTTTTGAAA
65 TGT-TTCA-TATTATGTTTTCAAAA
* * * *
8498 GAATCAGCTCATATTGCAAGAGGTGAGTTGAGCCTCAGGT-CACGCCGAGGTATTTTCAATCT-C
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTACACG-CGAGGTATTTTCAATTTCC
**
8561 TGTTTCATTATTATGTTTTTGAAA
65 TGTTTCA-TATTATGTTTTCAAAA
* * * *
8585 GAATCAACTCGTATTGCGAGAGGCCGAGTT-AGCCTCAGGTCACACGTCAAGGTATTTTCAATTT
1 AAATCAACTCATATTGCGAGAGG-TGAGTTGAGCCTCAGGT-ACACG-CGAGGTATTTTCAATTT
* *
8649 CCGTTTTTCA-ATTCCTGTCTTTCAAAA
63 CC-TGTTTCATATT-ATGT-TTTCAAAA
*
8676 AAATCAACTCATA-TGCGAGAGGTGAGTTGAGCCTCAGG-ACACGCTGAGGTAATTTCAATTT-C
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTACACGC-GAGGTATTTTCAATTTCC
8738 TG--------T-TG---TCAAAA
65 TGTTTCATATTATGTTTTCAAAA
* * * *
8749 AAATCAACTCGTATTGTGAGAGGCGAGTTGAGCCTCAGGTCACACGCCAAGGTATTTTCAATTT-
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGT-ACACG-CGAGGTATTTTCAATTTC
* *
8813 CTGTTTTCA-ATTTCTGCCTTTCAAAAAA
64 CTG-TTTCATA-TTATG-TTTTC--AAAA
8841 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
8876 TGGCTCACGC
Statistics
Matches: 317, Mismatches: 28, Indels: 58
0.79 0.07 0.14
Matches are distributed among these distances:
73 18 0.06
74 23 0.07
76 22 0.07
77 3 0.01
79 1 0.00
84 28 0.09
85 2 0.01
86 22 0.07
87 53 0.17
88 35 0.11
89 27 0.09
90 24 0.08
91 23 0.07
92 36 0.11
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.32
Consensus pattern (87 bp):
AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTACACGCGAGGTATTTTCAATTTCCT
GTTTCATATTATGTTTTCAAAA
Found at i:8772 original size:164 final size:166
Alignment explanation
Indices: 8586--8950 Score: 524
Period size: 164 Copynumber: 2.2 Consensus size: 166
8576 TTTTTGAAAG
* *
8586 AATCAACTCGTATTGCGAGAGGCCGAGTT-AGCCTCAGGTCACACGTCAAGGTATTTTCAATTTC
1 AATCAACTCGTATTGTGAGAGG-CGAGTTGAGCCTCAGGTCACACGCCAAGGTATTTTCAATTTC
*
8650 CGTTTTTCAATTCCTGTCTTTC-AAAAAAATCAACTCATA-TGCGAGAGGTGAGTTGAGCCTCAG
65 CG-TTTTCAATTCCTGCCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-AG
*
8713 G-ACACGCTGAGGTAATTTCAATTTCTGT-TGTCAAAAA
128 GCACACGCTGAGCTAATTTCAATTTCTGTCTGTCAAAAA
*
8750 AATCAACTCGTATTGTGAGAGGCGAGTTGAGCCTCAGGTCACACGCCAAGGTATTTTCAATTTCT
1 AATCAACTCGTATTGTGAGAGGCGAGTTGAGCCTCAGGTCACACGCCAAGGTATTTTCAATTTCC
* *
8815 GTTTTCAATTTCTGCCTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGC
66 GTTTTCAATTCCTGCCTTTC-AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGG-
* * *
8880 TCACGCGCTGAGCTATTTTCAATTTCTGTCTTTCAAAAA
129 -CACACGCTGAGCTAATTTCAATTTCTGTCTGTCAAAAA
* * *
8919 AATCAACTCATATTGTAAGAGGTGAGTTGAGC
1 AATCAACTCGTATTGTGAGAGGCGAGTTGAGC
8951 TTTAGATCAC
Statistics
Matches: 180, Mismatches: 13, Indels: 11
0.88 0.06 0.05
Matches are distributed among these distances:
163 23 0.13
164 56 0.31
165 19 0.11
166 21 0.12
168 24 0.13
169 37 0.21
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.31
Consensus pattern (166 bp):
AATCAACTCGTATTGTGAGAGGCGAGTTGAGCCTCAGGTCACACGCCAAGGTATTTTCAATTTCC
GTTTTCAATTCCTGCCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGGCA
CACGCTGAGCTAATTTCAATTTCTGTCTGTCAAAAA
Found at i:8777 original size:74 final size:74
Alignment explanation
Indices: 8654--8822 Score: 232
Period size: 74 Copynumber: 2.3 Consensus size: 74
8644 AATTTCCGTT
* *
8654 TTTCAATTCCTGTCTTTCAAAAAAATCAACTCATATGCGAGAGGTGAGTTGAGCCTCAGG-ACAC
1 TTTCAATTTCTGT-TTTCAAAAAAATCAACTCATATGCGAGAGGCGAGTTGAGCCTCAGGCACAC
**
8718 GCTGAGGTAA
65 GCCAAGGTAA
* * *
8728 TTTCAATTTCTGTTGTCAAAAAAATCAACTCGTATTGTGAGAGGCGAGTTGAGCCTCAGGTCACA
1 TTTCAATTTCTGTTTTCAAAAAAATCAACTCATA-TGCGAGAGGCGAGTTGAGCCTCAGG-CACA
*
8793 CGCCAAGGTAT
64 CGCCAAGGTAA
8804 TTTCAATTTCTGTTTTCAA
1 TTTCAATTTCTGTTTTCAA
8823 TTTCTGCCTT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
73 19 0.23
74 35 0.42
76 29 0.35
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (74 bp):
TTTCAATTTCTGTTTTCAAAAAAATCAACTCATATGCGAGAGGCGAGTTGAGCCTCAGGCACACG
CCAAGGTAA
Found at i:8819 original size:13 final size:13
Alignment explanation
Indices: 8803--8828 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8793 CGCCAAGGTA
8803 TTTTCAATTTCTG
1 TTTTCAATTTCTG
8816 TTTTCAATTTCTG
1 TTTTCAATTTCTG
8829 CCTTTCAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.08, T:0.62
Consensus pattern (13 bp):
TTTTCAATTTCTG
Found at i:8897 original size:92 final size:93
Alignment explanation
Indices: 8745--8915 Score: 247
Period size: 92 Copynumber: 1.8 Consensus size: 93
8735 TTCTGTTGTC
* * *
8745 AAAAAAATCAACTCGTATTGTGAGAGGCGAGTTGAGCCTCAGGTCACACGCCAAGGTATTTTCAA
1 AAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCCAAGCTATTTTCAA
8810 TTTCTGT-TTTCAATTTCTGCCTTTCAA
66 TTTCTGTCTTTCAATTTCTGCCTTTCAA
* * * **
8837 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TGGCTCACGCGCTGAGCTATTTTCA
1 AAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGG-TCACACGCCAAGCTATTTTCA
8901 ATTTCTGTCTTTCAA
65 ATTTCTGTCTTTCAA
8916 AAAAATCAAC
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
91 2 0.03
92 61 0.88
93 6 0.09
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.32
Consensus pattern (93 bp):
AAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGCCAAGCTATTTTCAA
TTTCTGTCTTTCAATTTCTGCCTTTCAA
Found at i:9039 original size:78 final size:79
Alignment explanation
Indices: 8837--9193 Score: 233
Period size: 77 Copynumber: 4.5 Consensus size: 79
8827 TGCCTTTCAA
* * * *
8837 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTA--TTTTC
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGATCACACGTTGAGGTATTTTTTC
* *
8900 AATTTCTGTCTTTC
66 AATTTATATCTTTC
** * * *
8914 AAAAAAATCAACTCATATTGTAAGAGGTGAGTTGAGCTTTAGATCACACATTGAGGTATTTTTTC
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGATCACACGTTGAGGTATTTTTTC
*
8979 AATTTATATTTTTC
66 AATTTATATCTTTC
* * * * * * * *
8993 -AAAAAATTAACTTACATTGCGAGATGTGAGTTGAGCCTCGGGTCACATGTCGAGGTATTTTCAA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGATCACACGTTGAGGTATTTT---
* * * *
9057 AATCTATTTTTCAGATTCTGTTT
63 -TTC-A-ATTT-ATA-TCT-TTC
** * * * * ** * *
9080 TCAAAAATTAACTCATATTGCGAGAAGTGAG-TGAGCCTTAGCTCACGTGCTGAGCTA--TTTTC
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGATCACACGTTGAGGTATTTTTTC
* * *
9142 -ATTTCTTTTTTTTC
66 AATTT-ATATCTTTC
9156 AAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGC
1 AAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGC
9194 TTTTTAATTT
Statistics
Matches: 214, Mismatches: 52, Indels: 27
0.73 0.18 0.09
Matches are distributed among these distances:
76 7 0.03
77 73 0.34
78 57 0.27
79 16 0.07
81 2 0.01
82 2 0.01
83 1 0.00
84 3 0.01
85 4 0.02
86 2 0.01
87 21 0.10
88 26 0.12
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.36
Consensus pattern (79 bp):
AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGATCACACGTTGAGGTATTTTTTC
AATTTATATCTTTC
Found at i:9051 original size:247 final size:238
Alignment explanation
Indices: 8653--9196 Score: 632
Period size: 243 Copynumber: 2.2 Consensus size: 238
8643 CAATTTCCGT
* * *
8653 TTTTCAATTCCTGTCTTTCAAAAAAATCAACTCATA-TGCGAGAGGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTTAGGACA
* * ** *
8717 CGCTGAGGTAATTTCAATTTCTGTTGTCAAAAAAATCAACTCGTATTGTGAGAGGCGAGTTGAGC
66 CACTGAGGTAATTTCAATTTATGTTGTCAAAAAAATCAACTCACATTGCGAGAGGCGAGTTGAGC
**
8782 CTCAGGTCACACGCCAAGGTATTTTCAATTTCT-GTTTTCA-ATTTCTGCCTTTCAAAAAAAAAT
131 CTCAGGTCACACGCCAAGGTATTTTCAAAATCTAGTTTTCAGA-TTCTG-CTTTC----AAAAAT
* *
8845 CAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTA
190 CAACTCATATTGCGAGAAGTGAG-TGAGCCTTAGCTCACGCGCTGAGCTA
**
8895 TTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGTAAGAGGTGAGTTGAGCTTTA-GATC
1 TTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTTAGGA-C
* * * * * * *
8959 ACACATTGAGGTATTTTTTCAATTTATATTTTTC-AAAAAATTAACTTACATTGCGAGATGTGAG
65 ACAC--TGAGGTA--ATTTCAATTTAT-GTTGTCAAAAAAATCAACTCACATTGCGAGAGGCGAG
* * * * * *
9023 TTGAGCCTCGGGTCACATGTCGAGGTATTTTCAAAATCTATTTTTCAGATTCTGTTTTCAAAAAT
125 TTGAGCCTCAGGTCACACGCCAAGGTATTTTCAAAATCTAGTTTTCAGATTCTGCTTTCAAAAAT
* *
9088 TAACTCATATTGCGAGAAGTGAGTGAGCCTTAGCTCACGTGCTGAGCTA
190 CAACTCATATTGCGAGAAGTGAGTGAGCCTTAGCTCACGCGCTGAGCTA
* *
9137 TTTTC-ATTTCTTTTTTTTCAAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCTTT
1 TTTTCAATTTC-TGTCTTTCAAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCTTT
9197 TTAATTTCTG
Statistics
Matches: 258, Mismatches: 33, Indels: 21
0.83 0.11 0.07
Matches are distributed among these distances:
241 5 0.02
242 79 0.31
243 81 0.31
245 7 0.03
247 70 0.27
248 15 0.06
249 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (238 bp):
TTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTTAGGACA
CACTGAGGTAATTTCAATTTATGTTGTCAAAAAAATCAACTCACATTGCGAGAGGCGAGTTGAGC
CTCAGGTCACACGCCAAGGTATTTTCAAAATCTAGTTTTCAGATTCTGCTTTCAAAAATCAACTC
ATATTGCGAGAAGTGAGTGAGCCTTAGCTCACGCGCTGAGCTA
Found at i:9190 original size:243 final size:239
Alignment explanation
Indices: 8653--9351 Score: 704
Period size: 247 Copynumber: 2.9 Consensus size: 239
8643 CAATTTCCGT
* * *
8653 TTTTCAATTCCTGTCTTTCAAAAAAATCAACTCATA-TGCGAGAGGTGAGTTGAGCCTCAGGA-C
1 TTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTTA-GATC
* * * * * * *
8716 ACGC--TGAGGTA-ATTTCAATTTCTGTTGTCAAAAAAATCAACTCGTATTGTGAGAGGCGAGTT
65 ACACATTGAGGTATTTTTCAATTTCTATTTTC-AAAAAATCAACTCATATTGCGAGA-GTGAGTT
* * * ** * *
8778 GAGCCTCAGGTCACACGCCAAGGTATTTTCAATTTCTGTTTTCAATTTCTGCCTTTCAAAAAAAA
128 GAGCCTCAGGTCACATGTCGAGGTATTTTCAAAATCTCTTTTCAAGTTCTG--TTTC---AAAAA
* *
8843 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGCGCTGAGCTA
188 ATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTAGCTCACGCGCTGAGCTA
**
8895 TTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGTAAGAGGTGAGTTGAGCTTTAGATCA
1 TTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTTAGATCA
* * * *
8960 CACATTGAGGTATTTTTTCAATTTATATTTTTCAAAAAATTAACTTACATTGCGAGATGTGAGTT
66 CACATTGAGGTA-TTTTTCAATTTCTA-TTTTCAAAAAATCAACTCATATTGCGAGA-GTGAGTT
* *
9025 GAGCCTCGGGTCACATGTCGAGGTATTTTCAAAATCTATTTTTC-AGATTCTGTTTTC-AAAAAT
128 GAGCCTCAGGTCACATGTCGAGGTATTTTCAAAATCT-CTTTTCAAG-TTCTG-TTTCAAAAAAT
* *
9088 TAACTCATATTGCGAGAAGTGAG-TGAGCCTTAGCTCACGTGCTGAGCTA
190 CAACTCATATTGCGAGAAGTGAGTTGAGCCTTAGCTCACGCGCTGAGCTA
* *
9137 TTTTC-ATTTCTTTTTTTTCAAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCTTTTTA-
1 TTTTCAATTTC-TGTCTTTCAAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGC--TTTAG
* * * *
9200 ATTTCTGCGAGAGTTGAGTTGAGTCTTTT-AATTTCTATTTTCAAAAAATCAACTCATATTACGA
62 A--TC-AC-ACA-TTGAGGT-A-T-TTTTCAATTTCTATTTTCAAAAAATCAACTCATATTGCGA
* * **
9264 GAGTGAGTTGAACCTCCA-GTCACATATCGAGGTATTTTCAAAATCTGCTTTTCAAGTTAAG-TT
119 GAGTGAGTTGAGCCT-CAGGTCACATGTCGAGGTATTTTCAAAATCT-CTTTTCAAGTTCTGTTT
9327 CAAAAAATCAACTCATATTGCGAGA
182 CAAAAAATCAACTCATATTGCGAGA
9352 GAGTAGAGAA
Statistics
Matches: 383, Mismatches: 51, Indels: 41
0.81 0.11 0.09
Matches are distributed among these distances:
241 5 0.01
242 79 0.21
243 78 0.20
244 1 0.00
245 11 0.03
246 5 0.01
247 94 0.25
248 63 0.16
249 34 0.09
250 9 0.02
251 4 0.01
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (239 bp):
TTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTTAGATCA
CACATTGAGGTATTTTTCAATTTCTATTTTCAAAAAATCAACTCATATTGCGAGAGTGAGTTGAG
CCTCAGGTCACATGTCGAGGTATTTTCAAAATCTCTTTTCAAGTTCTGTTTCAAAAAATCAACTC
ATATTGCGAGAAGTGAGTTGAGCCTTAGCTCACGCGCTGAGCTA
Found at i:9211 original size:30 final size:30
Alignment explanation
Indices: 9175--9235 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
9165 CAACTCATAT
9175 TGCGAGAGGTGAGTTGAG-CTTTTTAATTTC
1 TGCGAGAGGTGAGTTGAGTC-TTTTAATTTC
*
9205 TGCGAGAGTTGAGTTGAGTCTTTTAATTTC
1 TGCGAGAGGTGAGTTGAGTCTTTTAATTTC
9235 T
1 T
9236 ATTTTCAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.20, C:0.10, G:0.28, T:0.43
Consensus pattern (30 bp):
TGCGAGAGGTGAGTTGAGTCTTTTAATTTC
Found at i:10010 original size:25 final size:24
Alignment explanation
Indices: 9940--10010 Score: 101
Period size: 25 Copynumber: 2.9 Consensus size: 24
9930 AGCCCTCCCC
9940 AAAAAAAA-AAAAACCTAA-CCAA
1 AAAAAAAAGAAAAACCTAACCCAA
9962 AAAAAAGAAGAAAAAACCTAACCCAA
1 AAAAAA-AAG-AAAAACCTAACCCAA
9988 AAAGAAAAAGAAAAACCTAACCC
1 AAA-AAAAAGAAAAACCTAACCC
10011 CCCCCAAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.14
23 2 0.05
25 23 0.52
26 10 0.23
27 3 0.07
ACGTcount: A:0.70, C:0.20, G:0.06, T:0.04
Consensus pattern (24 bp):
AAAAAAAAGAAAAACCTAACCCAA
Found at i:12961 original size:24 final size:24
Alignment explanation
Indices: 12929--12989 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
12919 TGATGAGGGG
*
12929 AATATATATT-TATATATTAAAATA
1 AATATATATTGAAT-TATTAAAATA
* *
12953 AATATATATTGAATTTTTTAAATA
1 AATATATATTGAATTATTAAAATA
12977 AATATATATTGAA
1 AATATATATTGAA
12990 ATTTATTGAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 31 0.94
25 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (24 bp):
AATATATATTGAATTATTAAAATA
Found at i:14260 original size:106 final size:105
Alignment explanation
Indices: 14068--14262 Score: 354
Period size: 106 Copynumber: 1.8 Consensus size: 105
14058 AATCCGGAGG
* *
14068 AATTACATAGTTTGTTTTAAAAACTCAGAAGTTTAATCCTAGCTTTTGGAATCATGAAATCTAAA
1 AATTACATAGTTTGTTTTAAAAACTCAGAAATTTAATCCTAGCTTTTGAAATCATGAAATCTAAA
14133 AATATCATTTTCAGCCAAAACATTGACATGTTATTTTGGA
66 AATATCATTTTCAGCCAAAACATTGACATGTTATTTTGGA
*
14173 AATTACATTAGTTTGTTTTAAAAACTCAGAAATTTAATCCTAGCTTTTGAAATCGTGAAATCTAA
1 AATTACA-TAGTTTGTTTTAAAAACTCAGAAATTTAATCCTAGCTTTTGAAATCATGAAATCTAA
14238 AAATATCATTTTCAGCCAAAACATT
65 AAATATCATTTTCAGCCAAAACATT
14263 TGTAACGCCC
Statistics
Matches: 86, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
105 7 0.08
106 79 0.92
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (105 bp):
AATTACATAGTTTGTTTTAAAAACTCAGAAATTTAATCCTAGCTTTTGAAATCATGAAATCTAAA
AATATCATTTTCAGCCAAAACATTGACATGTTATTTTGGA
Found at i:14636 original size:25 final size:25
Alignment explanation
Indices: 14602--14649 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
14592 AATTGTAATA
14602 GGTTAGGTAAATGTTCCATGATATG
1 GGTTAGGTAAATGTTCCATGATATG
*
14627 GGTTAGGTAAATGTTTCATGATA
1 GGTTAGGTAAATGTTCCATGATA
14650 AGAATTTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.06, G:0.27, T:0.38
Consensus pattern (25 bp):
GGTTAGGTAAATGTTCCATGATATG
Found at i:19051 original size:24 final size:25
Alignment explanation
Indices: 19003--19052 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
18993 ATTGTATATG
*
19003 TATATTTCCTTAAATAATAAGTAAA
1 TATATTTCATTAAATAATAAGTAAA
* *
19028 TATATTT-ATTAAATATTAATTAAA
1 TATATTTCATTAAATAATAAGTAAA
19052 T
1 T
19053 TATAAATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (25 bp):
TATATTTCATTAAATAATAAGTAAA
Found at i:22219 original size:26 final size:26
Alignment explanation
Indices: 22181--22260 Score: 112
Period size: 26 Copynumber: 3.2 Consensus size: 26
22171 TGATACAAAT
*
22181 TGATAATGTGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
22207 TGATAATGGGTTAGG--CAT-TTACCA
1 TGATAATGGGTTAGGTAAATGTT-CCA
22231 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
22257 TGAT
1 TGAT
22261 GGGAATTTCA
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
23 2 0.04
24 20 0.43
26 23 0.49
27 2 0.04
ACGTcount: A:0.30, C:0.09, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Done.