Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013767.1 Kokia drynarioides strain JFW-HI SEQ_128795, 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: 205168
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 78 characters in sequence are not A, C, G, or T
Found at i:181 original size:3 final size:3
Alignment explanation
Indices: 173--221 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
163 ACAATTTCAT
* *
173 TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TTAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
219 TAA
1 TAA
222 ATAAAAAAGG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:489 original size:19 final size:19
Alignment explanation
Indices: 453--491 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
443 AAAAAAAGGG
*
453 AGGAGTAAAAGGGAGAAGA
1 AGGAGTAAAACGGAGAAGA
472 AGGAGTAAAAACGG-GAAGA
1 AGGAGT-AAAACGGAGAAGA
491 A
1 A
492 AGGACTTTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.54, C:0.03, G:0.38, T:0.05
Consensus pattern (19 bp):
AGGAGTAAAACGGAGAAGA
Found at i:1179 original size:28 final size:29
Alignment explanation
Indices: 1143--1284 Score: 101
Period size: 29 Copynumber: 4.9 Consensus size: 29
1133 ATAGGTCCCT
* *
1143 AACTGTCCAAAATT-TTTTTTTACCCTCG
1 AACTTTCCAAAATTACTTTTTTACCCTCG
* * *
1171 AACTTTCCAAAATTCCATTTTTAACCT-G
1 AACTTTCCAAAATTACTTTTTTACCCTCG
* ** *
1199 AATTTTTCCAAAATTACCATTTTACCCCCG
1 AA-CTTTCCAAAATTACTTTTTTACCCTCG
* * *
1229 AAC-TTCCAAAAATTTCTTTTTTAGCGTCG
1 AACTTTCC-AAAATTACTTTTTTACCCTCG
** *
1258 ATTTTTCCAACAATTACATTTTTACCC
1 AACTTTCCAA-AATTACTTTTTTACCC
1285 CTAAATTTTT
Statistics
Matches: 85, Mismatches: 23, Indels: 10
0.72 0.19 0.08
Matches are distributed among these distances:
28 20 0.24
29 46 0.54
30 19 0.22
ACGTcount: A:0.29, C:0.25, G:0.05, T:0.41
Consensus pattern (29 bp):
AACTTTCCAAAATTACTTTTTTACCCTCG
Found at i:1206 original size:29 final size:29
Alignment explanation
Indices: 1159--1343 Score: 116
Period size: 29 Copynumber: 6.3 Consensus size: 29
1149 CCAAAATTTT
*
1159 TTTTTACCCTCGAA-CTTTCCAAAATTCCA
1 TTTTTACCCT-GAATTTTTCCAAAATTCCA
*
1188 TTTTTAACCTGAATTTTTCCAAAATTACCA
1 TTTTTACCCTGAATTTTTCCAAAATT-CCA
* * * *
1218 -TTTTACCCCCGAA--CTTCCAAAAATTTCT
1 TTTTTA-CCCTGAATTTTTCC-AAAATTCCA
* * *
1246 TTTTTAGCGTCG-ATTTTTCCAACAATTACA
1 TTTTTACCCT-GAATTTTTCCAA-AATTCCA
* *
1276 TTTTTACCCCTAAATTTTT-CATAATTCCA
1 TTTTTA-CCCTGAATTTTTCCAAAATTCCA
* *
1305 TTTTTGGCCCCG-ATTTTTCCAAAATTACCA
1 TTTTT-ACCCTGAATTTTTCCAAAATT-CCA
1335 -TTTTACCCT
1 TTTTTACCCT
1344 CGGATGTCTA
Statistics
Matches: 118, Mismatches: 24, Indels: 29
0.69 0.14 0.17
Matches are distributed among these distances:
28 19 0.16
29 63 0.53
30 28 0.24
31 8 0.07
ACGTcount: A:0.27, C:0.26, G:0.05, T:0.42
Consensus pattern (29 bp):
TTTTTACCCTGAATTTTTCCAAAATTCCA
Found at i:1241 original size:58 final size:57
Alignment explanation
Indices: 1160--1472 Score: 181
Period size: 58 Copynumber: 5.4 Consensus size: 57
1150 CAAAATTTTT
*
1160 TTTTACCCTCGAACTTTCC-AAAATTCCATTTTTAACCTGAATTTTTCCAAAATTACCA
1 TTTTACCCCCGAA--TTCCAAAAATTCCATTTTTAACCTGAATTTTTCCAAAATTACCA
* * * *
1218 TTTTACCCCCGAACTTCCAAAAATTTCTTTTTTAGCGTCG-ATTTTTCCAACAATTA-CA
1 TTTTACCCCCGAA-TTCCAAAAATTCCATTTTTAACCT-GAATTTTTCCAA-AATTACCA
** * * ** *
1276 TTTTTACCCCTAAATTTTTC-ATAATTCCATTTTTGGCCCCG-ATTTTTCCAAAATTACCA
1 -TTTTACCCCCGAA--TTCCAAAAATTCCATTTTT-AACCTGAATTTTTCCAAAATTACCA
* * * * * * * * *
1335 TTTTACCCTCGGATGTCTAAAAATTTCATTTTAAACCTTGAA-CTTCCCAAAAATCACAA
1 TTTTACCCCCGAAT-TCCAAAAATTCCATTTTTAACC-TGAATTTTTCC-AAAATTACCA
* * * * * * *
1394 TTTTACCCCTGAATGTCTAAAAATTCC-TTTTTGACCCGAACTTTCCCAATATTACCA
1 TTTTACCCCCGAAT-TCCAAAAATTCCATTTTTAACCTGAATTTTTCCAAAATTACCA
**
1451 TTTTACCCTTGAATGTCCAAAA
1 TTTTACCCCCGAAT-TCCAAAA
1473 TCACCATTTT
Statistics
Matches: 196, Mismatches: 46, Indels: 27
0.73 0.17 0.10
Matches are distributed among these distances:
56 1 0.01
57 37 0.19
58 81 0.41
59 73 0.37
60 4 0.02
ACGTcount: A:0.30, C:0.26, G:0.06, T:0.39
Consensus pattern (57 bp):
TTTTACCCCCGAATTCCAAAAATTCCATTTTTAACCTGAATTTTTCCAAAATTACCA
Found at i:1398 original size:117 final size:116
Alignment explanation
Indices: 1179--1472 Score: 288
Period size: 117 Copynumber: 2.5 Consensus size: 116
1169 CGAACTTTCC
* * *
1179 AAAATTCCATTTTTAACCTGAATTTTTCCAAAATTACCATTTTACCCCCGAACTTCCAAAAATTT
1 AAAATTCC-TTTTTGACCCGAATTTTTCCAAAATTACCATTTTACCCTCGAACTTCCAAAAATTT
* * * * ** * * * * * * *
1244 CTTTTTTAGCGTCGATTTTTCCAACAATTACATTTTTACCCCTAAATTTTTC
65 CATTTTAAACCTCGAACTTCCCAAAAATCACAATTTTACCCCTAAATGTCTA
* * * *
1296 ATAATTCCATTTTTGGCCCCG-ATTTTTCCAAAATTACCATTTTACCCTCGGA-TGTCTAAAAAT
1 AAAATTCC-TTTTT-GACCCGAATTTTTCCAAAATTACCATTTTACCCTCGAACT-TCCAAAAAT
* *
1359 TTCATTTTAAACCTTGAACTTCCCAAAAATCACAATTTTACCCCTGAATGTCTA
63 TTCATTTTAAACCTCGAACTTCCCAAAAATCACAATTTTACCCCTAAATGTCTA
* * * *
1413 AAAATTCCTTTTTGACCCGAACTTTCCCAATATTACCATTTTACCCTTGAA-TGTCCAAAA
1 AAAATTCCTTTTTGACCCGAATTTTTCCAAAATTACCATTTTACCCTCGAACT-TCCAAAA
1473 TCACCATTTT
Statistics
Matches: 144, Mismatches: 30, Indels: 7
0.80 0.17 0.04
Matches are distributed among these distances:
115 5 0.03
116 40 0.28
117 96 0.67
118 3 0.02
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.38
Consensus pattern (116 bp):
AAAATTCCTTTTTGACCCGAATTTTTCCAAAATTACCATTTTACCCTCGAACTTCCAAAAATTTC
ATTTTAAACCTCGAACTTCCCAAAAATCACAATTTTACCCCTAAATGTCTA
Found at i:1464 original size:57 final size:58
Alignment explanation
Indices: 1323--1472 Score: 169
Period size: 57 Copynumber: 2.6 Consensus size: 58
1313 CCCGATTTTT
* * *
1323 CCAAAATTACCATTTTACCCTCGGATGTCTAAAAATTTCATTTTAAACCTTGAACTTC
1 CCAAAATTACCATTTTACCCTTGAATGTCTAAAAATTTCATTTTAAACCTCGAACTTC
* * * * **
1381 CCAAAAATCACAATTTTACCCCTGAATGTCTAAAAA-TTCCTTTTTGACC-CGAACTTTC
1 CC-AAAATTACCATTTTACCCTTGAATGTCTAAAAATTTCATTTTAAACCTCGAAC-TTC
* *
1439 CCAATATTACCATTTTACCCTTGAATGTCCAAAA
1 CCAAAATTACCATTTTACCCTTGAATGTCTAAAA
1473 TCACCATTTT
Statistics
Matches: 76, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
57 31 0.41
58 17 0.22
59 28 0.37
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.34
Consensus pattern (58 bp):
CCAAAATTACCATTTTACCCTTGAATGTCTAAAAATTTCATTTTAAACCTCGAACTTC
Found at i:3710 original size:29 final size:29
Alignment explanation
Indices: 3665--3947 Score: 194
Period size: 30 Copynumber: 9.7 Consensus size: 29
3655 TGGATGCCCG
*
3665 AGGGTAAAATGGTAATTTTTGGAAAGTTC
1 AGGGTAAAATGGTAATTTTTGGAAAGTTT
* *
3694 AAGGTCAAAATGG-AATTTTT-GAAA-ATT
1 AGGGT-AAAATGGTAATTTTTGGAAAGTTT
* ** *
3721 CGGGATAAAATGGTAATTTTTAAAAATTTT
1 AGGG-TAAAATGGTAATTTTTGGAAAGTTT
3751 AGGGTTAAAAGTGG-AATTTTTGGAAA-TTT
1 AGGG-TAAAA-TGGTAATTTTTGGAAAGTTT
* *
3780 AGGGGTAAAATGGTAA-TTTTGGGAAGTTC
1 A-GGGTAAAATGGTAATTTTTGGAAAGTTT
* *
3809 ATGGGCAAAAATGAG-ATTTTTTGG-AAGTTT
1 A-GGG-TAAAATG-GTAATTTTTGGAAAGTTT
*
3839 GAGAGTAAAATGGTAATTTTTGG-AAGTTT
1 -AGGGTAAAATGGTAATTTTTGGAAAGTTT
*
3868 AGGGGCAAAAAT-GTAATTTTTGTG-AAGTTT
1 A-GGG-TAAAATGGTAATTTTTG-GAAAGTTT
** *
3898 AGGGGTAAAATATTAATTTTTGAAAAGTTT
1 A-GGGTAAAATGGTAATTTTTGGAAAGTTT
* *
3928 GGGGTTCAAATGG-AATTTTT
1 AGGG-TAAAATGGTAATTTTT
3948 AGGGTTTAGG
Statistics
Matches: 205, Mismatches: 29, Indels: 40
0.75 0.11 0.15
Matches are distributed among these distances:
27 10 0.05
28 25 0.12
29 78 0.38
30 81 0.40
31 11 0.05
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.37
Consensus pattern (29 bp):
AGGGTAAAATGGTAATTTTTGGAAAGTTT
Found at i:3830 original size:59 final size:58
Alignment explanation
Indices: 3666--3922 Score: 218
Period size: 59 Copynumber: 4.4 Consensus size: 58
3656 GGATGCCCGA
* * * *
3666 GGGTAAAATGGTAATTTTTGGAAAGTTCAAGGTC-AAAATGGAATTTTT-GAAAATTCG
1 GGGTAAAATGGTAA-TTTTGGAAAGTTCATGGGCAAAAATGGAATTTTTGGAAATTTAG
* ** * * * *
3723 GGATAAAATGGTAATTTTTAAAAATT-TTAGGGTTAAAAGTGGAATTTTTGGAAATTTAG
1 GGGTAAAATGGTAATTTTGGAAAGTTCAT-GGG-CAAAAATGGAATTTTTGGAAATTTAG
* * *
3782 GGGTAAAATGGTAATTTTGGGAAGTTCATGGGCAAAAATGAGATTTTTTGGAAGTTT-G
1 GGGTAAAATGGTAATTTTGGAAAGTTCATGGGCAAAAATG-GAATTTTTGGAAATTTAG
* * * * *
3840 AGAGTAAAATGGTAATTTTTGG-AAGTTTAGGGGCAAAAATGTAATTTTTGTGAAGTTTAG
1 -GGGTAAAATGGTAA-TTTTGGAAAGTTCATGGGCAAAAATGGAATTTTTG-GAAATTTAG
** *
3900 GGGTAAAATATTAATTTTTGAAA
1 GGGTAAAATGGTAATTTTGGAAA
3923 AGTTTGGGGT
Statistics
Matches: 159, Mismatches: 30, Indels: 20
0.76 0.14 0.10
Matches are distributed among these distances:
56 11 0.07
57 13 0.08
58 32 0.20
59 95 0.60
60 8 0.05
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.36
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTGGAAAGTTCATGGGCAAAAATGGAATTTTTGGAAATTTAG
Found at i:5501 original size:17 final size:18
Alignment explanation
Indices: 5452--5502 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 18
5442 TTTTATTTCA
*
5452 AAATAAATTTAAAC-TCC
1 AAATAAATTTAAACTTAC
**
5469 AAATAAGCTTAAACTTAC
1 AAATAAATTTAAACTTAC
5487 -AATAAATTTAAACTTA
1 AAATAAATTTAAACTTA
5503 AAAAGAATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
17 26 0.93
18 2 0.07
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.31
Consensus pattern (18 bp):
AAATAAATTTAAACTTAC
Found at i:6275 original size:209 final size:208
Alignment explanation
Indices: 5906--6685 Score: 929
Period size: 209 Copynumber: 3.7 Consensus size: 208
5896 CTCTCGGTTT
* * * * * * *
5906 ACTTCTCTATATCTCATCAGGAAGTTAATCACTTTATTGCTTCGACTTGCTTCTTAGTATGTCAT
1 ACTTCTCTGTATCTCATCAGGAAGCTAACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTAAT
* * * * * *
5971 CAGGAAGCTGTGGTTCGAAGATTTGCTCACTTTGAGTCTAGTTTCATTGATTTGATCTACTTCTC
66 CA-GAAGCTGGGGTTCGAAGATTTGCTCACATTGAGTCTGGTTTCATTGAGTTGGTATACTTCTC
* * * *
6036 AGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTGTGTCTCATCAGGAA
130 AATATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCGCTTCTCTGTATCTCATCAGGAA
6101 GACGAATCTAGTTC
195 GACGAATCTAGTTC
*
6115 ACTTATCTGTATCTCATCAGGAAGCTAACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTAAT
1 ACTTCTCTGTATCTCATCAGGAAGCTAACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTAAT
* * *
6180 CAGTAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGTCTGGTTTCATTGATTTGGTTTACTTCTC
66 CAG-AAGCTGGGGTTCGAAGATTTGCTCACATTGAGTCTGGTTTCATTGAGTTGGTATACTTCTC
* *
6245 AATATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCGCTTCTCTATATCTTATCAGGAA
130 AATATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCGCTTCTCTGTATCTCATCAGGAA
*
6310 GACGAATCTTGTTC
195 GACGAATCTAGTTC
* * * * * * *
6324 ACTTCTCTGTATCTCATCAGGAAGTTGACTATTTTATTGCTTCGACCCGCTTCTTAGTATCTCAT
1 ACTTCTCTGTATCTCATCAGGAAGCTAACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTAAT
* * * * * * *
6389 CAAGAAGCT-AGGTTCGAAGTTTTCCTCCCATCGAGCTTTGGTTTCATTGAGCTGGTATACTTCT
66 C-AGAAGCTGGGGTTCGAAGATTTGCTCACATTGAG-TCTGGTTTCATTGAGTTGGTATACTTCT
** * * *
6453 CTGTATCTCATCAGGAAGATGACCACCTCACTTGTTTTAATTCGCTTCTCTGTATCTCATCAGGA
129 CAATATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCGCTTCTCTGTATCTCATCAGGA
* *
6518 AGACGAATTTGGTTC
194 AGACGAATCTAGTTC
* * * * *
6533 ACTTCTCTGTACCGCATTAGGAAGCTAACCATTTTATTGCGTCGACCTGCTTCTCAGTATC-ATA
1 ACTTCTCTGTATCTCATCAGGAAGCTAACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTA-A
* ** * * *
6597 TTAGAAATTTGGGGTTCAAAG-TTTCGCTCACATTGAG-CTTTGTTTCATTGAGATGGTATACTT
65 TCAG-AAGCTGGGGTTCGAAGATTT-GCTCACATTGAGTC-TGGTTTCATTGAGTTGGTATACTT
* * *
6660 CTCTATATCTCTTCAGGAAAATGACC
127 CTCAATATCTCATCAGGAAGATGACC
6686 ACCTCGTTGT
Statistics
Matches: 493, Mismatches: 70, Indels: 16
0.85 0.12 0.03
Matches are distributed among these distances:
208 23 0.05
209 451 0.91
210 19 0.04
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (208 bp):
ACTTCTCTGTATCTCATCAGGAAGCTAACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTAAT
CAGAAGCTGGGGTTCGAAGATTTGCTCACATTGAGTCTGGTTTCATTGAGTTGGTATACTTCTCA
ATATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCGCTTCTCTGTATCTCATCAGGAAG
ACGAATCTAGTTC
Found at i:18858 original size:30 final size:29
Alignment explanation
Indices: 18768--19231 Score: 228
Period size: 29 Copynumber: 15.9 Consensus size: 29
18758 GGATGCCCGA
*
18768 GGGTAAAATAGTAATTTTTGAAAAGTTT-G
1 GGGTAAAATGGTAATTTTTG-AAAGTTTAG
* * *
18797 AGATCAAAAAT-GAAATTTTTGGAAA-TTTAG
1 GGGT--AAAATGGTAATTTTT-GAAAGTTTAG
18827 GGGTAAAATGGTAATTTTTGAAAAGTTTAG
1 GGGTAAAATGGTAATTTTTG-AAAGTTTAG
* * *
18857 GGTTAAAAT--TAGATTTTTTGGAAA-TTCAA
1 GGGTAAAATGGTA-A-TTTTT-GAAAGTTTAG
* * * * *
18886 GGGTAAAATCGTAATTTTAGGAAGTTCAA
1 GGGTAAAATGGTAATTTTTGAAAGTTTAG
** *
18915 ATGTAAAAAT-G-AGATTTTTGAAAG-TTCG
1 GGGT-AAAATGGTA-ATTTTTGAAAGTTTAG
* * *
18943 AGAGTAAAATGGTAATTTTTGGAAG-TTCG
1 -GGGTAAAATGGTAATTTTTGAAAGTTTAG
* * ** * *
18972 TGAGCAAAATTTTAATTTTTGTGAAGTTCAG
1 -GGGTAAAATGGTAATTTTTG-AAAGTTTAG
19003 GGGTAAAATGGTAATTTTTGAAAAGTTTAG
1 GGGTAAAATGGTAATTTTTG-AAAGTTTAG
* *
19033 GGTTAAAAATGG-AATTTTTGGAAA--TTCG
1 GGGT-AAAATGGTAATTTTT-GAAAGTTTAG
* * ** *
19061 AGGTAAAAGGGTAATTTTCAAAAG-TTAA
1 GGGTAAAATGGTAATTTTTGAAAGTTTAG
* *
19089 AGCTCAAAATGG-AATTTTTGGAAA-TTTAG
1 GGGT-AAAATGGTAATTTTT-GAAAGTTTAG
* *
19118 GGGTAAAATAGTAATTTTTGGAAG-TTAG
1 GGGTAAAATGGTAATTTTTGAAAGTTTAG
* * *
19146 GGAGCAAAATAGG-ATTTTTTGGAAGTTTAG
1 GG-GTAAAAT-GGTAATTTTTGAAAGTTTAG
* *
19176 GGGTAAAATGGTAATTTTGGAAAGTTCAAG
1 GGGTAAAATGGTAATTTTTGAAAGTT-TAG
*
19206 GGTTAAAAT-GTAATTTTTAGAAAGTT
1 GGGTAAAATGGTAATTTTT-GAAAGTT
19232 CAAGGGTTAA
Statistics
Matches: 337, Mismatches: 63, Indels: 69
0.72 0.13 0.15
Matches are distributed among these distances:
27 9 0.03
28 57 0.17
29 146 0.43
30 106 0.31
31 19 0.06
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.36
Consensus pattern (29 bp):
GGGTAAAATGGTAATTTTTGAAAGTTTAG
Found at i:18950 original size:117 final size:116
Alignment explanation
Indices: 18768--19255 Score: 338
Period size: 117 Copynumber: 4.2 Consensus size: 116
18758 GGATGCCCGA
* ** * * * * *
18768 GGGTAAAATAGTAATTTTTGAAAAGTTTGAGATCAAAAATGAAATTTTTGGAAATTTAGGGGTAA
1 GGGTAAAATAGTAATTTTTG-GAAGTTAAAGGTTAAAAATGAGATTTTTGGAAA-TTCGAGGTAA
* * *
18833 AATGGTAATTTTTGAAAAGTTTAGGGTTAAAATTAGATTTTTTGGAAATTCAA
64 AATGGTAATTTTTGAAAAGTTTAGGGTCAAAATTAGAATTTTTGGAAATTCAG
* * *
18886 GGGTAAAATCGTAATTTTAGGAAGTTCAAATG-TAAAAATGAGATTTTT-GAAAGTTCGAGAGTA
1 GGGTAAAATAGTAATTTTTGGAAGTT-AAAGGTTAAAAATGAGATTTTTGGAAA-TTCGAG-GTA
* * ** *
18949 AAATGGTAATTTTTG-GAAGTTCGT-GAG-CAAAATTTTAATTTTTGTGAAGTTCAG
63 AAATGGTAATTTTTGAAAAGTT--TAGGGTCAAAATTAGAATTTTTG-GAAATTCAG
* * * *
19003 GGGTAAAATGGTAATTTTTGAAAAGTTTAGGGTTAAAAATG-GAATTTTTGGAAATTCGAGGTAA
1 GGGTAAAATAGTAATTTTTG-GAAGTTAAAGGTTAAAAATGAG-ATTTTTGGAAATTCGAGGTAA
* * * * * * *
19067 AAGGGTAA-TTTTCAAAAGTTAAAGCTCAAAA-TGGAATTTTTGGAAATTTAG
64 AATGGTAATTTTTGAAAAGTTTAGGGTCAAAATTAGAATTTTTGGAAATTCAG
* *** * * *
19118 GGGTAAAATAGTAATTTTTGGAAGTT-AGGGAGCAAAAT-AGGATTTTTTGGAAGTTTAGGGGTA
1 GGGTAAAATAGTAATTTTTGGAAGTTAAAGGTTAAAAATGA-GA-TTTTTGGAA-ATTCGAGGTA
* * * *
19181 AAATGGTAA-TTTTGGAAAGTTCAAGGGTTAAAA-T-GTAATTTTTAGAAAGTTCAAG
63 AAATGGTAATTTTTGAAAAGTT-TAGGGTCAAAATTAG-AATTTTTGGAAA-TTC-AG
* *
19236 GGTTAAAATA-TGATTTTTGG
1 GGGTAAAATAGTAATTTTTGG
19256 GCAATAAAAC
Statistics
Matches: 295, Mismatches: 55, Indels: 41
0.75 0.14 0.10
Matches are distributed among these distances:
113 10 0.03
114 15 0.05
115 52 0.18
116 59 0.20
117 99 0.34
118 56 0.19
119 4 0.01
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.36
Consensus pattern (116 bp):
GGGTAAAATAGTAATTTTTGGAAGTTAAAGGTTAAAAATGAGATTTTTGGAAATTCGAGGTAAAA
TGGTAATTTTTGAAAAGTTTAGGGTCAAAATTAGAATTTTTGGAAATTCAG
Found at i:19223 original size:58 final size:58
Alignment explanation
Indices: 18768--19228 Score: 334
Period size: 58 Copynumber: 7.9 Consensus size: 58
18758 GGATGCCCGA
* * * * *
18768 GGGTAAAATAGTAATTTTTGAAAAGTT-TGAGATCAAAAATGAAATTTTTGGAAATTTAG
1 GGGTAAAATGGTAATTTTTGGAAAGTTAAG-GGTC-AAAATGGAATTTTTGGAAATTTAG
* * * * * * *
18827 GGGTAAAATGGTAATTTTTGAAAAGTTTAGGGTTAAAATTAGATTTTTTGGAAATTCAA
1 GGGTAAAATGGTAATTTTTGGAAAGTTAAGGGTCAAAA-TGGAATTTTTGGAAATTTAG
* * ** * * *
18886 GGGTAAAATCGTAATTTTAGG-AAGTTCAAATGTAAAAAT-GAGATTTTT-GAAAGTTCG
1 GGGTAAAATGGTAATTTTTGGAAAGTT-AAGGGTCAAAATGGA-ATTTTTGGAAATTTAG
* * ** * *
18943 AGAGTAAAATGGTAATTTTTGG-AAGTT-CGTGAG-CAAAATTTTAATTTTTGTGAAGTTCAG
1 -GGGTAAAATGGTAATTTTTGGAAAGTTAAG-G-GTCAAAA-TGGAATTTTTG-GAAATTTAG
* * * *
19003 GGGTAAAATGGTAATTTTTGAAAAGTTTAGGGTTAAAAATGGAATTTTTGGAAA-TTCG
1 GGGTAAAATGGTAATTTTTGGAAAGTTAAGGG-TCAAAATGGAATTTTTGGAAATTTAG
* * ** * *
19061 AGGTAAAAGGGTAA-TTTTCAAAAGTTAAAGCTCAAAATGGAATTTTTGGAAATTTAG
1 GGGTAAAATGGTAATTTTTGGAAAGTTAAGGGTCAAAATGGAATTTTTGGAAATTTAG
* * * *
19118 GGGTAAAATAGTAATTTTTGG-AAGTT-AGGGAGCAAAATAGGATTTTTTGGAAGTTTAG
1 GGGTAAAATGGTAATTTTTGGAAAGTTAAGGG-TCAAAAT-GGAATTTTTGGAAATTTAG
* * *
19176 GGGTAAAATGGTAA-TTTTGGAAAGTTCAAGGGTTAAAATGTAATTTTTAGAAA
1 GGGTAAAATGGTAATTTTTGGAAAGTT-AAGGGTCAAAATGGAATTTTTGGAAA
19229 GTTCAAGGGT
Statistics
Matches: 313, Mismatches: 67, Indels: 45
0.74 0.16 0.11
Matches are distributed among these distances:
56 22 0.07
57 55 0.18
58 109 0.35
59 97 0.31
60 25 0.08
61 5 0.02
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTTGGAAAGTTAAGGGTCAAAATGGAATTTTTGGAAATTTAG
Found at i:21122 original size:17 final size:17
Alignment explanation
Indices: 21096--21134 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
21086 TTTTTATTTC
*
21096 AAAATAAATTTAAACTT
1 AAAATAAATTAAAACTT
* *
21113 AAAATGAATTAAAATTT
1 AAAATAAATTAAAACTT
21130 AAAAT
1 AAAAT
21135 CTAAAATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (17 bp):
AAAATAAATTAAAACTT
Found at i:24007 original size:26 final size:26
Alignment explanation
Indices: 23978--24029 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
23968 AAAATATCGC
*
23978 GGGAATTCTACAATTAACATTGTTAT
1 GGGAATTCTACAATCAACATTGTTAT
24004 GGGAATTCTACAATCAACATTGTTAT
1 GGGAATTCTACAATCAACATTGTTAT
24030 TGGTTTAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (26 bp):
GGGAATTCTACAATCAACATTGTTAT
Found at i:28506 original size:27 final size:27
Alignment explanation
Indices: 28471--28529 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
28461 GGTTTAAAAT
28471 TTTAAGA-TTTA-GTGTTGAGGCTTACAA
1 TTTAAGATTTTATGT-TTG-GGCTTACAA
* *
28498 TTTATGATTTTATGTTTGGGTTTACAA
1 TTTAAGATTTTATGTTTGGGCTTACAA
28525 TTTAA
1 TTTAA
28530 ACCTTTTGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
27 18 0.67
28 7 0.26
29 2 0.07
ACGTcount: A:0.27, C:0.05, G:0.19, T:0.49
Consensus pattern (27 bp):
TTTAAGATTTTATGTTTGGGCTTACAA
Found at i:37510 original size:19 final size:18
Alignment explanation
Indices: 37475--37527 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
37465 TTTGAGAAAT
*
37475 AAAAAATTTAAAA-TTCA
1 AAAAAATTAAAAAGTTCA
37492 AAAAAATATAAAAAGTTCA
1 AAAAAAT-TAAAAAGTTCA
*
37511 TAAAAATTCAAAAAGTT
1 AAAAAATT-AAAAAGTT
37528 AACATGGAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 7 0.23
18 6 0.19
19 18 0.58
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26
Consensus pattern (18 bp):
AAAAAATTAAAAAGTTCA
Found at i:42365 original size:25 final size:25
Alignment explanation
Indices: 42318--42367 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
42308 AGAAGAATAA
* *
42318 AAATAAATAAATAAATAACAAAAGT
1 AAATAAATAAAGAAATAAAAAAAGT
42343 AAATAAATAAAGAAAAATAAAAAAA
1 AAATAAATAAAG--AAATAAAAAAA
42368 TGAATTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 11 0.52
27 10 0.48
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (25 bp):
AAATAAATAAAGAAATAAAAAAAGT
Found at i:46543 original size:24 final size:24
Alignment explanation
Indices: 46499--46544 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
46489 ATTTGTAGGT
*
46499 AAAATAAATTATGCTAATAAATGC
1 AAAATAAATTATGATAATAAATGC
*
46523 AAAATATATTAT-ATAACTAAAT
1 AAAATAAATTATGATAA-TAAAT
46545 CTTCTAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.16
24 16 0.84
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (24 bp):
AAAATAAATTATGATAATAAATGC
Found at i:55993 original size:28 final size:28
Alignment explanation
Indices: 55803--55994 Score: 149
Period size: 28 Copynumber: 6.9 Consensus size: 28
55793 AAACCCAAAA
* * *
55803 TAATGCTCTTTCGAGCCAGATTACAGAA
1 TAATGCTCTTACGAGCCAGAATACAGAG
* * * *
55831 T-ATCACTCTTCCGAGCCAGAATGCAGAA
1 TAAT-GCTCTTACGAGCCAGAATACAGAG
* * *
55859 T-ATCGCTCTTCCGAGCCAGAATACAAAA
1 TAAT-GCTCTTACGAGCCAGAATACAGAG
* * *
55887 T-ATCGCTCTTTCGAGCTAGAATTCA-ATG
1 TAAT-GCTCTTACGAGCCAGAATACAGA-G
* * *
55915 TAATGCTCATACGAGCCAGAACACTGAG
1 TAATGCTCTTACGAGCCAGAATACAGAG
*
55943 TAATGCTCTTATGAGCCAGAATACAGAG
1 TAATGCTCTTACGAGCCAGAATACAGAG
* *
55971 TAATACTCTTACGAGCTAGAATAC
1 TAATGCTCTTACGAGCCAGAATAC
55995 TAAATATTTG
Statistics
Matches: 136, Mismatches: 24, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
27 3 0.02
28 130 0.96
29 3 0.02
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (28 bp):
TAATGCTCTTACGAGCCAGAATACAGAG
Found at i:63539 original size:22 final size:20
Alignment explanation
Indices: 63511--63579 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 20
63501 ATATTGATTT
63511 TTTTTGCTGTTTCTAGTGTGTG
1 TTTTTGCTGTTT-TAGTGT-TG
* *
63533 TTTTTGCTATTTTGGTGTTG
1 TTTTTGCTGTTTTAGTGTTG
**
63553 TTTTTGCTGTTATTTTTGTTG
1 TTTTTGCTGTT-TTAGTGTTG
63574 TTTTTG
1 TTTTTG
63580 TTTTTTAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
20 12 0.29
21 18 0.44
22 11 0.27
ACGTcount: A:0.04, C:0.06, G:0.23, T:0.67
Consensus pattern (20 bp):
TTTTTGCTGTTTTAGTGTTG
Found at i:65049 original size:18 final size:18
Alignment explanation
Indices: 64994--65050 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 18
64984 ATATGGATCC
*
64994 AAAATTTAATTAAATAATA
1 AAAATATAATT-AATAATA
*
65013 ATAAATATAACATTGATAATA
1 A-AAATAT-A-ATTAATAATA
65034 AAAATATAATTAATAAT
1 AAAATATAATTAATAAT
65051 TAAATAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 8 0.25
19 2 0.06
20 11 0.34
21 8 0.25
22 3 0.09
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (18 bp):
AAAATATAATTAATAATA
Found at i:65056 original size:8 final size:8
Alignment explanation
Indices: 65039--65070 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
65029 TAATAAAAAT
65039 ATAATT-A
1 ATAATTAA
65046 ATAATTAA
1 ATAATTAA
65054 ATAATTAA
1 ATAATTAA
65062 ATAATTAA
1 ATAATTAA
65070 A
1 A
65071 ATTTTACATT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 6 0.25
8 18 0.75
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATAATTAA
Found at i:69927 original size:9 final size:9
Alignment explanation
Indices: 69903--69931 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
69893 TATTGTATAA
69903 GGTGTAAAT
1 GGTGTAAAT
69912 GGT-TAAAT
1 GGTGTAAAT
69920 GGTGTAAAT
1 GGTGTAAAT
69929 GGT
1 GGT
69932 CATATGTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (9 bp):
GGTGTAAAT
Found at i:72454 original size:39 final size:39
Alignment explanation
Indices: 72400--72483 Score: 150
Period size: 39 Copynumber: 2.2 Consensus size: 39
72390 GGAACATGGA
72400 CGTGTGAGTGCCCGTGTAACCAACATTGAGTTACACGCC
1 CGTGTGAGTGCCCGTGTAACCAACATTGAGTTACACGCC
**
72439 CGTGTGAGTGCCCGTGTGTCCAACATTGAGTTACACGCC
1 CGTGTGAGTGCCCGTGTAACCAACATTGAGTTACACGCC
72478 CGTGTG
1 CGTGTG
72484 TCTAGCCATG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.19, C:0.27, G:0.29, T:0.25
Consensus pattern (39 bp):
CGTGTGAGTGCCCGTGTAACCAACATTGAGTTACACGCC
Found at i:72636 original size:63 final size:62
Alignment explanation
Indices: 72516--72636 Score: 145
Period size: 63 Copynumber: 1.9 Consensus size: 62
72506 CTTAAATAGC
* **
72516 AAAACAGTAGCCACACAAGTCTAGCACACGCCCGTGTGGCCTGGCCGTGTGTGTCAAATTAG
1 AAAACAGTAGCCACACAAGTCTAGCACACGCCCATGTGGCCTGGCCGTGTGCCTCAAATTAG
* * * * *
72578 AAAAGAGTAGCCACACACGGTCTGGCACATGCTCATGTGG-CTGGCCCGTGTGCCTCAAA
1 AAAACAGTAGCCACACA-AGTCTAGCACACGCCCATGTGGCCTGG-CCGTGTGCCTCAAA
72637 ATAGTAGCCA
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
62 20 0.41
63 29 0.59
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.19
Consensus pattern (62 bp):
AAAACAGTAGCCACACAAGTCTAGCACACGCCCATGTGGCCTGGCCGTGTGCCTCAAATTAG
Found at i:72988 original size:16 final size:17
Alignment explanation
Indices: 72969--73002 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
72959 ATAAAATATC
*
72969 AGTAATGAAA-AGGGAA
1 AGTAACGAAAGAGGGAA
72985 AGTAACGAAAGAGGGAA
1 AGTAACGAAAGAGGGAA
73002 A
1 A
73003 ACTAAAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.56, C:0.03, G:0.32, T:0.09
Consensus pattern (17 bp):
AGTAACGAAAGAGGGAA
Found at i:75457 original size:57 final size:57
Alignment explanation
Indices: 75369--75487 Score: 238
Period size: 57 Copynumber: 2.1 Consensus size: 57
75359 AATGGGTTAA
75369 GGTGAATGTGGATGGCTCGGTGTTAACAACGAGACCAAAGGCATCCATAAGGGGAGT
1 GGTGAATGTGGATGGCTCGGTGTTAACAACGAGACCAAAGGCATCCATAAGGGGAGT
75426 GGTGAATGTGGATGGCTCGGTGTTAACAACGAGACCAAAGGCATCCATAAGGGGAGT
1 GGTGAATGTGGATGGCTCGGTGTTAACAACGAGACCAAAGGCATCCATAAGGGGAGT
75483 GGTGA
1 GGTGA
75488 GTGGACTAAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 62 1.00
ACGTcount: A:0.29, C:0.15, G:0.36, T:0.19
Consensus pattern (57 bp):
GGTGAATGTGGATGGCTCGGTGTTAACAACGAGACCAAAGGCATCCATAAGGGGAGT
Found at i:77253 original size:6 final size:6
Alignment explanation
Indices: 77242--77266 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
77232 CAAATTAAAT
77242 GCTCAA GCTCAA GCTCAA GCTCAA G
1 GCTCAA GCTCAA GCTCAA GCTCAA G
77267 TATAAGCAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.32, G:0.20, T:0.16
Consensus pattern (6 bp):
GCTCAA
Found at i:77602 original size:28 final size:27
Alignment explanation
Indices: 77557--77637 Score: 90
Period size: 28 Copynumber: 2.9 Consensus size: 27
77547 AACACAGAAG
*
77557 AAGTGCGAACTTCTACAGTGAAGCTACA
1 AAGTGCGAACTTC-ACAGTGAACCTACA
* *
77585 AAGTGCGAGCTATCACAGTGAACCTGCA
1 AAGTGCGAACT-TCACAGTGAACCTACA
* *
77613 AAGTACGAACTCTCAAAGTGAACCT
1 AAGTGCGAACT-TCACAGTGAACCT
77638 GTGAAGTAAC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 43 0.96
29 2 0.04
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20
Consensus pattern (27 bp):
AAGTGCGAACTTCACAGTGAACCTACA
Found at i:78071 original size:11 final size:12
Alignment explanation
Indices: 78050--78158 Score: 86
Period size: 11 Copynumber: 9.3 Consensus size: 12
78040 GATTTATTTC
*
78050 TAAAATTAAATT
1 TAAATTTAAATT
*
78062 T-ACTTTAAATT
1 TAAATTTAAATT
78073 TAAATTTAAA-T
1 TAAATTTAAATT
*
78084 TAATTTTTTAAATT
1 TAA--ATTTAAATT
*
78098 TAAATTT-ATTT
1 TAAATTTAAATT
78109 TAAATTTAAATT
1 TAAATTTAAATT
*
78121 T-AGTTTAAATT
1 TAAATTTAAATT
*
78132 TGAAA--TAATTT
1 T-AAATTTAAATT
*
78143 TAAACTTAAATT
1 TAAATTTAAATT
78155 TAAA
1 TAAA
78159 ATCAATTACA
Statistics
Matches: 77, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
10 3 0.04
11 39 0.51
12 24 0.31
13 7 0.09
14 4 0.05
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (12 bp):
TAAATTTAAATT
Found at i:78074 original size:6 final size:6
Alignment explanation
Indices: 78050--78158 Score: 86
Period size: 6 Copynumber: 18.7 Consensus size: 6
78040 GATTTATTTC
* * *
78050 TAAAAT TAAATT T-ACTT TAAATT TAAATT TAAA-T TAATTTTT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAA--ATT TAAATT
* * *
78098 TAAATT T-ATTT TAAATT TAAATT T-AGTT TAAATT TGAAA-- TAATTT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT T-AAATT TAAATT
*
78143 TAAACT TAAATT TAAA
1 TAAATT TAAATT TAAA
78159 ATCAATTACA
Statistics
Matches: 81, Mismatches: 13, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
4 2 0.02
5 17 0.21
6 55 0.68
7 3 0.04
8 4 0.05
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (6 bp):
TAAATT
Found at i:78095 original size:19 final size:17
Alignment explanation
Indices: 78071--78156 Score: 102
Period size: 17 Copynumber: 4.9 Consensus size: 17
78061 TTACTTTAAA
*
78071 TTTAAATTTAAATTAATTT
1 TTTAAATTTAAATT--TAT
78090 TTTAAATTTAAATTTAT
1 TTTAAATTTAAATTTAT
*
78107 TTTAAATTTAAATTTAG
1 TTTAAATTTAAATTTAT
*
78124 TTTAAATTTGAAA-TAAT
1 TTTAAATTT-AAATTTAT
*
78141 TTTAAACTTAAATTTA
1 TTTAAATTTAAATTTA
78157 AAATCAATTA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.05
17 39 0.66
18 3 0.05
19 14 0.24
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.53
Consensus pattern (17 bp):
TTTAAATTTAAATTTAT
Found at i:80009 original size:30 final size:29
Alignment explanation
Indices: 79941--80309 Score: 311
Period size: 30 Copynumber: 12.5 Consensus size: 29
79931 GAAGGTCCCT
* *
79941 AAACTATCCAAAAATTCCATTTT-ACCCCT
1 AAACT-TCCAAAAATCCCATTTTGACCCCA
79970 AAACTTCCAAAAATCCCATTTTCGACCCCA
1 AAACTTCCAAAAATCCCATTTT-GACCCCA
* * * **
80000 AAACCTCCAAAAATTCCATTTTCACCCTT
1 AAACTTCCAAAAATCCCATTTTGACCCCA
* *
80029 GAACTTCCAAAAATCCCATTTTTGACCCTA
1 AAACTTCCAAAAATCCCA-TTTTGACCCCA
* * *
80059 AAACTTCCAAAAATTCCATTTTTACCCTTA
1 AAACTTCCAAAAATCCCATTTTGACCC-CA
*
80089 AAA-TTCCAAAAATCCCATTTTTAACCCCA
1 AAACTTCCAAAAATCCCA-TTTTGACCCCA
* *
80118 AAACTTCTAAAAATATCCACTTTT-ACCCTC-
1 AAACTTCCAAAAAT-CCCA-TTTTGACCC-CA
* *
80148 GAACTTCCAAAAATCCCATTTTTTTA-CCCA
1 AAACTTCCAAAAATCCCA--TTTTGACCCCA
* * **
80178 GAAACTTCCAAAAATTCCATTTTTACCCTT
1 -AAACTTCCAAAAATCCCATTTTGACCCCA
*
80208 AAACTTCCAAAAATCCCATTTTTGTCCCCA
1 AAACTTCCAAAAATCCCA-TTTTGACCCCA
** *
80238 AAACTTCC-AAAATTTCATTTTTACCCCTA
1 AAACTTCCAAAAATCCCATTTTGACCCC-A
* **
80267 AAA-TTCAAAAAATCCCATTTTTGACCTTA
1 AAACTTCCAAAAATCCCA-TTTTGACCCCA
80296 AAACTTCCAAAAAT
1 AAACTTCCAAAAAT
80310 TTCCTTTTTA
Statistics
Matches: 277, Mismatches: 45, Indels: 35
0.78 0.13 0.10
Matches are distributed among these distances:
28 27 0.10
29 98 0.35
30 127 0.46
31 25 0.09
ACGTcount: A:0.37, C:0.30, G:0.02, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATCCCATTTTGACCCCA
Found at i:80046 original size:59 final size:59
Alignment explanation
Indices: 79941--80319 Score: 505
Period size: 59 Copynumber: 6.4 Consensus size: 59
79931 GAAGGTCCCT
* *
79941 AAACTATCCAAAAATTCCA-TTTTACCCCTAAACTTCCAAAAATCCCATTTTCGACCCCA
1 AAACT-TCCAAAAATTCCATTTTTACCCTTAAACTTCCAAAAATCCCATTTTTGACCCCA
* * * *
80000 AAACCTCCAAAAATTCCATTTTCACCCTTGAACTTCCAAAAATCCCATTTTTGACCCTA
1 AAACTTCCAAAAATTCCATTTTTACCCTTAAACTTCCAAAAATCCCATTTTTGACCCCA
* *
80059 AAACTTCCAAAAATTCCATTTTTACCCTTAAAATTCCAAAAATCCCATTTTTAACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCTTAAACTTCCAAAAATCCCATTTTTGACCCCA
* * ** *
80118 AAACTTCTAAAAATATCCACTTTTACCCTCGAACTTCCAAAAATCCCATTTTTTTA-CCCA
1 AAACTTCCAAAAAT-TCCATTTTTACCCTTAAACTTCCAAAAATCCCA-TTTTTGACCCCA
*
80178 GAAACTTCCAAAAATTCCATTTTTACCCTTAAACTTCCAAAAATCCCATTTTTGTCCCCA
1 -AAACTTCCAAAAATTCCATTTTTACCCTTAAACTTCCAAAAATCCCATTTTTGACCCCA
* * * * **
80238 AAACTTCC-AAAATTTCATTTTTACCCCTAAAATTCAAAAAATCCCATTTTTGACCTTA
1 AAACTTCCAAAAATTCCATTTTTACCCTTAAACTTCCAAAAATCCCATTTTTGACCCCA
80296 AAACTTCCAAAAATTTCC-TTTTTA
1 AAACTTCCAAAAA-TTCCATTTTTA
80320 AACTCGAATT
Statistics
Matches: 281, Mismatches: 32, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
58 64 0.23
59 128 0.46
60 70 0.25
61 19 0.07
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.33
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCTTAAACTTCCAAAAATCCCATTTTTGACCCCA
Found at i:80318 original size:30 final size:29
Alignment explanation
Indices: 79937--80319 Score: 377
Period size: 29 Copynumber: 13.0 Consensus size: 29
79927 CCCTGAAGGT
79937 CCCT-AAACTATCCAAAAATTCCA-TTTTA
1 CCCTAAAACT-TCCAAAAATTCCATTTTTA
* *
79965 CCCCT-AAACTTCCAAAAATCCCATTTTCGA
1 -CCCTAAAACTTCCAAAAATTCCATTTT-TA
* * *
79995 CCCCAAAACCTCCAAAAATTCCATTTTCA
1 CCCTAAAACTTCCAAAAATTCCATTTTTA
** *
80024 CCCTTGAACTTCCAAAAATCCCATTTTTGA
1 CCCTAAAACTTCCAAAAATTCCATTTTT-A
80054 CCCTAAAACTTCCAAAAATTCCATTTTTA
1 CCCTAAAACTTCCAAAAATTCCATTTTTA
*
80083 CCCTTAAAA-TTCCAAAAATCCCATTTTTAA
1 CCC-TAAAACTTCCAAAAATTCCATTTTT-A
* * *
80113 CCCCAAAACTTCTAAAAATATCCACTTTTA
1 CCCTAAAACTTCCAAAAAT-TCCATTTTTA
** *
80143 CCCTCGAACTTCCAAAAATCCCATTTTTTTA
1 CCCTAAAACTTCCAAAAATTCCA--TTTTTA
80174 CCC-AGAAACTTCCAAAAATTCCATTTTTA
1 CCCTA-AAACTTCCAAAAATTCCATTTTTA
* * *
80203 CCCTTAAACTTCCAAAAATCCCATTTTTGT
1 CCCTAAAACTTCCAAAAATTCCATTTTT-A
* *
80233 CCCCAAAACTTCC-AAAATTTCATTTTTA
1 CCCTAAAACTTCCAAAAATTCCATTTTTA
* *
80261 CCCCTAAAA-TTCAAAAAATCCCATTTTTGA
1 -CCCTAAAACTTCCAAAAATTCCATTTTT-A
*
80291 CCTTAAAACTTCCAAAAATTTCC-TTTTTA
1 CCCTAAAACTTCCAAAAA-TTCCATTTTTA
80320 AACTCGAATT
Statistics
Matches: 292, Mismatches: 44, Indels: 36
0.78 0.12 0.10
Matches are distributed among these distances:
28 15 0.05
29 137 0.47
30 106 0.36
31 34 0.12
ACGTcount: A:0.36, C:0.30, G:0.02, T:0.33
Consensus pattern (29 bp):
CCCTAAAACTTCCAAAAATTCCATTTTTA
Found at i:80696 original size:46 final size:44
Alignment explanation
Indices: 80630--80722 Score: 159
Period size: 46 Copynumber: 2.1 Consensus size: 44
80620 TTAACTTACT
80630 AGGTGCAATTTTTTCAAATCGAAATAATCAAATACCCTTAATCG
1 AGGTGCAATTTTTTCAAATCGAAATAATCAAATACCCTTAATCG
*
80674 AGGTGCAAATTTTTTTCAAATCGAAATAATCGAATACCCTTAATCG
1 AGGTGC-AA-TTTTTTCAAATCGAAATAATCAAATACCCTTAATCG
80720 AGG
1 AGG
80723 CAATGTTTCT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 6 0.13
45 2 0.04
46 38 0.83
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (44 bp):
AGGTGCAATTTTTTCAAATCGAAATAATCAAATACCCTTAATCG
Found at i:85405 original size:14 final size:14
Alignment explanation
Indices: 85386--85413 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
85376 ACAGAACAAC
85386 CATTTTGGTTAAAA
1 CATTTTGGTTAAAA
85400 CATTTTGGTTAAAA
1 CATTTTGGTTAAAA
85414 AAGGAGTAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (14 bp):
CATTTTGGTTAAAA
Found at i:89279 original size:15 final size:15
Alignment explanation
Indices: 89255--89297 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
89245 TTCCAAGAAG
*
89255 CAATCAACAGTTGCT
1 CAATCCACAGTTGCT
89270 CAATCCACAGTTGCT
1 CAATCCACAGTTGCT
89285 CAATCCACAGTTG
1 CAATCCACAGTTG
89298 AGGCTAAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.26
Consensus pattern (15 bp):
CAATCCACAGTTGCT
Found at i:89711 original size:38 final size:38
Alignment explanation
Indices: 89660--89733 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
89650 ATTCATATGG
*
89660 CGAACACATTTGGCGAGCTTATCTAGAATGGCGAGCAA
1 CGAACACATTTGGCGAGCTCATCTAGAATGGCGAGCAA
*
89698 CGAACACATTTGGCGAGCTCATCTAGATTGGCGAGC
1 CGAACACATTTGGCGAGCTCATCTAGAATGGCGAGC
89734 TCACAACAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.22
Consensus pattern (38 bp):
CGAACACATTTGGCGAGCTCATCTAGAATGGCGAGCAA
Found at i:89748 original size:18 final size:18
Alignment explanation
Indices: 89727--89772 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
89717 CATCTAGATT
89727 GGCGAGCTCACAACAAGA
1 GGCGAGCTCACAACAAGA
* * *
89745 GGCGAGCTCCCAAGAAGT
1 GGCGAGCTCACAACAAGA
*
89763 TGCGAGCTCA
1 GGCGAGCTCA
89773 TTAATTTTGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.30, C:0.28, G:0.30, T:0.11
Consensus pattern (18 bp):
GGCGAGCTCACAACAAGA
Found at i:89864 original size:28 final size:28
Alignment explanation
Indices: 89819--89879 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
89809 AACATAAAAC
*
89819 AAGTGTGAACTTGTACAGTGAAGTTGCG
1 AAGTGTGAACTTGTACAGTGAACTTGCG
* *
89847 AAGTGT-AAGTTGTCACAGTGAACTTGTG
1 AAGTGTGAACTTGT-ACAGTGAACTTGCG
89875 AAGTG
1 AAGTG
89880 CAAACTCTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 6 0.21
28 23 0.79
ACGTcount: A:0.30, C:0.10, G:0.31, T:0.30
Consensus pattern (28 bp):
AAGTGTGAACTTGTACAGTGAACTTGCG
Found at i:91199 original size:2 final size:2
Alignment explanation
Indices: 91192--91218 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
91182 TTATCAAACT
91192 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 T
91219 TGAAAAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:108119 original size:34 final size:34
Alignment explanation
Indices: 108080--108146 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
108070 TATTTGGTTT
*
108080 TAGTGGGAGTTTGTACTTTTAAATGTTTTTATGG
1 TAGTGGGAGTTTGTACTTTTAAATGCTTTTATGG
108114 TAGTGGGAGTTTGTACTTTTAAATGCTTTTATG
1 TAGTGGGAGTTTGTACTTTTAAATGCTTTTATG
108147 TTATAGACAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.21, C:0.04, G:0.25, T:0.49
Consensus pattern (34 bp):
TAGTGGGAGTTTGTACTTTTAAATGCTTTTATGG
Found at i:112770 original size:49 final size:48
Alignment explanation
Indices: 112712--112805 Score: 170
Period size: 49 Copynumber: 1.9 Consensus size: 48
112702 AATGAAAGTT
*
112712 GTTACAACAATATTTATAGAGTTATTAGTAGTTAATTAAAATTTATAGA
1 GTTACAACAATATTTATAAAGTTATTAGTAGTTAATT-AAATTTATAGA
112761 GTTACAACAATATTTATAAAGTTATTAGTAGTTAATTAAATTTAT
1 GTTACAACAATATTTATAAAGTTATTAGTAGTTAATTAAATTTAT
112806 TTAAAAATGT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 8 0.18
49 36 0.82
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.43
Consensus pattern (48 bp):
GTTACAACAATATTTATAAAGTTATTAGTAGTTAATTAAATTTATAGA
Found at i:113051 original size:26 final size:26
Alignment explanation
Indices: 113011--113073 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
113001 TTTGATTATT
* * *
113011 TAATTAAAATTATAACTTAATATTTA
1 TAATTAATATCATAACTAAATATTTA
*
113037 TTATTAATATCATAACTAAATATTTA
1 TAATTAATATCATAACTAAATATTTA
*
113063 TAATTATTATC
1 TAATTAATATC
113074 TATTAAAACT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (26 bp):
TAATTAATATCATAACTAAATATTTA
Found at i:113930 original size:104 final size:98
Alignment explanation
Indices: 113677--113939 Score: 283
Period size: 98 Copynumber: 2.6 Consensus size: 98
113667 GCTGTTTCAA
* * * * *
113677 AGTTACGAGCTTAGCTCAGCTAACTCAAAAAACTAGAGGTTGTAAGCTTAACTCAGCTAACCTTT
1 AGTTGCGAGCTTAACTCAGCTAACTCAAATAATTAGAGGTTGCAAGCTTAACTCAGCTAACCTTT
*
113742 AATCATCAATTGGGAACGTTCGAACTGTTTTGG
66 AATCATCAATTGGGAACGTTCCAACTGTTTTGG
* * * ** ** *
113775 TGTTGCGAGGTTAACTTAGCTAACTTGAATAATTAGATATTGCAAGCTTAACTCAACTAACCTTT
1 AGTTGCGAGCTTAACTCAGCTAACTCAAATAATTAGAGGTTGCAAGCTTAACTCAGCTAACCTTT
* *
113840 ATTCATCAATTGGGAACATAGATTCACAAGTTGTTTTGG
66 AATCATCAATTGGGAAC---G-TTC-CAA-CTGTTTTGG
* * * * *
113879 AGTTGTGAGCTTAACTCAGCTAACTCAAATAATTGGAGGTTACGAGTTTAACTCAGCTAAC
1 AGTTGCGAGCTTAACTCAGCTAACTCAAATAATTAGAGGTTGCAAGCTTAACTCAGCTAAC
113940 TCAAATAACC
Statistics
Matches: 130, Mismatches: 29, Indels: 6
0.79 0.18 0.04
Matches are distributed among these distances:
98 68 0.52
101 1 0.01
102 3 0.02
103 2 0.02
104 56 0.43
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (98 bp):
AGTTGCGAGCTTAACTCAGCTAACTCAAATAATTAGAGGTTGCAAGCTTAACTCAGCTAACCTTT
AATCATCAATTGGGAACGTTCCAACTGTTTTGG
Found at i:113956 original size:37 final size:37
Alignment explanation
Indices: 113885--113976 Score: 112
Period size: 37 Copynumber: 2.5 Consensus size: 37
113875 TTGGAGTTGT
****
113885 GAGCTTAACTCAGCTAACTCAAATAATTGGAGGTTAC
1 GAGCTTAACTCAGCTAACTCAAATAACCAAAGGTTAC
* **
113922 GAGTTTAACTCAGCTAACTCAAATAACCAAAGGTTGT
1 GAGCTTAACTCAGCTAACTCAAATAACCAAAGGTTAC
*
113959 GAGCTTAACTCAACTAAC
1 GAGCTTAACTCAGCTAAC
113977 CCTTAATCAT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (37 bp):
GAGCTTAACTCAGCTAACTCAAATAACCAAAGGTTAC
Found at i:119096 original size:27 final size:26
Alignment explanation
Indices: 119066--119117 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
119056 TTGAATAAAG
* *
119066 TCCTAAAGAATATTTACATATTAATTA
1 TCCTAAACAATATTTA-AAATTAATTA
*
119093 TCCTATACAATATTTAAAATTAATT
1 TCCTAAACAATATTTAAAATTAATT
119118 TAAAACACTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.42
Consensus pattern (26 bp):
TCCTAAACAATATTTAAAATTAATTA
Found at i:120558 original size:157 final size:151
Alignment explanation
Indices: 120133--120631 Score: 473
Period size: 157 Copynumber: 3.3 Consensus size: 151
120123 CTTTTGGAAA
* * * *
120133 AAAAATCTAAAGCTTTCTTTTTTTTAAAACAAAATC---A--TTACTTTACTTAAAAAT-TAATA
1 AAAAATATAAA-CTTTC-TTTTTTTAAAAGAAAATCATTATTTTACTTTACTTGAAAATCCAA-A
* * * * *
120192 TTTTTATTTCGAAATAGTT-AAAAAATTAAACTTTTTTTAAAAA-TTAAACTTTTTCTTTTGAAA
63 CTTTTATTTCGAAATAATTAAAAAAATAAAACTTTGTTTAAAAATTTAAACTTTTTC-TTTAAAA
*
120255 TGCCTAAAAAACATATTTTTTTTATTTTT
127 TGACTAAAAAACATA---TTTTTA-TTTT
** ** * *
120284 AAAAATATAAACTTT-TCTTTTTTAAAA-AAAAAAATTA-AATACTTTACTTGAAAATCTAAATT
1 AAAAATATAAACTTTCT-TTTTTTAAAAGAAAATCATTATTTTACTTTACTTGAAAATCCAAACT
** *
120346 TTTATTTCGAAATTTTTAAAAAAATTAAAACTTTGTTTAAAAATTTGAACTTTTTCTTTAAAATG
65 TTTATTTCGAAATAATTAAAAAAA-TAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATG
120411 ACTAAAAAACATATTTTTATTTT
129 ACTAAAAAACATATTTTTATTTT
* * * * **
120434 AAAAAATTTAAAATTTCTTTTTTTAAAAGAAAATCATTATTTTTCTGATTTTCTTTTAAATCCAA
1 -AAAAATATAAACTTTCTTTTTTTAAAAGAAAATCATTATTTTAC---TTTACTTGAAAATCCAA
* * * *
120499 GCTTTTATTTCGAAATAATTAAAAAAAATCAAAACTTGGTTTAAAAATTTAAAATTTTTCTTTTA
62 ACTTTTATTTCGAAATAATT-AAAAAAAT-AAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAA
* *
120564 AATGACTAAAAAATAGATTTTTATTTT
125 AATGACTAAAAAACATATTTTTATTTT
* *
120591 TAAAATCTAAACTTTC-TTTTTTAAAAGAAAATCATTATTTT
1 AAAAATATAAACTTTCTTTTTTTAAAAGAAAATCATTATTTT
120632 CTTAAAAATC
Statistics
Matches: 294, Mismatches: 36, Indels: 32
0.81 0.10 0.09
Matches are distributed among these distances:
148 5 0.02
149 10 0.03
150 8 0.03
151 40 0.14
152 42 0.14
153 11 0.04
154 36 0.12
155 36 0.12
156 43 0.15
157 63 0.21
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.45
Consensus pattern (151 bp):
AAAAATATAAACTTTCTTTTTTTAAAAGAAAATCATTATTTTACTTTACTTGAAAATCCAAACTT
TTATTTCGAAATAATTAAAAAAATAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATGAC
TAAAAAACATATTTTTATTTT
Found at i:121110 original size:3 final size:3
Alignment explanation
Indices: 121102--121138 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
121092 CATGAAACCT
*
121102 TAA TAA TAA TAA TAA TAA CAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
121139 TTGGGCCCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:130070 original size:6 final size:6
Alignment explanation
Indices: 130058--130105 Score: 69
Period size: 6 Copynumber: 8.0 Consensus size: 6
130048 TCACATGTAT
* * *
130058 ATCTCA GTCTCA GTCTCA ATCTCA ATCTCG ATCTCA ATCTCA ATCTCA
1 ATCTCA ATCTCA ATCTCA ATCTCA ATCTCA ATCTCA ATCTCA ATCTCA
130106 TGATATTACA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.27, C:0.33, G:0.06, T:0.33
Consensus pattern (6 bp):
ATCTCA
Found at i:142817 original size:17 final size:17
Alignment explanation
Indices: 142795--142830 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
142785 TCAACTCAAA
142795 AAGAAAAACGAAA-AAAG
1 AAGAAAAA-GAAAGAAAG
142812 AAGAAAAAGAAAGAAAG
1 AAGAAAAAGAAAGAAAG
142829 AA
1 AA
142831 AAGACTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (17 bp):
AAGAAAAAGAAAGAAAG
Found at i:153804 original size:23 final size:23
Alignment explanation
Indices: 153774--153820 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
153764 AATTGAGATT
*
153774 GTTGATTCTATAGGCGGAACATA
1 GTTGATTCTATAGGCAGAACATA
153797 GTTGATTCTATAGGCAGAACATA
1 GTTGATTCTATAGGCAGAACATA
153820 G
1 G
153821 CAACTCATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.30
Consensus pattern (23 bp):
GTTGATTCTATAGGCAGAACATA
Found at i:159123 original size:16 final size:16
Alignment explanation
Indices: 159102--159140 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
159092 TAAGTGTAAC
159102 AAAAAT-GAAGAAATTG
1 AAAAATAGAA-AAATTG
*
159118 AAAAATAGAAAGATTG
1 AAAAATAGAAAAATTG
159134 AAAAATA
1 AAAAATA
159141 TAATTTGTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 18 0.86
17 3 0.14
ACGTcount: A:0.67, C:0.00, G:0.15, T:0.18
Consensus pattern (16 bp):
AAAAATAGAAAAATTG
Found at i:159941 original size:23 final size:24
Alignment explanation
Indices: 159902--159946 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
159892 ACTCAAAAGT
*
159902 AAAACCCAAAAGTTACA-AAAATG
1 AAAACCCAAAAGATACAGAAAATG
159925 AAAA-CCAAAACGATACAGAAAA
1 AAAACCCAAAA-GATACAGAAAA
159947 AACTCTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 6 0.32
23 9 0.47
24 4 0.21
ACGTcount: A:0.64, C:0.18, G:0.09, T:0.09
Consensus pattern (24 bp):
AAAACCCAAAAGATACAGAAAATG
Found at i:166774 original size:10 final size:10
Alignment explanation
Indices: 166742--166775 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
166732 GATTAAAAAT
166742 AATTTTTTAA
1 AATTTTTTAA
166752 AATATTTTT-A
1 AAT-TTTTTAA
166762 AATTTTTTAA
1 AATTTTTTAA
166772 AATT
1 AATT
166776 AAGGTTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 5 0.23
10 12 0.55
11 5 0.23
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
AATTTTTTAA
Found at i:170556 original size:15 final size:17
Alignment explanation
Indices: 170536--170567 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
170526 TCAAACATAT
170536 ACGATA-TGA-TTATTA
1 ACGATATTGATTTATTA
170551 ACGATATTGATTTATTA
1 ACGATATTGATTTATTA
170568 CACTTTGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 3 0.20
17 6 0.40
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (17 bp):
ACGATATTGATTTATTA
Found at i:171727 original size:13 final size:14
Alignment explanation
Indices: 171653--171727 Score: 50
Period size: 14 Copynumber: 5.5 Consensus size: 14
171643 TTTAAGGTTC
171653 AGGTTT-GGATTTG
1 AGGTTTAGGATTTG
* * **
171666 AGATTTGGGATTCA
1 AGGTTTAGGATTTG
*
171680 AGCTTTAGG-TTT-
1 AGGTTTAGGATTTG
*
171692 AGGGTTAAAGGATTTG
1 A-GGTT-TAGGATTTG
171708 AGGTTTAGGATTTG
1 AGGTTTAGGATTTG
171722 -GGTTTA
1 AGGTTTA
171728 AGGTTCAAGG
Statistics
Matches: 48, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
12 1 0.02
13 16 0.33
14 23 0.48
15 7 0.15
16 1 0.02
ACGTcount: A:0.23, C:0.03, G:0.33, T:0.41
Consensus pattern (14 bp):
AGGTTTAGGATTTG
Found at i:185786 original size:34 final size:34
Alignment explanation
Indices: 185747--185819 Score: 128
Period size: 34 Copynumber: 2.1 Consensus size: 34
185737 AAACTAAACT
185747 CAAATATTTTTAATGTTTTACCTTTTATCTTACC
1 CAAATATTTTTAATGTTTTACCTTTTATCTTACC
* *
185781 TAAATATTTTTAATTTTTTACCTTTTATCTTACC
1 CAAATATTTTTAATGTTTTACCTTTTATCTTACC
185815 CAAAT
1 CAAAT
185820 GTTGTTTACT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.29, C:0.16, G:0.01, T:0.53
Consensus pattern (34 bp):
CAAATATTTTTAATGTTTTACCTTTTATCTTACC
Found at i:192396 original size:2 final size:2
Alignment explanation
Indices: 192389--192429 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
192379 TCAACAAAAC
*
192389 TA TA TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
192430 AATTCAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:194101 original size:31 final size:31
Alignment explanation
Indices: 194039--194233 Score: 160
Period size: 31 Copynumber: 6.4 Consensus size: 31
194029 TTAATATAAT
* * *
194039 ATTTGGTACCTAAATTTGACATTTTTTTTCTTA
1 ATTTGGTACCTAAACTTGACA--CTTTTTCCTA
*
194072 ATTTGGTACCTAAACTTGACACTTTTTCTTA
1 ATTTGGTACCTAAACTTGACACTTTTTCCTA
*
194103 ATTTGGTACCTAAA-TT-----TTTTTGACCCA
1 ATTTGGTACCTAAACTTGACACTTTTT--CCTA
194130 ATTTGGTACCTAAACTTGACACTTTTTCCTA
1 ATTTGGTACCTAAACTTGACACTTTTTCCTA
*
194161 ATTTGGTACCTAAACTT-----TTTTTGGACCCA
1 ATTTGGTACCTAAACTTGACACTTTTT---CCTA
* * *
194190 ATTTGGTATCTAAACTTGATATTTTTTCCTA
1 ATTTGGTACCTAAACTTGACACTTTTTCCTA
*
194221 ATTTGGTATCTAA
1 ATTTGGTACCTAA
194234 GATTTTTTTT
Statistics
Matches: 138, Mismatches: 8, Indels: 34
0.77 0.04 0.19
Matches are distributed among these distances:
25 5 0.04
26 5 0.04
27 16 0.12
28 2 0.01
29 19 0.14
30 2 0.01
31 59 0.43
33 25 0.18
34 5 0.04
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.47
Consensus pattern (31 bp):
ATTTGGTACCTAAACTTGACACTTTTTCCTA
Found at i:194148 original size:58 final size:59
Alignment explanation
Indices: 194071--194242 Score: 274
Period size: 60 Copynumber: 2.9 Consensus size: 59
194061 TTTTTTTCTT
*
194071 AATTTGGTACCTAAACTTGACACTTTTTCTTAATTTGGTACCTAAATTTTTTT-GACCC
1 AATTTGGTACCTAAACTTGACACTTTTTCCTAATTTGGTACCTAAATTTTTTTGGACCC
194129 AATTTGGTACCTAAACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTTGGACCC
1 AATTTGGTACCTAAACTTGACACTTTTTCCTAATTTGGTACCTAAA-TTTTTTTGGACCC
* * * *
194189 AATTTGGTATCTAAACTTGATATTTTTTCCTAATTTGGTATCTAAGATTTTTTT
1 AATTTGGTACCTAAACTTGACACTTTTTCCTAATTTGGTACCTAA-ATTTTTTT
194243 TTTATATTCA
Statistics
Matches: 106, Mismatches: 5, Indels: 4
0.92 0.04 0.03
Matches are distributed among these distances:
58 45 0.42
59 7 0.07
60 53 0.50
61 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.47
Consensus pattern (59 bp):
AATTTGGTACCTAAACTTGACACTTTTTCCTAATTTGGTACCTAAATTTTTTTGGACCC
Found at i:198396 original size:31 final size:31
Alignment explanation
Indices: 198358--198421 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
198348 TTAATGGGCT
198358 AGTCAAAAAGTGTTATAAAAGGTAGGAGGGG
1 AGTCAAAAAGTGTTATAAAAGGTAGGAGGGG
198389 AGTCAAAAAGTGTTATAAAAGGTAGGAGGGG
1 AGTCAAAAAGTGTTATAAAAGGTAGGAGGGG
198420 AG
1 AG
198422 AGAAAGAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.42, C:0.03, G:0.36, T:0.19
Consensus pattern (31 bp):
AGTCAAAAAGTGTTATAAAAGGTAGGAGGGG
Done.