Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold975
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: 287369
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:166522 original size:44 final size:44
Alignment explanation
Indices: 166466--167490 Score: 514
Period size: 44 Copynumber: 23.6 Consensus size: 44
166456 CATTTTGGTC
166466 TGACGTATGGTTACCACCCTAGTCAGATTCTTTTCATTCTGATT
1 TGACGTATGGTTACCACCCTAGTCAGATTCTTTTCATTCTGATT
* * * * * * * * *
166510 TAACGCAGGGTTACC-TCTTAGTTAAATTCTTCTCATT-TCGATC
1 TGACGTATGGTTACCACCCTAGTCAGATTCTTTTCATTCT-GATT
* * * * *
166553 TAACGTATGGTTAACACCCTGGTCAGATTCTTTTCATTTTAATT
1 TGACGTATGGTTACCACCCTAGTCAGATTCTTTTCATTCTGATT
* * * ** *
166597 TGACGCATTGTTACCACCCTAGTCA-AATCTACCTCCTTCCT-ATT
1 TGACGTATGGTTACCACCCTAGTCAGATTCT-TTTCATT-CTGATT
* * * * *
166641 TGACGTATGGTTACCACCCTAGTCAAACTCTTTTCATTTTGGTC
1 TGACGTATGGTTACCACCCTAGTCAGATTCTTTTCATTCTGATT
* * *
166685 TGACGTATGGTTACCACCCTGGTTAGATTTTTTTCATTCTGATT
1 TGACGTATGGTTACCACCCTAGTCAGATTCTTTTCATTCTGATT
* * * *
166729 TGATGCATGGTTACCACCCTAGTCA-AATCTGCCTTC-TTCCTG-TT
1 TGACGTATGGTTACCACCCTAGTCAGATTCT--TTTCATT-CTGATT
* * *
166773 TGACGTTTGGTTACCACCCTAGTCAGATTATTTTTATTCTGATT
1 TGACGTATGGTTACCACCCTAGTCAGATTCTTTTCATTCTGATT
* * * * * * *
166817 TGATGCATGGTTACCACTCTGGTCAAATTTGCCTTT--TTCTTATT
1 TGACGTATGGTTACCACCCTAGTCAGA-TT-CTTTTCATTCTGATT
* ** * * * *
166861 TGATGTATGGTTACCACCCCGGTCAAACTCTTTTCATTTTGATC
1 TGACGTATGGTTACCACCCTAGTCAGATTCTTTTCATTCTGATT
* *
166905 TGACATATGGTTACCACCCTGGTCAGATTCTTTTCATTCTGATT
1 TGACGTATGGTTACCACCCTAGTCAGATTCTTTTCATTCTGATT
* * * ** *
166949 TGATGCATGGTT--CA----AATCAGCCTC-CTTC--T-TG-TT
1 TGACGTATGGTTACCACCCTAGTCAGATTCTTTTCATTCTGATT
* * * * * *
166982 TGACATATGGTTACCACCAT-GATCAAACTCTTCTT-ATTTTGGTT
1 TGACGTATGGTTACCACCCTAG-TCAGATTCTT-TTCATTCTGATT
* * * *
167026 TGATGTATGGTTACCACCTTGGTTAGATTCTTTTCATTCTGATT
1 TGACGTATGGTTACCACCCTAGTCAGATTCTTTTCATTCTGATT
* * * ** *
167070 TGACGCATGGTTACTACCCTAGTCA-AATCTACCTCTTTCCT-ATT
1 TGACGTATGGTTACCACCCTAGTCAGATTCT-TTTCATT-CTGATT
* * * * * * *
167114 TGACGTATGGTTATCGCCCTGGTCAAACTCTTTTCATT-TCGGTC
1 TGACGTATGGTTACCACCCTAGTCAGATTCTTTTCATTCT-GATT
* * *
167158 TGACGTATGGTTACCACCTTTGTCAAATTCTTTTCATTCTGATT
1 TGACGTATGGTTACCACCCTAGTCAGATTCTTTTCATTCTGATT
* * * **
167202 TGATGTATGGTTACCACCCTGGTCAAATCTCCCTTC-TTCCT-ATT
1 TGACGTATGGTTACCACCCTAGTCAGAT-TCTTTTCATT-CTGATT
* * * * * *
167246 TAACGTATGGTTACCACCTTAGTCAAACTCTTCTT-ATT-TCGGTC
1 TGACGTATGGTTACCACCCTAGTCAGATTCTT-TTCATTCT-GATT
* * * * * *
167290 TAATGTATGGTTACTACCCTAATCAGATTCTTTTCATTTTGACT
1 TGACGTATGGTTACCACCCTAGTCAGATTCTTTTCATTCTGATT
* * * * ** *
167334 TGACATATGGTTGCCA-CCTTGTTCA-AATCTGCCTCTTTCTTG-TT
1 TGACGTATGGTTACCACCCTAG-TCAGATTCT-TTTCATTC-TGATT
* * * * * * * * * *
167378 TAATGTATGGTTACCACCCTGGTCAAACTCTTCTAATTTTGGTC
1 TGACGTATGGTTACCACCCTAGTCAGATTCTTTTCATTCTGATT
* * * *
167422 TAACGTATGGTTACCACCTTACTCA-ATTTTTTTTCATTCTGATT
1 TGACGTATGGTTACCACCCTAGTCAGA-TTCTTTTCATTCTGATT
** *
167466 TGACACATGGTTACCACTCTAGTCA
1 TGACGTATGGTTACCACCCTAGTCA
167491 AATCTGCCTT
Statistics
Matches: 728, Mismatches: 200, Indels: 106
0.70 0.19 0.10
Matches are distributed among these distances:
33 11 0.02
34 2 0.00
35 3 0.00
37 3 0.00
38 6 0.01
39 6 0.01
41 2 0.00
42 10 0.01
43 68 0.09
44 571 0.78
45 43 0.06
46 3 0.00
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (44 bp):
TGACGTATGGTTACCACCCTAGTCAGATTCTTTTCATTCTGATT
Found at i:167492 original size:132 final size:132
Alignment explanation
Indices: 166960--167522 Score: 614
Period size: 132 Copynumber: 4.3 Consensus size: 132
166950 GATGCATGGT
* * * * * * *
166960 TCAAATCAGCCTCCTTCTTGTTTGACATATGGTTACCACCATGATCAAACTCTTCTTATTTTGGT
1 TCAAATCTGCCTCTTTCCTGTTTGACGTATGGTTACCACCCTGGTCAAACTCTTCTTATTTCGGT
* * * * * * *
167025 TTGATGTATGGTTACCACCTTGGTTAGATTCTTTTCATTCTGATTTGACGCATGGTTACTACCCT
66 CTAACGTATGGTTACCACCTTAGTCAGATTCTTTTCATTCTGATTTGACACATGGTTACCACCCT
167090 AG
131 AG
* * * *
167092 TCAAATCTACCTCTTTCCTATTTGACGTATGGTTATCGCCCTGGTCAAACTCTT-TTCATTTCGG
1 TCAAATCTGCCTCTTTCCTGTTTGACGTATGGTTACCACCCTGGTCAAACTCTTCTT-ATTTCGG
* * * ***
167156 TCTGACGTATGGTTACCACCTTTGTCAAATTCTTTTCATTCTGATTTGATGTATGGTTACCACCC
65 TCTAACGTATGGTTACCACCTTAGTCAGATTCTTTTCATTCTGATTTGACACATGGTTACCACCC
*
167221 TGG
130 TAG
* * * * *
167224 TCAAATCTCCCT-TCTTCCTATTTAACGTATGGTTACCACCTTAGTCAAACTCTTCTTATTTCGG
1 TCAAATCTGCCTCT-TTCCTGTTTGACGTATGGTTACCACCCTGGTCAAACTCTTCTTATTTCGG
* * * * * * * *
167288 TCTAATGTATGGTTACTACCCTAATCAGATTCTTTTCATTTTGACTTGACATATGGTTGCCA-CC
65 TCTAACGTATGGTTACCACCTTAGTCAGATTCTTTTCATTCTGATTTGACACATGGTTACCACCC
*
167352 TTG
130 TAG
* * * * *
167355 TTCAAATCTGCCTCTTTCTTGTTTAATGTATGGTTACCACCCTGGTCAAACTCTTCTAATTTTGG
1 -TCAAATCTGCCTCTTTCCTGTTTGACGTATGGTTACCACCCTGGTCAAACTCTTCTTATTTCGG
* * *
167420 TCTAACGTATGGTTACCACCTTACTCA-ATTTTTTTTCATTCTGATTTGACACATGGTTACCACT
65 TCTAACGTATGGTTACCACCTTAGTCAGA-TTCTTTTCATTCTGATTTGACACATGGTTACCACC
167484 CTAG
129 CTAG
* *
167488 TCAAATCTGCCT-TTTTCTGTTTGATGTATGGTTAC
1 TCAAATCTGCCTCTTTCCTGTTTGACGTATGGTTAC
167523 TAAAAGTGGC
Statistics
Matches: 363, Mismatches: 61, Indels: 15
0.83 0.14 0.03
Matches are distributed among these distances:
131 28 0.08
132 329 0.91
133 6 0.02
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (132 bp):
TCAAATCTGCCTCTTTCCTGTTTGACGTATGGTTACCACCCTGGTCAAACTCTTCTTATTTCGGT
CTAACGTATGGTTACCACCTTAGTCAGATTCTTTTCATTCTGATTTGACACATGGTTACCACCCT
AG
Found at i:167650 original size:16 final size:16
Alignment explanation
Indices: 167631--167683 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
167621 AAATAGCCTT
*
167631 AACCCGAGAAAACCCG
1 AACCCGAGAAAGCCCG
*
167647 AACCCGAGAAAGCCCA
1 AACCCGAGAAAGCCCG
* *
167663 AACCTGAGAAAGCTCG
1 AACCCGAGAAAGCCCG
167679 AACCC
1 AACCC
167684 AAAAAAAACT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.42, C:0.36, G:0.19, T:0.04
Consensus pattern (16 bp):
AACCCGAGAAAGCCCG
Found at i:167715 original size:16 final size:16
Alignment explanation
Indices: 167694--167739 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
167684 AAAAAAAACT
167694 TGAACCTGAAAGAACC
1 TGAACCTGAAAGAACC
*
167710 TGAACCCGAAAGAACC
1 TGAACCTGAAAGAACC
*
167726 T-AAACTCGAAAGAA
1 TGAACCT-GAAAGAA
167740 TGCGAACCTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 3 0.12
16 23 0.88
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.11
Consensus pattern (16 bp):
TGAACCTGAAAGAACC
Found at i:171561 original size:99 final size:100
Alignment explanation
Indices: 171399--171586 Score: 247
Period size: 99 Copynumber: 1.9 Consensus size: 100
171389 AGTTTTGATT
* * *
171399 ATTATATTTTTAATTAATTAATGATATTTTTATTAAAATTAAAATATTGAGTAATTTTATTATTA
1 ATTATATTCTTAATTAATTAATGATATTTTTATTAAAATTAAAACATTGAATAATTTTATTATTA
*
171464 -ATCTTGAATTCTTTATTAACGTAATAGTATAGACC
66 TA-CCTGAATTCTTTATTAACGTAATAGTATAGACC
* * * *
171499 ATTATGTTCTTAATTAATTAATGAT-TTTTTATTTAGATTAAAACA-TGAAATAATTTTCTTATT
1 ATTATATTCTTAATTAATTAATGATATTTTTATTAAAATTAAAACATTG-AATAATTTTATTATT
* *
171562 GTACCTGAATTCTTTATTCACGTAA
65 ATACCTGAATTCTTTATTAACGTAA
171587 ATATTTCATA
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
98 2 0.03
99 50 0.66
100 24 0.32
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (100 bp):
ATTATATTCTTAATTAATTAATGATATTTTTATTAAAATTAAAACATTGAATAATTTTATTATTA
TACCTGAATTCTTTATTAACGTAATAGTATAGACC
Found at i:172014 original size:16 final size:16
Alignment explanation
Indices: 171995--172051 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 16
171985 GAATAATCCT
* *
171995 GAACCTGAATAAGCTC
1 GAACCCGAAAAAGCTC
172011 GAACCCGAAAAAGCTC
1 GAACCCGAAAAAGCTC
* * * *
172027 AAACTCAAAAAAGTTC
1 GAACCCGAAAAAGCTC
*
172043 AAACCCGAA
1 GAACCCGAA
172052 CGAGCCCGAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.47, C:0.26, G:0.14, T:0.12
Consensus pattern (16 bp):
GAACCCGAAAAAGCTC
Found at i:172069 original size:16 final size:16
Alignment explanation
Indices: 172044--172172 Score: 104
Period size: 16 Copynumber: 8.2 Consensus size: 16
172034 AAAAAGTTCA
*
172044 AACCCGAACGAGCCCG
1 AACCTGAACGAGCCCG
*
172060 AA-CTCGAACGAGCCTG
1 AACCT-GAACGAGCCCG
* *
172076 AA-CTCGAATGAGCCCA
1 AACCT-GAACGAGCCCG
*
172092 AACCTGAACGAGCCCA
1 AACCTGAACGAGCCCG
* *
172108 AACCTGAATGAGCTCG
1 AACCTGAACGAGCCCG
* **
172124 AACCTGAACGAACTTG
1 AACCTGAACGAGCCCG
*
172140 -ACCCGAACGAGCCCG
1 AACCTGAACGAGCCCG
*
172155 AACCTGAACCAG-CCG
1 AACCTGAACGAGCCCG
172170 AAC
1 AAC
172173 TCACCTAATT
Statistics
Matches: 92, Mismatches: 18, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
15 18 0.20
16 72 0.78
17 2 0.02
ACGTcount: A:0.34, C:0.35, G:0.22, T:0.09
Consensus pattern (16 bp):
AACCTGAACGAGCCCG
Found at i:172089 original size:32 final size:32
Alignment explanation
Indices: 172048--172174 Score: 118
Period size: 32 Copynumber: 4.0 Consensus size: 32
172038 AGTTCAAACC
172048 CGAACGAGCCCGAA-CTCGAACGAGCCTGAACT
1 CGAACGAGCCCGAACCT-GAACGAGCCTGAACT
* * **
172080 CGAATGAGCCCAAACCTGAACGAGCCCAAAC-
1 CGAACGAGCCCGAACCTGAACGAGCCTGAACT
* * * * *
172111 CTGAATGAGCTCGAACCTGAACGAACTTG-ACC
1 C-GAACGAGCCCGAACCTGAACGAGCCTGAACT
*
172143 CGAACGAGCCCGAACCTGAACCAGCC-GAACT
1 CGAACGAGCCCGAACCTGAACGAGCCTGAACT
172174 C
1 C
172175 ACCTAATTAA
Statistics
Matches: 75, Mismatches: 16, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
30 1 0.01
31 26 0.35
32 46 0.61
33 2 0.03
ACGTcount: A:0.33, C:0.35, G:0.22, T:0.10
Consensus pattern (32 bp):
CGAACGAGCCCGAACCTGAACGAGCCTGAACT
Found at i:180432 original size:132 final size:132
Alignment explanation
Indices: 180059--180441 Score: 452
Period size: 132 Copynumber: 2.9 Consensus size: 132
180049 ATCTCCAAGA
* ** * *
180059 GGATACTCTAACCTTATTTTTACTT-TCAAGACATCGAATTTTTAATTTATGGGATACTCTAACC
1 GGATACTCCAACCCCATTTTTACTTCT-AAAACATCGAATTTTTAATCTATGGGATACTCTAACC
* * * * * *
180123 CTATAATTTTTACTTCTACAATACCAAATTCTTCATCTCTAAGGATGCTCCAACCATCACCTCTG
65 CTATATTTTTTACTTCCACAATACCAAATTCTTCACCTCTAGGGATACTCCAACCATCACCTCTA
180188 AAG
130 AAG
* * * * *
180191 GGATACTCCAACCCCATTTTTACTTCCAAAACATCGAATTTTTGATCTTTTGGATATTCTAACCC
1 GGATACTCCAACCCCATTTTTACTTCTAAAACATCGAATTTTTAATCTATGGGATACTCTAACCC
* * *
180256 TATATTTTGTACTTCCACAATACCGAATTCTTCATCC-CTAGGGATACTCCAACC-TCTACCTTT
66 TATATTTTTTACTTCCACAATACCAAATTCTTCA-CCTCTAGGGATACTCCAACCATC-ACCTCT
180319 AAAG
129 AAAG
* * * *
180323 GGATACTCCAACCCCGTTTTTACTTCTAAAACATTGAATTTTTCATCTATGGGGATACTCCAACC
1 GGATACTCCAACCCCATTTTTACTTCTAAAACATCGAATTTTTAATCTAT-GGGATACTCTAACC
* * *
180388 CCAT-TTTTTTACTTCCACAATACCAAACTCTTTACCTC-AGGGGATACTCCAACC
65 CTATATTTTTTACTTCCACAATACCAAATTCTTCACCTCTA-GGGATACTCCAACC
180442 CCACCATCTC
Statistics
Matches: 213, Mismatches: 32, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
131 5 0.02
132 193 0.91
133 15 0.07
ACGTcount: A:0.29, C:0.27, G:0.09, T:0.35
Consensus pattern (132 bp):
GGATACTCCAACCCCATTTTTACTTCTAAAACATCGAATTTTTAATCTATGGGATACTCTAACCC
TATATTTTTTACTTCCACAATACCAAATTCTTCACCTCTAGGGATACTCCAACCATCACCTCTAA
AG
Found at i:181075 original size:20 final size:21
Alignment explanation
Indices: 181035--181085 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 21
181025 TTTTGCAATT
*
181035 TGTATCGATACAATTAGTGAA
1 TGTATCGATACAATAAGTGAA
*
181056 TGTATTGATAC-ATAAGTGAA
1 TGTATCGATACAATAAGTGAA
181076 TGTATCGATA
1 TGTATCGATA
181086 TAGGACCATG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.37, C:0.08, G:0.20, T:0.35
Consensus pattern (21 bp):
TGTATCGATACAATAAGTGAA
Found at i:183632 original size:14 final size:14
Alignment explanation
Indices: 183613--183640 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
183603 TTTGACTCCT
183613 TTTTCAAAAAAATA
1 TTTTCAAAAAAATA
183627 TTTTCAAAAAAATA
1 TTTTCAAAAAAATA
183641 AATACCCGTC
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:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (14 bp):
TTTTCAAAAAAATA
Found at i:184416 original size:20 final size:20
Alignment explanation
Indices: 184391--184444 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
184381 TTACCACTGT
* *
184391 TTGTATCGATACATGGCACA
1 TTGTATCGATACATGACAAA
*
184411 TTGTATCGATACATGATAAA
1 TTGTATCGATACATGACAAA
*
184431 CTGTATCGATACAT
1 TTGTATCGATACAT
184445 TGCTTATAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (20 bp):
TTGTATCGATACATGACAAA
Found at i:190628 original size:13 final size:13
Alignment explanation
Indices: 190610--190635 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
190600 AAAATATTCT
190610 TTGTATCGATACA
1 TTGTATCGATACA
190623 TTGTATCGATACA
1 TTGTATCGATACA
190636 AGGGTTACTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:190755 original size:21 final size:22
Alignment explanation
Indices: 190731--190780 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
190721 ATCAAATCTG
* *
190731 CTTCAAATTTCTT-ATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
190752 CTTCAAAATACTTCATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
190774 --TCAAAAT
1 CTTCAAAAT
190781 CATCAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 7 0.27
21 11 0.42
22 8 0.31
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (22 bp):
CTTCAAAATACTTCATTTTTCA
Found at i:194509 original size:33 final size:33
Alignment explanation
Indices: 194467--194529 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
194457 TACCACTATT
* *
194467 TGTATCGATACATTGCA-CATTGTATCGATATAA
1 TGTATCGATACA-TGAAGAATTGTATCGATATAA
194500 TGTATCGATACATGAAGAATTGTATCGATA
1 TGTATCGATACATGAAGAATTGTATCGATA
194530 CATTATCCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 3 0.11
33 24 0.89
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (33 bp):
TGTATCGATACATGAAGAATTGTATCGATATAA
Found at i:200717 original size:20 final size:21
Alignment explanation
Indices: 200692--200731 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
200682 ATTTTTTAGA
*
200692 ATGTATTGATACAT-TGAAAG
1 ATGTATCGATACATCTGAAAG
200712 ATGTATCGATACATCTGAAA
1 ATGTATCGATACATCTGAAA
200732 AAATCCAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATCTGAAAG
Found at i:202217 original size:34 final size:33
Alignment explanation
Indices: 202154--202222 Score: 93
Period size: 34 Copynumber: 2.1 Consensus size: 33
202144 AAACCAGTTA
* * * *
202154 TCACTTTCGCAGCGCATTGATGAGCACTTTAGT
1 TCACTTTAGCAGCACATGGATGAGAACTTTAGT
202187 TCACTTTAGCACGCACATGGATGAGAACTTTAGT
1 TCACTTTAGCA-GCACATGGATGAGAACTTTAGT
202221 TC
1 TC
202223 TCTTAACCGA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 10 0.32
34 21 0.68
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (33 bp):
TCACTTTAGCAGCACATGGATGAGAACTTTAGT
Found at i:203189 original size:13 final size:13
Alignment explanation
Indices: 203171--203197 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
203161 ACATTATGCT
203171 TTGTATCGATACA
1 TTGTATCGATACA
203184 TTGTATCGATACA
1 TTGTATCGATACA
203197 T
1 T
203198 GTTCATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:204765 original size:6 final size:6
Alignment explanation
Indices: 204754--204793 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
204744 TTCTGCATAC
*
204754 ATATAA ATATAA TTATAA ATATAA ATAT-A ATATAA ATATA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATA
204794 TATTTTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
ATATAA
Found at i:204777 original size:18 final size:17
Alignment explanation
Indices: 204754--204793 Score: 71
Period size: 18 Copynumber: 2.3 Consensus size: 17
204744 TTCTGCATAC
204754 ATATAAATATAATTATAA
1 ATATAAATATAA-TATAA
204772 ATATAAATATAATATAA
1 ATATAAATATAATATAA
204789 ATATA
1 ATATA
204794 TATTTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATATAAATATAATATAA
Found at i:205232 original size:15 final size:15
Alignment explanation
Indices: 205214--205242 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
205204 GTTCTATTTA
205214 TTATATTTTTATTCT
1 TTATATTTTTATTCT
205229 TTATATTTTTATTC
1 TTATATTTTTATTC
205243 AACAAACATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (15 bp):
TTATATTTTTATTCT
Found at i:205827 original size:23 final size:25
Alignment explanation
Indices: 205801--205846 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
205791 AAAATTATAA
205801 CACATG-A-TAACATAAAA-TAATGC
1 CACATGTATTAACA-AAAACTAATGC
205824 CACATGTATTAACAAAAACTAAT
1 CACATGTATTAACAAAAACTAAT
205847 AATTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.30
24 5 0.25
25 9 0.45
ACGTcount: A:0.52, C:0.17, G:0.07, T:0.24
Consensus pattern (25 bp):
CACATGTATTAACAAAAACTAATGC
Found at i:206799 original size:17 final size:18
Alignment explanation
Indices: 206764--206802 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
206754 TTTCGATATG
206764 TTTTTTAAAAAATATTAA
1 TTTTTTAAAAAATATTAA
*
206782 TTTTTTAAGAAATA-TAA
1 TTTTTTAAAAAATATTAA
206799 TTTT
1 TTTT
206803 ACATTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TTTTTTAAAAAATATTAA
Found at i:207844 original size:21 final size:20
Alignment explanation
Indices: 207793--207844 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
207783 CATTATAAAT
* *
207793 TTAATTTTAGTGTTACGATA
1 TTAATTTTATTGTTACAATA
*
207813 TTCAATATTATTGTTACAATAA
1 TT-AATTTTATTGTTACAAT-A
207835 TTAATTTTAT
1 TTAATTTTAT
207845 CATCAATGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 2 0.08
21 21 0.81
22 3 0.12
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.52
Consensus pattern (20 bp):
TTAATTTTATTGTTACAATA
Found at i:208418 original size:5 final size:6
Alignment explanation
Indices: 208403--208427 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
208393 TTGAGATTAA
208403 AAAAAG AAAAAG AAAAAG AAAAAG A
1 AAAAAG AAAAAG AAAAAG AAAAAG A
208428 CCACCAAGTA
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:213907 original size:18 final size:20
Alignment explanation
Indices: 213877--213917 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 20
213867 TATAAAAGAA
213877 TTATTAAAGTATC-AA-AAG
1 TTATTAAAGTATCTAATAAG
213895 TTATATAAA-TATCTAATAAG
1 TTAT-TAAAGTATCTAATAAG
213915 TTA
1 TTA
213918 AATACAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
18 8 0.40
19 6 0.30
20 6 0.30
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (20 bp):
TTATTAAAGTATCTAATAAG
Found at i:214102 original size:28 final size:30
Alignment explanation
Indices: 214032--214102 Score: 76
Period size: 28 Copynumber: 2.4 Consensus size: 30
214022 ATAACATGAC
*
214032 TATATAATATGAAGACAATATAGAAAAAATAA
1 TATA-AATAT-AAAACAATATAGAAAAAATAA
*
214064 T-TAAAACATAAAACAATA-AG-AAAAATAA
1 TAT-AAATATAAAACAATATAGAAAAAATAA
214092 TATAAATATAA
1 TATAAATATAA
214103 CATGAATACA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
28 16 0.47
29 3 0.09
30 8 0.24
31 5 0.15
32 2 0.06
ACGTcount: A:0.66, C:0.04, G:0.06, T:0.24
Consensus pattern (30 bp):
TATAAATATAAAACAATATAGAAAAAATAA
Found at i:221267 original size:19 final size:21
Alignment explanation
Indices: 221229--221267 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
221219 CATGCAGCAT
*
221229 CCCAACACCAGACCTTCATCC
1 CCCAACACCAGACCTCCATCC
221250 CCCAACACC-GACC-CCATC
1 CCCAACACCAGACCTCCATC
221268 GTCGTTCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 4 0.24
21 9 0.53
ACGTcount: A:0.28, C:0.56, G:0.05, T:0.10
Consensus pattern (21 bp):
CCCAACACCAGACCTCCATCC
Found at i:225850 original size:33 final size:33
Alignment explanation
Indices: 225808--225873 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
225798 GTGGCAAAAG
*
225808 AACAGGAACCACTTTCAGTAGTAGTGGAAAACT
1 AACAGGAACCACTTTCAGTAGTAGTGAAAAACT
* *
225841 AACAGGAACCATTTTCATTAGTAGTGAAAAACT
1 AACAGGAACCACTTTCAGTAGTAGTGAAAAACT
225874 GGTTTCAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (33 bp):
AACAGGAACCACTTTCAGTAGTAGTGAAAAACT
Found at i:235142 original size:13 final size:13
Alignment explanation
Indices: 235124--235150 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
235114 ACATTATGCT
235124 TTGTATCGATACA
1 TTGTATCGATACA
235137 TTGTATCGATACA
1 TTGTATCGATACA
235150 T
1 T
235151 ATTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:235147 original size:33 final size:32
Alignment explanation
Indices: 235105--235169 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
235095 CACACTCAGA
*
235105 TGTATCGATACATTATGCTTTGTATCGATACAT
1 TGTATCGATACA-TATGCATTGTATCGATACAT
* *
235138 TGTATCGATACATATTCATTGTATTGATACAT
1 TGTATCGATACATATGCATTGTATCGATACAT
235170 GGACAATTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (32 bp):
TGTATCGATACATATGCATTGTATCGATACAT
Found at i:235159 original size:19 final size:19
Alignment explanation
Indices: 235134--235189 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
235124 TTGTATCGAT
*
235134 ACATTGTATCGATACATAT
1 ACATTGTATCGATACATAG
* * *
235153 TCATTGTATTGATACATGG
1 ACATTGTATCGATACATAG
235172 ACAATTGTATCGATACAT
1 AC-ATTGTATCGATACAT
235190 GAAACTGGCA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (19 bp):
ACATTGTATCGATACATAG
Found at i:235253 original size:13 final size:13
Alignment explanation
Indices: 235235--235287 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
235225 CGATACATGG
235235 TACATTGTATCGA
1 TACATTGTATCGA
235248 TACATTGTATCGA
1 TACATTGTATCGA
235261 TACA-TG-AT-G-
1 TACATTGTATCGA
235270 -A-ATTGTATCGA
1 TACATTGTATCGA
235281 TACATTG
1 TACATTG
235288 CTTCTAACGG
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
7 1 0.03
8 3 0.09
9 2 0.06
10 2 0.06
11 2 0.06
12 3 0.09
13 21 0.62
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:235261 original size:33 final size:33
Alignment explanation
Indices: 235219--235287 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
235209 CTACCACTGT
*
235219 TTGTATCGATACATGGT-ACATTGTATCGATACA
1 TTGTATCGATACATGATGA-ATTGTATCGATACA
235252 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGATGAATTGTATCGATACA
235285 TTG
1 TTG
235288 CTTCTAACGG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 33 0.97
34 1 0.03
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.38
Consensus pattern (33 bp):
TTGTATCGATACATGATGAATTGTATCGATACA
Found at i:241462 original size:13 final size:13
Alignment explanation
Indices: 241444--241470 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
241434 ACAATATTCC
241444 TTGTATCGATACA
1 TTGTATCGATACA
241457 TTGTATCGATACA
1 TTGTATCGATACA
241470 T
1 T
241471 GGGTTACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:245369 original size:78 final size:79
Alignment explanation
Indices: 245278--245626 Score: 310
Period size: 79 Copynumber: 4.4 Consensus size: 79
245268 TATTTTGGAG
* * * * **
245278 ATAAAAACGGAGTTGGAGTATCCCCTCAAAAATAACGGGGTTAGAGTATCCCCAATGGTGAAAAA
1 ATAAAATCAGAGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAA
* *
245343 TCGATGTTTGAAAA
66 TCGATGTTTTAGAA
* * * ** * * *
245357 ATAAAATC-GAGTTTAGAGCATCCTCTCAAAAATAACGCAGTTGAAGTATCCCTGATTATGAGAA
1 ATAAAATCAGAG-TTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAA
245421 ATCGATGTTTTAGAA
65 ATCGATGTTTTAGAA
* * * * * ** * *
245436 ATAAAACCAGGGTTGGAGTATCTCCTCAGAAATAATGGGGTTGGAGTATCTTCGATTGTGGAAAA
1 ATAAAATCAGAGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAA
245501 TC-AGTGTTTTAGAA
66 TCGA-TGTTTTAGAA
* * * ** * * * * *
245515 ATCAAA-CTGGGTTGGAGTATTGCCTCGAAAATAACAGGATTGGAATATCCTCGATTATGAAAAA
1 ATAAAATCAGAGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAA
245579 TCGATGTTTTAGAA
66 TCGATGTTTTAGAA
* *
245593 ATAAAATCA-AGATTGGAGTATCTCCTCGAAAATA
1 ATAAAATCAGAG-TTGGAGTATCCCCTCAAAAATA
245627 CGATTGGAGT
Statistics
Matches: 214, Mismatches: 50, Indels: 12
0.78 0.18 0.04
Matches are distributed among these distances:
78 68 0.32
79 144 0.67
80 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (79 bp):
ATAAAATCAGAGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAA
TCGATGTTTTAGAA
Found at i:247043 original size:15 final size:15
Alignment explanation
Indices: 247015--247051 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
247005 CATTTTTATG
*
247015 GAAAG-AAAATATAA
1 GAAAGAAAAAAATAA
247029 GAAAGAAAAAAATAA
1 GAAAGAAAAAAATAA
247044 GAAA-AAAA
1 GAAAGAAAA
247052 TGCATGGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (15 bp):
GAAAGAAAAAAATAA
Found at i:248751 original size:97 final size:97
Alignment explanation
Indices: 248639--248824 Score: 250
Period size: 97 Copynumber: 1.9 Consensus size: 97
248629 AAATATCCTC
* * ** * * *
248639 TCAGAGGAATGGGGTTGGAGTGTCC-CTAATGATGACAATTTAGGTGAAAAA-AAGATTTAAATC
1 TCAGAAGAATGGGGTTGGAGTATCCTC-AACAATGACAATTTAAG-CAAAAATAAGATTTAAATA
* *
248702 TTGATAAGTTTAAAAGCAAGGTTGGAATGCCCCT
64 TTGACAAGTTTAAAAACAAGGTTGGAATGCCCCT
248736 TCAGAAGAATGGGGTTGGAGTATCCTCAACAATGACAATTTAAGCAAAAATAAGATTTAAATATT
1 TCAGAAGAATGGGGTTGGAGTATCCTCAACAATGACAATTTAAGCAAAAATAAGATTTAAATATT
*
248801 GACAAGTTTAAAAATAAGGTTGGA
66 GACAAGTTTAAAAACAAGGTTGGA
248825 GTATCTCCTC
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
96 5 0.06
97 71 0.92
98 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.23, T:0.27
Consensus pattern (97 bp):
TCAGAAGAATGGGGTTGGAGTATCCTCAACAATGACAATTTAAGCAAAAATAAGATTTAAATATT
GACAAGTTTAAAAACAAGGTTGGAATGCCCCT
Found at i:248848 original size:97 final size:97
Alignment explanation
Indices: 248670--248858 Score: 224
Period size: 97 Copynumber: 1.9 Consensus size: 97
248660 GTCCCTAATG
* * * * *
248670 ATGACAATTTAGGTGAAAAAAAGATTTAAATCTTGATAAGTTTAAAAGCAAGGTTGGAATGCCCC
1 ATGACAATTTAAGTCAAAAAAAGATTTAAATATTGACAAGTTTAAAAACAAGGTTGGAATGCCCC
* *
248735 TTCAGAAGAATGGGGTTGGAGTATCCTCAACA
66 TTCAGAAAAAAGGGGTTGGAGTATCCTCAACA
*
248767 ATGACAATTTAAG-CAAAAATAAGATTTAAATATTGACAAGTTTAAAAATAAGGTTGGAGTAT-C
1 ATGACAATTTAAGTCAAAAA-AAGATTTAAATATTGACAAGTTTAAAAACAAGGTTGGA--ATGC
* *
248830 TCC-TC-GAAAAAAGAGGGTTTGAGTATCCT
63 CCCTTCAGAAAAAAG-GGGTTGGAGTATCCT
248859 TGTGAATAAA
Statistics
Matches: 78, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
96 11 0.14
97 62 0.79
98 3 0.04
99 2 0.03
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (97 bp):
ATGACAATTTAAGTCAAAAAAAGATTTAAATATTGACAAGTTTAAAAACAAGGTTGGAATGCCCC
TTCAGAAAAAAGGGGTTGGAGTATCCTCAACA
Found at i:255757 original size:814 final size:814
Alignment explanation
Indices: 254189--255811 Score: 3228
Period size: 814 Copynumber: 2.0 Consensus size: 814
254179 AGCTAATCCT
254189 CATTGATTGAGGCTAGCTTGAACTTAACTTGGGGAGGTGTTTAAAAATCTACTTTAAGGCAAACA
1 CATTGATTGAGGCTAGCTTGAACTTAACTTGGGGAGGTGTTTAAAAATCTACTTTAAGGCAAACA
254254 AGTATGATGATCATGCAAAAACATGATGAACAACATTCATGGAGGTGCTGAACATGCCATAAATG
66 AGTATGATGATCATGCAAAAACATGATGAACAACATTCATGGAGGTGCTGAACATGCCATAAATG
254319 CATGAAGCATAGTAAAAATGCATGATCAAGGTTTATCAAAATGATAGAGATGGATATGGCATGTT
131 CATGAAGCATAGTAAAAATGCATGATCAAGGTTTATCAAAATGATAGAGATGGATATGGCATGTT
254384 AGGCACACAAATGGCTTCAAATCATCAAAATCATCAAAATAATCCCTATACTACCACATCCAAAG
196 AGGCACACAAATGGCTTCAAATCATCAAAATCATCAAAATAATCCCTATACTACCACATCCAAAG
254449 CCACAATCATGCATGATGATCCTAAGAGGGTCTTGGAAACGTGTTAGGATCACTAAATGATGATA
261 CCACAATCATGCATGATGATCCTAAGAGGGTCTTGGAAACGTGTTAGGATCACTAAATGATGATA
254514 AACACATAAGCAGAAAAATAAAAGGATCAAAGTTCAGAAAGTATACCAACACAAGCCACTATGCT
326 AACACATAAGCAGAAAAATAAAAGGATCAAAGTTCAGAAAGTATACCAACACAAGCCACTATGCT
254579 GATTTGCTGGTTTAGAGTGACCAAACAGCTTGTTTAACACCTCTTTGGGGTTGTAAACAAGCTGA
391 GATTTGCTGGTTTAGAGTGACCAAACAGCTTGTTTAACACCTCTTTGGGGTTGTAAACAAGCTGA
254644 AAATGAGTTGTTTGAGTTATGGTATTGAGGAGAAATGGTTTGGAGTAGTGTATGAACTAAGGAGG
456 AAATGAGTTGTTTGAGTTATGGTATTGAGGAGAAATGGTTTGGAGTAGTGTATGAACTAAGGAGG
*
254709 AAGTGTTTTTGAGGTGTTTTTGTGGTAAGGAAGGAGGAGCTACGGGATTTTGTGTTTCCTGAAAT
521 AAGTGTTTTTGAGGTGTTTTTATGGTAAGGAAGGAGGAGCTACGGGATTTTGTGTTTCCTGAAAT
254774 GGGAAGTGTTTGTGGGAGCTAGAAGATGCTGGAGAGGTGTTCAGCCAAAAACCTCTTTTGCTGAA
586 GGGAAGTGTTTGTGGGAGCTAGAAGATGCTGGAGAGGTGTTCAGCCAAAAACCTCTTTTGCTGAA
254839 AACAAAATCAGCCTTTTATAGGCAAGATTTGTGGAAACAAAGTAAGGGTACTTGAGACATTTCAC
651 AACAAAATCAGCCTTTTATAGGCAAGATTTGTGGAAACAAAGTAAGGGTACTTGAGACATTTCAC
254904 TCTCAAGCATTGAATGAAAAGCTTACTGGCTGAGGTGGCTGATATCATTGCCTATGGTAGCTGGC
716 TCTCAAGCATTGAATGAAAAGCTTACTGGCTGAGGTGGCTGATATCATTGCCTATGGTAGCTGGC
254969 AAAGCTCAAGGAGAAGATAGGGTGGCTGGCAAAA
781 AAAGCTCAAGGAGAAGATAGGGTGGCTGGCAAAA
255003 CATTGATTGAGGCTAGCTTGAACTTAACTTGGGGAGGTGTTTAAAAATCTACTTTAAGGCAAACA
1 CATTGATTGAGGCTAGCTTGAACTTAACTTGGGGAGGTGTTTAAAAATCTACTTTAAGGCAAACA
255068 AGTATGATGATCATGCAAAAACATGATGAACAACATTCATGGAGGTGCTGAACATGCCATAAATG
66 AGTATGATGATCATGCAAAAACATGATGAACAACATTCATGGAGGTGCTGAACATGCCATAAATG
255133 CATGAAGCATAGTAAAAATGCATGATCAAGGTTTATCAAAATGATAGAGATGGATATGGCATGTT
131 CATGAAGCATAGTAAAAATGCATGATCAAGGTTTATCAAAATGATAGAGATGGATATGGCATGTT
*
255198 AGGCACACAAATGGCTTCAAATCATCAAAATCATCAAAATAATCCCTATACTTCCACATCCAAAG
196 AGGCACACAAATGGCTTCAAATCATCAAAATCATCAAAATAATCCCTATACTACCACATCCAAAG
255263 CCACAATCATGCATGATGATCCTAAGAGGGTCTTGGAAACGTGTTAGGATCACTAAATGATGATA
261 CCACAATCATGCATGATGATCCTAAGAGGGTCTTGGAAACGTGTTAGGATCACTAAATGATGATA
255328 AACACATAAGCAGAAAAATAAAAGGATCAAAGTTCAGAAAGTATACCAACACAAGCCACTATGCT
326 AACACATAAGCAGAAAAATAAAAGGATCAAAGTTCAGAAAGTATACCAACACAAGCCACTATGCT
255393 GATTTGCTGGTTTAGAGTGACCAAACAGCTTGTTTAACACCTCTTTGGGGTTGTAAACAAGCTGA
391 GATTTGCTGGTTTAGAGTGACCAAACAGCTTGTTTAACACCTCTTTGGGGTTGTAAACAAGCTGA
255458 AAATGAGTTGTTTGAGTTATGGTATTGAGGAGAAATGGTTTGGAGTAGTGTATGAACTAAGGAGG
456 AAATGAGTTGTTTGAGTTATGGTATTGAGGAGAAATGGTTTGGAGTAGTGTATGAACTAAGGAGG
255523 AAGTGTTTTTGAGGTGTTTTTATGGTAAGGAAGGAGGAGCTACGGGATTTTGTGTTTCCTGAAAT
521 AAGTGTTTTTGAGGTGTTTTTATGGTAAGGAAGGAGGAGCTACGGGATTTTGTGTTTCCTGAAAT
255588 GGGAAGTGTTTGTGGGAGCTAGAAGATGCTGGAGAGGTGTTCAGCCAAAAACCTCTTTTGCTGAA
586 GGGAAGTGTTTGTGGGAGCTAGAAGATGCTGGAGAGGTGTTCAGCCAAAAACCTCTTTTGCTGAA
255653 AACAAAATCAGCCTTTTATAGGCAAGATTTGTGGAAACAAAGTAAGGGTACTTGAGACATTTCAC
651 AACAAAATCAGCCTTTTATAGGCAAGATTTGTGGAAACAAAGTAAGGGTACTTGAGACATTTCAC
255718 TCTCAAGCATTGAATGAAAAGCTTACTGGCTGAGGTGGCTGATATCATTGCCTATGGTAGCTGGC
716 TCTCAAGCATTGAATGAAAAGCTTACTGGCTGAGGTGGCTGATATCATTGCCTATGGTAGCTGGC
255783 AAAGCTCAAGGAGAAGATAGGGTGGCTGG
781 AAAGCTCAAGGAGAAGATAGGGTGGCTGG
255812 AGTTAATGCT
Statistics
Matches: 807, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
814 807 1.00
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.27
Consensus pattern (814 bp):
CATTGATTGAGGCTAGCTTGAACTTAACTTGGGGAGGTGTTTAAAAATCTACTTTAAGGCAAACA
AGTATGATGATCATGCAAAAACATGATGAACAACATTCATGGAGGTGCTGAACATGCCATAAATG
CATGAAGCATAGTAAAAATGCATGATCAAGGTTTATCAAAATGATAGAGATGGATATGGCATGTT
AGGCACACAAATGGCTTCAAATCATCAAAATCATCAAAATAATCCCTATACTACCACATCCAAAG
CCACAATCATGCATGATGATCCTAAGAGGGTCTTGGAAACGTGTTAGGATCACTAAATGATGATA
AACACATAAGCAGAAAAATAAAAGGATCAAAGTTCAGAAAGTATACCAACACAAGCCACTATGCT
GATTTGCTGGTTTAGAGTGACCAAACAGCTTGTTTAACACCTCTTTGGGGTTGTAAACAAGCTGA
AAATGAGTTGTTTGAGTTATGGTATTGAGGAGAAATGGTTTGGAGTAGTGTATGAACTAAGGAGG
AAGTGTTTTTGAGGTGTTTTTATGGTAAGGAAGGAGGAGCTACGGGATTTTGTGTTTCCTGAAAT
GGGAAGTGTTTGTGGGAGCTAGAAGATGCTGGAGAGGTGTTCAGCCAAAAACCTCTTTTGCTGAA
AACAAAATCAGCCTTTTATAGGCAAGATTTGTGGAAACAAAGTAAGGGTACTTGAGACATTTCAC
TCTCAAGCATTGAATGAAAAGCTTACTGGCTGAGGTGGCTGATATCATTGCCTATGGTAGCTGGC
AAAGCTCAAGGAGAAGATAGGGTGGCTGGCAAAA
Found at i:256110 original size:13 final size:13
Alignment explanation
Indices: 256092--256119 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
256082 ATACAAAGAT
256092 CAATGTATCGATA
1 CAATGTATCGATA
256105 CAATGTATCGATA
1 CAATGTATCGATA
256118 CA
1 CA
256120 TTGAATAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:256184 original size:13 final size:13
Alignment explanation
Indices: 256166--256191 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
256156 CAAGGTAGCT
256166 TTGTATCGATACA
1 TTGTATCGATACA
256179 TTGTATCGATACA
1 TTGTATCGATACA
256192 ACACTCATGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:257067 original size:52 final size:50
Alignment explanation
Indices: 256924--257935 Score: 188
Period size: 39 Copynumber: 22.3 Consensus size: 50
256914 CAGCTAACGG
* * *
256924 TATTGGGCTTGAAGATATG-AAGAATGACAATGTGCTGATTCATGGCCAGCGA
1 TATTGGGCTT-AA-AAATGAAAG-ATGCCAATGTGCTGATTCAAGGCCAGCGA
* * * * ** * *
256976 CATTAGACTT--GAA-G-AAGAATGCCAATGTGCTGAGACAAGGTCGGCGA
1 TATTGGGCTTAAAAATGAAAG-ATGCCAATGTGCTGATTCAAGGCCAGCGA
* * * * *
257023 CATTGGGCTTAGGAATATTAAAGATGCCAATATGCTGATTCAAGGCCAACGA
1 TATTGGGCTTA--AAAATGAAAGATGCCAATGTGCTGATTCAAGGCCAGCGA
* *
257075 TATCGGACTTAAAAATGAAAG-TGCCAATGTGCTGATTCAAGGCCAGCGA
1 TATTGGGCTTAAAAATGAAAGATGCCAATGTGCTGATTCAAGGCCAGCGA
*
257124 TATTGGGC-T-----T----G-TGCCAATGTGCTGATTCAAGGCCAACGA
1 TATTGGGCTTAAAAATGAAAGATGCCAATGTGCTGATTCAAGGCCAGCGA
* * ** * * * **
257163 CATTGGTCTTAGGAA-CAAGGA-GCCAATATGCTGATTCAAGGCTGGCGA
1 TATTGGGCTTAAAAATGAAAGATGCCAATGTGCTGATTCAAGGCCAGCGA
* ** * *
257211 TATTAGGC-------T----CCTGCTAATGTGTTGATTCAAGGCCAGCGA
1 TATTGGGCTTAAAAATGAAAGATGCCAATGTGCTGATTCAAGGCCAGCGA
* * * * *
257250 CATTGGTCTTAAAGATGGTTAAGGTGCCAATGTGCTGATTCAAGGCCCA-CGA
1 TATTGGGCTTAAAAAT-G-AAAGATGCCAATGTGCTGATTCAAGG-CCAGCGA
* * * * * * * *
257302 CATCGGTCTTAAAGATG-AAGGTGCC-ATATGCTGATTCAAGGCTAGCAA
1 TATTGGGCTTAAAAATGAAAGATGCCAATGTGCTGATTCAAGGCCAGCGA
*
257350 TATTGGGC-T-----T----G-TGCCAATGTGCTGATTCAAGGCCAACGA
1 TATTGGGCTTAAAAATGAAAGATGCCAATGTGCTGATTCAAGGCCAGCGA
* * * * * *
257389 CATTGGTCTT--AAAGGCAAGGTGCCAATATGCTGATTCAAGGCCAGCGA
1 TATTGGGCTTAAAAATGAAAGATGCCAATGTGCTGATTCAAGGCCAGCGA
* *
257437 TATTGGGC-T-----T-----ATGCTAATGTGCTGATTCAAGGCTAGCGA
1 TATTGGGCTTAAAAATGAAAGATGCCAATGTGCTGATTCAAGGCCAGCGA
* * * * *
257476 CATTGGTCTT--AGA-GACAAGGTGCCAATATGCTGATTCAAGGCCAGCGA
1 TATTGGGCTTAAAAATGA-AAGATGCCAATGTGCTGATTCAAGGCCAGCGA
* *
257524 TATTGGGC-T-----T-----ATGCCAATGTGCTGATTCAAGGCTAGCAA
1 TATTGGGCTTAAAAATGAAAGATGCCAATGTGCTGATTCAAGGCCAGCGA
* * * * *
257563 CATTGGTCTT--AGA-GACAAGGTGCCAATATGCTGATTCAAGGCCAGCGA
1 TATTGGGCTTAAAAATGA-AAGATGCCAATGTGCTGATTCAAGGCCAGCGA
* *
257611 TATTGGGC-T-----T-----ATGCCAATGTGTTGATTCAAGGTCAGCG-
1 TATTGGGCTTAAAAATGAAAGATGCCAATGTGCTGATTCAAGGCCAGCGA
* * * * *
257649 TCATTGGTCTT--AGA-GACAAGGTGCCAATATGCTGATTCGAGGCCAGCGA
1 T-ATTGGGCTTAAAAATGA-AAGATGCCAATGTGCTGATTCAAGGCCAGCGA
* *
257698 TATTGGGC-T-----T-----ATGCCAATGTGTTGATTCAAGGTCAGCGA
1 TATTGGGCTTAAAAATGAAAGATGCCAATGTGCTGATTCAAGGCCAGCGA
* * * * * * * *
257737 CATTGGTCTTAGAGAT--AAGGTGCCAATATGCTGATTCAAGACTAGCGA
1 TATTGGGCTTAAAAATGAAAGATGCCAATGTGCTGATTCAAGGCCAGCGA
* *
257785 TATTGGGC-T-----TG---CA--CCAATGTACTGATTCAAGGCCAGCGA
1 TATTGGGCTTAAAAATGAAAGATGCCAATGTGCTGATTCAAGGCCAGCGA
* * * * *
257824 CATTGGTCTT--AAA-GACAGGGTGCCAATATGCTGATTCAAGGCCAGCGA
1 TATTGGGCTTAAAAATGA-AAGATGCCAATGTGCTGATTCAAGGCCAGCGA
* * * * * *
257872 TATTGGAC-TCAAGATGGTAAAGGTGCCAATATGCTGATTCAAGGCCAGTGA
1 TATTGGGCTTAAAAAT-G-AAAGATGCCAATGTGCTGATTCAAGGCCAGCGA
257923 TATTGGGCTTAAA
1 TATTGGGCTTAAA
257936 GGTGCCATAG
Statistics
Matches: 712, Mismatches: 143, Indels: 210
0.67 0.13 0.20
Matches are distributed among these distances:
38 5 0.01
39 237 0.33
40 7 0.01
42 3 0.00
43 1 0.00
45 1 0.00
46 1 0.00
47 46 0.06
48 235 0.33
49 43 0.06
50 8 0.01
51 40 0.06
52 79 0.11
53 6 0.01
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.26
Consensus pattern (50 bp):
TATTGGGCTTAAAAATGAAAGATGCCAATGTGCTGATTCAAGGCCAGCGA
Found at i:257213 original size:87 final size:88
Alignment explanation
Indices: 257047--257262 Score: 263
Period size: 87 Copynumber: 2.5 Consensus size: 88
257037 ATATTAAAGA
* * * * * * *
257047 TGCCAATATGCTGATTCAAGGCCAACGATATCGGACTTAAAAATGAAAGTGCCAATGTGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAAATCAAAGAGCCAATATGCTGATT
* **
257112 CAAGGCCAGCGATATTGGGCTTG
66 CAAGGCCAGCGATATTAGGCTCC
** *
257135 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAGGAA-CAAGGAGCCAATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAAATCAAAGAGCCAATATGCTGATT
**
257199 CAAGGCTGGCGATATTAGGCTCC
66 CAAGGCCAGCGATATTAGGCTCC
* * *
257222 TGCTAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAA
1 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAA
257263 GATGGTTAAG
Statistics
Matches: 108, Mismatches: 20, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
87 71 0.66
88 37 0.34
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (88 bp):
TGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAAATCAAAGAGCCAATATGCTGATT
CAAGGCCAGCGATATTAGGCTCC
Found at i:257302 original size:139 final size:135
Alignment explanation
Indices: 257134--257432 Score: 402
Period size: 139 Copynumber: 2.2 Consensus size: 135
257124 TATTGGGCTT
* *
257134 GTGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTT-AGGAACAAGGAGCCAATATGCTGAT
1 GTGCCAATGTGCTGATTCAAGGCCAACGACATCGGTCTTAAAGAACAAGGAGCC-ATATGCTGAT
* * * * *
257198 TCAAGGCTGGCGATATTAGGCTCCTGCTAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAA
65 TCAAGGCTAGCAATATTAGGCTCCTGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTT-AA
*
257263 GATGGTTAAG
129 -A-GG-CAAG
* ** *
257273 GTGCCAATGTGCTGATTCAAGGCCCACGACATCGGTCTTAAAGATGAAGGTGCCATATGCTGATT
1 GTGCCAATGTGCTGATTCAAGGCCAACGACATCGGTCTTAAAGAACAAGGAGCCATATGCTGATT
* **
257338 CAAGGCTAGCAATATTGGGCTTGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAG
66 CAAGGCTAGCAATATTAGGCTCCTGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAG
257403 GCAAG
131 GCAAG
*
257408 GTGCCAATATGCTGATTCAAGGCCA
1 GTGCCAATGTGCTGATTCAAGGCCA
257433 GCGATATTGG
Statistics
Matches: 142, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
135 26 0.18
136 2 0.01
137 1 0.01
138 2 0.01
139 101 0.71
140 10 0.07
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (135 bp):
GTGCCAATGTGCTGATTCAAGGCCAACGACATCGGTCTTAAAGAACAAGGAGCCATATGCTGATT
CAAGGCTAGCAATATTAGGCTCCTGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAG
GCAAG
Found at i:257342 original size:48 final size:52
Alignment explanation
Indices: 257233--257343 Score: 160
Period size: 52 Copynumber: 2.2 Consensus size: 52
257223 GCTAATGTGT
* *
257233 TGATTCAAGG-CCAGCGACATTGGTCTTAAAGATGGTTAAGGTGCCAATGTGC
1 TGATTCAAGGCCCAGCGACATCGGTCTTAAAGATGG-TAAGGTGCCAATATGC
257285 TGATTCAAGGCCCA-CGACATCGGTCTTAAAGAT-G-AAGGTGCC-ATATGC
1 TGATTCAAGGCCCAGCGACATCGGTCTTAAAGATGGTAAGGTGCCAATATGC
257333 TGATTCAAGGC
1 TGATTCAAGGC
257344 TAGCAATATT
Statistics
Matches: 56, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
48 16 0.29
49 8 0.14
51 1 0.02
52 28 0.50
53 3 0.05
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (52 bp):
TGATTCAAGGCCCAGCGACATCGGTCTTAAAGATGGTAAGGTGCCAATATGC
Found at i:257375 original size:39 final size:39
Alignment explanation
Indices: 257322--257877 Score: 261
Period size: 48 Copynumber: 12.9 Consensus size: 39
257312 AAAGATGAAG
* *
257322 GTGCC-ATATGCTGATTCAAGGCTAGCAATATTGGGCTT
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT
* * * *
257360 GTGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTT
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT
257399 AAAGGCAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT
1 ---------GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT
* * * * * *
257447 ATGCTAATGTGCTGATTCAAGGCTAGCGACATTGGTCTT
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT
257486 AGAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT
1 ---------GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT
* * * * * *
257534 ATGCCAATGTGCTGATTCAAGGCTAGCAACATTGGTCTT
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT
257573 AGAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT
1 ---------GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT
* * * * *
257621 ATGCCAATGTGTTGATTCAAGGTCAGCG-TCATTGGTCTT
1 GTGCCAATATGCTGATTCAAGGCCAGCGAT-ATTGGGCTT
*
257660 AGAGACAAGGTGCCAATATGCTGATTCGAGGCCAGCGATATTGGGCTT
1 ---------GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT
* * * * * *
257708 ATGCCAATGTGTTGATTCAAGGTCAGCGACATTGGTCTTAGAGAT
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGC-T-----T
* *
257753 AAGGTGCCAATATGCTGATTCAAGACTAGCGATATTGGGCTT
1 ---GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT
** * * * *
257795 GCACCAATGTACTGATTCAAGGCCAGCGACATTGGTCTT
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT
257834 AAAGACAGGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGG
1 ---------GTGCCAATATGCTGATTCAAGGCCAGCGATATTGG
257878 ACTCAAGATG
Statistics
Matches: 388, Mismatches: 73, Indels: 104
0.69 0.13 0.18
Matches are distributed among these distances:
38 6 0.02
39 186 0.48
40 1 0.00
42 1 0.00
45 1 0.00
47 1 0.00
48 191 0.49
49 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (39 bp):
GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT
Found at i:257377 original size:87 final size:87
Alignment explanation
Indices: 257274--257877 Score: 924
Period size: 87 Copynumber: 6.9 Consensus size: 87
257264 ATGGTTAAGG
* * *
257274 TGCCAATGTGCTGATTCAAGGCCCA-CGACATCGGTCTTAAAGATGAAGGTGCC-ATATGCTGAT
1 TGCCAATGTGCTGATTCAAGG-CCAGCGACATTGGTCTTAGAGA-CAAGGTGCCAATATGCTGAT
* * *
257337 TCAAGGCTAGCAATATTGGGCTTG
64 TCAAGGCCAGCGATATTGGGCTTA
* * *
257361 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGGCAAGGTGCCAATATGCTGATTC
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAGAGACAAGGTGCCAATATGCTGATTC
257426 AAGGCCAGCGATATTGGGCTTA
66 AAGGCCAGCGATATTGGGCTTA
* *
257448 TGCTAATGTGCTGATTCAAGGCTAGCGACATTGGTCTTAGAGACAAGGTGCCAATATGCTGATTC
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAGAGACAAGGTGCCAATATGCTGATTC
257513 AAGGCCAGCGATATTGGGCTTA
66 AAGGCCAGCGATATTGGGCTTA
* *
257535 TGCCAATGTGCTGATTCAAGGCTAGCAACATTGGTCTTAGAGACAAGGTGCCAATATGCTGATTC
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAGAGACAAGGTGCCAATATGCTGATTC
257600 AAGGCCAGCGATATTGGGCTTA
66 AAGGCCAGCGATATTGGGCTTA
* * *
257622 TGCCAATGTGTTGATTCAAGGTCAGCGTCATTGGTCTTAGAGACAAGGTGCCAATATGCTGATTC
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAGAGACAAGGTGCCAATATGCTGATTC
*
257687 GAGGCCAGCGATATTGGGCTTA
66 AAGGCCAGCGATATTGGGCTTA
* * *
257709 TGCCAATGTGTTGATTCAAGGTCAGCGACATTGGTCTTAGAGATAAGGTGCCAATATGCTGATTC
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAGAGACAAGGTGCCAATATGCTGATTC
* * *
257774 AAGACTAGCGATATTGGGCTTG
66 AAGGCCAGCGATATTGGGCTTA
** * * *
257796 CACCAATGTACTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAGGGTGCCAATATGCTGATTC
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAGAGACAAGGTGCCAATATGCTGATTC
257861 AAGGCCAGCGATATTGG
66 AAGGCCAGCGATATTGG
257878 ACTCAAGATG
Statistics
Matches: 480, Mismatches: 35, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
86 11 0.02
87 469 0.98
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (87 bp):
TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAGAGACAAGGTGCCAATATGCTGATTC
AAGGCCAGCGATATTGGGCTTA
Found at i:257416 original size:226 final size:222
Alignment explanation
Indices: 257047--257519 Score: 698
Period size: 226 Copynumber: 2.1 Consensus size: 222
257037 ATATTAAAGA
* *
257047 TGCCAATATGCTGATTCAAGGCCAACGATATCGGACTTAAAAATGAAAGTGCCAATGTGCTGATT
1 TGCCAATATGCTGATTCAAGGCCAACGACATCGGACTTAAAAATGAAAGTGCCAATATGCTGATT
*
257112 CAAGGCCAGCGATATTGGGCTTGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAGGA
66 CAAGGCCAGCAATATTGGGCTTGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAGG-
** * *
257177 ACAAGGAGCCAATATGCTGATTCAAGGCTGGCGATATTAGGCTCCTGCTAATGTGTTGATTCAAG
130 ACAAGGAGCCAATATGCTGATTCAAGGCCAGCGATATTAGGCTCATGCTAATGTGCTGATTCAAG
**
257242 GCCAGCGACATTGGTCTTAAAGATGGTTAAGG
195 GCCAGCGACATTGGTCTT--AGA--GACAAGG
* * * * *
257274 TGCCAATGTGCTGATTCAAGGCCCACGACATCGGTCTTAAAGATGAAGGTGCC-ATATGCTGATT
1 TGCCAATATGCTGATTCAAGGCCAACGACATCGGACTTAAAAATGAAAGTGCCAATATGCTGATT
*
257338 CAAGGCTAGCAATATTGGGCTTGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAG
66 CAAGGCCAGCAATATTGGGCTTGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTT--AG
* * *
257403 G-CAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTATGCTAATGTGCTGATTCAA
129 GACAAGGAGCCAATATGCTGATTCAAGGCCAGCGATATTAGGCTCATGCTAATGTGCTGATTCAA
*
257467 GGCTAGCGACATTGGTCTTAGAGACAAGG
194 GGCCAGCGACATTGGTCTTAGAGACAAGG
257496 TGCCAATATGCTGATTCAAGGCCA
1 TGCCAATATGCTGATTCAAGGCCA
257520 GCGATATTGG
Statistics
Matches: 223, Mismatches: 21, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
222 27 0.12
224 3 0.01
226 143 0.64
227 47 0.21
228 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (222 bp):
TGCCAATATGCTGATTCAAGGCCAACGACATCGGACTTAAAAATGAAAGTGCCAATATGCTGATT
CAAGGCCAGCAATATTGGGCTTGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAGGA
CAAGGAGCCAATATGCTGATTCAAGGCCAGCGATATTAGGCTCATGCTAATGTGCTGATTCAAGG
CCAGCGACATTGGTCTTAGAGACAAGG
Found at i:258081 original size:33 final size:33
Alignment explanation
Indices: 257933--258472 Score: 555
Period size: 33 Copynumber: 16.8 Consensus size: 33
257923 TATTGGGCTT
** *
257933 AAAGGTGCCATAGAGTTGTGGACTTACAA-GAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* * *
257965 AAAGGGATGCCACAGAGGTGTGGGCTTAAAAGGGAA
1 AAA-GG-TGCCACGGAGTTGTGGACTTAAAA-GGAA
** *
258001 AAAGGTGCCACGGAGTCATGGACTTAAAAAG-A
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
*
258033 AAAGGTGCCACGGAGTCGTGGACTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
258066 CAAGGTGCCAGGGAGTTGTGGACTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
258099 AAAGATGCCACGGAGTTATGGACTTAAAA-G--
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
*
258129 ---GGTGCCACGAAGTTGTGGACTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
258159 AAATGGATGCCACGGAGGTGTGGGCTTAAAAGGGAA
1 AAA-GG-TGCCACGGAGTTGTGGACTTAAAA-GGAA
* * *
258195 AAGGGTGCCACGGAGTCGTGGACTTAAAAAG-A
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
*
258227 AAAGGTGCCACGGAGTTATGGACTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
258260 CAAGGTGCCACGGAGTTATGGACTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
258293 AAAGATGCCATGGAGTTGTGGACTTAAAA-G--
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
258323 ---GGTGCCACGGAGTTGTGGACTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
258353 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAGGAA
1 AAAG-GTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
258387 AAAGATGCCATGGAGTTGTGGACTT------AA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
258414 AAAGGTGCCACGGAGTTATGGACTTTGAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGAC-TTAAAAGGAA
** *
258448 AAAGGTGCCATAGAGTCGTGGACTT
1 AAAGGTGCCACGGAGTTGTGGACTT
258473 TGGGAAGAGA
Statistics
Matches: 426, Mismatches: 53, Indels: 57
0.79 0.10 0.11
Matches are distributed among these distances:
27 69 0.16
28 4 0.01
32 63 0.15
33 139 0.33
34 114 0.27
35 25 0.06
36 12 0.03
ACGTcount: A:0.35, C:0.13, G:0.33, T:0.19
Consensus pattern (33 bp):
AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
Found at i:258184 original size:194 final size:193
Alignment explanation
Indices: 257946--258472 Score: 773
Period size: 194 Copynumber: 2.8 Consensus size: 193
257936 GGTGCCATAG
* *
257946 AGTTGTGGACTTACAA-GAAAAAGGGATGCCACAGAGGTGTGGGCTTAAAAGGGAAAAAGGTGCC
1 AGTTGTGGACTTAAAAGGAAAAA-GGATGCCACGGAGGTGTGGGCTTAAAAGGGAAAAAGGTGCC
* **
258010 ACGGAGTCATGGACTTAAAAAGAAAAGGTGCCACGGAGTCGTGGACTTAAAAGGAACAAGGTGCC
65 ACGGAGTCGTGGACTTAAAAAGAAAAGGTGCCACGGAGTTATGGACTTAAAAGGAACAAGGTGCC
*
258075 AGGGAGTTGTGGACTTAAAAGGAAAAAGATGCCACGGAGTTATGGACTTAAAAGGGTGCCACGA
130 ACGGAGTTGTGGACTTAAAAGGAAAAAGATGCCACGGAGTTATGGACTTAAAAGGGTGCCACGA
*
258139 AGTTGTGGACTTAAAAGGAAAAATGGATGCCACGGAGGTGTGGGCTTAAAAGGGAAAAGGGTGCC
1 AGTTGTGGACTTAAAAGGAAAAA-GGATGCCACGGAGGTGTGGGCTTAAAAGGGAAAAAGGTGCC
258204 ACGGAGTCGTGGACTTAAAAAGAAAAGGTGCCACGGAGTTATGGACTTAAAAGGAACAAGGTGCC
65 ACGGAGTCGTGGACTTAAAAAGAAAAGGTGCCACGGAGTTATGGACTTAAAAGGAACAAGGTGCC
* * * *
258269 ACGGAGTTATGGACTTAAAAGGAAAAAGATGCCATGGAGTTGTGGACTTAAAAGGGTGCCACGG
130 ACGGAGTTGTGGACTTAAAAGGAAAAAGATGCCACGGAGTTATGGACTTAAAAGGGTGCCACGA
* * *
258333 AGTTGTGGACTTAAAAGGAAAAA-GAGTGCCACGGAGTTGTGGGCTTTAAA-GGAAAAAGATGCC
1 AGTTGTGGACTTAAAAGGAAAAAGGA-TGCCACGGAGGTGTGGGCTTAAAAGGGAAAAAGGTGCC
* * * *
258396 ATGGAGTTGTGGACTT----A-AAAAGGTGCCACGGAGTTATGGACTTTGAAAGGAAAAAGGTGC
65 ACGGAGTCGTGGACTTAAAAAGAAAAGGTGCCACGGAGTTATGGAC-TTAAAAGGAACAAGGTGC
** *
258456 CATAGAGTCGTGGACTT
129 CACGGAGTTGTGGACTT
258473 TGGGAAGAGA
Statistics
Matches: 307, Mismatches: 24, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
187 24 0.08
188 30 0.10
192 27 0.09
193 37 0.12
194 189 0.62
ACGTcount: A:0.35, C:0.13, G:0.33, T:0.19
Consensus pattern (193 bp):
AGTTGTGGACTTAAAAGGAAAAAGGATGCCACGGAGGTGTGGGCTTAAAAGGGAAAAAGGTGCCA
CGGAGTCGTGGACTTAAAAAGAAAAGGTGCCACGGAGTTATGGACTTAAAAGGAACAAGGTGCCA
CGGAGTTGTGGACTTAAAAGGAAAAAGATGCCACGGAGTTATGGACTTAAAAGGGTGCCACGA
Found at i:258322 original size:26 final size:26
Alignment explanation
Indices: 258292--258349 Score: 89
Period size: 27 Copynumber: 2.2 Consensus size: 26
258282 CTTAAAAGGA
*
258292 AAAAGATGCCATGGAGTTGTGGACTT
1 AAAAGATGCCACGGAGTTGTGGACTT
*
258318 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAA-GATGCCACGGAGTTGTGGACTT
258345 AAAAG
1 AAAAG
258350 GAAAAAGAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 5 0.17
27 24 0.83
ACGTcount: A:0.33, C:0.12, G:0.33, T:0.22
Consensus pattern (26 bp):
AAAAGATGCCACGGAGTTGTGGACTT
Found at i:258416 original size:61 final size:61
Alignment explanation
Indices: 258351--258663 Score: 219
Period size: 65 Copynumber: 5.0 Consensus size: 61
258341 ACTTAAAAGG
* * * *
258351 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAGGAAAAAGATGCCATGGAGTTGTGGACTT
1 AAAAAG-GTGCCACGGAGTTATGGACTTTGAAAGGAAAAAGATGCCATAGAGTCGTGGACTT
*
258412 AAAAAGGTGCCACGGAGTTATGGACTTTGAAAGGAAAAAGGTGCCATAGAGTCGTGGACTTT
1 AAAAAGGTGCCACGGAGTTATGGACTTTGAAAGGAAAAAGATGCCATAGAGTCGTGGAC-TT
* * * * * * * *
258474 GGGAAGAGATGCCACTGAGTCATGGACTCTG--A-G-AAGAGATTGCCACT-GAATCGTGGACTT
1 --AAAAAGGTGCCACGGAGTTATGGACTTTGAAAGGAAAAAGA-TGCCA-TAGAGTCGTGGACTT
* * * ** *
258534 GGAAGAAAAGATGCCACTGAGTCATGGACTTTGAAAAAAAAAAGATGCCATTGAGTCGTGGACTT
1 ---A-AAAAGGTGCCACGGAGTTATGGACTTTGAAAGGAAAAAGATGCCATAGAGTCGTGGAC-T
258599 T
61 T
* ** *
258600 GAAGAAAAGATTGCCATTGAGTTATGGACTTT-AAAGAAAAAAGATGCCACT-GAGTCGTGGACT
1 --A-AAAAG-GTGCCACGGAGTTATGGACTTTGAAAGGAAAAAGATGCCA-TAGAGTCGTGGACT
258663 T
61 T
258664 TGAGAAAAGA
Statistics
Matches: 211, Mismatches: 25, Indels: 29
0.80 0.09 0.11
Matches are distributed among these distances:
60 26 0.12
61 50 0.24
62 30 0.14
64 27 0.13
65 51 0.24
66 27 0.13
ACGTcount: A:0.34, C:0.14, G:0.29, T:0.23
Consensus pattern (61 bp):
AAAAAGGTGCCACGGAGTTATGGACTTTGAAAGGAAAAAGATGCCATAGAGTCGTGGACTT
Found at i:258473 original size:34 final size:32
Alignment explanation
Indices: 258413--258765 Score: 257
Period size: 31 Copynumber: 11.0 Consensus size: 32
258403 TGTGGACTTA
* * *
258413 AAAAGGTGCCACGGAGTTATGGACTTTGAAAGG
1 AAAAGATGCCACTGAGTCATGGACTTTGAAA-G
* * *
258446 AAAAAGGTGCCA-TAGAGTCGTGGACTTTG--GG
1 -AAAAGATGCCACT-GAGTCATGGACTTTGAAAG
* *
258477 AAGAGATGCCACTGAGTCATGGACTCTG--AG
1 AAAAGATGCCACTGAGTCATGGACTTTGAAAG
* * * *
258507 AAGAGATTGCCACTGAATCGTGGAC-TTGGAAG
1 AAAAGA-TGCCACTGAGTCATGGACTTTGAAAG
*
258539 AAAAGATGCCACTGAGTCATGGACTTTGAAAAAA
1 AAAAGATGCCACTGAGTCATGGACTTTG--AAAG
* *
258573 AAAAGATGCCATTGAGTCGTGGACTTTG-AAG
1 AAAAGATGCCACTGAGTCATGGACTTTGAAAG
* *
258604 AAAAGATTGCCATTGAGTTATGGACTTT-AAAG
1 AAAAGA-TGCCACTGAGTCATGGACTTTGAAAG
*
258636 AAAAAAGATGCCACTGAGTCGTGGACTTTGAGAA-
1 --AAAAGATGCCACTGAGTCATGGACTTTGA-AAG
* * * *
258670 AAGAGACGCCACTAAGTTATGGACTTTG--AG
1 AAAAGATGCCACTGAGTCATGGACTTTGAAAG
* *
258700 AAGAGATTGTCACTGAGTCATGGACTTTG--AG
1 AAAAGA-TGCCACTGAGTCATGGACTTTGAAAG
*
258731 AAGAGATTGCCACT-AGGTCATGGACTTTGAGAAG
1 AAAAGA-TGCCACTGA-GTCATGGACTTTGA-AAG
258765 A
1 A
258766 GAGATTTGAA
Statistics
Matches: 264, Mismatches: 35, Indels: 40
0.78 0.10 0.12
Matches are distributed among these distances:
29 1 0.00
30 38 0.14
31 88 0.33
32 55 0.21
33 18 0.07
34 62 0.23
35 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.28, T:0.24
Consensus pattern (32 bp):
AAAAGATGCCACTGAGTCATGGACTTTGAAAG
Found at i:258521 original size:31 final size:30
Alignment explanation
Indices: 258460--258767 Score: 276
Period size: 31 Copynumber: 9.8 Consensus size: 30
258450 AGGTGCCATA
* *
258460 GAGTCGTGGACTTTGGGAAGAGATGCCACT
1 GAGTCATGGACTTTGAGAAGAGATGCCACT
*
258490 GAGTCATGGACTCTGAGAAGAGATTGCCACT
1 GAGTCATGGACTTTGAGAAGAGA-TGCCACT
* * * *
258521 GAATCGTGGACTTGGAAGAAAAGATGCCACT
1 GAGTCATGGACTTTG-AGAAGAGATGCCACT
* * *
258552 GAGTCATGGACTTTGAAAAAAAAAAGATGCCATT
1 GAGTCATGGACTTTG----AGAAGAGATGCCACT
* * *
258586 GAGTCGTGGACTTTGAAGAAAAGATTGCCATT
1 GAGTCATGGACTTTG-AGAAGAGA-TGCCACT
* * *
258618 GAGTTATGGACTTTAAAGAAAAAAGATGCCACT
1 GAGTCATGGACTTT---GAGAAGAGATGCCACT
* *
258651 GAGTCGTGGACTTTGAGAAAAGAGACGCCACT
1 GAGTCATGGACTTTGAG--AAGAGATGCCACT
* * *
258683 AAGTTATGGACTTTGAGAAGAGATTGTCACT
1 GAGTCATGGACTTTGAGAAGAGA-TGCCACT
258714 GAGTCATGGACTTTGAGAAGAGATTGCCACT
1 GAGTCATGGACTTTGAGAAGAGA-TGCCACT
258745 -AGGTCATGGACTTTGAGAAGAGA
1 GA-GTCATGGACTTTGAGAAGAGA
258768 GATTTGAAGA
Statistics
Matches: 233, Mismatches: 32, Indels: 25
0.80 0.11 0.09
Matches are distributed among these distances:
30 29 0.12
31 99 0.42
32 51 0.22
33 18 0.08
34 35 0.15
35 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.28, T:0.24
Consensus pattern (30 bp):
GAGTCATGGACTTTGAGAAGAGATGCCACT
Found at i:258606 original size:65 final size:63
Alignment explanation
Indices: 258385--258760 Score: 319
Period size: 65 Copynumber: 6.0 Consensus size: 63
258375 GCTTTAAAGG
* * * * *
258385 AAAAAGATGCCA-TGGAGTTGTGGAC-TT-A-AAAAGGTGCCACGGAGTTATGGACTTTGAAAGG
1 AAAAAGATGCCACT-GAGTCGTGGACTTTGAGAAAAGATGCCACTGAGTCATGGACTTTGAAA-A
* * * *
258446 AAAAAGGTGCCA-TAGAGTCGTGGACTTTGGGAAGAGATGCCACTGAGTCATGGACTCTG---A
1 AAAAAGATGCCACT-GAGTCGTGGACTTTGAGAAAAGATGCCACTGAGTCATGGACTTTGAAAA
* * * *
258506 GAAGAGATTGCCACTGAATCGTGGACTTGGAAGAAAAGATGCCACTGAGTCATGGACTTTGAAAA
1 AAAAAGA-TGCCACTGAGTCGTGGACTTTG-AGAAAAGATGCCACTGAGTCATGGACTTTG-AAA
258571 A
63 A
* * *
258572 AAAAAGATGCCATTGAGTCGTGGACTTTGAAGAAAAGATTGCCATTGAGTTATGGACTTT-AAAG
1 AAAAAGATGCCACTGAGTCGTGGACTTTG-AGAAAAGA-TGCCACTGAGTCATGGACTTTGAAA-
258636 A
63 A
* * *
258637 AAAAAGATGCCACTGAGTCGTGGACTTTGAGAAAAGAGACGCCACTAAGTTATGGACTTTG---A
1 AAAAAGATGCCACTGAGTCGTGGACTTTGAG-AAA-AGATGCCACTGAGTCATGGACTTTGAAAA
* * * * *
258699 GAAGAGATTGTCACTGAGTCATGGACTTTGAGAAGAGATTGCCACT-AGGTCATGGACTTTGA
1 AAAAAGA-TGCCACTGAGTCGTGGACTTTGAGAAAAGA-TGCCACTGA-GTCATGGACTTTGA
258761 GAAGAGAGAT
Statistics
Matches: 260, Mismatches: 36, Indels: 36
0.78 0.11 0.11
Matches are distributed among these distances:
60 4 0.02
61 44 0.17
62 56 0.22
63 22 0.08
64 28 0.11
65 78 0.30
66 28 0.11
ACGTcount: A:0.34, C:0.14, G:0.28, T:0.24
Consensus pattern (63 bp):
AAAAAGATGCCACTGAGTCGTGGACTTTGAGAAAAGATGCCACTGAGTCATGGACTTTGAAAA
Found at i:258726 original size:193 final size:187
Alignment explanation
Indices: 258385--258760 Score: 481
Period size: 193 Copynumber: 2.0 Consensus size: 187
258375 GCTTTAAAGG
* *
258385 AAAAAGATGCCATGGAGTTGTGGACTTAAAAAGGTGCCACGGAGTTATGGACTTTGAAAGGAAAA
1 AAAAAGATGCCATGGAGTCGTGGACTTAAAAAGGTGCCACGGAGTTATGGACTTTGAAAGAAAAA
* * * *
258450 AGGTGCCATAGAGTCGTGGACTTTGGGAAGAGATGCCACTGAGTCATGGACTCTGAGAAGAGATT
66 AGATGCCATAGAGTCGTGGACTTTGGAAAGAGACGCCACTAAGTCATGGACTCTGAGAAGAGATT
*
258515 GCCACTGAATCGTGGACTTGGAAGAAAAGA-TGCCACT-GAGTCATGGACTTTGAAAAA
131 GCCACTGAATCATGGACTTGG-AGAAAAGATTGCCACTAG-GTCATGGACTTTGAAAAA
* * **
258572 AAAAAGATGCCATTGAGTCGTGGACTTTGAAGAAAAGATTGCCATTGAGTTATGGACTTT-AAAG
1 AAAAAGATGCCATGGAGTCGTGGAC-TT--A-AAAAG-GTGCCACGGAGTTATGGACTTTGAAAG
* *
258636 AAAAAAGATGCCACT-GAGTCGTGGACTTTGAGAAAAGAGACGCCACTAAGTTATGGACTTTGAG
61 AAAAAAGATGCCA-TAGAGTCGTGGACTTTG-G-AAAGAGACGCCACTAAGTCATGGACTCTGAG
* * * *
258700 AAGAGATTGTCACTGAGTCATGGACTTTGAGAAGAGATTGCCACTAGGTCATGGACTTTGA
123 AAGAGATTGCCACTGAATCATGGACTTGGAGAAAAGATTGCCACTAGGTCATGGACTTTGA
258761 GAAGAGAGAT
Statistics
Matches: 162, Mismatches: 17, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
187 23 0.14
188 2 0.01
190 1 0.01
191 35 0.22
192 28 0.17
193 72 0.44
194 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.28, T:0.24
Consensus pattern (187 bp):
AAAAAGATGCCATGGAGTCGTGGACTTAAAAAGGTGCCACGGAGTTATGGACTTTGAAAGAAAAA
AGATGCCATAGAGTCGTGGACTTTGGAAAGAGACGCCACTAAGTCATGGACTCTGAGAAGAGATT
GCCACTGAATCATGGACTTGGAGAAAAGATTGCCACTAGGTCATGGACTTTGAAAAA
Found at i:260057 original size:14 final size:14
Alignment explanation
Indices: 260038--260072 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
260028 CTTTGCATTC
260038 TTTTTTTGTGTGTG
1 TTTTTTTGTGTGTG
* *
260052 TTTTTTTGTTTTTG
1 TTTTTTTGTGTGTG
260066 TTTTTTT
1 TTTTTTT
260073 TTTCGTGCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (14 bp):
TTTTTTTGTGTGTG
Found at i:266893 original size:15 final size:15
Alignment explanation
Indices: 266873--266903 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
266863 ATGAGTTTGG
266873 ATATGAAAATTTGAA
1 ATATGAAAATTTGAA
266888 ATATGAAAATTTGAA
1 ATATGAAAATTTGAA
266903 A
1 A
266904 ATGTCTCGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (15 bp):
ATATGAAAATTTGAA
Found at i:268894 original size:13 final size:12
Alignment explanation
Indices: 268876--268936 Score: 54
Period size: 13 Copynumber: 4.9 Consensus size: 12
268866 TATCGGTCAT
268876 TTTTTTTTCATTC
1 TTTTTTTTC-TTC
268889 TTTTTTTT-TTAC
1 TTTTTTTTCTT-C
*
268901 TTTGATTTT-TTC
1 TTT-TTTTTCTTC
268913 TTTTTTTTCCTTC
1 TTTTTTTT-CTTC
*
268926 ATTTTTTTCTT
1 TTTTTTTTCTT
268937 TTCATATCTA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
11 6 0.15
12 11 0.27
13 24 0.59
ACGTcount: A:0.07, C:0.13, G:0.02, T:0.79
Consensus pattern (12 bp):
TTTTTTTTCTTC
Found at i:268918 original size:21 final size:22
Alignment explanation
Indices: 268892--268938 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
268882 TTCATTCTTT
* *
268892 TTTTTTTACTTTGA-TTTTTTC
1 TTTTTTTACCTTCATTTTTTTC
*
268913 TTTTTTTTCCTTCATTTTTTTC
1 TTTTTTTACCTTCATTTTTTTC
268935 TTTT
1 TTTT
268939 CATATCTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.06, C:0.13, G:0.02, T:0.79
Consensus pattern (22 bp):
TTTTTTTACCTTCATTTTTTTC
Found at i:275435 original size:14 final size:14
Alignment explanation
Indices: 275405--275438 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
275395 ATTTTAATTC
275405 AGTTGTCTTATACA
1 AGTTGTCTTATACA
275419 AGTT-TCTTATACAA
1 AGTTGTCTTATAC-A
275433 AGTTGT
1 AGTTGT
275439 GTTGTCTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 8 0.44
14 9 0.50
15 1 0.06
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (14 bp):
AGTTGTCTTATACA
Found at i:275544 original size:170 final size:170
Alignment explanation
Indices: 275255--275563 Score: 528
Period size: 170 Copynumber: 1.8 Consensus size: 170
275245 TCAGTTGTCT
*
275255 TTATACGAAGTTGTGTTATCTCATAAGAAACTTCTTTGAATAGTCACTGAAGTATTAAGTTTCTT
1 TTATACAAAGTTGTGTTATCTCATAAGAAACTTCTTTGAATAGTCACTGAAGTATTAAGTTTCTT
*
275320 ATTTATTATGCATTATTTTGAATTTAAGTGTTACTAAATGAAGCAATTTAGTGCTTTGATTGTTA
66 ATTTATTATGCATTATTTTGAATTTAAGTGTCACTAAATGAAGCAATTTAGTGCTTTGATTGTTA
275385 TTTATGATGTATTTTAATTCAGTTGTCTTATACAAGTTTC
131 TTTATGATGTATTTTAATTCAGTTGTCTTATACAAGTTTC
* * * * *
275425 TTATACAAAGTTGTGTTGTCTTATAAGAAGCTTCTTTGTATGGTCACTGAAGTATTAAGTTTCTT
1 TTATACAAAGTTGTGTTATCTCATAAGAAACTTCTTTGAATAGTCACTGAAGTATTAAGTTTCTT
* *
275490 ATTTATTATGTATTATTTTGAATTTAAGTGTCACTATATGAAGCAATTTAGTGCTTTGATTGTTA
66 ATTTATTATGCATTATTTTGAATTTAAGTGTCACTAAATGAAGCAATTTAGTGCTTTGATTGTTA
*
275555 TTTCTGATG
131 TTTATGATG
275564 AAGAAAGGCA
Statistics
Matches: 129, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
170 129 1.00
ACGTcount: A:0.28, C:0.09, G:0.16, T:0.47
Consensus pattern (170 bp):
TTATACAAAGTTGTGTTATCTCATAAGAAACTTCTTTGAATAGTCACTGAAGTATTAAGTTTCTT
ATTTATTATGCATTATTTTGAATTTAAGTGTCACTAAATGAAGCAATTTAGTGCTTTGATTGTTA
TTTATGATGTATTTTAATTCAGTTGTCTTATACAAGTTTC
Found at i:283699 original size:83 final size:83
Alignment explanation
Indices: 283560--283821 Score: 515
Period size: 83 Copynumber: 3.2 Consensus size: 83
283550 ACACGCTCCA
283560 ATGTATCGATACAATTCATAATGTATCGATACATGCATTTGAAATTATAGCCGTTGGGCTTTTAT
1 ATGTATCGATACAATTCATAATGTATCGATACATGCATTTGAAATTATAGCCGTTGGGCTTTTAT
283625 TAAATAGTGTGAACAGTG
66 TAAATAGTGTGAACAGTG
283643 ATGTATCGATACAATTCATAATGTATCGATACATGCATTTGAAATTATAGCCGTTGGGCTTTTAT
1 ATGTATCGATACAATTCATAATGTATCGATACATGCATTTGAAATTATAGCCGTTGGGCTTTTAT
*
283708 TAAATAGTGTGAATAGTG
66 TAAATAGTGTGAACAGTG
283726 ATGTATCGATACAATTCATAATGTATCGATACATGCATTTGAAATTATAGCCGTTGGGCTTTTAT
1 ATGTATCGATACAATTCATAATGTATCGATACATGCATTTGAAATTATAGCCGTTGGGCTTTTAT
283791 TAAATAGTGTGAACAGTG
66 TAAATAGTGTGAACAGTG
283809 ATGTATCGATACA
1 ATGTATCGATACA
283822 TGAATAGTGA
Statistics
Matches: 177, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 177 1.00
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (83 bp):
ATGTATCGATACAATTCATAATGTATCGATACATGCATTTGAAATTATAGCCGTTGGGCTTTTAT
TAAATAGTGTGAACAGTG
Found at i:283915 original size:22 final size:22
Alignment explanation
Indices: 283860--283915 Score: 105
Period size: 21 Copynumber: 2.6 Consensus size: 22
283850 AGTAACAGCG
283860 ATGAACAGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
283882 ATGAA-AGTGATGTATCGATAC
1 ATGAACAGTGATGTATCGATAC
283903 ATGAACAGTGATG
1 ATGAACAGTGATG
283916 AATAGTGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.38, C:0.11, G:0.25, T:0.27
Consensus pattern (22 bp):
ATGAACAGTGATGTATCGATAC
Found at i:284083 original size:21 final size:21
Alignment explanation
Indices: 284043--284083 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
284033 GTCAACCTTG
*
284043 TGTATTGATATCAATAGTATA
1 TGTATTGATATCAACAGTATA
284064 TGTATTGATA-CAACACGTAT
1 TGTATTGATATCAACA-GTAT
284084 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.39
Consensus pattern (21 bp):
TGTATTGATATCAACAGTATA
Done.