Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 106 of 378
Found at i:29315719 original size:6 final size:6
Alignment explanation
Indices: 29315705--29315739 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
29315695 GAGACAATGG
* *
29315705 AATAAA AATAGA AATAAA GATAAA AATAAA AATAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAA
29315740 TAGTAAAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (6 bp):
AATAAA
Found at i:29320205 original size:37 final size:37
Alignment explanation
Indices: 29320155--29320228 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
29320145 GTGTTACTAG
* *
29320155 GTAAACTTCCTGGTGGTCTTTCTGAAATTATCTTAGC
1 GTAAACTTCCTGGTGGTCTTTCTAAAATCATCTTAGC
29320192 GTAAACTTCCTGGTGGTCTTTCTAAAATCATCTTAGC
1 GTAAACTTCCTGGTGGTCTTTCTAAAATCATCTTAGC
29320229 CAGCTACCCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (37 bp):
GTAAACTTCCTGGTGGTCTTTCTAAAATCATCTTAGC
Found at i:29322261 original size:40 final size:40
Alignment explanation
Indices: 29322184--29322401 Score: 343
Period size: 40 Copynumber: 5.5 Consensus size: 40
29322174 AAACCAAGTA
* *
29322184 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
29322223 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
29322263 CCTTCGGGACCTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
29322303 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
29322343 CCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
29322383 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
29322402 TTATCATCCG
Statistics
Matches: 168, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
39 15 0.09
40 153 0.91
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:29330513 original size:40 final size:40
Alignment explanation
Indices: 29330436--29330653 Score: 343
Period size: 40 Copynumber: 5.5 Consensus size: 40
29330426 AAACCAAGTA
* *
29330436 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
29330475 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
29330515 CCTTCGGGACCTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
29330555 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
29330595 CCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
29330635 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
29330654 TTATCATCCG
Statistics
Matches: 168, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
39 15 0.09
40 153 0.91
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:29333383 original size:26 final size:26
Alignment explanation
Indices: 29333354--29333406 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
29333344 AAAAGTAAAA
*
29333354 TGGCTAAAGTAATAAAAATTGAGTGT
1 TGGCTAAAGTAATAAAAATCGAGTGT
29333380 TGGCTAAAGTAATAAAAATCGAGTGT
1 TGGCTAAAGTAATAAAAATCGAGTGT
29333406 T
1 T
29333407 CCTAATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.06, G:0.23, T:0.30
Consensus pattern (26 bp):
TGGCTAAAGTAATAAAAATCGAGTGT
Found at i:29334927 original size:28 final size:28
Alignment explanation
Indices: 29334895--29334951 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
29334885 TGGTTTTGAT
29334895 GCTTTTATAATTTTAACTGTTATGACTG
1 GCTTTTATAATTTTAACTGTTATGACTG
29334923 GCTTTTATAATTTTAACTGTTATGACTG
1 GCTTTTATAATTTTAACTGTTATGACTG
29334951 G
1 G
29334952 GAGTATTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.25, C:0.11, G:0.16, T:0.49
Consensus pattern (28 bp):
GCTTTTATAATTTTAACTGTTATGACTG
Found at i:29334961 original size:28 final size:28
Alignment explanation
Indices: 29334900--29334961 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
29334890 TTGATGCTTT
** *
29334900 TATAATTTTAACTGTTATGACTGGCTTT
1 TATAATTTTAACTGTTATGACTGGAGTA
29334928 TATAATTTTAACTGTTATGACTGGGAGTA
1 TATAATTTTAACTGTTATGACT-GGAGTA
29334957 T-TAAT
1 TATAAT
29334962 GAAATTTTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 26 0.87
29 4 0.13
ACGTcount: A:0.29, C:0.08, G:0.16, T:0.47
Consensus pattern (28 bp):
TATAATTTTAACTGTTATGACTGGAGTA
Found at i:29335343 original size:89 final size:89
Alignment explanation
Indices: 29335220--29335398 Score: 263
Period size: 89 Copynumber: 2.0 Consensus size: 89
29335210 AACGATAATG
* * * *
29335220 AATTGACGGATTACGATTATTATTCACTCGAGTATCCTTTGAATTTCAAATAGGTACAAC-GAGT
1 AATTGACAGATTACGATTATTATTCACCCCAGTATCCTTTGAATTTCAAATAGGTACAACAG-GC
29335284 ACAAATAATGTTATACAGATGAGTT
65 ACAAATAATGTTATACAGATGAGTT
* *
29335309 AATTGACAGATTACTGA-TATTATTCACCCCAGTATCCTTTGAATTTCTAATAGGTTCAACAGGC
1 AATTGACAGATTAC-GATTATTATTCACCCCAGTATCCTTTGAATTTCAAATAGGTACAACAGGC
*
29335373 ACAAATAATGTTATACGGATGAGTT
65 ACAAATAATGTTATACAGATGAGTT
29335398 A
1 A
29335399 CGGTTTATAA
Statistics
Matches: 81, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
89 78 0.96
90 3 0.04
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (89 bp):
AATTGACAGATTACGATTATTATTCACCCCAGTATCCTTTGAATTTCAAATAGGTACAACAGGCA
CAAATAATGTTATACAGATGAGTT
Found at i:29343197 original size:6 final size:6
Alignment explanation
Indices: 29343179--29343237 Score: 59
Period size: 6 Copynumber: 9.7 Consensus size: 6
29343169 AAGAAACATT
*
29343179 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGA ATCAGT ATCAGTTA A-CAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAG--A ATCAGA
*
29343228 ATCAAA ATCA
1 ATCAGA ATCA
29343238 AAATGTGAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
5 3 0.07
6 37 0.82
7 4 0.09
8 1 0.02
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.20
Consensus pattern (6 bp):
ATCAGA
Found at i:29343665 original size:27 final size:27
Alignment explanation
Indices: 29343635--29343776 Score: 178
Period size: 27 Copynumber: 5.3 Consensus size: 27
29343625 GGGGCAAAAT
* * *
29343635 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
29343662 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
29343689 GGTAATTCTACCCTAC-AGGCGTATTTT
1 GGTAATTCTACCCTACAAGG-GTATTTC
* * *
29343716 AGTAACTCTACCCTACAAGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
*
29343743 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
29343770 GATAATT
1 GGTAATT
29343777 TCACAAATCA
Statistics
Matches: 100, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
26 2 0.02
27 95 0.95
28 3 0.03
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:29343693 original size:54 final size:54
Alignment explanation
Indices: 29343634--29343803 Score: 184
Period size: 54 Copynumber: 3.1 Consensus size: 54
29343624 AGGGGCAAAA
* * *
29343634 TGGTAATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTT
* ** * *
29343688 CGGTAATTCTACCCTAC-AGGCGTATTTTAGTAACTCTACCCTACAAGGGTATTT
1 TGGTAATTCTACCCTACAAGG-GTATTTCGGTAATTCTACCCTACAGGGGTATTT
* * **
29343742 TGGTAATTCTACCCTACAGGGGTATTTCGATAATT-T-CACAAATCAGGGGTATTT
1 TGGTAATTCTACCCTACAAGGGTATTTCGGTAATTCTAC-CCTA-CAGGGGTATTT
29343796 TGGTAATT
1 TGGTAATT
29343804 TTACAAACCA
Statistics
Matches: 95, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
52 1 0.01
53 6 0.06
54 86 0.91
55 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (54 bp):
TGGTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTT
Found at i:29343794 original size:81 final size:81
Alignment explanation
Indices: 29343643--29343801 Score: 214
Period size: 81 Copynumber: 2.0 Consensus size: 81
29343633 ATGGTAATTT
* **
29343643 TACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGG
1 TACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACAATACAGG
29343708 CGTATTTTAGTAACTC
66 CGTATTTTAGTAACTC
* * *
29343724 TACCCTACAAGGGTATTTTGGTAATTCTACCCTACAGGGGTATTTCGATAATT-TCACAA-ATCA
1 TACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCGATAATTCT-ACAATA-CA
* *
29343787 GGGGTATTTTGGTAA
64 GGCGTATTTTAGTAA
29343802 TTTTACAAAC
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
80 2 0.03
81 66 0.97
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.33
Consensus pattern (81 bp):
TACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACAATACAGG
CGTATTTTAGTAACTC
Found at i:29343816 original size:54 final size:54
Alignment explanation
Indices: 29343733--29343900 Score: 153
Period size: 54 Copynumber: 3.1 Consensus size: 54
29343723 CTACCCTACA
* **
29343733 AGGGTATTTTGGTAATTCTACCCTA-CAGGGGTATTTCGATAATTTCACAAATC-
1 AGGGTATTTTGGTAATTTTA-CAAACCAGGGGTATTTCGATAATTTCACAAATCG
* * * ***
29343786 AGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATTGATCG
1 A-GGGTATTTTGGTAATTTTACAAACCAGGGGTATTTCGATAATTTCACAAATCG
** * * *
29343841 AGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTC-AGTAATTTTATAAATCG
1 AGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTCGA-TAATTTCACAAATCG
*
29343895 ATGGTA
1 AGGGTA
29343901 AAATGGTAAT
Statistics
Matches: 94, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
53 3 0.03
54 90 0.96
55 1 0.01
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.39
Consensus pattern (54 bp):
AGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTCGATAATTTCACAAATCG
Found at i:29343819 original size:81 final size:81
Alignment explanation
Indices: 29343649--29343830 Score: 208
Period size: 81 Copynumber: 2.2 Consensus size: 81
29343639 ATTTTACCCC
* * * **
29343649 ACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGCGTATT
1 ACAAGGGTATTTTGGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACAATACAGGCGTATT
**
29343714 TTAGTAACTCTACCCT
66 TTAGTAACTCTACCAA
*
29343730 ACAAGGGTATTTTGGTAATTCTACCCTACAGGGGTATTTCGATAATT-TCACAA-ATCAGGGGTA
1 ACAAGGGTATTTTGGTAATTCTACCCTACAGGGGTATTTCGATAATTCT-ACAATA-CAGGCGTA
* * *
29343793 TTTTGGTAATTTTA-CAA
64 TTTTAGTAACTCTACCAA
*
29343810 ACCAGGGGTATTTTGGTAATT
1 A-CAAGGGTATTTTGGTAATT
29343831 TTATTGATCG
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
80 4 0.05
81 82 0.95
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (81 bp):
ACAAGGGTATTTTGGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACAATACAGGCGTATT
TTAGTAACTCTACCAA
Found at i:29343832 original size:27 final size:27
Alignment explanation
Indices: 29343734--29343887 Score: 132
Period size: 27 Copynumber: 5.7 Consensus size: 27
29343724 TACCCTACAA
* **
29343734 GGGTATTTTGGTAATTCTACCCTA-CAG
1 GGGTATTTTGGTAATTTTA-CAAACCAG
* * * *
29343761 GGGTATTTCGATAATTTCACAAATCAG
1 GGGTATTTTGGTAATTTTACAAACCAG
29343788 GGGTATTTTGGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAG
*** *
29343815 GGGTATTTTGGTAATTTTATTGATC-G
1 GGGTATTTTGGTAATTTTACAAACCAG
** *
29343841 AGGGTATTTTGGTAATTTTGTAAACCAA
1 -GGGTATTTTGGTAATTTTACAAACCAG
**
29343869 GGGTATTTCAGTAATTTTA
1 GGGTATTTTGGTAATTTTA
29343888 TAAATCGATG
Statistics
Matches: 102, Mismatches: 22, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
26 3 0.03
27 99 0.97
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.40
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACCAG
Found at i:29343900 original size:27 final size:27
Alignment explanation
Indices: 29343761--29344039 Score: 164
Period size: 27 Copynumber: 10.6 Consensus size: 27
29343751 TACCCTACAG
* * * *
29343761 GGGTATTTCGATAATTTCACAAATC-A
1 GGGTATTTTGGTAATTTTATAAATCGA
* *
29343787 GGGGTATTTTGGTAATTTTACAAA-CCA
1 -GGGTATTTTGGTAATTTTATAAATCGA
**
29343814 GGGGTATTTTGGTAATTTTATTGATCGA
1 -GGGTATTTTGGTAATTTTATAAATCGA
* * *
29343842 GGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTATAAATCGA
**
29343869 GGGTATTTCAGTAATTTTATAAATCGA
1 GGGTATTTTGGTAATTTTATAAATCGA
* *** * *
29343896 TGGTAAAATGGTAATTCTGTAAATCGA
1 GGGTATTTTGGTAATTTTATAAATCGA
*** *
29343923 GGGTAAAATGGTAA--TTCT--ATC--
1 GGGTATTTTGGTAATTTTATAAATCGA
* * *
29343944 --TTATTTCGGTAATTTTACAAATCGA
1 GGGTATTTTGGTAATTTTATAAATCGA
* * *
29343969 GGATATTTGGGTAATTTTATAAATCGG
1 GGGTATTTTGGTAATTTTATAAATCGA
* * *
29343996 GGGTACTTTGGTAATTTTACAAGTCGA
1 GGGTATTTTGGTAATTTTATAAATCGA
**
29344023 GGGTATTTCAGTAATTT
1 GGGTATTTTGGTAATTT
29344040 GGTAAACTAA
Statistics
Matches: 194, Mismatches: 48, Indels: 20
0.74 0.18 0.08
Matches are distributed among these distances:
19 7 0.04
21 2 0.01
23 6 0.03
25 2 0.01
26 1 0.01
27 174 0.90
28 2 0.01
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.39
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTATAAATCGA
Found at i:29345136 original size:26 final size:25
Alignment explanation
Indices: 29345112--29345197 Score: 90
Period size: 24 Copynumber: 3.5 Consensus size: 25
29345102 CCATAGCTCG
*
29345112 TATGAGCTTACTGATATATCAGCTCA
1 TATGAGCTTACTGAT-TATCAACTCA
*
29345138 TAAGAGCTTACT-ATTATCAACTCA
1 TATGAGCTTACTGATTATCAACTCA
* *
29345162 T-TGGAGCTTACCG-TT-TCAACTCG
1 TAT-GAGCTTACTGATTATCAACTCA
29345185 TATGAGCTTACTG
1 TATGAGCTTACTG
29345198 TTCAGCTCAA
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
23 17 0.33
24 21 0.41
25 2 0.04
26 11 0.22
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (25 bp):
TATGAGCTTACTGATTATCAACTCA
Found at i:29345213 original size:22 final size:22
Alignment explanation
Indices: 29345188--29345246 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 22
29345178 CAACTCGTAT
29345188 GAGCTTACTGTTCAGCTCAATA
1 GAGCTTACTGTTCAGCTCAATA
*
29345210 GAGCTTACCGCTTCAGCTCAATA
1 GAGCTTACTG-TTCAGCTCAATA
*
29345233 GAGCTTACTATTCA
1 GAGCTTACTGTTCA
29345247 TTAGCTTGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 13 0.39
23 20 0.61
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (22 bp):
GAGCTTACTGTTCAGCTCAATA
Found at i:29345228 original size:23 final size:22
Alignment explanation
Indices: 29345165--29345240 Score: 91
Period size: 23 Copynumber: 3.4 Consensus size: 22
29345155 CAACTCATTG
* *
29345165 GAGCTTACCGTTTCAACTC-GTA
1 GAGCTTACCG-TTCAGCTCAATA
*
29345187 TGAGCTTACTGTTCAGCTCAATA
1 -GAGCTTACCGTTCAGCTCAATA
29345210 GAGCTTACCGCTTCAGCTCAATA
1 GAGCTTACCG-TTCAGCTCAATA
29345233 GAGCTTAC
1 GAGCTTAC
29345241 TATTCATTAG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
22 16 0.34
23 31 0.66
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.30
Consensus pattern (22 bp):
GAGCTTACCGTTCAGCTCAATA
Found at i:29349826 original size:40 final size:40
Alignment explanation
Indices: 29349771--29350020 Score: 385
Period size: 40 Copynumber: 6.2 Consensus size: 40
29349761 AACATTGGAA
29349771 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
29349811 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
29349851 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
29349891 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
29349931 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
29349970 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
29350011 CTATATCCGG
1 ATATATCCGG
29350021 TTAAATCCCG
Statistics
Matches: 191, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
39 2 0.01
40 189 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:29357099 original size:40 final size:40
Alignment explanation
Indices: 29357044--29357293 Score: 385
Period size: 40 Copynumber: 6.2 Consensus size: 40
29357034 AACATTGGAA
29357044 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
29357084 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
29357124 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
29357164 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
29357204 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
29357243 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
29357284 CTATATCCGG
1 ATATATCCGG
29357294 TTAAATCCCG
Statistics
Matches: 191, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
39 2 0.01
40 189 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:29361372 original size:25 final size:24
Alignment explanation
Indices: 29361309--29361377 Score: 93
Period size: 24 Copynumber: 2.8 Consensus size: 24
29361299 CTCTTTTAAT
*
29361309 AACTAGGGCAAAGCCCTTTCTGATA
1 AACT-GGGCAAAGCCCTTTTTGATA
*
29361334 AACTGGGCAAAGCCCTTTTTGGTA
1 AACTGGGCAAAGCCCTTTTTGATA
*
29361358 AACTGGGGCAGAGCCCTTTT
1 AACT-GGGCAAAGCCCTTTT
29361378 AGCACTTCCT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
24 22 0.55
25 18 0.45
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (24 bp):
AACTGGGCAAAGCCCTTTTTGATA
Found at i:29361377 original size:24 final size:23
Alignment explanation
Indices: 29361296--29361377 Score: 85
Period size: 24 Copynumber: 3.4 Consensus size: 23
29361286 CTGGAGGCCT
*
29361296 AGCCTCTTTTAAT-AACTAGGGCAA
1 AGCC-CTTTTGATAAACT-GGGCAA
29361320 AGCCCTTTCTGATAAACTGGGCAA
1 AGCCCTTT-TGATAAACTGGGCAA
* *
29361344 AGCCCTTTTTGGTAAACTGGGGCAG
1 AGCCC-TTTTGATAAACT-GGGCAA
29361369 AGCCCTTTT
1 AGCCCTTTT
29361378 AGCACTTCCT
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
23 4 0.08
24 30 0.59
25 17 0.33
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (23 bp):
AGCCCTTTTGATAAACTGGGCAA
Found at i:29362217 original size:27 final size:27
Alignment explanation
Indices: 29362187--29362251 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
29362177 GGGCATATTC
29362187 GTCATTTTACCATACAAGGG-TATTACG
1 GTCATTTTACCATACAAGGGCT-TTACG
* * *
29362214 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCATTTTACCATACAAGGGCTTTACG
*
29362241 GTCTTTTTACC
1 GTCATTTTACC
29362252 TATTAGGGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCATACAAGGGCTTTACG
Found at i:29374263 original size:8 final size:8
Alignment explanation
Indices: 29374250--29374274 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
29374240 TTATCAGCTC
29374250 TTATTATT
1 TTATTATT
29374258 TTATTATT
1 TTATTATT
29374266 TTATTATT
1 TTATTATT
29374274 T
1 T
29374275 CGACTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTATTATT
Found at i:29374751 original size:17 final size:17
Alignment explanation
Indices: 29374729--29374767 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
29374719 TTTATTGTTC
*
29374729 TATTTATTTATCTTAGT
1 TATTTATTTATCTTAAT
*
29374746 TATTTATTTATTTTAAT
1 TATTTATTTATCTTAAT
29374763 TATTT
1 TATTT
29374768 TATCTAACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (17 bp):
TATTTATTTATCTTAAT
Found at i:29378297 original size:41 final size:41
Alignment explanation
Indices: 29378252--29378334 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 41
29378242 TATCTCTGTC
* *
29378252 AACCTTATCATGAAA-TTTTGTAATAAATAAATTAAATCAAA
1 AACCTTATCATCAAACCTTT-TAATAAATAAATTAAATCAAA
* *
29378293 AACCTTATCATCAAACCTTTTAATAATTTAATTAAATCAAA
1 AACCTTATCATCAAACCTTTTAATAAATAAATTAAATCAAA
29378334 A
1 A
29378335 GTCAAATGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
41 34 0.92
42 3 0.08
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.35
Consensus pattern (41 bp):
AACCTTATCATCAAACCTTTTAATAAATAAATTAAATCAAA
Found at i:29382682 original size:18 final size:18
Alignment explanation
Indices: 29382647--29382684 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
29382637 TTTCAGCTCC
*
29382647 ATATTTTCTCTTCTTTTT
1 ATATTTTCTCTTCATTTT
29382665 ATATTTTCT-TATCATTTT
1 ATATTTTCTCT-TCATTTT
29382683 AT
1 AT
29382685 TTTATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.18, C:0.13, G:0.00, T:0.68
Consensus pattern (18 bp):
ATATTTTCTCTTCATTTT
Found at i:29386480 original size:15 final size:15
Alignment explanation
Indices: 29386458--29386496 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
29386448 ATCTTGTTGT
29386458 TTTTTAATTT-TATA
1 TTTTTAATTTCTATA
*
29386472 TTTTGTAATTTCTTTA
1 TTTT-TAATTTCTATA
29386488 TTTTTAATT
1 TTTTTAATT
29386497 GTTTTTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 4 0.18
15 11 0.50
16 7 0.32
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (15 bp):
TTTTTAATTTCTATA
Found at i:29393518 original size:40 final size:40
Alignment explanation
Indices: 29393462--29393665 Score: 286
Period size: 40 Copynumber: 5.1 Consensus size: 40
29393452 TGGGATTTAA
* * * *
29393462 CCGGATATAGCT-ACTCGCTCGAATACCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
*
29393502 CCGGACATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
29393542 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
29393582 CCGGATATAGTAACTCGCACAAATGCCTTTGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * * *
29393622 TCGGA-ACTAGTCACTAGCGCAAATGCCTTCGGGACTTAGC
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGC
29393662 CCGG
1 CCGG
29393666 TTATCATCCA
Statistics
Matches: 149, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
39 2 0.01
40 147 0.99
ACGTcount: A:0.26, C:0.28, G:0.24, T:0.22
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:29395462 original size:28 final size:27
Alignment explanation
Indices: 29395399--29395468 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
29395389 ATAGTGAGTC
29395399 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
29395426 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
29395454 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29395469 GTACAAATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:29403855 original size:40 final size:40
Alignment explanation
Indices: 29403772--29404029 Score: 351
Period size: 40 Copynumber: 6.5 Consensus size: 40
29403762 AAGCCAAGTA
* * * * *
29403772 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATA
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* * *
29403811 CCTTCGGGACATAGCCTGGACATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
29403851 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
29403891 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
29403931 CCTTCAGGACTTAGCCCGGATATAGTAACTCGCACATATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
29403971 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
29404011 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
29404030 TTATCATCCA
Statistics
Matches: 198, Mismatches: 18, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
39 13 0.07
40 185 0.93
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.22
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:29412213 original size:42 final size:41
Alignment explanation
Indices: 29412096--29412213 Score: 146
Period size: 43 Copynumber: 2.8 Consensus size: 41
29412086 ATACCAATGA
29412096 CATATCCCAGATATGGTCTTACATGAGATCTCATATAGATGG
1 CATATCCCAGATATGGTCTTACATGA-ATCTCATATAGATGG
* * * *
29412138 CAATAGCCCAGCTATGGTCTTACATGAAGTCTCATATCGATGT
1 C-ATATCCCAGATATGGTCTTACATGAA-TCTCATATAGATGG
* *
29412181 CATATCCCAGATATAGTCTTACACGTAATCTCA
1 CATATCCCAGATATGGTCTTACATG-AATCTCA
29412214 AATAACCCCA
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
42 27 0.42
43 38 0.58
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.31
Consensus pattern (41 bp):
CATATCCCAGATATGGTCTTACATGAATCTCATATAGATGG
Found at i:29413577 original size:24 final size:24
Alignment explanation
Indices: 29413550--29413605 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
29413540 TGGAGGAACG
* * *
29413550 AGATGAAGGTGAAGATAAAGATGA
1 AGATGAAGCTCAAGATAAAAATGA
* *
29413574 AGATGGAGCTCAAGGTAAAAATGA
1 AGATGAAGCTCAAGATAAAAATGA
29413598 AGATGAAG
1 AGATGAAG
29413606 AATATGAGGA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.48, C:0.04, G:0.32, T:0.16
Consensus pattern (24 bp):
AGATGAAGCTCAAGATAAAAATGA
Found at i:29418212 original size:27 final size:27
Alignment explanation
Indices: 29418177--29418254 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
29418167 TTCTCTATAG
* *
29418177 AGGCGTTCCTTTCATGTTGCGCCAAAA
1 AGGCGTTCCTTTCATATTGCACCAAAA
* *
29418204 AGGCTTTCCTTTCATATTGCACCACAA
1 AGGCGTTCCTTTCATATTGCACCAAAA
*
29418231 AGACGTTCCTTTCATAATT-CACCA
1 AGGCGTTCCTTTCAT-ATTGCACCA
29418255 GAACGACAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
27 41 0.93
28 3 0.07
ACGTcount: A:0.26, C:0.28, G:0.14, T:0.32
Consensus pattern (27 bp):
AGGCGTTCCTTTCATATTGCACCAAAA
Found at i:29418348 original size:27 final size:27
Alignment explanation
Indices: 29418298--29418382 Score: 93
Period size: 27 Copynumber: 3.1 Consensus size: 27
29418288 TTGCGCCATA
* * * *
29418298 TTCCTTTCATAATGCGCTATAAAGGCT
1 TTCCTTTCATATTGCACCACAAAGGCT
29418325 TTCCTTTCATATTGCACCACAAAGG-T
1 TTCCTTTCATATTGCACCACAAAGGCT
*
29418351 GTTCCTTTCATAATT-CACCACAAAGGCG
1 -TTCCTTTCAT-ATTGCACCACAAAGGCT
29418379 TTCC
1 TTCC
29418383 ATTCCTGACA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
26 1 0.02
27 46 0.92
28 3 0.06
ACGTcount: A:0.26, C:0.27, G:0.13, T:0.34
Consensus pattern (27 bp):
TTCCTTTCATATTGCACCACAAAGGCT
Found at i:29419917 original size:40 final size:40
Alignment explanation
Indices: 29419872--29420038 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
29419862 CGGAATATAA
29419872 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
29419912 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
29419952 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
29419992 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
29420031 CCGGATAT
1 CCGGATAT
29420039 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:29420885 original size:17 final size:19
Alignment explanation
Indices: 29420862--29420907 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
29420852 AAGAAGCATG
29420862 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
29420880 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
29420898 AATCATGCTC
1 AATCATGCTC
29420908 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:29427898 original size:40 final size:40
Alignment explanation
Indices: 29427853--29428019 Score: 194
Period size: 40 Copynumber: 4.2 Consensus size: 40
29427843 CGGAATATAA
29427853 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
29427893 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
29427933 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
29427973 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
29428012 CCGGATAT
1 CCGGATAT
29428020 CATTCAATTT
Statistics
Matches: 109, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
39 14 0.13
40 95 0.87
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:29428864 original size:17 final size:19
Alignment explanation
Indices: 29428841--29428886 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
29428831 AAGAAGCATG
29428841 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
29428859 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
29428877 AATCATGCTC
1 AATCATGCTC
29428887 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:29433568 original size:43 final size:41
Alignment explanation
Indices: 29433511--29433636 Score: 121
Period size: 43 Copynumber: 3.0 Consensus size: 41
29433501 AATGCCAACG
29433511 TCCCAGAC-GTGGTCTTACATGTAATCAAACATCGATGCCACTA
1 TCCCAGACAG-GGTCTTACATGTAATCAAA-ATCGATGCCA-TA
* * *
29433554 TCCCAGACAGGGTCTTAAATGAAATC-AAATACGATGTCGATA
1 TCCCAGACAGGGTCTTACATGTAATCAAAAT-CGATG-CCATA
* * *
29433596 TCCCAGACATGGTCTTACACGTAAATCATAAGTCGATGCCA
1 TCCCAGACAGGGTCTTACATGT-AATCA-AAATCGATGCCA
29433637 ACGTCCTAGA
Statistics
Matches: 68, Mismatches: 9, Indels: 12
0.76 0.10 0.13
Matches are distributed among these distances:
41 2 0.03
42 27 0.40
43 30 0.44
44 6 0.09
45 3 0.04
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (41 bp):
TCCCAGACAGGGTCTTACATGTAATCAAAATCGATGCCATA
Found at i:29445958 original size:42 final size:43
Alignment explanation
Indices: 29445876--29445980 Score: 117
Period size: 42 Copynumber: 2.5 Consensus size: 43
29445866 ACGTCCTGGG
* * *
29445876 CGTGGTCTTACATGTAATTCAATATCGATGCCACTATCCCAGA
1 CGTGGTCTTACACGTAAATCAATATCGATGCCAATATCCCAGA
*
29445919 CAG-GGTCTTACACG-AAATCAGATAT-GATGCCAATGTCCCAGA
1 C-GTGGTCTTACACGTAAATCA-ATATCGATGCCAATATCCCAGA
* *
29445961 CGTGGTCTTATACATAAATC
1 CGTGGTCTTACACGTAAATC
29445981 TGAATCGAGG
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
41 1 0.02
42 30 0.58
43 20 0.38
44 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (43 bp):
CGTGGTCTTACACGTAAATCAATATCGATGCCAATATCCCAGA
Found at i:29468494 original size:80 final size:79
Alignment explanation
Indices: 29468361--29468537 Score: 229
Period size: 80 Copynumber: 2.2 Consensus size: 79
29468351 TGGATGATAA
*
29468361 CCGGGCTAAGTCCCGAAGGCATTTTCGCTAGTGACTAGTTCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTTCGCGAGTGACTAGTTCCGGGCTAAGTCCCGAAGGCA-TTG
29468426 TA-CGAGCTA-CTATAT
65 -AGCGAG-TAGCTATAT
* *
29468441 CCGGGCTAAGTCCCGAAGGCATTTGT-GCGAGTTACTA-TATCCGGGCTATGTCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTT-TCGCGAGTGACTAGT-TCCGGGCTAAGTCCCGAAGGCATT
29468504 GAGCGAGTAGCTATAT
64 GAGCGAGTAGCTATAT
* *
29468520 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
29468538 TACTTGGCTT
Statistics
Matches: 88, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
78 17 0.19
79 16 0.18
80 54 0.61
81 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTTCGCGAGTGACTAGTTCCGGGCTAAGTCCCGAAGGCATTGA
GCGAGTAGCTATAT
Found at i:29468521 original size:39 final size:40
Alignment explanation
Indices: 29468361--29468537 Score: 204
Period size: 40 Copynumber: 4.5 Consensus size: 40
29468351 TGGATGATAA
** *
29468361 CCGGGCTAAGTCCCGAAGGCATTTTCGCTAG-TGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGCT-ACTA-TAT
29468401 CCGGGCTAAGTCCCGAAGGCATTTGTA-CGAGCTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTG-AGCGAGCTACTATAT
* *
29468441 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGCTACTATAT
*
29468481 CCGGGCTATGTCCCGAAGGCA-TTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGCTA-CTATAT
* *
29468520 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
29468538 TACTTGGCTT
Statistics
Matches: 122, Mismatches: 10, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
38 15 0.12
39 17 0.14
40 89 0.73
41 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGCTACTATAT
Found at i:29476568 original size:40 final size:39
Alignment explanation
Indices: 29476513--29476689 Score: 207
Period size: 40 Copynumber: 4.5 Consensus size: 39
29476503 TGGATGATAA
* *
29476513 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT-ACTA-TAT
29476553 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAT
* * *
29476593 CTGGGCTATGTCCTGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAT
* *
29476633 CCGGGCTATGTCCCGAAGGCA-TTGAGCGAGTAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTA-CTATAT
* *
29476672 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
29476690 TACTTGGCTT
Statistics
Matches: 122, Mismatches: 12, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
38 15 0.12
39 17 0.14
40 89 0.73
41 1 0.01
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.26
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTATAT
Found at i:29478307 original size:79 final size:81
Alignment explanation
Indices: 29478206--29478390 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
29478196 ACGACTCGCT
** * *
29478206 CAAATGCCTTCGGGACGAAGCCCGG-TTATAGTGACTCGCACGAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACGAATGCCTTC-GGATCCTAACCC
* *
29478269 GGGTTTAGTAACTT-GCA
64 GGATATAGTAACTTAGCA
* **
29478286 CAAATGCCTTCGGG-CTTAGCCCGGATTTATTAACTCGCACGAATGCCTTCGGATCCTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG
*
29478350 ATATAGTCACTTAGCA
66 ATATAGTAACTTAGCA
29478366 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
29478391 CATCATTCGA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCTTCGGATCCTAACCCGG
ATATAGTAACTTAGCA
Found at i:29478390 original size:40 final size:39
Alignment explanation
Indices: 29478199--29478390 Score: 163
Period size: 40 Copynumber: 4.8 Consensus size: 39
29478189 GGATATAACG
* ** * *
29478199 ACTCGCTCAAATGCCTTCGGGACGAAGCCCGGTTATAGTG
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * * *
29478239 ACTCGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA
1 ACTCGCAC-AAAGCCTTCGGGACTTAGCCCGGATATAGTA
* * *
29478279 ACTTGCACAAATGCCTTCGGG-CTTAGCCCGGATTTATTA
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * * *
29478318 ACTCGCACGAATGCCTTC-GGATCCTAGTCCGGATATAGTC
1 ACTCGCAC-AAAGCCTTCGGGA-CTTAGCCCGGATATAGTA
*
29478358 ACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAAAGCCTTCGGGACTTAGCCCGGA
29478391 CATCATTCGA
Statistics
Matches: 121, Mismatches: 24, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
38 2 0.02
39 30 0.25
40 79 0.65
41 10 0.08
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.24
Consensus pattern (39 bp):
ACTCGCACAAAGCCTTCGGGACTTAGCCCGGATATAGTA
Found at i:29481347 original size:27 final size:27
Alignment explanation
Indices: 29481317--29481377 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
29481307 AGACTATCCC
* * * *
29481317 TTCATGATTCACTACAAAGGCGTTCCT
1 TTCATAATGCACTACAAAAGCATTCCT
*
29481344 TTCATAATGCCCTACAAAAGCATTCCT
1 TTCATAATGCACTACAAAAGCATTCCT
*
29481371 TTAATAA
1 TTCATAA
29481378 ATTGCCATAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.25, G:0.10, T:0.33
Consensus pattern (27 bp):
TTCATAATGCACTACAAAAGCATTCCT
Found at i:29502227 original size:30 final size:30
Alignment explanation
Indices: 29502193--29502252 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
29502183 TATTTTATTA
*
29502193 TTAATTTTGTTATTATTTTATAGACATTTG
1 TTAATTTTGTTATTATTTTAGAGACATTTG
*
29502223 TTAATTTTGTTATTATTTTAGAGGCATTTG
1 TTAATTTTGTTATTATTTTAGAGACATTTG
29502253 CTTGTTAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.25, C:0.03, G:0.13, T:0.58
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAGAGACATTTG
Found at i:29502373 original size:17 final size:19
Alignment explanation
Indices: 29502333--29502373 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
29502323 AGAAAATATT
*
29502333 TATTTTGATGTTGTTAGTA
1 TATTTTGATGTTATTAGTA
29502352 T-TTTTGATG-TATTA-TA
1 TATTTTGATGTTATTAGTA
29502368 TATTTT
1 TATTTT
29502374 TAAAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 8 0.40
19 1 0.05
ACGTcount: A:0.22, C:0.00, G:0.15, T:0.63
Consensus pattern (19 bp):
TATTTTGATGTTATTAGTA
Found at i:29507839 original size:40 final size:40
Alignment explanation
Indices: 29507784--29507947 Score: 170
Period size: 40 Copynumber: 4.1 Consensus size: 40
29507774 TGAATGATAC
* * * *
29507784 CCGGGCTAAGTCCCGAAGGCATTTATGTTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
*
29507824 CCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCAATT-GTGCTAG-TGATTATAT
* * * * * *
29507864 CCGGGTTAAAACCCGAAGGCAATTGTGCAAGTTACTAAAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
* * *
29507904 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
29507944 CCGG
1 CCGG
29507948 TTAAATGCCG
Statistics
Matches: 102, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
39 3 0.03
40 94 0.92
41 5 0.05
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTATAT
Found at i:29511783 original size:48 final size:48
Alignment explanation
Indices: 29511722--29511935 Score: 374
Period size: 48 Copynumber: 4.4 Consensus size: 48
29511712 ATATACACAC
* * *
29511722 ATCTCCTATATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
29511770 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
29511818 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
29511866 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCAC--ATATACAT
*
29511916 TTCTCATACATATTTCACAT
1 ATCTCATACATATTTCACAT
29511936 ATTCACTACA
Statistics
Matches: 160, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
48 133 0.83
50 27 0.17
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.36
Consensus pattern (48 bp):
ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
Found at i:29523914 original size:23 final size:25
Alignment explanation
Indices: 29523888--29523986 Score: 81
Period size: 24 Copynumber: 4.3 Consensus size: 25
29523878 AAACTTGATT
29523888 GAGCT-AAAACGGTAAGCTCTAT-C
1 GAGCTGAAAACGGTAAGCTCTATAC
*
29523911 GAGCTGAATAA---TAAGCTC-ATAA
1 GAGCTGAA-AACGGTAAGCTCTATAC
* * *
29523933 GAG-TTAAAACGGTAAGCTCCA-AT
1 GAGCTGAAAACGGTAAGCTCTATAC
*
29523956 GAGTTGAAAACGGTAAGCTCT-TAC
1 GAGCTGAAAACGGTAAGCTCTATAC
29523980 GAGCTGA
1 GAGCTGA
29523987 TATAGGAGCT
Statistics
Matches: 60, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
20 2 0.03
21 5 0.08
22 10 0.17
23 16 0.27
24 25 0.42
25 2 0.03
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.22
Consensus pattern (25 bp):
GAGCTGAAAACGGTAAGCTCTATAC
Found at i:29524513 original size:29 final size:27
Alignment explanation
Indices: 29524472--29524532 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
29524462 ATCTTTCATT
29524472 ATTTTACATATTTAACCACCATATTTTAC
1 ATTTTACATATTTAACC-CC-TATTTTAC
* *
29524501 ATTTTCACA-ATTTAATCCCTATTTTGC
1 ATTTT-ACATATTTAACCCCTATTTTAC
29524528 ATTTT
1 ATTTT
29524533 TGCCAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 12 0.41
28 2 0.07
29 12 0.41
30 3 0.10
ACGTcount: A:0.30, C:0.20, G:0.02, T:0.49
Consensus pattern (27 bp):
ATTTTACATATTTAACCCCTATTTTAC
Found at i:29528409 original size:48 final size:48
Alignment explanation
Indices: 29528336--29528621 Score: 295
Period size: 48 Copynumber: 6.0 Consensus size: 48
29528326 AAAAGGGTGA
* ** * *
29528336 AATGCCGATGCCATGTCCCGGACATGGTCTTGCACTGGCTCACATAAC
1 AATGCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATC
* * * * *
29528384 AATGCTGATGGCATGTTCCAAACATGGACTTACACTGGCTCATATATT
1 AATGCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATC
* * * * * * *
29528432 GAGGCCAATGCCATG-TCCAGACATGATCTTACACTAGCTCTCATATC
1 AATGCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATC
* * *
29528479 AATGTCGATGCCATGTTCCAAACATGGTCTTACACTGGATCACATATT
1 AATGCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATC
* * * * * *
29528527 GAGGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATC
1 AATGCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATC
* * * *
29528575 AGTGCCGATGCCATGCTCCAAAAATGGTCTTACACTGGCTCATATAT
1 AATGCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATAT
29528622 TGAGGTTAAT
Statistics
Matches: 186, Mismatches: 51, Indels: 2
0.78 0.21 0.01
Matches are distributed among these distances:
47 36 0.19
48 150 0.81
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (48 bp):
AATGCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATC
Found at i:29528602 original size:96 final size:96
Alignment explanation
Indices: 29528343--29528668 Score: 465
Period size: 96 Copynumber: 3.4 Consensus size: 96
29528333 TGAAATGCCG
* * * * * * *
29528343 ATGCCATGTCCCGGACATGGTCTTGCACTGGCTCACATAACAATGCTGATGGCATGTTCCAAACA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATGCCGATGCCATGTTCCAAACA
*
29528408 TGGACTTACACTGGCTCATATATTGAGGCCA
66 TGGTCTTACACTGGCTCATATATTGAGGCCA
* *
29528439 ATGCCATGT-CCAGACATGATCTTACACTAGCTCTCATATCAATGTCGATGCCATGTTCCAAACA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATGCCGATGCCATGTTCCAAACA
* * *
29528503 TGGTCTTACACTGGATCACATATTGAGGCCG
66 TGGTCTTACACTGGCTCATATATTGAGGCCA
* * *
29528534 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAGTGCCGATGCCATGCTCCAAAAA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATGCCGATGCCATGTTCCAAACA
**
29528599 TGGTCTTACACTGGCTCATATATTGAGGTTA
66 TGGTCTTACACTGGCTCATATATTGAGGCCA
* *
29528630 ATGTCATTTCCCAGACATGGTCTTACACTAGCTCTCATA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATA
29528669 ACCCTAGTAT
Statistics
Matches: 204, Mismatches: 25, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
95 82 0.40
96 122 0.60
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (96 bp):
ATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAATGCCGATGCCATGTTCCAAACA
TGGTCTTACACTGGCTCATATATTGAGGCCA
Found at i:29528650 original size:48 final size:48
Alignment explanation
Indices: 29528339--29528663 Score: 232
Period size: 48 Copynumber: 6.8 Consensus size: 48
29528329 AGGGTGAAAT
* * * * * *** *
29528339 GCCGATGCCATGTCCCGGACATGGTCTTGCACTGGCTCACATAACAAT
1 GCCGATGCCATTTCCCAGACATGGTCTTACACTAGCTCATATATTGAG
* * * * *
29528387 GCTGATGGCATGTT-CCAAACATGGACTTACACTGGCTCATATATTGAG
1 GCCGATGCCAT-TTCCCAGACATGGTCTTACACTAGCTCATATATTGAG
* * * ** *
29528435 GCCAATGCCATGT-CCAGACATGATCTTACACTAGCTC-TCATATCAAT
1 GCCGATGCCATTTCCCAGACATGGTCTTACACTAGCTCAT-ATATTGAG
* * * * *
29528482 GTCGATGCCATGTT-CCAAACATGGTCTTACACTGGATCACATATTGAG
1 GCCGATGCCAT-TTCCCAGACATGGTCTTACACTAGCTCATATATTGAG
* *
29528530 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTC-TCATA-TCAG
1 GCCGATGCCATTTCCCAGACATGGTCTTACACTAGCTCAT-ATATTGAG
* * * *
29528577 TGCCGATGCCA-TGCTCCAAAAATGGTCTTACACTGGCTCATATATTGAG
1 -GCCGATGCCATTTC-CCAGACATGGTCTTACACTAGCTCATATATTGAG
*** *
29528626 GTTAATGTCATTTCCCAGACATGGTCTTACACTAGCTC
1 GCCGATGCCATTTCCCAGACATGGTCTTACACTAGCTC
29528664 TCATAACCCT
Statistics
Matches: 211, Mismatches: 55, Indels: 22
0.73 0.19 0.08
Matches are distributed among these distances:
46 1 0.00
47 40 0.19
48 163 0.77
49 7 0.03
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (48 bp):
GCCGATGCCATTTCCCAGACATGGTCTTACACTAGCTCATATATTGAG
Found at i:29531373 original size:28 final size:29
Alignment explanation
Indices: 29531342--29531418 Score: 111
Period size: 29 Copynumber: 2.7 Consensus size: 29
29531332 TGACCCACTT
* *
29531342 GGCCCAA-TCTCATTTATATGGCCCATCA
1 GGCCCAATTCACATTCATATGGCCCATCA
29531370 GGCCCAATTCACATTCATATGGCCCATCA
1 GGCCCAATTCACATTCATATGGCCCATCA
* *
29531399 GGCCCAAATCACATGCATAT
1 GGCCCAATTCACATTCATAT
29531419 TCATGCTCAC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
28 7 0.16
29 37 0.84
ACGTcount: A:0.29, C:0.32, G:0.14, T:0.25
Consensus pattern (29 bp):
GGCCCAATTCACATTCATATGGCCCATCA
Found at i:29531499 original size:17 final size:18
Alignment explanation
Indices: 29531477--29531520 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
29531467 TGCCTATTAT
29531477 GGGCCCA-ATAGCCCATC
1 GGGCCCATATAGCCCATC
*
29531494 GGGCCCATTTAGCCCATTC
1 GGGCCCATATAGCCCA-TC
*
29531513 TGGCCCAT
1 GGGCCCAT
29531521 TTGGCCAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 7 0.30
18 7 0.30
19 9 0.39
ACGTcount: A:0.18, C:0.39, G:0.23, T:0.20
Consensus pattern (18 bp):
GGGCCCATATAGCCCATC
Found at i:29531508 original size:18 final size:19
Alignment explanation
Indices: 29531485--29531532 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
29531475 ATGGGCCCAA
29531485 TAGCCCA-TCGGGCCCATT
1 TAGCCCATTCGGGCCCATT
*
29531503 TAGCCCATTCTGGCCCATT
1 TAGCCCATTCGGGCCCATT
* *
29531522 TGGCCAATTCG
1 TAGCCCATTCG
29531533 TAACCCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.17, C:0.35, G:0.21, T:0.27
Consensus pattern (19 bp):
TAGCCCATTCGGGCCCATT
Found at i:29536270 original size:42 final size:42
Alignment explanation
Indices: 29536207--29536365 Score: 167
Period size: 42 Copynumber: 3.6 Consensus size: 42
29536197 CCAGACATAA
*
29536207 TCTTACATTGGCTCACATATTGAGGCCATGATCCAAACAAGG
1 TCTTACACTGGCTCACATATTGAGGCCATGATCCAAACAAGG
** * * *
29536249 TCTTACACTGGCTCATGTATTGAGGCCGATATCATGTCCCAGACATA-A
1 TCTTACACTGGCTCACATATTGAGGCC---ATGA--T-CCAAACA-AGG
*
29536297 TCTTACACTGGCTCACATATTGAGGCCATGATCCAAACATGG
1 TCTTACACTGGCTCACATATTGAGGCCATGATCCAAACAAGG
* *
29536339 TCTTACATTGGCTCACATATTAAGGCC
1 TCTTACACTGGCTCACATATTGAGGCC
29536366 GATGTCATGT
Statistics
Matches: 95, Mismatches: 14, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
42 55 0.58
43 1 0.01
45 6 0.06
47 1 0.01
48 31 0.33
49 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.28
Consensus pattern (42 bp):
TCTTACACTGGCTCACATATTGAGGCCATGATCCAAACAAGG
Found at i:29536317 original size:90 final size:90
Alignment explanation
Indices: 29536164--29536400 Score: 384
Period size: 90 Copynumber: 2.6 Consensus size: 90
29536154 GCTCTGATAC
*
29536164 CACTGGCTCACATATTGAGGCCGATGTCATGTCCCAGACATAATCTTACATTGGCTCACATATTG
1 CACTGGCTCACATATTGAGGCCGATGTCATGTCCCAGACATAATCTTACACTGGCTCACATATTG
29536229 AGGCCATGATCCAAACAAGGTCTTA
66 AGGCCATGATCCAAACAAGGTCTTA
** *
29536254 CACTGGCTCATGTATTGAGGCCGATATCATGTCCCAGACATAATCTTACACTGGCTCACATATTG
1 CACTGGCTCACATATTGAGGCCGATGTCATGTCCCAGACATAATCTTACACTGGCTCACATATTG
*
29536319 AGGCCATGATCCAAACATGGTCTTA
66 AGGCCATGATCCAAACAAGGTCTTA
* * ** *
29536344 CATTGGCTCACATATTAAGGCCGATGTCATGTCCCAGACATGGTCTTACACTAGCTC
1 CACTGGCTCACATATTGAGGCCGATGTCATGTCCCAGACATAATCTTACACTGGCTC
29536401 TCGTAACCCT
Statistics
Matches: 134, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 134 1.00
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.27
Consensus pattern (90 bp):
CACTGGCTCACATATTGAGGCCGATGTCATGTCCCAGACATAATCTTACACTGGCTCACATATTG
AGGCCATGATCCAAACAAGGTCTTA
Found at i:29536320 original size:48 final size:48
Alignment explanation
Indices: 29536164--29536400 Score: 230
Period size: 48 Copynumber: 5.2 Consensus size: 48
29536154 GCTCTGATAC
* *
29536164 CACTGGCTCACATATTGAGGCCGATGTCATGTCCCAGACATAATCTTA
1 CACTGGCTCACATATTGAGGCCGATATCATGTCCCAGACATAGTCTTA
* * *
29536212 CATTGGCTCACATATTGAGGCC---ATGA--T-CCAAACA-AGGTCTTA
1 CACTGGCTCACATATTGAGGCCGATATCATGTCCCAGACATA-GTCTTA
** *
29536254 CACTGGCTCATGTATTGAGGCCGATATCATGTCCCAGACATAATCTTA
1 CACTGGCTCACATATTGAGGCCGATATCATGTCCCAGACATAGTCTTA
* * *
29536302 CACTGGCTCACATATTGAGGCC---ATGA--T-CCAAACATGGTCTTA
1 CACTGGCTCACATATTGAGGCCGATATCATGTCCCAGACATAGTCTTA
* * * *
29536344 CATTGGCTCACATATTAAGGCCGATGTCATGTCCCAGACATGGTCTTA
1 CACTGGCTCACATATTGAGGCCGATATCATGTCCCAGACATAGTCTTA
*
29536392 CACTAGCTC
1 CACTGGCTC
29536401 TCGTAACCCT
Statistics
Matches: 151, Mismatches: 24, Indels: 28
0.74 0.12 0.14
Matches are distributed among these distances:
41 1 0.01
42 62 0.41
43 2 0.01
45 10 0.07
47 2 0.01
48 73 0.48
49 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.27
Consensus pattern (48 bp):
CACTGGCTCACATATTGAGGCCGATATCATGTCCCAGACATAGTCTTA
Found at i:29539576 original size:40 final size:40
Alignment explanation
Indices: 29539532--29539660 Score: 145
Period size: 40 Copynumber: 3.2 Consensus size: 40
29539522 TGCTGGAAAT
* * *
29539532 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGAC
* * *
29539572 TATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGCGAGTTAT
1 TATATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGTGAC
* * *
29539612 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ATGTGAT
1 TATATCCGGGCTAAGACCCGAAGGCAATTGTGCGA-GTGAC
29539652 TATATCCGG
1 TATATCCGG
29539661 TTATATTCCG
Statistics
Matches: 75, Mismatches: 11, Indels: 6
0.82 0.12 0.07
Matches are distributed among these distances:
39 4 0.05
40 69 0.92
41 2 0.03
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGAC
Found at i:29542288 original size:47 final size:47
Alignment explanation
Indices: 29542215--29542499 Score: 428
Period size: 47 Copynumber: 6.1 Consensus size: 47
29542205 ACACGTTTCG
* * * * * * *
29542215 CATTAGCCGTTCGGCTTTACCACATATATACACT-TCCACGTTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCA-TGTTCACATTCATCA
* *
29542262 CATTGGCCATTCTGCCTTGTCACATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
29542309 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
*
29542356 CATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
29542403 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
* * **
29542450 CATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
29542497 CAT
1 CAT
29542500 AAAATCCTAA
Statistics
Matches: 220, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
46 1 0.00
47 219 1.00
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.34
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
Found at i:29555381 original size:40 final size:40
Alignment explanation
Indices: 29555344--29555531 Score: 227
Period size: 40 Copynumber: 4.7 Consensus size: 40
29555334 GCTACTCGTT
* *
29555344 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
29555384 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
29555424 CAAATGCCTTCGAGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
29555464 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
* * *
29555505 CAAAAGCCTTTGGGACTTAGCCCGGAT
1 CAAATGCCTTCGGGACTTAACCCGGAT
29555532 ATCATTCGAA
Statistics
Matches: 131, Mismatches: 13, Indels: 7
0.87 0.09 0.05
Matches are distributed among these distances:
39 2 0.02
40 100 0.76
41 26 0.20
42 3 0.02
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:29563709 original size:41 final size:40
Alignment explanation
Indices: 29563550--29563718 Score: 189
Period size: 40 Copynumber: 4.2 Consensus size: 40
29563540 CAGAATTTAA
** *
29563550 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
29563590 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
29563630 CCGAATTTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * * *
29563670 CCGGATATGGTTACTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
29563711 CCGGATAT
1 CCGGATAT
29563719 CATTCGAATA
Statistics
Matches: 108, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
39 4 0.04
40 74 0.69
41 27 0.25
42 3 0.03
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:29569157 original size:13 final size:13
Alignment explanation
Indices: 29569139--29569165 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29569129 AGATCCTCGC
29569139 TCTCTTCAACTCA
1 TCTCTTCAACTCA
29569152 TCTCTTCAACTCA
1 TCTCTTCAACTCA
29569165 T
1 T
29569166 TGTTGTAGAA
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:0.22, C:0.37, G:0.00, T:0.41
Consensus pattern (13 bp):
TCTCTTCAACTCA
Found at i:29570816 original size:22 final size:19
Alignment explanation
Indices: 29570777--29570818 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
29570767 TGCAAAGTTG
29570777 ATAATAATTAATATATATT
1 ATAATAATTAATATATATT
29570796 ATAATAGATATAATTATATATT
1 ATAATA-AT-TAA-TATATATT
29570818 A
1 A
29570819 ATGATTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 3 0.15
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
ATAATAATTAATATATATT
Found at i:29581665 original size:2 final size:2
Alignment explanation
Indices: 29581658--29581696 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
29581648 CAATTACACT
* *
29581658 TA TA TA TA TA TA AA TG TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29581697 TCTTCTTTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:29581994 original size:39 final size:39
Alignment explanation
Indices: 29581951--29582084 Score: 135
Period size: 39 Copynumber: 3.4 Consensus size: 39
29581941 CCAGACATAT
* * *
29581951 TTCCAGCGCGTAGCCTACGGACCTTAAGTCCAGTTATAA
1 TTCCAGCACATAGCCTACGGACCTTAAGTCCAGGTATAA
* * *
29581990 TTCCAACACATAGCCTGCGGACCTTAAGTCCGGGTATAA
1 TTCCAGCACATAGCCTACGGACCTTAAGTCCAGGTATAA
* * * * *
29582029 TTCCAGCATATAGCCTGCGGGTCTTTAAG-CCCGGATATAA
1 TTCCAGCACATAGCCTAC-GGACCTTAAGTCCAGG-TATAA
*
29582069 TTCCAGCATATAGCCT
1 TTCCAGCACATAGCCT
29582085 GCAGGTCTTT
Statistics
Matches: 82, Mismatches: 11, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
39 53 0.65
40 29 0.35
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (39 bp):
TTCCAGCACATAGCCTACGGACCTTAAGTCCAGGTATAA
Found at i:29582068 original size:40 final size:39
Alignment explanation
Indices: 29581985--29582105 Score: 170
Period size: 40 Copynumber: 3.1 Consensus size: 39
29581975 TAAGTCCAGT
* * * * * *
29581985 TATAATTCCAACACATAGCCTGCGGACCTTAAGTCCGGG
1 TATAATTCCAGCATATAGCCTGCGGTCTTTAAGCCCGGA
29582024 TATAATTCCAGCATATAGCCTGCGGGTCTTTAAGCCCGGA
1 TATAATTCCAGCATATAGCCTGC-GGTCTTTAAGCCCGGA
29582064 TATAATTCCAGCATATAGCCTGCAGGTCTTTAAGCCCGGA
1 TATAATTCCAGCATATAGCCTGC-GGTCTTTAAGCCCGGA
29582104 TA
1 TA
29582106 CACATCAAAT
Statistics
Matches: 74, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 21 0.28
40 53 0.72
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (39 bp):
TATAATTCCAGCATATAGCCTGCGGTCTTTAAGCCCGGA
Found at i:29589971 original size:40 final size:40
Alignment explanation
Indices: 29589916--29589997 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
29589906 ACCTTCTGGG
*
29589916 TATAATTCCAGCATATAGCCTGTGGGTCTTTAAGCCCGGA
1 TATAATTCCAGCATATAGCCTGCGGGTCTTTAAGCCCGGA
29589956 TATAATTCCAGCATATAGCCTGCGGGTCTTTAAGCCCGGA
1 TATAATTCCAGCATATAGCCTGCGGGTCTTTAAGCCCGGA
29589996 TA
1 TA
29589998 CACAACAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (40 bp):
TATAATTCCAGCATATAGCCTGCGGGTCTTTAAGCCCGGA
Found at i:29593926 original size:27 final size:27
Alignment explanation
Indices: 29593896--29594089 Score: 244
Period size: 27 Copynumber: 7.2 Consensus size: 27
29593886 TACTAAAATG
* *
29593896 CCCTCGATTTGTAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCGTTTTA
* *
29593923 CCCTCAATTTATAGAATTACCGTTTCA
1 CCCTCGATTTATAGAATTACCGTTTTA
* * *
29593950 CCCTCGATTTACAAAATTACTGTTTTA
1 CCCTCGATTTATAGAATTACCGTTTTA
*
29593977 CCCTCGATTTATAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCGTTTTA
**
29594004 CCCTCGATTTATAGAATTATTGTTTTA
1 CCCTCGATTTATAGAATTACCGTTTTA
* * *
29594031 CCCTCGATTTACAAAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCGTTTTA
* * *
29594058 CCCTCAATTTACAAAATTACCGTTTTA
1 CCCTCGATTTATAGAATTACCGTTTTA
29594085 CCCTC
1 CCCTC
29594090 AATTGTGAAA
Statistics
Matches: 144, Mismatches: 23, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 144 1.00
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.40
Consensus pattern (27 bp):
CCCTCGATTTATAGAATTACCGTTTTA
Found at i:29594014 original size:81 final size:81
Alignment explanation
Indices: 29593896--29594093 Score: 297
Period size: 81 Copynumber: 2.4 Consensus size: 81
29593886 TACTAAAATG
*
29593896 CCCTCGATTTGTAGAATTACCATTTTACCCTCAATTTATAGAATTACCGTTTCACCCTCGATTTA
1 CCCTCGATTTATAGAATTACCATTTTACCCTCAATTTATAGAATTACCGTTTCACCCTCGATTTA
**
29593961 CAAAATTACTGTTTTA
66 CAAAATTACCATTTTA
* ** *
29593977 CCCTCGATTTATAGAATTACCATTTTACCCTCGATTTATAGAATTATTGTTTTACCCTCGATTTA
1 CCCTCGATTTATAGAATTACCATTTTACCCTCAATTTATAGAATTACCGTTTCACCCTCGATTTA
29594042 CAAAATTACCATTTTA
66 CAAAATTACCATTTTA
* * * *
29594058 CCCTCAATTTACAAAATTACCGTTTTACCCTCAATT
1 CCCTCGATTTATAGAATTACCATTTTACCCTCAATT
29594094 GTGAAATTAC
Statistics
Matches: 105, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 105 1.00
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.40
Consensus pattern (81 bp):
CCCTCGATTTATAGAATTACCATTTTACCCTCAATTTATAGAATTACCGTTTCACCCTCGATTTA
CAAAATTACCATTTTA
Found at i:29594163 original size:54 final size:53
Alignment explanation
Indices: 29594092--29594247 Score: 195
Period size: 54 Copynumber: 2.9 Consensus size: 53
29594082 TTACCCTCAA
* ** * *
29594092 TTGTGAAATTACTAAAATACCCCTATAGGATAGAATTACCAAAATACCTCTAGT
1 TTGTGAAATTACCAAAATACCCCTATTTG-TAAAATTACCAAAATACCACTAGT
* * *
29594146 TTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCGAAATACCACTGGT
1 TTGTGAAATTACCAAAATACCCCTA-TTTGTAAAATTACCAAAATACCACTAGT
* *
29594200 TTGTGAAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACC
1 TTGTGAAATTACCAAAATACCC-CTATTTGTAAAATTACCAAAATACC
29594248 CTTGATTTAC
Statistics
Matches: 88, Mismatches: 12, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
54 84 0.95
55 4 0.05
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.29
Consensus pattern (53 bp):
TTGTGAAATTACCAAAATACCCCTATTTGTAAAATTACCAAAATACCACTAGT
Found at i:29594249 original size:27 final size:27
Alignment explanation
Indices: 29594029--29594249 Score: 146
Period size: 27 Copynumber: 8.2 Consensus size: 27
29594019 ATTATTGTTT
* ** ***
29594029 TACCCTCGATTTACAAAATTACCATTT
1 TACCCTCAATTTGTAAAATTACCAAAA
** ****
29594056 TACCCTCAATTTACAAAATTACCGTTT
1 TACCCTCAATTTGTAAAATTACCAAAA
* *
29594083 TACCCTCAA-TTGTGAAATTACTAAAA
1 TACCCTCAATTTGTAAAATTACCAAAA
* ** *
29594109 TACCC-CTATAGGATAGAATTACCAAAA
1 TACCCTCAATTTG-TAAAATTACCAAAA
*
29594136 TA-CCTCTAGTTTGTAAAATTACCAAAA
1 TACCCTC-AATTTGTAAAATTACCAAAA
* *
29594163 TACCC-CTAGTTTGTAAAATTACCGAAA
1 TACCCTC-AATTTGTAAAATTACCAAAA
** * *
29594190 TACCACT-GGTTTGTGAAATTACCGAAA
1 TACC-CTCAATTTGTAAAATTACCAAAA
29594217 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTCAATTTGTAAAATTACCAAAA
29594244 TACCCT
1 TACCCT
29594250 TGATTTACAC
Statistics
Matches: 158, Mismatches: 28, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
25 2 0.01
26 19 0.12
27 132 0.84
28 5 0.03
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (27 bp):
TACCCTCAATTTGTAAAATTACCAAAA
Found at i:29594255 original size:27 final size:27
Alignment explanation
Indices: 29594125--29594277 Score: 143
Period size: 27 Copynumber: 5.7 Consensus size: 27
29594115 TATAGGATAG
*
29594125 AATTACCAAAATACCTCTAG-TTTGTAA
1 AATTACCAAAATACC-CTTGATTTGTAA
*
29594152 AATTACCAAAATACCCCT-AGTTTGTAA
1 AATTACCAAAATACCCTTGA-TTTGTAA
* * *
29594179 AATTACCGAAATACCAC-TGGTTTGTGA
1 AATTACCAAAATACC-CTTGATTTGTAA
* **
29594206 AATTACCGAAATACCCTCAATTTGTAA
1 AATTACCAAAATACCCTTGATTTGTAA
** *
29594233 AATTACCAAAATACCCTTGATTTACAC
1 AATTACCAAAATACCCTTGATTTGTAA
29594260 AATTA-CAGAAATACCCTT
1 AATTACCA-AAATACCCTT
29594278 AACTTTCTAA
Statistics
Matches: 105, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
26 4 0.04
27 100 0.95
28 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.30
Consensus pattern (27 bp):
AATTACCAAAATACCCTTGATTTGTAA
Found at i:29594264 original size:54 final size:54
Alignment explanation
Indices: 29594125--29594332 Score: 167
Period size: 54 Copynumber: 3.8 Consensus size: 54
29594115 TATAGGATAG
* * * * *
29594125 AATTACCAAAATACCTCTAGTTTGTA-AAATTACCAAAATACCC-CTAGTTTGTAA
1 AATTACCAAAATACCACTTGGTT-TACAAATTACCGAAATACCCTC-AATTTGTAA
* **
29594179 AATTACCGAAATACCAC-TGGTTTGTGAAATTACCGAAATACCCTCAATTTGTAA
1 AATTACCAAAATACCACTTGGTTT-ACAAATTACCGAAATACCCTCAATTTGTAA
* * * *
29594233 AATTACCAAAATACC-CTTGATTTACACAATTACAGAAATACCCTTAACTTTCTAAA
1 AATTACCAAAATACCACTTGGTTTACA-AATTACCGAAATACCCTCAA-TTTGT-AA
* * *
29594289 AATTA-TAGAAATACTA-TTGGTTTACAAAATTACTGAAATACCCT
1 AATTACCA-AAATACCACTTGGTTTAC-AAATTACCGAAATACCCT
29594333 TGGTTTGTAG
Statistics
Matches: 126, Mismatches: 18, Indels: 18
0.78 0.11 0.11
Matches are distributed among these distances:
52 1 0.01
53 5 0.04
54 76 0.60
55 6 0.05
56 37 0.29
57 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (54 bp):
AATTACCAAAATACCACTTGGTTTACAAATTACCGAAATACCCTCAATTTGTAA
Found at i:29594264 original size:81 final size:81
Alignment explanation
Indices: 29594125--29594274 Score: 207
Period size: 81 Copynumber: 1.9 Consensus size: 81
29594115 TATAGGATAG
* * *
29594125 AATTACCAAAATACCTCTAGTTTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCGAAA
1 AATTACCAAAATACCTCTAATTTGTAAAATTACCAAAATACCCCTAGATTGTAAAATTACAGAAA
29594190 TACCACTGGTTTGTGA
66 TACCACTGGTTTGTGA
* *
29594206 AATTACCGAAATACC-CTCAATTTGTAAAATTACCAAAATA-CCCTTGATT-TACACAATTACAG
1 AATTACCAAAATACCTCT-AATTTGTAAAATTACCAAAATACCCCTAGATTGTA-A-AATTACAG
29594268 AAATACC
63 AAATACC
29594275 CTTAACTTTC
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
79 2 0.03
80 10 0.16
81 49 0.80
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (81 bp):
AATTACCAAAATACCTCTAATTTGTAAAATTACCAAAATACCCCTAGATTGTAAAATTACAGAAA
TACCACTGGTTTGTGA
Found at i:29594326 original size:27 final size:27
Alignment explanation
Indices: 29594287--29594338 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
29594277 TAACTTTCTA
*
29594287 AAAATTATAGAAATACTATTGGTTTAC
1 AAAATTATAGAAATACCATTGGTTTAC
*
29594314 AAAATTACT-GAAATACCCTTGGTTT
1 AAAATTA-TAGAAATACCATTGGTTT
29594339 GTAGATTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (27 bp):
AAAATTATAGAAATACCATTGGTTTAC
Found at i:29594434 original size:27 final size:27
Alignment explanation
Indices: 29594392--29594456 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
29594382 ACCTATAATA
* *
29594392 GGTAAAAAGACCGTAA-AGCCCCTGTAG
1 GGTAAAATGACTGTAATA-CCCCTGTAG
* * *
29594419 GGTAAAGTGACTGTAATACCCTTGTAT
1 GGTAAAATGACTGTAATACCCCTGTAG
29594446 GGTAAAATGAC
1 GGTAAAATGAC
29594457 GAATATGCCC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
27 30 0.97
28 1 0.03
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (27 bp):
GGTAAAATGACTGTAATACCCCTGTAG
Found at i:29595188 original size:20 final size:20
Alignment explanation
Indices: 29595163--29595229 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
29595153 GATATGATAT
*
29595163 ACATGAT-TGATATGATATGC
1 ACATGATATG-TATGAAATGC
*
29595183 ACATGATATGTATAAAATGC
1 ACATGATATGTATGAAATGC
29595203 ACATGATATGTATGAAATGC
1 ACATGATATGTATGAAATGC
29595223 ACATGAT
1 ACATGAT
29595230 GTATTCATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 41 0.95
21 2 0.05
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.31
Consensus pattern (20 bp):
ACATGATATGTATGAAATGC
Found at i:29595376 original size:25 final size:26
Alignment explanation
Indices: 29595279--29595401 Score: 178
Period size: 26 Copynumber: 4.8 Consensus size: 26
29595269 GAGGAAGTGC
* **
29595279 AAAAGGGCTTATGCCCTAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
29595305 AGAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
29595331 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
29595357 AAAAGGGCTT-TGCCCCAGTTTACCA
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
29595382 AAAAGGGCTT-TTCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
29595402 ATTAAAAGAG
Statistics
Matches: 90, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
25 33 0.37
26 57 0.63
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:29595606 original size:42 final size:42
Alignment explanation
Indices: 29595547--29595638 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
29595537 TAGTCTCCCC
* * *
29595547 AAATGGGCTTGCATACATTCATTGGTATTTCATATGATATTG
1 AAATGGGCTTGCATACATCCATTGATATTACATATGATATTG
*
29595589 AAATGGGCTTGCATACATCCATTGATATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGATATTACATATGATATTG
29595631 AAATGGGC
1 AAATGGGC
29595639 CTATGGGCCA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGATATTACATATGATATTG
Found at i:29595697 original size:31 final size:31
Alignment explanation
Indices: 29595662--29595742 Score: 128
Period size: 31 Copynumber: 2.6 Consensus size: 31
29595652 CGTTTACAGT
* *
29595662 AAAGGCTTCAGCCCAGTGAA-ATGGTTTATGA
1 AAAGGCTTCGGCCCAGT-AATATGATTTATGA
29595693 AAAGGCTTCGGCCCAGTAATATGATTTATGA
1 AAAGGCTTCGGCCCAGTAATATGATTTATGA
29595724 AAAGGCTTCGGCCCAGTAA
1 AAAGGCTTCGGCCCAGTAA
29595743 CCGTTAAACG
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
30 2 0.04
31 45 0.96
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGATTTATGA
Found at i:29597358 original size:21 final size:21
Alignment explanation
Indices: 29597334--29597403 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
29597324 CGATCTGAAC
29597334 TCATTGAGTTGTGGTCTGAGT
1 TCATTGAGTTGTGGTCTGAGT
* * * **
29597355 TCA-TGATATATGTGACATTTGAAC
1 TCATTGA-GT-TGTG--GTCTGAGT
29597379 TCATTGAGTTGTGGTCTGAGT
1 TCATTGAGTTGTGGTCTGAGT
29597400 TCAT
1 TCAT
29597404 GATGCATGTG
Statistics
Matches: 34, Mismatches: 10, Indels: 10
0.63 0.19 0.19
Matches are distributed among these distances:
20 3 0.09
21 12 0.35
22 4 0.12
23 4 0.12
24 8 0.24
25 3 0.09
ACGTcount: A:0.21, C:0.11, G:0.26, T:0.41
Consensus pattern (21 bp):
TCATTGAGTTGTGGTCTGAGT
Found at i:29597393 original size:45 final size:45
Alignment explanation
Indices: 29597329--29597416 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 45
29597319 CTATGCGATC
*
29597329 TGAACTCATTGAGTTGTGGTCTGAGTTCATGATATATGTGACATT
1 TGAACTCATTGAGTTGTGGTCTGAGTTCATGATACATGTGACATT
*
29597374 TGAACTCATTGAGTTGTGGTCTGAGTTCATGATGCATGTGACA
1 TGAACTCATTGAGTTGTGGTCTGAGTTCATGATACATGTGACA
29597417 CATGTTTTGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.24, C:0.12, G:0.26, T:0.38
Consensus pattern (45 bp):
TGAACTCATTGAGTTGTGGTCTGAGTTCATGATACATGTGACATT
Found at i:29600036 original size:42 final size:44
Alignment explanation
Indices: 29599972--29600072 Score: 109
Period size: 48 Copynumber: 2.2 Consensus size: 44
29599962 TGTCCACAAC
**
29599972 ATGGTCTTACATGGGTCTACAT-A-CCGATGCCATATCCCAGAT
1 ATGGTCTTACATGAATCTACATAAGCCGATGCCATATCCCAGAT
*
29600014 ATGGTCTTACATGAAATC-ACATACCAAGGCCGATGCCATATCCTAGAT
1 ATGGTCTTACATG-AATCTACAT---AA-GCCGATGCCATATCCCAGAT
29600062 ATGGTCTTACA
1 ATGGTCTTACA
29600073 CTGGCACACA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
42 17 0.35
43 2 0.04
46 1 0.02
48 29 0.59
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.28
Consensus pattern (44 bp):
ATGGTCTTACATGAATCTACATAAGCCGATGCCATATCCCAGAT
Found at i:29600083 original size:48 final size:47
Alignment explanation
Indices: 29599995--29600173 Score: 171
Period size: 48 Copynumber: 3.7 Consensus size: 47
29599985 GGTCTACATA
* ** *
29599995 CCGATGCCATATCCCAGATATGGTCTTACA-TGAAATCACATACCAAGG
1 CCGATGCCATATCCCAGACATGGTCTTACACTGGCA-CACATACC-ATG
* * *
29600043 CCGATGCCATATCCTAGATATGGTCTTACACTGGCACACATATCGATG
1 CCGATGCCATATCCCAGACATGGTCTTACACTGGCACACATA-CCATG
** * * * *
29600091 CCGATGTTATGTCCCAGACATGGTCTTATACTGGCTCTCATATCCATG
1 CCGATGCCATATCCCAGACATGGTCTTACACTGGCACACATA-CCATG
* * *
29600139 TCGATGCCATGTCTCAGACATGGTCTTACACTGGC
1 CCGATGCCATATCCCAGACATGGTCTTACACTGGC
29600174 TCTCATAAAT
Statistics
Matches: 110, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
48 106 0.96
49 4 0.04
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (47 bp):
CCGATGCCATATCCCAGACATGGTCTTACACTGGCACACATACCATG
Found at i:29604419 original size:25 final size:25
Alignment explanation
Indices: 29604391--29604439 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
29604381 TTGTTTTTGA
*
29604391 TAGTATATCTTGAAACTGCTATAGG
1 TAGTATATCTTGAAACTACTATAGG
* *
29604416 TAGTATATGTTGAGACTACTATAG
1 TAGTATATCTTGAAACTACTATAG
29604440 ATAGACTGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (25 bp):
TAGTATATCTTGAAACTACTATAGG
Found at i:29609788 original size:223 final size:223
Alignment explanation
Indices: 29609400--29609843 Score: 861
Period size: 223 Copynumber: 2.0 Consensus size: 223
29609390 TATCAGAATG
29609400 GGCCTACTGGTCTGGTGGTTAGGAGGAATGTTGGTGAGTAGAGGTCCTGAGTTTGAATCCCTGCA
1 GGCCTACTGGTCTGGTGGTTAGGAGGAATGTTGGTGAGTAGAGGTCCTGAGTTTGAATCCCTGCA
29609465 AGGGAGTTTATTTTTGCCTAGTGTTGCGGTGAGAGTTTCGGTGAAACCAAAATTCTGTAGAAGTT
66 AGGGAGTTTATTTTTGCCTAGTGTTGCGGTGAGAGTTTCGGTGAAACCAAAATTCTGTAGAAGTT
* *
29609530 ATCTGTTGTGTGGATAGAGTAGAGAATTAAGGGGTTGTGGGAATATCCCTTGATTGTTCTTTTGC
131 ATCTGTTGTGTGGATAGAGTAGAGAAGTAAGGGGTTGTGGGAATATCCCTTAATTGTTCTTTTGC
29609595 TAATTCTTTTTCTCTCTCTGCCAAAATA
196 TAATTCTTTTTCTCTCTCTGCCAAAATA
*
29609623 GGCCTACTGGTCTGGTGGTTAGGAGGAATGTTGGTGAGTAGAGGTCCTGAGTTTGAATCCCTGTA
1 GGCCTACTGGTCTGGTGGTTAGGAGGAATGTTGGTGAGTAGAGGTCCTGAGTTTGAATCCCTGCA
29609688 AGGGAGTTTATTTTTGCCTAGTGTTGCGGTGAGAGTTTCGGTGAAACCAAAATTCTGTAGAAGTT
66 AGGGAGTTTATTTTTGCCTAGTGTTGCGGTGAGAGTTTCGGTGAAACCAAAATTCTGTAGAAGTT
29609753 ATCTGTTGTGTGGATAGAGTAGAGAAGTAAGGGGTTGTGGGAATATCCCTTAATTGTTCTTTTGC
131 ATCTGTTGTGTGGATAGAGTAGAGAAGTAAGGGGTTGTGGGAATATCCCTTAATTGTTCTTTTGC
29609818 TAATTCTTTTTCTCTCTCTGCCAAAA
196 TAATTCTTTTTCTCTCTCTGCCAAAA
29609844 ATTCCCTACC
Statistics
Matches: 218, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
223 218 1.00
ACGTcount: A:0.22, C:0.13, G:0.29, T:0.36
Consensus pattern (223 bp):
GGCCTACTGGTCTGGTGGTTAGGAGGAATGTTGGTGAGTAGAGGTCCTGAGTTTGAATCCCTGCA
AGGGAGTTTATTTTTGCCTAGTGTTGCGGTGAGAGTTTCGGTGAAACCAAAATTCTGTAGAAGTT
ATCTGTTGTGTGGATAGAGTAGAGAAGTAAGGGGTTGTGGGAATATCCCTTAATTGTTCTTTTGC
TAATTCTTTTTCTCTCTCTGCCAAAATA
Found at i:29612395 original size:21 final size:21
Alignment explanation
Indices: 29612356--29612395 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
29612346 CCATATATCA
* *
29612356 AGCTAATCACTAAAGGTATTT
1 AGCTAATCACCAAAAGTATTT
*
29612377 AGCTAATGACCAAAAGTAT
1 AGCTAATCACCAAAAGTAT
29612396 ATCAAGTTTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (21 bp):
AGCTAATCACCAAAAGTATTT
Found at i:29614644 original size:25 final size:25
Alignment explanation
Indices: 29614615--29614662 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
29614605 TTATAATATG
* * *
29614615 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
29614640 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
29614663 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:29614731 original size:20 final size:20
Alignment explanation
Indices: 29614706--29614764 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
29614696 TAAATATGGT
29614706 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
* *
29614726 ATGTATGATACGCACATGAT
1 ATGTATGATATGCACATGAA
29614746 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
29614765 GGTAATCATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:29614884 original size:47 final size:48
Alignment explanation
Indices: 29614815--29614933 Score: 172
Period size: 47 Copynumber: 2.5 Consensus size: 48
29614805 GAGGAAGTGA
29614815 AAAAGGGCTTATGCCCCAGTTATCGAAAGGGCTTAT-GCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATCGAAAGGGCTT-TGGCCCCAGTTATT
*
29614862 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTGGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATCGAAAGGGCTTTGGCCCCAGTTATT
*
29614910 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
29614934 ATGATAAAGC
Statistics
Matches: 66, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
46 1 0.02
47 43 0.65
48 11 0.17
49 11 0.17
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (48 bp):
AAAAGGGCTTATGCCCCAGTTATCGAAAGGGCTTTGGCCCCAGTTATT
Found at i:29614909 original size:24 final size:24
Alignment explanation
Indices: 29614815--29614933 Score: 154
Period size: 24 Copynumber: 5.0 Consensus size: 24
29614805 GAGGAAGTGA
*
29614815 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
*
29614839 GAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
29614862 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
29614886 GAAAGGGCTT-TGGCCCCAGTTATT
1 AAAAGGGCTTAT-GCCCCAGTTATT
*
29614910 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
29614934 ATGATAAAGC
Statistics
Matches: 84, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
23 22 0.26
24 51 0.61
25 11 0.13
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:29615160 original size:31 final size:31
Alignment explanation
Indices: 29615125--29615226 Score: 123
Period size: 31 Copynumber: 3.1 Consensus size: 31
29615115 CGTTTACAGT
29615125 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
29615156 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
1 AAAGGCTTCGGCCCAG-----T--AATATGAAATATGA
*
29615194 AAAGGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
29615225 AA
1 AA
29615227 TATGAAAAGG
Statistics
Matches: 61, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
31 30 0.49
33 1 0.02
36 1 0.02
38 29 0.48
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:29615194 original size:38 final size:38
Alignment explanation
Indices: 29615142--29615249 Score: 189
Period size: 38 Copynumber: 2.8 Consensus size: 38
29615132 TCGGCCCAGT
29615142 AATATGAAATATGAAAAGGCTTCGGCCCAGTATTATGA
1 AATATGAAATATGAAAAGGCTTCGGCCCAGTATTATGA
*
29615180 AATATGAAACATGAAAAGGCTTCGGCCCAGTATTATGA
1 AATATGAAATATGAAAAGGCTTCGGCCCAGTATTATGA
*
29615218 AATATGAAATATGAAAAGGGCTACGGCCCAGT
1 AATATGAAATATGAAAA-GGCTTCGGCCCAGT
29615250 GCATGATTGA
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
38 53 0.80
39 13 0.20
ACGTcount: A:0.40, C:0.15, G:0.22, T:0.23
Consensus pattern (38 bp):
AATATGAAATATGAAAAGGCTTCGGCCCAGTATTATGA
Found at i:29622971 original size:25 final size:25
Alignment explanation
Indices: 29622942--29622989 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
29622932 TTATAATATG
* * *
29622942 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
29622967 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
29622990 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:29623058 original size:20 final size:20
Alignment explanation
Indices: 29623033--29623091 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
29623023 TAAATATGGT
29623033 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
* *
29623053 ATGTATGATACGCACATGAT
1 ATGTATGATATGCACATGAA
29623073 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
29623092 GGTAATCATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:29623211 original size:47 final size:48
Alignment explanation
Indices: 29623142--29623260 Score: 172
Period size: 47 Copynumber: 2.5 Consensus size: 48
29623132 GAGGAAGTGA
29623142 AAAAGGGCTTATGCCCCAGTTATCGAAAGGGCTTAT-GCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATCGAAAGGGCTT-TGGCCCCAGTTATT
*
29623189 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTGGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATCGAAAGGGCTTTGGCCCCAGTTATT
*
29623237 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
29623261 ATGATAAAGC
Statistics
Matches: 66, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
46 1 0.02
47 43 0.65
48 11 0.17
49 11 0.17
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (48 bp):
AAAAGGGCTTATGCCCCAGTTATCGAAAGGGCTTTGGCCCCAGTTATT
Found at i:29623236 original size:24 final size:24
Alignment explanation
Indices: 29623142--29623260 Score: 154
Period size: 24 Copynumber: 5.0 Consensus size: 24
29623132 GAGGAAGTGA
*
29623142 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
*
29623166 GAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
29623189 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
29623213 GAAAGGGCTT-TGGCCCCAGTTATT
1 AAAAGGGCTTAT-GCCCCAGTTATT
*
29623237 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
29623261 ATGATAAAGC
Statistics
Matches: 84, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
23 22 0.26
24 51 0.61
25 11 0.13
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:29623487 original size:31 final size:31
Alignment explanation
Indices: 29623452--29623553 Score: 123
Period size: 31 Copynumber: 3.1 Consensus size: 31
29623442 CGTTTACAGT
29623452 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
29623483 AAAGGCTTCGGCCCAGTATTATGAAATATGAAACATGA
1 AAAGGCTTCGGCCCAG-----T--AATATGAAATATGA
*
29623521 AAAGGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
29623552 AA
1 AA
29623554 TATGAAATGA
Statistics
Matches: 61, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
31 30 0.49
33 1 0.02
36 1 0.02
38 29 0.48
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:29623521 original size:38 final size:38
Alignment explanation
Indices: 29623469--29623560 Score: 175
Period size: 38 Copynumber: 2.4 Consensus size: 38
29623459 TCGGCCCAGT
29623469 AATATGAAATATGAAAAGGCTTCGGCCCAGTATTATGA
1 AATATGAAATATGAAAAGGCTTCGGCCCAGTATTATGA
*
29623507 AATATGAAACATGAAAAGGCTTCGGCCCAGTATTATGA
1 AATATGAAATATGAAAAGGCTTCGGCCCAGTATTATGA
29623545 AATATGAAATATGAAA
1 AATATGAAATATGAAA
29623561 TGAAAAGGGC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.43, C:0.12, G:0.20, T:0.25
Consensus pattern (38 bp):
AATATGAAATATGAAAAGGCTTCGGCCCAGTATTATGA
Found at i:29624874 original size:46 final size:46
Alignment explanation
Indices: 29624770--29624980 Score: 162
Period size: 46 Copynumber: 4.6 Consensus size: 46
29624760 GATTGGAGGG
* * * * *
29624770 TGCCAT-GATGTCTTTCAACCATGGTCTTTTTTATTCTCGA-C-TTT
1 TGCCATAG-TGTCTTTCAACCATGGTCTTATTCATTTTCTATCGTGT
* *
29624814 ATGCCATAGTGTCTTTCAGCCATTGTCTTATTCATTTT-TCATCGTGT
1 -TGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTTCT-ATCGTGT
** *
29624861 TGCCATAGTGTCTTTCAATTATGGTTTTATTCATTTTCTATCGTGT
1 TGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTTCTATCGTGT
* * ** * ** * *
29624907 TGCTATAGTGTCTTTTAATTATGGTCTTATTCGTTTGAT-TCATGA
1 TGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTTCTATCGTGT
* * *
29624952 TGCCATAGCGTCTTTCAGCTATGGTCTTA
1 TGCCATAGTGTCTTTCAACCATGGTCTTA
29624981 CTCGGTAGAA
Statistics
Matches: 136, Mismatches: 25, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
45 59 0.43
46 74 0.54
47 3 0.02
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.48
Consensus pattern (46 bp):
TGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTTCTATCGTGT
Found at i:29624977 original size:45 final size:45
Alignment explanation
Indices: 29624814--29625122 Score: 185
Period size: 45 Copynumber: 6.8 Consensus size: 45
29624804 TCTCGACTTT
* *
29624814 ATGCCATAGTGTCTTTCAGCCATTGTCTTATTCATTT--TTCATCGTG
1 ATGCCATAGTGTCTTTCAGCTATGGTCTTATTCATTTGATTCA---TG
* ** * ** *
29624860 TTGCCATAGTGTCTTTCAATTATGGTTTTATTCATTTTCTATCGTG
1 ATGCCATAGTGTCTTTCAGCTATGGTCTTATTCATTTGAT-TCATG
* * * ** *
29624906 TTGCTATAGTGTCTTTTAATTATGGTCTTATTCGTTTGATTCATG
1 ATGCCATAGTGTCTTTCAGCTATGGTCTTATTCATTTGATTCATG
* * ** * *
29624951 ATGCCATAGCGTCTTTCAGCTATGGTCTTACTCGGTAGAAT-AGTG
1 ATGCCATAGTGTCTTTCAGCTATGGTCTTATTCATTTGATTCA-TG
** * * * * * * *
29624996 ATATCATAATGTCTTTCAGCTATGGCCTTACTCAATAGAATCGTG
1 ATGCCATAGTGTCTTTCAGCTATGGTCTTATTCATTTGATTCATG
** * * **
29625041 ATGCCATAACGTCTTTCAGCTATGGTCTTACTCATTT-CTGGAATG
1 ATGCCATAGTGTCTTTCAGCTATGGTCTTATTCATTTGAT-TCATG
* * *
29625086 GTGCCATAGTGTCTTTCATCTATGGTCTTATTTATTT
1 ATGCCATAGTGTCTTTCAGCTATGGTCTTATTCATTT
29625123 CTGGTATAGA
Statistics
Matches: 208, Mismatches: 49, Indels: 13
0.77 0.18 0.05
Matches are distributed among these distances:
44 1 0.00
45 137 0.66
46 67 0.32
48 1 0.00
49 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.17, T:0.44
Consensus pattern (45 bp):
ATGCCATAGTGTCTTTCAGCTATGGTCTTATTCATTTGATTCATG
Found at i:29625144 original size:45 final size:45
Alignment explanation
Indices: 29624948--29625148 Score: 135
Period size: 45 Copynumber: 4.5 Consensus size: 45
29624938 CGTTTGATTC
** ** * *
29624948 ATGATGCCATAGCGTCTTTCAGCTATGGTCTTACTC-GGT-AGAA
1 ATGATGCCATAATGTCTTTCAGCTATGGTCTTACTCATTTCTGGA
** * * *
29624991 TAGTGATATCATAATGTCTTTCAGCTATGGCCTTACTCA---ATAGA
1 -A-TGATGCCATAATGTCTTTCAGCTATGGTCTTACTCATTTCTGGA
*
29625035 ATCGTGATGCCATAACGTCTTTCAGCTATGGTCTTACTCATTTCTGGA
1 A---TGATGCCATAATGTCTTTCAGCTATGGTCTTACTCATTTCTGGA
* * * * * *
29625083 ATGGTGCCATAGTGTCTTTCATCTATGGTCTTATTTATTTCTGGT
1 ATGATGCCATAATGTCTTTCAGCTATGGTCTTACTCATTTCTGGA
*
29625128 ATAGAT-TCATAATGTCTTTCA
1 AT-GATGCCATAATGTCTTTCA
29625149 ACTAATGTCT
Statistics
Matches: 124, Mismatches: 24, Indels: 17
0.75 0.15 0.10
Matches are distributed among these distances:
43 1 0.01
44 2 0.02
45 115 0.93
46 2 0.02
48 4 0.03
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.39
Consensus pattern (45 bp):
ATGATGCCATAATGTCTTTCAGCTATGGTCTTACTCATTTCTGGA
Found at i:29630896 original size:39 final size:39
Alignment explanation
Indices: 29630842--29631003 Score: 245
Period size: 39 Copynumber: 4.2 Consensus size: 39
29630832 TGTGTATGAA
*
29630842 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
29630881 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* ** *
29630920 GGTGCGACCTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* *
29630959 TGTGCGAGTTGTGATATCC-GGTTAAGTCCCGAAGGCATT
1 TGTGCGAGTTGTGATATCCGGGCTAAG-CCCGAAGGCAAT
29630998 TGTGCG
1 TGTGCG
29631004 GGTTACCATA
Statistics
Matches: 111, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
38 6 0.05
39 105 0.95
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.24
Consensus pattern (39 bp):
TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:29631019 original size:78 final size:78
Alignment explanation
Indices: 29630859--29631034 Score: 237
Period size: 78 Copynumber: 2.2 Consensus size: 78
29630849 ATTGTGATAT
29630859 CCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAATGGTG
1 CCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAATGGTG
** *
29630924 CGACCTATGATAT
66 CGACCTACCATAA
* * *
29630937 CCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTGTGATATCC-GGTTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTGTGATATCCGGGCTAAG-CCCGAAGGCAATGGT
***
29631001 GCGGGTTACCATAA
65 GCGACCTACCATAA
*
29631015 CCGGGCTATGTCCCGAAGGC
1 CCGGGCTAAG-CCCGAAGGC
29631035 GTTTGAACGA
Statistics
Matches: 86, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
77 6 0.07
78 71 0.83
79 9 0.10
ACGTcount: A:0.23, C:0.24, G:0.32, T:0.22
Consensus pattern (78 bp):
CCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAATGGTG
CGACCTACCATAA
Found at i:29633130 original size:79 final size:79
Alignment explanation
Indices: 29632999--29633160 Score: 324
Period size: 79 Copynumber: 2.1 Consensus size: 79
29632989 AAGAGTCAAG
29632999 AGACATCACATTATCACAGGTTATAAAATGGCATGCATTTCTAAACTCATACATGCTACACTTAG
1 AGACATCACATTATCACAGGTTATAAAATGGCATGCATTTCTAAACTCATACATGCTACACTTAG
29633064 TACAAGAACCAAAT
66 TACAAGAACCAAAT
29633078 AGACATCACATTATCACAGGTTATAAAATGGCATGCATTTCTAAACTCATACATGCTACACTTAG
1 AGACATCACATTATCACAGGTTATAAAATGGCATGCATTTCTAAACTCATACATGCTACACTTAG
29633143 TACAAGAACCAAAT
66 TACAAGAACCAAAT
29633157 AGAC
1 AGAC
29633161 TGTAGCTCTG
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 83 1.00
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.26
Consensus pattern (79 bp):
AGACATCACATTATCACAGGTTATAAAATGGCATGCATTTCTAAACTCATACATGCTACACTTAG
TACAAGAACCAAAT
Found at i:29637879 original size:46 final size:46
Alignment explanation
Indices: 29637780--29637937 Score: 156
Period size: 46 Copynumber: 3.5 Consensus size: 46
29637770 TGTCATGGTG
* * * * * * * *
29637780 TCTTTCAACCGTGGTCTTATTTATTCTCGA-CTTGATGCCATAATG
1 TCTTTCAACCATGGTCTTATTCATTTTCCATCATGTTGCCATAGTA
* *
29637825 TCTTTCAACCATAGTCTTATTCATTTTCCATCATGTTGCCATAGTT
1 TCTTTCAACCATGGTCTTATTCATTTTCCATCATGTTGCCATAGTA
* * ** *
29637871 TCTTTCAACTATGGTCTTTTTCATTTTCTGTCGTGTTGCCATAGTA
1 TCTTTCAACCATGGTCTTATTCATTTTCCATCATGTTGCCATAGTA
* *
29637917 TCTGTCAACTATGGTCTTATT
1 TCTTTCAACCATGGTCTTATT
29637938 GGTTTGATTC
Statistics
Matches: 94, Mismatches: 18, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
45 25 0.27
46 69 0.73
ACGTcount: A:0.19, C:0.22, G:0.13, T:0.46
Consensus pattern (46 bp):
TCTTTCAACCATGGTCTTATTCATTTTCCATCATGTTGCCATAGTA
Found at i:29638064 original size:24 final size:23
Alignment explanation
Indices: 29638037--29638113 Score: 59
Period size: 24 Copynumber: 3.3 Consensus size: 23
29638027 TCGTTTCTAG
29638037 TATGGTGCTATAGTGTCTTTCAAC
1 TATGGT-CTATAGTGTCTTTCAAC
* * * *
29638061 TATGGTCT-TA-TTTATTTCCAG
1 TATGGTCTATAGTGTCTTTCAAC
* *
29638082 TATAGTACCATAGTGTCTTTCAAC
1 TATGGT-CTATAGTGTCTTTCAAC
*
29638106 TATAGTCT
1 TATGGTCT
29638114 TAATCATTTC
Statistics
Matches: 39, Mismatches: 11, Indels: 7
0.68 0.19 0.12
Matches are distributed among these distances:
21 12 0.31
22 3 0.08
23 5 0.13
24 19 0.49
ACGTcount: A:0.23, C:0.17, G:0.16, T:0.44
Consensus pattern (23 bp):
TATGGTCTATAGTGTCTTTCAAC
Found at i:29638084 original size:45 final size:45
Alignment explanation
Indices: 29637766--29638124 Score: 210
Period size: 45 Copynumber: 7.9 Consensus size: 45
29637756 GGAGGGTGTC
* * ** * * *
29637766 ATGGTGTCATGGTGTCTTTCAACCGTGGTCTTATTTATTCTCGACT
1 ATGGTGCCATAGTGTCTTTCAACTATGGTCTTATTCATT-TCCAGT
* * * *
29637812 -TGATGCCATAATGTCTTTCAACCATAGTCTTATTCATTTTCCA-T
1 ATGGTGCCATAGTGTCTTTCAACTATGGTCTTATTCA-TTTCCAGT
* * * * *
29637856 CATGTTGCCATAGTTTCTTTCAACTATGGTCTTTTTCATTTTCTGT
1 -ATGGTGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCAGT
* * * * ** * *
29637902 CGTGTTGCCATAGTATCTGTCAACTATGGTCTTATTGGTTT-GATT
1 -ATGGTGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCAGT
* * * * *
29637947 CGTGATGCCATAGTGTCTTTCAGCTATGGTCTTACTTGA--T--AGA
1 -ATGGTGCCATAGTGTCTTTCAACTATGGTCTTA-TTCATTTCCAGT
** * * * * *
29637990 ATCGTGATGCCATAACGTCTTTTAGCTATGGTCTTACTCGTTTCTAGT
1 AT-G-G-TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCAGT
* *
29638038 ATGGTGCTATAGTGTCTTTCAACTATGGTCTTATTTATTTCCAGT
1 ATGGTGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCAGT
* * * *
29638083 ATAGTACCATAGTGTCTTTCAACTATAGTCTTAATCATTTCC
1 ATGGTGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCC
29638125 TTCAAGCCAA
Statistics
Matches: 245, Mismatches: 56, Indels: 25
0.75 0.17 0.08
Matches are distributed among these distances:
42 1 0.00
43 2 0.01
44 3 0.01
45 161 0.66
46 73 0.30
47 1 0.00
48 4 0.02
ACGTcount: A:0.20, C:0.19, G:0.17, T:0.44
Consensus pattern (45 bp):
ATGGTGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCAGT
Found at i:29643557 original size:46 final size:45
Alignment explanation
Indices: 29643490--29643664 Score: 210
Period size: 46 Copynumber: 3.8 Consensus size: 45
29643480 TGTAACCCGC
*
29643490 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGTAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGC-TTCGTAT
* *
29643536 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGT-T
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG--GCTTCGTAT
* * * * *
29643582 ACATTTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCA--TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGC-TTCGTAT
29643629 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
29643665 ATGCTCAACC
Statistics
Matches: 109, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
45 3 0.03
46 68 0.62
47 34 0.31
48 4 0.04
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCTTCGTAT
Found at i:29643610 original size:93 final size:93
Alignment explanation
Indices: 29643498--29643668 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
29643488 GCCCATAAGT
* * *
29643498 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGTATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
29643563 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
*
29643591 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
29643656 CGAGTTCGGATGC
66 CGAGTTCGGATGC
29643669 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:29644125 original size:30 final size:30
Alignment explanation
Indices: 29644091--29644150 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
29644081 ATTTAATACG
*
29644091 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTACCCCTA
* * *
29644121 AACTTTTGCATAATTACACTTTTACCCCTA
1 AACTTTGGAAAAATTACACTTTTACCCCTA
29644151 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTACCCCTA
Found at i:29646069 original size:8 final size:8
Alignment explanation
Indices: 29646058--29646084 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
29646048 CATGGCTAGG
29646058 GCTTCCAA
1 GCTTCCAA
29646066 GCTTCCAA
1 GCTTCCAA
29646074 GCTTCCAA
1 GCTTCCAA
29646082 GCT
1 GCT
29646085 CGATTGTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.22, C:0.37, G:0.15, T:0.26
Consensus pattern (8 bp):
GCTTCCAA
Found at i:29647272 original size:50 final size:49
Alignment explanation
Indices: 29647152--29647373 Score: 273
Period size: 49 Copynumber: 4.5 Consensus size: 49
29647142 TGAGGTCGCA
* ** * * *
29647152 TGTGTAGTACTAAGTGCAGGCTACTATGCATACCCGAAAACTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA-T-TGGTCACG
* * * **
29647203 TGTGTAGTACTAAGTGCAGGCTACCACGTGTATCAGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT-GGTCACG
* *
29647253 TGTGAAGTACTAAGTGCAGGCTACTACATGTACCGGATAATTGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACG
* *
29647302 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACG
*
29647351 TGTGTAGTACTATGTGCAGGCTA
1 TGTGTAGTACTAAGTGCAGGCTA
29647374 TTATACGTAC
Statistics
Matches: 148, Mismatches: 22, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
49 75 0.51
50 42 0.28
51 31 0.21
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.28
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCACG
Found at i:29647322 original size:99 final size:99
Alignment explanation
Indices: 29647145--29647373 Score: 284
Period size: 99 Copynumber: 2.3 Consensus size: 99
29647135 TCTATTGTGA
*
29647145 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCATACCCGAAAACTGTGATCACGTGTGTAG
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATG-ATACCCGAAAACTGTGATCACGTGTGTAG
* **
29647210 TACTAAGTGCAGGCTACCACGTGTATCAGATGGTT
65 TACTAAGTGCAGGCTACCACGTGTACCAGATAATT
* * * * *
29647245 AGGTCACGTGTGAAGTACTAAGTGCAGGCTACTACATG-TACCGGATAA-T-TGGTCACGTGTGT
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACT--ATGATACCCGAAAACTGTGATCACGTGTGT
* *
29647307 AGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT
63 AGTACTAAGTGCAGGCTACCACGTGTACCAGATAATT
* *
29647344 GGTCGCATGTGTAGTACTATGTGCAGGCTA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTA
29647374 TTATACGTAC
Statistics
Matches: 111, Mismatches: 15, Indels: 7
0.83 0.11 0.05
Matches are distributed among these distances:
98 26 0.23
99 44 0.40
100 1 0.01
101 37 0.33
103 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.28
Consensus pattern (99 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGATACCCGAAAACTGTGATCACGTGTGTAGT
ACTAAGTGCAGGCTACCACGTGTACCAGATAATT
Done.