Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A11
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: 113101708
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2797742 characters in sequence are not A, C, G, or T
File 82 of 352
Found at i:25777332 original size:18 final size:17
Alignment explanation
Indices: 25777309--25777358 Score: 66
Period size: 18 Copynumber: 2.9 Consensus size: 17
25777299 TAAATAAAGG
25777309 AAAATAAAATTAAAAAT
1 AAAATAAAATTAAAAAT
25777326 AAAAATAAAATTGAAAAAT
1 -AAAATAAAATT-AAAAAT
*
25777345 ATAATAAAA-TAAAA
1 AAAATAAAATTAAAA
25777359 GGGACTTGGG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 4 0.13
17 1 0.03
18 19 0.63
19 6 0.20
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (17 bp):
AAAATAAAATTAAAAAT
Found at i:25786958 original size:17 final size:17
Alignment explanation
Indices: 25786926--25786977 Score: 54
Period size: 16 Copynumber: 3.0 Consensus size: 17
25786916 CAGAAGCAAA
25786926 TAAAAGAAAAATTAAAAAT
1 TAAAA-AAAAA-TAAAAAT
25786945 TAAAAAAAAAT-AAAA-
1 TAAAAAAAAATAAAAAT
*
25786960 TACAATAAAAATAAAAAT
1 TA-AAAAAAAATAAAAAT
25786978 GGCTAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 2 0.07
16 12 0.41
17 5 0.17
18 5 0.17
19 5 0.17
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (17 bp):
TAAAAAAAAATAAAAAT
Found at i:25789915 original size:24 final size:24
Alignment explanation
Indices: 25789885--25789941 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
25789875 GAACGATTCA
25789885 TTTAGTGTTTTAGGAACATGT-TTG
1 TTTAGTGTTTTAGGAACAT-TCTTG
25789909 TTTAGTGTTTTAGGAACATTCTTG
1 TTTAGTGTTTTAGGAACATTCTTG
*
25789933 TTGAGTGTT
1 TTTAGTGTT
25789942 CACAAACGTG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 1 0.03
24 30 0.97
ACGTcount: A:0.19, C:0.05, G:0.25, T:0.51
Consensus pattern (24 bp):
TTTAGTGTTTTAGGAACATTCTTG
Found at i:25790956 original size:30 final size:30
Alignment explanation
Indices: 25790899--25790956 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
25790889 CTTTCGAGCA
* **
25790899 TAGGGGTAAAATGGTCATTTTGTCAAAGTC
1 TAGGGGCAAAATGGTCATTTTACCAAAGTC
25790929 TAGGGGCAAAATGGTCATTTTACCAAAG
1 TAGGGGCAAAATGGTCATTTTACCAAAG
25790957 ATGTAAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (30 bp):
TAGGGGCAAAATGGTCATTTTACCAAAGTC
Found at i:25791597 original size:50 final size:49
Alignment explanation
Indices: 25791536--25791708 Score: 215
Period size: 50 Copynumber: 3.5 Consensus size: 49
25791526 CATGTCAGTT
25791536 TAAGACCATGTCTGGGACATGGCATCGACATGGATACGCAAGAGCTAGTG
1 TAAGACCATGTCTGGGACATGGCATCGACATGGATACG-AAGAGCTAGTG
* * *
25791586 TAAGACAATGTCTAGGACATGGCATCGACATGTAAGTACG-AGAGCTAGTG
1 TAAGACCATGTCTGGGACATGGCATCGACATG-GA-TACGAAGAGCTAGTG
* * * * * *
25791636 TAAGACCATGTCTGGGACATGGCATCGGCCTCGAT-GGAGATAGCCAGTG
1 TAAGACCATGTCTGGGACATGGCATCGACATGGATACGA-AGAGCTAGTG
25791685 TAAGACCATGTCTGGGACATGGCA
1 TAAGACCATGTCTGGGACATGGCA
25791709 GCGAAAACTT
Statistics
Matches: 107, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
47 1 0.01
48 1 0.01
49 33 0.31
50 67 0.63
51 1 0.01
52 4 0.04
ACGTcount: A:0.29, C:0.20, G:0.30, T:0.21
Consensus pattern (49 bp):
TAAGACCATGTCTGGGACATGGCATCGACATGGATACGAAGAGCTAGTG
Found at i:25798624 original size:13 final size:13
Alignment explanation
Indices: 25798598--25798637 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
25798588 GCTTGGTATG
* *
25798598 GACACACCCGTGT
1 GACACGCCCATGT
25798611 GACACGCCCATGT
1 GACACGCCCATGT
25798624 GACACGCCCATGT
1 GACACGCCCATGT
25798637 G
1 G
25798638 CGATTAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.23, C:0.38, G:0.25, T:0.15
Consensus pattern (13 bp):
GACACGCCCATGT
Found at i:25799215 original size:31 final size:31
Alignment explanation
Indices: 25799177--25799238 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
25799167 ATCTAAGTAA
25799177 TTACCTTTGATTCATAATATCACAGAGTTTC
1 TTACCTTTGATTCATAATATCACAGAGTTTC
25799208 TTACCTTTGATTCATAATATCACAGAGTTTC
1 TTACCTTTGATTCATAATATCACAGAGTTTC
25799239 ACATCCTCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.42
Consensus pattern (31 bp):
TTACCTTTGATTCATAATATCACAGAGTTTC
Found at i:25804308 original size:9 final size:9
Alignment explanation
Indices: 25804294--25804318 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
25804284 TGTAAACCAT
25804294 CAAACTGAA
1 CAAACTGAA
25804303 CAAACTGAA
1 CAAACTGAA
25804312 CAAACTG
1 CAAACTG
25804319 CTGTATCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.52, C:0.24, G:0.12, T:0.12
Consensus pattern (9 bp):
CAAACTGAA
Found at i:25807520 original size:94 final size:95
Alignment explanation
Indices: 25807390--25807601 Score: 238
Period size: 94 Copynumber: 2.3 Consensus size: 95
25807380 AGACCATGTC
* * * *
25807390 TGGGACATGGCATCGGCATTGAGACGAGGGCTAGTGTAAGACGTGTTTAGGACATGCATCAGCCG
1 TGGGACATGGCATCGGCATAGAGACGAGGGCCAGTGTAAGACATGTCTAGGACATGCATCAGCCG
*
25807455 C-ATCATGATAGCCCGTGTAAGACAACGTT
66 CGATCATGATAGCCAGTGTAAGACAACGTT
** * *
25807484 TGGGACATGGCATCGG-AGTAGAGGTGAGTGCCAGTGTAAGACATGTCTAGGATATGCATCAGCC
1 TGGGACATGGCATCGGCA-TAGAGACGAGGGCCAGTGTAAGACATGTCTAGGACATGCATCAGCC
* * * *
25807548 TCGATGATGTTAGCCAGTGTAAGACATA--TC
65 GCGATCATGATAGCCAGTGTAAGACA-ACGTT
25807578 TGGGACAT-GCATCGGC-TACGAGAC
1 TGGGACATGGCATCGGCATA-GAGAC
25807602 ATGTCAATAT
Statistics
Matches: 98, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
92 2 0.02
93 11 0.11
94 64 0.65
95 20 0.20
96 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (95 bp):
TGGGACATGGCATCGGCATAGAGACGAGGGCCAGTGTAAGACATGTCTAGGACATGCATCAGCCG
CGATCATGATAGCCAGTGTAAGACAACGTT
Found at i:25807673 original size:50 final size:49
Alignment explanation
Indices: 25807615--25807783 Score: 157
Period size: 50 Copynumber: 3.4 Consensus size: 49
25807605 TCAATATAAA
*
25807615 ACCATGTTTGGGACATGGCATCGACATGGATACGCAAGAGCTAGTGTAAG
1 ACCATGTCTGGGACATGGCATCGACATGGATACG-AAGAGCTAGTGTAAG
* * *
25807665 ACCATGTTTAGGACATGAG-ATC-AGCATGTAAGTACG-AGAGCTAGTGTAAG
1 ACCATGTCTGGGACATG-GCATCGA-CATG-GA-TACGAAGAGCTAGTGTAAG
* * * * * * *
25807715 ACCTTGTCTGGGACATGACATCGGCCTCGATA-GAGATAGCCAGTGTAAG
1 ACCATGTCTGGGACATGGCATCGACATGGATACGA-AGAGCTAGTGTAAG
25807764 ACCATGTCTGGGACATGGCA
1 ACCATGTCTGGGACATGGCA
25807784 ACGGTAACTT
Statistics
Matches: 97, Mismatches: 14, Indels: 17
0.76 0.11 0.13
Matches are distributed among these distances:
47 1 0.01
48 2 0.02
49 32 0.33
50 56 0.58
51 2 0.02
52 4 0.04
ACGTcount: A:0.30, C:0.19, G:0.29, T:0.22
Consensus pattern (49 bp):
ACCATGTCTGGGACATGGCATCGACATGGATACGAAGAGCTAGTGTAAG
Found at i:25808624 original size:55 final size:55
Alignment explanation
Indices: 25808530--25808660 Score: 140
Period size: 55 Copynumber: 2.4 Consensus size: 55
25808520 CTCAAACTTT
* * * * * *
25808530 TAAA-TCAGTATTGTCCACAGTTAGGCCACACGGGTGTGTGCCATAGCCGTG-TC
1 TAAAGTCAGTATTGCCCACGGGTAGGCCACAAGGGCGTGTGCCATAGCCGTGCCC
* * *
25808583 TATAAGTCAGTATTGCCCACGGGTAGGCTACAAGGGCGTGTGTCATGGCCGTGCCC
1 TA-AAGTCAGTATTGCCCACGGGTAGGCCACAAGGGCGTGTGCCATAGCCGTGCCC
* *
25808639 TAAAGTCAGTGTTGCACACGGG
1 TAAAGTCAGTATTGCCCACGGG
25808661 CTGAGGACGT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
53 2 0.03
54 2 0.03
55 57 0.89
56 3 0.05
ACGTcount: A:0.22, C:0.24, G:0.30, T:0.24
Consensus pattern (55 bp):
TAAAGTCAGTATTGCCCACGGGTAGGCCACAAGGGCGTGTGCCATAGCCGTGCCC
Found at i:25811184 original size:15 final size:16
Alignment explanation
Indices: 25811164--25811196 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
25811154 CTTTGTGACA
25811164 TTTTTTTT-CTTGTTT
1 TTTTTTTTACTTGTTT
*
25811179 TTTTTTTTATTTGTTT
1 TTTTTTTTACTTGTTT
25811195 TT
1 TT
25811197 CTTCTTGAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.03, C:0.03, G:0.06, T:0.88
Consensus pattern (16 bp):
TTTTTTTTACTTGTTT
Found at i:25811960 original size:19 final size:19
Alignment explanation
Indices: 25811915--25811975 Score: 70
Period size: 19 Copynumber: 3.1 Consensus size: 19
25811905 ATCTAATTAC
25811915 AAATATTTAATTATTATATTT
1 AAATATTTAATTA-TA-ATTT
*
25811936 AAATATTTAAATATAATTT
1 AAATATTTAATTATAATTT
*
25811955 ATATATTCTAATTA-AATTT
1 AAATATT-TAATTATAATTT
25811974 AA
1 AA
25811976 TAAATAACTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
19 16 0.46
20 7 0.20
21 12 0.34
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
AAATATTTAATTATAATTT
Found at i:25812232 original size:13 final size:13
Alignment explanation
Indices: 25812211--25812281 Score: 79
Period size: 13 Copynumber: 5.5 Consensus size: 13
25812201 AAATTTTTCC
25812211 AAAGCACTTCTCA
1 AAAGCACTTCTCA
*
25812224 AAAGTACTTCTCA
1 AAAGCACTTCTCA
* * *
25812237 AAAACACTTTTCC
1 AAAGCACTTCTCA
* *
25812250 ACAGCACTTTTCA
1 AAAGCACTTCTCA
*
25812263 AAAGCACTTTTCA
1 AAAGCACTTCTCA
25812276 AAAGCA
1 AAAGCA
25812282 ATGAAAAACT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 49 1.00
ACGTcount: A:0.39, C:0.27, G:0.07, T:0.27
Consensus pattern (13 bp):
AAAGCACTTCTCA
Found at i:25812667 original size:6 final size:6
Alignment explanation
Indices: 25812652--25812685 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
25812642 ATCAAAGAAA
* *
25812652 ATATAT ATATAC ATATAC ATATAC ATATAT ATAT
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATAT
25812686 CCCGATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (6 bp):
ATATAC
Found at i:25812673 original size:12 final size:12
Alignment explanation
Indices: 25812652--25812685 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
25812642 ATCAAAGAAA
25812652 ATATATATATAC
1 ATATATATATAC
*
25812664 ATATACATATAC
1 ATATATATATAC
25812676 ATATATATAT
1 ATATATATAT
25812686 CCCGATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATATATATAC
Found at i:25823113 original size:126 final size:126
Alignment explanation
Indices: 25822888--25823139 Score: 504
Period size: 126 Copynumber: 2.0 Consensus size: 126
25822878 TTCCCCTATT
25822888 CATTTTCTCGGCAACCAAACACATTGTAAGCGCATAAAAACCTAATGAAAAGCTAAAATTAAGAA
1 CATTTTCTCGGCAACCAAACACATTGTAAGCGCATAAAAACCTAATGAAAAGCTAAAATTAAGAA
25822953 TTAACTAAAAAATAGGTACCACTAGTAAAAAGAGGAAACCGAAAACAGCAAACTCAAGAGA
66 TTAACTAAAAAATAGGTACCACTAGTAAAAAGAGGAAACCGAAAACAGCAAACTCAAGAGA
25823014 CATTTTCTCGGCAACCAAACACATTGTAAGCGCATAAAAACCTAATGAAAAGCTAAAATTAAGAA
1 CATTTTCTCGGCAACCAAACACATTGTAAGCGCATAAAAACCTAATGAAAAGCTAAAATTAAGAA
25823079 TTAACTAAAAAATAGGTACCACTAGTAAAAAGAGGAAACCGAAAACAGCAAACTCAAGAGA
66 TTAACTAAAAAATAGGTACCACTAGTAAAAAGAGGAAACCGAAAACAGCAAACTCAAGAGA
25823140 GAGAAAAGAA
Statistics
Matches: 126, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
126 126 1.00
ACGTcount: A:0.50, C:0.18, G:0.14, T:0.17
Consensus pattern (126 bp):
CATTTTCTCGGCAACCAAACACATTGTAAGCGCATAAAAACCTAATGAAAAGCTAAAATTAAGAA
TTAACTAAAAAATAGGTACCACTAGTAAAAAGAGGAAACCGAAAACAGCAAACTCAAGAGA
Found at i:25824028 original size:16 final size:17
Alignment explanation
Indices: 25824001--25824045 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
25823991 GAAAAAAGAC
25824001 AATAAA-ATAATA-GAA
1 AATAAATATAATATGAA
25824016 AATAAATATAATATGAA
1 AATAAATATAATATGAA
*
25824033 AAT-GATATAATAT
1 AATAAATATAATAT
25824046 ATATATGATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 6 0.22
16 15 0.56
17 6 0.22
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (17 bp):
AATAAATATAATATGAA
Found at i:25845233 original size:29 final size:28
Alignment explanation
Indices: 25845186--25845264 Score: 99
Period size: 28 Copynumber: 2.8 Consensus size: 28
25845176 GACTGTAAAA
25845186 GTGATTGGG-CTAGTGGGCCATAT-AGAT
1 GTGATTGGGCCTAGTGGGCCATATGA-AT
*
25845213 GTGATTTGGGCCTAATGGGCCATATGAAT
1 GTGA-TTGGGCCTAGTGGGCCATATGAAT
**
25845242 AAGATTGGGCCTAGTGGGCCATA
1 GTGATTGGGCCTAGTGGGCCATA
25845265 AGCATGTATG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
27 4 0.09
28 23 0.51
29 17 0.38
30 1 0.02
ACGTcount: A:0.24, C:0.14, G:0.34, T:0.28
Consensus pattern (28 bp):
GTGATTGGGCCTAGTGGGCCATATGAAT
Found at i:25847152 original size:3 final size:3
Alignment explanation
Indices: 25847144--25847176 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
25847134 ATGTCTACCC
25847144 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
25847177 ATTTTCAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:25848223 original size:17 final size:17
Alignment explanation
Indices: 25848201--25848244 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
25848191 AGATGACATA
25848201 TTGGTCTTTCAATCGAT
1 TTGGTCTTTCAATCGAT
25848218 TTGGTCTTTCAATCGAT
1 TTGGTCTTTCAATCGAT
*
25848235 TTGCTCTTTC
1 TTGGTCTTTC
25848245 CTGATTAGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.14, C:0.20, G:0.16, T:0.50
Consensus pattern (17 bp):
TTGGTCTTTCAATCGAT
Found at i:25849169 original size:21 final size:21
Alignment explanation
Indices: 25849145--25849188 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
25849135 AGTTGATAAG
* *
25849145 TTTTCTTTTTGTTAGTTATTA
1 TTTTCTCTTTATTAGTTATTA
*
25849166 TTTTCTCTTTATTATTTATTA
1 TTTTCTCTTTATTAGTTATTA
25849187 TT
1 TT
25849189 ATTTGCTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.07, G:0.05, T:0.73
Consensus pattern (21 bp):
TTTTCTCTTTATTAGTTATTA
Found at i:25859527 original size:20 final size:20
Alignment explanation
Indices: 25859502--25859546 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
25859492 AGGGACTAAA
* *
25859502 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTCTAAAATTTG
*
25859522 ATGAAAAATTCTAAAATTTT
1 ATGAAAAATTCTAAAATTTG
25859542 ATGAA
1 ATGAA
25859547 TACATATGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTCTAAAATTTG
Found at i:25861467 original size:47 final size:47
Alignment explanation
Indices: 25861413--25861542 Score: 172
Period size: 47 Copynumber: 2.8 Consensus size: 47
25861403 GTGTGAATAA
* * * * *
25861413 TACCTTGATTTAGCTACAGGCCATGGTATAGGTATTGAAAGAGT-GGT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCAAAGA-TAAGT
* *
25861460 TACCTTGATTTGGCTACGGGCCATGGTATAGGTGCTCTAAGATAAGT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCAAAGATAAGT
*
25861507 TACCTTGATTTGGCTATGGGCCATGGTATAGGTACT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACT
25861543 TATTGATTGA
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
46 1 0.01
47 72 0.99
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (47 bp):
TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCAAAGATAAGT
Found at i:25873424 original size:16 final size:16
Alignment explanation
Indices: 25873399--25873435 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
25873389 AGCAAAGAAA
*
25873399 AGAGGGAAGCAGATTC
1 AGAGGAAAGCAGATTC
25873415 AGAGGAAAGCAGATTC
1 AGAGGAAAGCAGATTC
25873431 AGAGG
1 AGAGG
25873436 CTAGAGACAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.41, C:0.11, G:0.38, T:0.11
Consensus pattern (16 bp):
AGAGGAAAGCAGATTC
Found at i:25876671 original size:40 final size:42
Alignment explanation
Indices: 25876627--25876707 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
25876617 CAAGGTTTTT
25876627 AGACACGGG-C-TAGGATACG-G-GCGTGTCATGGCCGTGTGAG
1 AGACACGGGCCATA-GATACGAGCGCGTGTCA-GGCCGTGTGAG
*
25876667 AGACACGGGCCATAGATACGAGCGTGTGTCAGGCCGTGTGA
1 AGACACGGGCCATAGATACGAGCGCGTGTCAGGCCGTGTGA
25876708 AAACCCCTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
40 9 0.25
41 7 0.19
42 13 0.36
43 7 0.19
ACGTcount: A:0.22, C:0.21, G:0.40, T:0.17
Consensus pattern (42 bp):
AGACACGGGCCATAGATACGAGCGCGTGTCAGGCCGTGTGAG
Found at i:25878075 original size:36 final size:36
Alignment explanation
Indices: 25878030--25878106 Score: 145
Period size: 36 Copynumber: 2.1 Consensus size: 36
25878020 TGAAAAAGAG
25878030 ACAGATGGGTAAATCATTTCAGTCTTCATTGAAGGA
1 ACAGATGGGTAAATCATTTCAGTCTTCATTGAAGGA
*
25878066 ACAGGTGGGTAAATCATTTCAGTCTTCATTGAAGGA
1 ACAGATGGGTAAATCATTTCAGTCTTCATTGAAGGA
25878102 ACAGA
1 ACAGA
25878107 AGTAATTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (36 bp):
ACAGATGGGTAAATCATTTCAGTCTTCATTGAAGGA
Found at i:25889687 original size:43 final size:42
Alignment explanation
Indices: 25889537--25889710 Score: 124
Period size: 43 Copynumber: 4.0 Consensus size: 42
25889527 ACATAGGATT
* *
25889537 TCGATATGTG-TTATCATGTAAGACCACGTCTGGGACATTGGCA
1 TCGATATTTGATTA-CATGTAAGACC-CGTCTGGGACAGTGGCA
** ** *
25889580 TCGACT-TGAGATTTACATGTAAGACCATATCTGGAACA-TCGGGCA
1 TCGA-TATTTGA-TTACATGTAAGACC-CGTCTGGGACAGT--GGCA
* *
25889625 TCG-TATTTGATTTCGTGTAAGACCCTGTCTGGGACAGTGGCA
1 TCGATATTTGATTACATGTAAGACCC-GTCTGGGACAGTGGCA
* *
25889667 TCGATATTTGACTACATGTAAGATCACGTCTGGGAC-GTTGGCA
1 TCGATATTTGATTACATGTAAGA-CCCGTCTGGGACAG-TGGCA
25889710 T
1 T
25889711 TGTATCAGCT
Statistics
Matches: 105, Mismatches: 15, Indels: 22
0.74 0.11 0.15
Matches are distributed among these distances:
42 8 0.08
43 60 0.57
44 27 0.26
45 10 0.10
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (42 bp):
TCGATATTTGATTACATGTAAGACCCGTCTGGGACAGTGGCA
Found at i:25897435 original size:25 final size:26
Alignment explanation
Indices: 25897372--25897435 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
25897362 AGCAAGCCAT
* *
25897372 ATCGAGAAGCTCACAAAGAGCCAATTA
1 ATCGGGAAGCTCACAAAGAGCC-AGTA
*
25897399 A-CGGGAAACTCACAAAGAGCC-GTA
1 ATCGGGAAGCTCACAAAGAGCCAGTA
25897423 ATCGGGAAGCTCA
1 ATCGGGAAGCTCA
25897436 TAAGAGCTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 3 0.09
25 10 0.31
26 18 0.56
27 1 0.03
ACGTcount: A:0.41, C:0.23, G:0.23, T:0.12
Consensus pattern (26 bp):
ATCGGGAAGCTCACAAAGAGCCAGTA
Found at i:25897513 original size:23 final size:24
Alignment explanation
Indices: 25897487--25897537 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
25897477 CTATCGAGAC
* *
25897487 GCTCCGAAGAGCT-ATAATGGGAA
1 GCTCAGAAGAGCTAATAACGGGAA
*
25897510 GCTCAGAAGAGCTAATAACGGGAC
1 GCTCAGAAGAGCTAATAACGGGAA
25897534 GCTC
1 GCTC
25897538 TTTCGAGTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 12 0.50
24 12 0.50
ACGTcount: A:0.33, C:0.22, G:0.29, T:0.16
Consensus pattern (24 bp):
GCTCAGAAGAGCTAATAACGGGAA
Found at i:25903518 original size:27 final size:27
Alignment explanation
Indices: 25903488--25903722 Score: 231
Period size: 27 Copynumber: 8.7 Consensus size: 27
25903478 TTTGGTTTAC
*
25903488 AAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
25903515 AAAATTACCAAAATACCCCTGGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
*
25903542 AAAATTACCAAAATACCCTTGGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
* *
25903569 AAAATTACCAAAATACCCCTGGCTTCT
1 AAAATTACCAAAATACCCCTGGTTTGT
* * *
25903596 AAAATTACCAAAATACCCATGATTTAT
1 AAAATTACCAAAATACCCCTGGTTTGT
* * **
25903623 AAAATTA-CAGAAATACCCTTGACTTTCA
1 AAAATTACCA-AAATACCCCTG-GTTTGT
** ** **
25903651 AAAATT-GTAGAAATACCATTGGTTTAC
1 AAAATTACCA-AAATACCCCTGGTTTGT
* *
25903678 AAAATTACTAAAATACCCTTGGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGT
* * *
25903705 AGATTTACCAAAACACCC
1 AAAATTACCAAAATACCC
25903723 TTGTAGGATG
Statistics
Matches: 178, Mismatches: 26, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
26 2 0.01
27 153 0.86
28 23 0.13
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (27 bp):
AAAATTACCAAAATACCCCTGGTTTGT
Found at i:25903794 original size:27 final size:27
Alignment explanation
Indices: 25903719--25903820 Score: 73
Period size: 27 Copynumber: 3.8 Consensus size: 27
25903709 TTACCAAAAC
* * * * *
25903719 ACCCTTGTAGGATGAAATGACTAAAAT
1 ACCCCTGTAGGGTAAAATGACCATAAT
* * *
25903746 ACCCCTAATA-GGTAAAAAGACCGTAA-
1 ACCCCT-GTAGGGTAAAATGACCATAAT
* *
25903772 AGCCTCTGTAGGGTAAAGTGACCATAAT
1 A-CCCCTGTAGGGTAAAATGACCATAAT
*
25903800 ACCCCTGTATGGTAAAATGAC
1 ACCCCTGTAGGGTAAAATGAC
25903821 GAATATGCCC
Statistics
Matches: 55, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
26 3 0.05
27 49 0.89
28 3 0.05
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (27 bp):
ACCCCTGTAGGGTAAAATGACCATAAT
Found at i:25904520 original size:10 final size:10
Alignment explanation
Indices: 25904501--25904565 Score: 78
Period size: 10 Copynumber: 6.4 Consensus size: 10
25904491 TGAGATTTTT
25904501 ATAT-ACATG
1 ATATGACATG
25904510 ATATGACATG
1 ATATGACATG
25904520 ATATGACATG
1 ATATGACATG
25904530 ATATGCACATG
1 ATATG-ACATG
**
25904541 ATATGTTATG
1 ATATGACATG
*
25904551 AGATGCACATG
1 ATATG-ACATG
25904562 ATAT
1 ATAT
25904566 ACTCATTATA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
9 4 0.09
10 27 0.57
11 16 0.34
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.32
Consensus pattern (10 bp):
ATATGACATG
Found at i:25904541 original size:21 final size:21
Alignment explanation
Indices: 25904501--25904565 Score: 89
Period size: 21 Copynumber: 3.2 Consensus size: 21
25904491 TGAGATTTTT
25904501 ATAT-ACATGATATG-ACATG
1 ATATGACATGATATGCACATG
25904520 ATATGACATGATATGCACATG
1 ATATGACATGATATGCACATG
** *
25904541 ATATGTTATGAGATGCACATG
1 ATATGACATGATATGCACATG
25904562 ATAT
1 ATAT
25904566 ACTCATTATA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 4 0.10
20 10 0.24
21 27 0.66
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.32
Consensus pattern (21 bp):
ATATGACATGATATGCACATG
Found at i:25904577 original size:32 final size:31
Alignment explanation
Indices: 25904500--25904577 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
25904490 ATGAGATTTT
* ** *
25904500 TATATACATGATATGACATGATATGACATGA
1 TATACACATGATATGTTATGAGATGACATGA
*
25904531 TATGCACATGATATGTTATGAGATGCACATGA
1 TATACACATGATATGTTATGAGATG-ACATGA
* *
25904563 TATACTCATTATATG
1 TATACACATGATATG
25904578 CATGGGTTGG
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
31 20 0.53
32 18 0.47
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.35
Consensus pattern (31 bp):
TATACACATGATATGTTATGAGATGACATGA
Found at i:25910756 original size:28 final size:29
Alignment explanation
Indices: 25910691--25910789 Score: 125
Period size: 28 Copynumber: 3.5 Consensus size: 29
25910681 CATGAGATTG
* *
25910691 GCACTAAGTGTGCG-GGTTCAAATTGTATA
1 GCACTAAGTGTGCGAGGTTC-GATTATATA
25910720 GCACTAAGTGTGCGAGGTT-GATTATATA
1 GCACTAAGTGTGCGAGGTTCGATTATATA
*
25910748 GCACTAAGTGTGCGA-GTTCGACTAT-TAA
1 GCACTAAGTGTGCGAGGTTCGATTATAT-A
25910776 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
25910790 GGCTTATTAT
Statistics
Matches: 64, Mismatches: 3, Indels: 7
0.86 0.04 0.09
Matches are distributed among these distances:
27 4 0.06
28 42 0.66
29 14 0.22
30 4 0.06
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (29 bp):
GCACTAAGTGTGCGAGGTTCGATTATATA
Found at i:25928060 original size:46 final size:45
Alignment explanation
Indices: 25928001--25928167 Score: 142
Period size: 46 Copynumber: 3.6 Consensus size: 45
25927991 GCCCATAAAC
25928001 GAACTCGGACTCAACTCAAAGAGCTCGGGCGTTCGTATCCATAAGT
1 GAACTCGGACTCAACTCAAAGAGCTCGGGC-TTCGTATCCATAAGT
* * * * * *
25928047 GAACTCGGACTCAACTCAACA-AGCTTGGATGCCTAGT-TACATCTCA-C
1 GAACTCGGACTCAACTCAA-AGAGCTCGG--GCTTCGTATCCA--TAAGT
* * * *
25928094 GAACTCGGACTCAACTCAACGAGCTCGGACATCCGCATCCATAAGT
1 GAACTCGGACTCAACTCAAAGAGCTCGGGC-TTCGTATCCATAAGT
* *
25928140 GAACTCAGACTCAACTCAACGAGCTCGG
1 GAACTCGGACTCAACTCAAAGAGCTCGG
25928168 ATGCCCAAAT
Statistics
Matches: 95, Mismatches: 17, Indels: 18
0.73 0.13 0.14
Matches are distributed among these distances:
45 3 0.03
46 56 0.59
47 32 0.34
48 4 0.04
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (45 bp):
GAACTCGGACTCAACTCAAAGAGCTCGGGCTTCGTATCCATAAGT
Found at i:25928107 original size:93 final size:93
Alignment explanation
Indices: 25927999--25928172 Score: 276
Period size: 93 Copynumber: 1.9 Consensus size: 93
25927989 CCGCCCATAA
* * * * *
25927999 ACGAACTCGGACTCAACTCAAAGAGCTCGGGCGTTCGTATCCATAAGTGAACTCGGACTCAACTC
1 ACGAACTCGGACTCAACTCAAAGAGCTCGGACATCCGCATCCATAAGTGAACTCAGACTCAACTC
*
25928064 AACAAGCTTGGATGCCTAGTTACATCTC
66 AACAAGCTCGGATGCCTAGTTACATCTC
*
25928092 ACGAACTCGGACTCAACTCAACGAGCTCGGACATCCGCATCCATAAGTGAACTCAGACTCAACTC
1 ACGAACTCGGACTCAACTCAAAGAGCTCGGACATCCGCATCCATAAGTGAACTCAGACTCAACTC
*
25928157 AACGAGCTCGGATGCC
66 AACAAGCTCGGATGCC
25928173 CAAATATCCT
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (93 bp):
ACGAACTCGGACTCAACTCAAAGAGCTCGGACATCCGCATCCATAAGTGAACTCAGACTCAACTC
AACAAGCTCGGATGCCTAGTTACATCTC
Found at i:25936464 original size:21 final size:21
Alignment explanation
Indices: 25936440--25936479 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
25936430 AATTTAACTC
*
25936440 AATTTAATACAATTCACATTA
1 AATTCAATACAATTCACATTA
*
25936461 AATTCAATCCAATTCACAT
1 AATTCAATACAATTCACAT
25936480 CCTAGGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.20, G:0.00, T:0.35
Consensus pattern (21 bp):
AATTCAATACAATTCACATTA
Found at i:25939917 original size:37 final size:37
Alignment explanation
Indices: 25939849--25939919 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
25939839 TTTAAGTTGC
*
25939849 AAGTATATGATTATTTGATACGTGAATGAAAATGAGT
1 AAGTATATGATTATTTGATACATGAATGAAAATGAGT
* * *
25939886 AAGTGTATGGTTATTTGATATATGTAA-GAAAATG
1 AAGTATATGATTATTTGATACATG-AATGAAAATG
25939920 TTCAAAAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 27 0.93
38 2 0.07
ACGTcount: A:0.39, C:0.01, G:0.23, T:0.37
Consensus pattern (37 bp):
AAGTATATGATTATTTGATACATGAATGAAAATGAGT
Found at i:25941412 original size:13 final size:13
Alignment explanation
Indices: 25941390--25941422 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
25941380 AAGGGTTTGT
25941390 TTAT-TAAACTAA
1 TTATCTAAACTAA
25941402 TTATCTAAACTAA
1 TTATCTAAACTAA
*
25941415 TTAACTAA
1 TTATCTAA
25941423 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:25944337 original size:31 final size:31
Alignment explanation
Indices: 25944279--25944340 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
25944269 TTTTCATATC
*
25944279 TCATATTTCATAACACTAGGCTAAAGCCTTT
1 TCATATTTCATAACACTAGGCCAAAGCCTTT
** * *
25944310 TCATATTTCATATTACTGGGCCGAAGCCTTT
1 TCATATTTCATAACACTAGGCCAAAGCCTTT
25944341 ACTATAAACG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (31 bp):
TCATATTTCATAACACTAGGCCAAAGCCTTT
Found at i:25944652 original size:25 final size:25
Alignment explanation
Indices: 25944548--25944655 Score: 132
Period size: 25 Copynumber: 4.4 Consensus size: 25
25944538 CTGGAGGCCT
25944548 AGCCTCTTTTAAT-AACTGGGGC-AA
1 AGCC-CTTTTAATAAACTGGGGCAAA
* *
25944572 AGCCCTTTTGACAAACTGGGGCAAA
1 AGCCCTTTTAATAAACTGGGGCAAA
25944597 AGCCCTTTTAATAAACTGGGGCAAA
1 AGCCCTTTTAATAAACTGGGGCAAA
* * *
25944622 AGCCCTTTTCAGTAAACTAGGGCATA
1 AGCCCTTTT-AATAAACTGGGGCAAA
25944648 A-CCCTTTT
1 AGCCCTTTT
25944656 TGCACTTCCT
Statistics
Matches: 74, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
23 6 0.08
24 13 0.18
25 41 0.55
26 14 0.19
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (25 bp):
AGCCCTTTTAATAAACTGGGGCAAA
Found at i:25944726 original size:20 final size:20
Alignment explanation
Indices: 25944703--25944749 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
25944693 TTATGAATAC
25944703 ATCATGTGCATATCATA-CA
1 ATCATGTGCATATCATATCA
25944722 TATCATGTGCATATCATATCA
1 -ATCATGTGCATATCATATCA
25944743 ATCATGT
1 ATCATGT
25944750 ATATCAAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (20 bp):
ATCATGTGCATATCATATCA
Found at i:25947315 original size:23 final size:22
Alignment explanation
Indices: 25947280--25947364 Score: 75
Period size: 23 Copynumber: 3.7 Consensus size: 22
25947270 TATGTCTTTC
*
25947280 AAAAT-AAAATAAAATTGAAATG
1 AAAATAAAAATAAAATT-AAAAG
25947302 AAAATAAAAATAAAAATTAAAAG
1 AAAATAAAAAT-AAAATTAAAAG
* *
25947325 AAAA-ATAAAATAAAAATAAAAT
1 AAAATA-AAAATAAAATTAAAAG
*
25947347 AAGAATAAATAAAAAAAT
1 AA-AATAAA-AATAAAAT
25947365 AAGAGGATTC
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
22 17 0.33
23 22 0.42
24 13 0.25
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (22 bp):
AAAATAAAAATAAAATTAAAAG
Found at i:25947316 original size:11 final size:11
Alignment explanation
Indices: 25947280--25947361 Score: 94
Period size: 11 Copynumber: 7.4 Consensus size: 11
25947270 TATGTCTTTC
25947280 AAAATAAAATA
1 AAAATAAAATA
* * *
25947291 AAATTGAAATG
1 AAAATAAAATA
25947302 AAAATAAAAATA
1 AAAAT-AAAATA
*
25947314 AAAATTAAAAGA
1 AAAA-TAAAATA
25947326 AAAATAAAATA
1 AAAATAAAATA
25947337 AAAATAAAATA
1 AAAATAAAATA
*
25947348 AGAAT-AAATA
1 AAAATAAAATA
25947358 AAAA
1 AAAA
25947362 AATAAGAGGA
Statistics
Matches: 59, Mismatches: 10, Indels: 5
0.80 0.14 0.07
Matches are distributed among these distances:
10 8 0.14
11 33 0.56
12 17 0.29
13 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:25947322 original size:7 final size:6
Alignment explanation
Indices: 25947280--25947366 Score: 76
Period size: 6 Copynumber: 15.2 Consensus size: 6
25947270 TATGTCTTTC
* * * * *
25947280 AAAAT- AAAAT- AAAATT GAAATG AAAATA AAAATA AAAATT AAAAGA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
*
25947326 AAAAT- AAAATA AAAAT- AAAATA AGAATA AATAA-A AAAATA A
1 AAAATA AAAATA AAAATA AAAATA AAAATA AA-AATA AAAATA A
25947367 GAGGATTCAA
Statistics
Matches: 67, Mismatches: 10, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
5 22 0.33
6 43 0.64
7 2 0.03
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (6 bp):
AAAATA
Found at i:25947363 original size:29 final size:29
Alignment explanation
Indices: 25947302--25947366 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
25947292 AATTGAAATG
*
25947302 AAAATAAAAATAAAAATTAAAAGAAAAAT
1 AAAATAAAAATAAAAATTAAAAGAAAAAA
*
25947331 AAAATAAAAAT-AAAA-TAAGAATAAATAAA
1 AAAATAAAAATAAAAATTAA-AAGAAA-AAA
25947360 AAAATAA
1 AAAATAA
25947367 GAGGATTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 3 0.09
28 9 0.28
29 20 0.62
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (29 bp):
AAAATAAAAATAAAAATTAAAAGAAAAAA
Found at i:25952756 original size:13 final size:13
Alignment explanation
Indices: 25952734--25952766 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
25952724 AAGGGTTTGT
25952734 TTAT-TAAACTAA
1 TTATCTAAACTAA
25952746 TTATCTAAACTAA
1 TTATCTAAACTAA
*
25952759 TTAACTAA
1 TTATCTAA
25952767 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:25954390 original size:44 final size:44
Alignment explanation
Indices: 25954327--25954422 Score: 147
Period size: 44 Copynumber: 2.2 Consensus size: 44
25954317 TCACAGCTCC
* * * *
25954327 TGTGAGCAGCATCGTGTAATGGTTAATGTCTGATTTATAGCTTG
1 TGTGAGCAGCATCATGTAATGGTTAATGTCTAATTCATAGCTGG
*
25954371 TGTGAGTAGCATCATGTAATGGTTAATGTCTAATTCATAGCTGG
1 TGTGAGCAGCATCATGTAATGGTTAATGTCTAATTCATAGCTGG
25954415 TGTGAGCA
1 TGTGAGCA
25954423 TTATTATCCC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.25, C:0.11, G:0.27, T:0.36
Consensus pattern (44 bp):
TGTGAGCAGCATCATGTAATGGTTAATGTCTAATTCATAGCTGG
Found at i:25957150 original size:11 final size:12
Alignment explanation
Indices: 25957125--25957154 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
25957115 CTAGCTTGGT
25957125 TAGTTTAATTTA
1 TAGTTTAATTTA
25957137 TAGTTTAA-TTA
1 TAGTTTAATTTA
25957148 TAGTTTA
1 TAGTTTA
25957155 TAAACCATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (12 bp):
TAGTTTAATTTA
Found at i:25960610 original size:3 final size:3
Alignment explanation
Indices: 25960604--25960649 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
25960594 TCCTCTTCTA
25960604 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
25960650 TTCTTCTTCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.35, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:25962353 original size:18 final size:18
Alignment explanation
Indices: 25962317--25962360 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
25962307 ATCTACCTCT
* *
25962317 TCCTCCTCTTCATCCTCA
1 TCCTCCTCCTCATCATCA
25962335 TCCTCCTCCTCATCATCA
1 TCCTCCTCCTCATCATCA
*
25962353 TCATCCTC
1 TCCTCCTC
25962361 TACCCCATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.50, G:0.00, T:0.36
Consensus pattern (18 bp):
TCCTCCTCCTCATCATCA
Found at i:25962369 original size:21 final size:21
Alignment explanation
Indices: 25962317--25962378 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
25962307 ATCTACCTCT
* *
25962317 TCCTCCTCTTCATCCTCATCC
1 TCCTCCCCATCATCCTCATCC
* *
25962338 TCCTCCTCATCATCATCATCC
1 TCCTCCCCATCATCCTCATCC
*
25962359 T-CTACCCCATCTTCCTCATC
1 TCCT-CCCCATCATCCTCATC
25962379 ATCATCACTA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
20 2 0.06
21 33 0.94
ACGTcount: A:0.15, C:0.50, G:0.00, T:0.35
Consensus pattern (21 bp):
TCCTCCCCATCATCCTCATCC
Found at i:25962731 original size:18 final size:18
Alignment explanation
Indices: 25962704--25962738 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
25962694 ATCATCCTCA
*
25962704 TCCTCATCCTCTTCATCT
1 TCCTCATCCTCCTCATCT
*
25962722 TCCTCTTCCTCCTCATC
1 TCCTCATCCTCCTCATC
25962739 ATCCGATTCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.09, C:0.49, G:0.00, T:0.43
Consensus pattern (18 bp):
TCCTCATCCTCCTCATCT
Found at i:25967930 original size:34 final size:36
Alignment explanation
Indices: 25967881--25967955 Score: 127
Period size: 35 Copynumber: 2.1 Consensus size: 36
25967871 CACTTACTCA
25967881 ATTTTGAAAAGTGATAA-TTATCATTCAATAGATAC
1 ATTTTGAAAAGTGATAATTTATCATTCAATAGATAC
*
25967916 ATTTTG-AAAGTGATAATTTATCATTCAATGGATAC
1 ATTTTGAAAAGTGATAATTTATCATTCAATAGATAC
25967951 ATTTT
1 ATTTT
25967956 CATTGGACAT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
34 10 0.26
35 28 0.74
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.41
Consensus pattern (36 bp):
ATTTTGAAAAGTGATAATTTATCATTCAATAGATAC
Found at i:25971001 original size:40 final size:40
Alignment explanation
Indices: 25970911--25971131 Score: 209
Period size: 40 Copynumber: 5.5 Consensus size: 40
25970901 CTCAAGTAAT
* * * *
25970911 CTTCGGGATTTAG-CCGGATATA-ACTACTTGCAC-AAGGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * *
25970949 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCACAGATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
25970989 CTTCGGGACTTAGCCCGGATATAATCGCTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * * *
25971029 CTTCGGGTCTTAGCTCGGATATAG-CAACTCGCACGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * * * *
25971069 CTTC-AGATCTTAGTCCGGTTATAGTCACCTTGCACAAAAGC
1 CTTCGGGA-CTTAGCCCGGATATAGTCA-CTAGCACAAATGC
25971110 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
25971132 CATTCGAATA
Statistics
Matches: 146, Mismatches: 29, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
38 11 0.08
39 17 0.12
40 89 0.61
41 27 0.18
42 2 0.01
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.26
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:25971120 original size:121 final size:118
Alignment explanation
Indices: 25970911--25971131 Score: 291
Period size: 121 Copynumber: 1.8 Consensus size: 118
25970901 CTCAAGTAAT
* * * * *
25970911 CTTCGGGATTTAGCCGGATATAACTACTTGCACAAGGCCTTCGGGTCTTAGCCCGGATATGGTCA
1 CTTCGGGATTTAGCCGGATATAACAACTCGCACAAGGCCTTCAGATCTTAGCCCGGATATAGTCA
* *
25970976 CTAGCACAGATGCCTTCGGGACTTAGCCCGGATATAATCGCTAGCACAAATGC
66 CTAGCACAAAAGCCTTCGGGACTTAGCCCGGATATAATCGCTAGCACAAATGC
* * * *
25971029 CTTCGGG-TCTTAGCTCGGATATAGCAACTCGCACGAATGCCTTCAGATCTTAGTCCGGTTATAG
1 CTTCGGGAT-TTAGC-CGGATATAACAACTCGCAC-AAGGCCTTCAGATCTTAGCCCGGATATAG
*
25971093 TCACCTTGCACAAAAGCCTTCGGGACTTAGCCCGGATAT
63 TCA-CTAGCACAAAAGCCTTCGGGACTTAGCCCGGATAT
25971132 CATTCGAATA
Statistics
Matches: 87, Mismatches: 12, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
117 1 0.01
118 12 0.14
119 16 0.18
120 26 0.30
121 32 0.37
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.26
Consensus pattern (118 bp):
CTTCGGGATTTAGCCGGATATAACAACTCGCACAAGGCCTTCAGATCTTAGCCCGGATATAGTCA
CTAGCACAAAAGCCTTCGGGACTTAGCCCGGATATAATCGCTAGCACAAATGC
Found at i:25973248 original size:42 final size:42
Alignment explanation
Indices: 25973170--25973249 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
25973160 GTGCAGGTTT
* * *
25973170 CACACGGCTAAGACATACGCCCGTGTTCTAGGCCGTGTAGCA
1 CACACGGCTAAGACACACACCCGTGTTCTAGCCCGTGTAGCA
25973212 CACACGGCTAAGACACACACCCGTG-TCTATGCCCGTGT
1 CACACGGCTAAGACACACACCCGTGTTCTA-GCCCGTGT
25973250 GCTCAATTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
41 4 0.12
42 30 0.88
ACGTcount: A:0.24, C:0.34, G:0.24, T:0.19
Consensus pattern (42 bp):
CACACGGCTAAGACACACACCCGTGTTCTAGCCCGTGTAGCA
Found at i:25973836 original size:16 final size:18
Alignment explanation
Indices: 25973804--25973842 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
25973794 ATTTTGGAAT
*
25973804 TAAAAATTATATTAAATG
1 TAAAAATTATATTAAATA
25973822 TAAAAA-TAT-TTAAATA
1 TAAAAATTATATTAAATA
25973838 TAAAA
1 TAAAA
25973843 TGTGAAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 11 0.55
17 3 0.15
18 6 0.30
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
TAAAAATTATATTAAATA
Found at i:25979815 original size:34 final size:35
Alignment explanation
Indices: 25979777--25979843 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
25979767 TGAATTTTGG
*
25979777 AAAGTGATAA-TTATCATTCAATAGATACATTTAT
1 AAAGTGATAATTTACCATTCAATAGATACATTTAT
*
25979811 AAAGTGATAATTTACCATTCAATGGATACATTT
1 AAAGTGATAATTTACCATTCAATAGATACATTT
25979844 CCATGGGACA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 10 0.33
35 20 0.67
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.37
Consensus pattern (35 bp):
AAAGTGATAATTTACCATTCAATAGATACATTTAT
Found at i:25990231 original size:5 final size:5
Alignment explanation
Indices: 25990221--25990252 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
25990211 TTGTGTGATC
25990221 TTTAT TTTA- TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
25990253 TCCCAAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:25990235 original size:9 final size:9
Alignment explanation
Indices: 25990221--25990251 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
25990211 TTGTGTGATC
25990221 TTTATTTTA
1 TTTATTTTA
25990230 TTTATTTTA
1 TTTATTTTA
25990239 TTTTATTTTA
1 -TTTATTTTA
25990249 TTT
1 TTT
25990252 TTCCCAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:25999005 original size:5 final size:5
Alignment explanation
Indices: 25998995--25999027 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
25998985 GGAAGCTGTG
*
25998995 AAAAT AAAAT AAAAT AAAAC AAAAT AAAA- AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
25999028 GAACACACAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.12
Consensus pattern (5 bp):
AAAAT
Found at i:26005962 original size:14 final size:14
Alignment explanation
Indices: 26005945--26005987 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
26005935 CATTCTTTCC
26005945 TTTTCTTTCTTC-T
1 TTTTCTTTCTTCTT
26005958 TTTT-TTT-TTCTT
1 TTTTCTTTCTTCTT
*
26005970 CTTTCTTTCTTCTT
1 TTTTCTTTCTTCTT
26005984 TTTT
1 TTTT
26005988 TGTTTGATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 3 0.12
12 7 0.28
13 7 0.28
14 8 0.32
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTCTTTCTTCTT
Found at i:26016233 original size:69 final size:69
Alignment explanation
Indices: 26016117--26016253 Score: 211
Period size: 69 Copynumber: 2.0 Consensus size: 69
26016107 TGGCTTTTAT
* *
26016117 TTTCCCAGTTAAACTCTATTTTTAGTTTTCAAATTACACTCTAATTAGTGTAGGTTATTTGAATA
1 TTTCCCAGTTAAACTCTATTTTTAGTTTCCAAATTAAACTCTAATTAGTGTAGGTTATTTGAATA
26016182 TTAG
66 TTAG
* * * * *
26016186 TTTCCCAGTTAAGCTCTATTTTTAGTTTCCCACTTAAACTCTGATTAGTGTAGGTTATTTTAATA
1 TTTCCCAGTTAAACTCTATTTTTAGTTTCCAAATTAAACTCTAATTAGTGTAGGTTATTTGAATA
26016251 TTA
66 TTA
26016254 TTTGACCTAC
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 61 1.00
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.47
Consensus pattern (69 bp):
TTTCCCAGTTAAACTCTATTTTTAGTTTCCAAATTAAACTCTAATTAGTGTAGGTTATTTGAATA
TTAG
Found at i:26019243 original size:19 final size:19
Alignment explanation
Indices: 26019207--26019243 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
26019197 TAATTAGGCT
* *
26019207 TTAATTAAGTGAATTTAGC
1 TTAATTAAGAGAAATTAGC
26019226 TTAATTAAGAGAAATTAG
1 TTAATTAAGAGAAATTAG
26019244 GAAAAAGGGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.16, T:0.38
Consensus pattern (19 bp):
TTAATTAAGAGAAATTAGC
Found at i:26019878 original size:2 final size:2
Alignment explanation
Indices: 26019871--26019907 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
26019861 TTATTAACTA
*
26019871 AT AT AT AT AT AT AT AT AG AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
26019908 AAAGAAAGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:26020360 original size:17 final size:18
Alignment explanation
Indices: 26020338--26020371 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
26020328 TAAATGAGTT
26020338 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
26020355 AATTAGGGTATAAATTG
1 AATTAGGATATAAATTG
26020372 AATAGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:26020531 original size:21 final size:21
Alignment explanation
Indices: 26020507--26020548 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
26020497 GGAGTAATCG
26020507 AACAAATCTGGGTTTGTATTA
1 AACAAATCTGGGTTTGTATTA
26020528 AACAAATCTGGGTTTGTATTA
1 AACAAATCTGGGTTTGTATTA
26020549 CTATAATTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (21 bp):
AACAAATCTGGGTTTGTATTA
Found at i:26020915 original size:15 final size:14
Alignment explanation
Indices: 26020879--26020918 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
26020869 ATTTGATTGG
26020879 AAAATGAATT-AAA
1 AAAATGAATTAAAA
*
26020892 AATATGAATTAAATA
1 AAAATGAATTAAA-A
26020907 AAAATGAATTAA
1 AAAATGAATTAA
26020919 TTTATGAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 9 0.39
14 2 0.09
15 12 0.52
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (14 bp):
AAAATGAATTAAAA
Found at i:26021215 original size:186 final size:186
Alignment explanation
Indices: 26021021--26021395 Score: 723
Period size: 186 Copynumber: 2.0 Consensus size: 186
26021011 ATATTGGTAT
26021021 TGAATTGTTTATTGATTAGAAAGTGGAAAAGTGAATTTGAATTGAATGAGAATTGAATTGAATGG
1 TGAATTGTTTATTGATTAGAAAGTGGAAAAGTGAATTTGAATTGAATGAGAATTGAATTGAATGG
26021086 TGAATGTGTATGTATAATTGAACTGTATATTGATTTGAATGTGAAATTGTAATTGAAAAGTGATC
66 TGAATGTGTATGTATAATTGAACTGTATATTGATTTGAATGTGAAATTGTAATTGAAAAGTGATC
*
26021151 TTGAATTGGAAATAAAAGTGAATTGAGAATTAAAGTACCGTATTAACTAGTCGGGC
131 TTGAATTGGAAATAAAAGTGAATTGAGAATTAAAGTACCCTATTAACTAGTCGGGC
*
26021207 TGAATTGTTTATTGATTAGAAAGTTGAAAAGTGAATTTGAATTGAATGAGAATTGAATTGAATGG
1 TGAATTGTTTATTGATTAGAAAGTGGAAAAGTGAATTTGAATTGAATGAGAATTGAATTGAATGG
26021272 TGAATGTGTATGTATAATTGAACTGTATATTGATTTGAATGTGAAATTGTAATTGAAAAGTGATC
66 TGAATGTGTATGTATAATTGAACTGTATATTGATTTGAATGTGAAATTGTAATTGAAAAGTGATC
*
26021337 TTGAATTGGAAATGAAAGTGAATTGAGAATTAAAGTACCCTATTAACTAGTCGGGC
131 TTGAATTGGAAATAAAAGTGAATTGAGAATTAAAGTACCCTATTAACTAGTCGGGC
26021393 TGA
1 TGA
26021396 GTCGGATATA
Statistics
Matches: 186, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
186 186 1.00
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.35
Consensus pattern (186 bp):
TGAATTGTTTATTGATTAGAAAGTGGAAAAGTGAATTTGAATTGAATGAGAATTGAATTGAATGG
TGAATGTGTATGTATAATTGAACTGTATATTGATTTGAATGTGAAATTGTAATTGAAAAGTGATC
TTGAATTGGAAATAAAAGTGAATTGAGAATTAAAGTACCCTATTAACTAGTCGGGC
Found at i:26022899 original size:29 final size:30
Alignment explanation
Indices: 26022853--26022914 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 30
26022843 AATTATTTTA
26022853 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
* *
26022883 TTGTTAA-TTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
26022912 TTG
1 TTG
26022915 CTTGTTAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 23 0.77
30 7 0.23
ACGTcount: A:0.26, C:0.03, G:0.15, T:0.56
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:26023391 original size:20 final size:19
Alignment explanation
Indices: 26023347--26023384 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
26023337 GTTGTGTGTT
26023347 TAATTAAGCTTTAATTAAG
1 TAATTAAGCTTTAATTAAG
*
26023366 TGAATTTAGC-TTAATTAAG
1 T-AATTAAGCTTTAATTAAG
26023385 AATAATTAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.39, C:0.05, G:0.13, T:0.42
Consensus pattern (19 bp):
TAATTAAGCTTTAATTAAG
Found at i:26023870 original size:8 final size:8
Alignment explanation
Indices: 26023853--26023890 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
26023843 TAAAGTAAAT
26023853 AAAG-ATA
1 AAAGAATA
26023860 AAAGAATA
1 AAAGAATA
*
26023868 AAAAAACTA
1 AAAGAA-TA
26023877 AAAGAATA
1 AAAGAATA
26023885 AAAGAA
1 AAAGAA
26023891 AGAAATGAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
7 4 0.15
8 16 0.59
9 7 0.26
ACGTcount: A:0.76, C:0.03, G:0.11, T:0.11
Consensus pattern (8 bp):
AAAGAATA
Found at i:26024281 original size:36 final size:37
Alignment explanation
Indices: 26024190--26024281 Score: 116
Period size: 37 Copynumber: 2.5 Consensus size: 37
26024180 ATATGTGTGG
*
26024190 AATTGAATTGAATAT-TGACTTGAAAATGGAAAAGTGA
1 AATTGAATTGAA-ATGTGACTTGAAAATGAAAAAGTGA
* * *
26024227 ATTTTGAATTGAATTGTGA-TTGAAAGTGAAAAAGTGA
1 A-ATTGAATTGAAATGTGACTTGAAAATGAAAAAGTGA
26024264 AATTGAATTGAAATGTGA
1 AATTGAATTGAAATGTGA
26024282 ATTTGGAGAC
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
36 15 0.32
37 19 0.40
38 13 0.28
ACGTcount: A:0.43, C:0.01, G:0.23, T:0.33
Consensus pattern (37 bp):
AATTGAATTGAAATGTGACTTGAAAATGAAAAAGTGA
Found at i:26025171 original size:12 final size:12
Alignment explanation
Indices: 26025130--26025171 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
26025120 TTAAATAGAA
26025130 ATGAATGAAATT
1 ATGAATGAAATT
*
26025142 ATCAAT-AAATT
1 ATGAATGAAATT
* *
26025153 TTGAATGATATT
1 ATGAATGAAATT
26025165 ATGAATG
1 ATGAATG
26025172 TTTATTTAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.45, C:0.02, G:0.14, T:0.38
Consensus pattern (12 bp):
ATGAATGAAATT
Found at i:26025280 original size:22 final size:22
Alignment explanation
Indices: 26025230--26025280 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
26025220 TATTCAAATG
26025230 TGAA-TTGGATTGGTTGTGATT
1 TGAATTTGGATTGGTTGTGATT
***
26025251 TTTGTTTGGATTGGTCT-TGATT
1 TGAATTTGGATTGGT-TGTGATT
26025273 TGAATTTG
1 TGAATTTG
26025281 TAGGGAATGT
Statistics
Matches: 22, Mismatches: 6, Indels: 3
0.71 0.19 0.10
Matches are distributed among these distances:
21 1 0.05
22 20 0.91
23 1 0.05
ACGTcount: A:0.16, C:0.02, G:0.29, T:0.53
Consensus pattern (22 bp):
TGAATTTGGATTGGTTGTGATT
Found at i:26025350 original size:17 final size:16
Alignment explanation
Indices: 26025324--26025366 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
26025314 TTGAGTTCGC
*
26025324 ATAAAAAAATTTAATAA
1 ATAAAAAAATATAA-AA
*
26025341 ATAAATAAATATAAAA
1 ATAAAAAAATATAAAA
26025357 ATATAAAAAA
1 ATA-AAAAAA
26025367 ATTCCCAAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAAAAAAATATAAAA
Found at i:26025630 original size:16 final size:16
Alignment explanation
Indices: 26025609--26025639 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
26025599 TTCCATCCCG
26025609 ATTTTGATTAAATTTT
1 ATTTTGATTAAATTTT
26025625 ATTTTGATTAAATTT
1 ATTTTGATTAAATTT
26025640 ATAATTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.61
Consensus pattern (16 bp):
ATTTTGATTAAATTTT
Found at i:26025825 original size:19 final size:21
Alignment explanation
Indices: 26025784--26025825 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 21
26025774 AAAATTATTG
**
26025784 ATTTTTAAAAATATTTATGAA
1 ATTTTTAAAAATATTTACCAA
26025805 ATTTTT-AAAAT-TTTACCAA
1 ATTTTTAAAAATATTTACCAA
26025824 AT
1 AT
26025826 AATATCCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 8 0.42
20 5 0.26
21 6 0.32
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (21 bp):
ATTTTTAAAAATATTTACCAA
Found at i:26028842 original size:57 final size:56
Alignment explanation
Indices: 26028769--26028903 Score: 162
Period size: 56 Copynumber: 2.4 Consensus size: 56
26028759 GTTAAAGTCT
* *** ** *
26028769 GGATTTAGCCTAGACTGGTAATCCAGATTGAGCTCTTTAGAGTATTTGTCACAGAAA
1 GGATTTAGCCTGGACTGGTAATCCAGACAAAGCTC-TTAGAACATATGTCACAGAAA
* * *
26028826 GGATTTAGCCTGGACTGGTAATCCTGACAAAGCTCTTAGAACATATGTTACAGACA
1 GGATTTAGCCTGGACTGGTAATCCAGACAAAGCTCTTAGAACATATGTCACAGAAA
*
26028882 GGATTTAGACTGGACTGGTAAT
1 GGATTTAGCCTGGACTGGTAAT
26028904 GCTGCTGTAT
Statistics
Matches: 67, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
56 37 0.55
57 30 0.45
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (56 bp):
GGATTTAGCCTGGACTGGTAATCCAGACAAAGCTCTTAGAACATATGTCACAGAAA
Found at i:26028895 original size:56 final size:57
Alignment explanation
Indices: 26028754--26028903 Score: 167
Period size: 57 Copynumber: 2.6 Consensus size: 57
26028744 AGCCTTTGAG
* * * * *** *
26028754 CATATGTTAAAGTCTGGATTTAGCCTAGACTGGTAATCCAGATTGAGCTCTTTAGAG
1 CATATGTTACAGACAGGATTTAGCCTGGACTGGTAATCCAGACAAAGCTCTTTAGAA
* * * * *
26028811 TATTTGTCACAGAAAGGATTTAGCCTGGACTGGTAATCCTGACAAAGCTC-TTAGAA
1 CATATGTTACAGACAGGATTTAGCCTGGACTGGTAATCCAGACAAAGCTCTTTAGAA
*
26028867 CATATGTTACAGACAGGATTTAGACTGGACTGGTAAT
1 CATATGTTACAGACAGGATTTAGCCTGGACTGGTAAT
26028904 GCTGCTGTAT
Statistics
Matches: 75, Mismatches: 18, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
56 37 0.49
57 38 0.51
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.31
Consensus pattern (57 bp):
CATATGTTACAGACAGGATTTAGCCTGGACTGGTAATCCAGACAAAGCTCTTTAGAA
Found at i:26033748 original size:25 final size:25
Alignment explanation
Indices: 26033714--26033810 Score: 106
Period size: 25 Copynumber: 3.9 Consensus size: 25
26033704 ACACACCACA
* *
26033714 GCTCTTATGAGCATCCTGATATTTG
1 GCTCTCATGAGCTTCCTGATATTTG
* *
26033739 GCTCTCATGAGCTTTCTGAT-TAATG
1 GCTCTCATGAGCTTCCTGATAT-TTG
* * *
26033764 GCTCTCTTGAGCTTCCCGATAATTG
1 GCTCTCATGAGCTTCCTGATATTTG
*
26033789 GCTCACATGAGCTTCCTGATAT
1 GCTCTCATGAGCTTCCTGATAT
26033811 ACAGCTCGAT
Statistics
Matches: 57, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
24 1 0.02
25 56 0.98
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.37
Consensus pattern (25 bp):
GCTCTCATGAGCTTCCTGATATTTG
Found at i:26033817 original size:25 final size:25
Alignment explanation
Indices: 26033789--26033854 Score: 98
Period size: 25 Copynumber: 2.6 Consensus size: 25
26033779 CCGATAATTG
26033789 GCTCACATGAGCTTCCTGATATACA
1 GCTCACATGAGCTTCCTGATATACA
* *
26033814 GCTCGA-TTGAGCTTCCTGTTATACA
1 GCTC-ACATGAGCTTCCTGATATACA
26033839 GCTCACATGAGCTTCC
1 GCTCACATGAGCTTCC
26033855 CATTACATGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 1 0.03
25 34 0.94
26 1 0.03
ACGTcount: A:0.23, C:0.29, G:0.18, T:0.30
Consensus pattern (25 bp):
GCTCACATGAGCTTCCTGATATACA
Found at i:26033824 original size:50 final size:49
Alignment explanation
Indices: 26033721--26033829 Score: 121
Period size: 50 Copynumber: 2.2 Consensus size: 49
26033711 ACAGCTCTTA
* * * * * **
26033721 TGAGCATCCTGATATTTGGCTCTCATGAGCTTTCTGATTAATGGCTCTCT
1 TGAGCTTCCCGATAATTGGCTCACATGAGCTTCCTGATTAA-GGCTCGAT
26033771 TGAGCTTCCCGATAATTGGCTCACATGAGCTTCCTGATATACA-GCTCGAT
1 TGAGCTTCCCGATAATTGGCTCACATGAGCTTCCTGAT-TA-AGGCTCGAT
26033821 TGAGCTTCC
1 TGAGCTTCC
26033830 TGTTATACAG
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
50 47 0.94
51 2 0.04
52 1 0.02
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (49 bp):
TGAGCTTCCCGATAATTGGCTCACATGAGCTTCCTGATTAAGGCTCGAT
Found at i:26033867 original size:25 final size:25
Alignment explanation
Indices: 26033737--26033889 Score: 59
Period size: 25 Copynumber: 6.1 Consensus size: 25
26033727 TCCTGATATT
* **
26033737 TGGCTCTCATGAGCTTTCTGATTA-A
1 TGGCTCACATGAGC-TTCCCATTACA
* *
26033762 TGGCTCTCTTGAGCTTCCCGA-TA-A
1 TGGCTCACATGAGCTTCCC-ATTACA
*
26033786 TTGGCTCACATGAGCTTCCTGATATACA
1 -TGGCTCACATGAGCTTCC-CAT-TACA
* ** *
26033814 --GCTCGA-TTGAGCTTCCTGTTATA
1 TGGCTC-ACATGAGCTTCCCATTACA
**
26033837 CAGCTCACATGAGCTTCCCATTACA
1 TGGCTCACATGAGCTTCCCATTACA
* *
26033862 TGGCTCTA-AAGAGCTTCCCGTTTACA
1 TGGCTC-ACATGAGCTTCCC-ATTACA
26033888 TG
1 TG
26033890 CTCGTATGGG
Statistics
Matches: 98, Mismatches: 18, Indels: 23
0.71 0.13 0.17
Matches are distributed among these distances:
23 3 0.03
24 8 0.08
25 75 0.77
26 9 0.09
27 2 0.02
28 1 0.01
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.33
Consensus pattern (25 bp):
TGGCTCACATGAGCTTCCCATTACA
Found at i:26033892 original size:25 final size:25
Alignment explanation
Indices: 26033822--26033892 Score: 67
Period size: 25 Copynumber: 2.8 Consensus size: 25
26033812 CAGCTCGATT
* *
26033822 GAGCTTCCTGTTATACA-GCTCACAT
1 GAGCTTCCCGTT-TACATGCTCACAA
*
26033847 GAGCTTCCC-ATTACATGGCTCTA-AA
1 GAGCTTCCCGTTTACAT-GCTC-ACAA
26033872 GAGCTTCCCGTTTACATGCTC
1 GAGCTTCCCGTTTACATGCTC
26033893 GTATGGGCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
23 4 0.11
24 1 0.03
25 26 0.68
26 7 0.18
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.31
Consensus pattern (25 bp):
GAGCTTCCCGTTTACATGCTCACAA
Found at i:26051128 original size:15 final size:15
Alignment explanation
Indices: 26051108--26051137 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
26051098 GTAAGTTTTC
26051108 TTTCTATTACACGAA
1 TTTCTATTACACGAA
*
26051123 TTTCTATTACGCGAA
1 TTTCTATTACACGAA
26051138 CTTACTAAGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (15 bp):
TTTCTATTACACGAA
Found at i:26059245 original size:35 final size:34
Alignment explanation
Indices: 26059155--26059343 Score: 107
Period size: 33 Copynumber: 5.6 Consensus size: 34
26059145 AATTGACGGA
* * * * * *
26059155 TAAGACCATAACTGGGTTATGGCACTATGA-ACG
1 TAAGACCATAGCTGGGCTATGGCAGTTTTATATG
* * * *
26059188 TAAGACCATGGTTGGACCATGGCAGTGTTTATATG
1 TAAGACCATAGCTGGGCTATGGCAGT-TTTATATG
* *
26059223 TAAGATCATAGCTGGGCTATGGCA-TTTT-GATG
1 TAAGACCATAGCTGGGCTATGGCAGTTTTATATG
* * * * * *
26059255 ATATGACCATAACTGGGTTATGGCACTATGA-ATG
1 -TAAGACCATAGCTGGGCTATGGCAGTTTTATATG
* * * *
26059289 TAAGACCATGGTTGGACCATGGCAGTGTTTATATG
1 TAAGACCATAGCTGGGCTATGGCAGT-TTTATATG
* *
26059324 TAAGACCAGAGTTGGGCTAT
1 TAAGACCATAGCTGGGCTAT
26059344 TGCATTCTGA
Statistics
Matches: 113, Mismatches: 36, Indels: 12
0.70 0.22 0.07
Matches are distributed among these distances:
32 3 0.03
33 60 0.53
34 10 0.09
35 40 0.35
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.30
Consensus pattern (34 bp):
TAAGACCATAGCTGGGCTATGGCAGTTTTATATG
Found at i:26059296 original size:33 final size:33
Alignment explanation
Indices: 26059155--26059297 Score: 108
Period size: 33 Copynumber: 4.3 Consensus size: 33
26059145 AATTGACGGA
* *
26059155 TAAGACCATAACTGGGTTATGGCACTATGAACG
1 TAAGACCATAACTGGGCTATGGCACTATGAATG
*** * * * * *
26059188 TAAGACCATGGTTGGACCATGGCAGTGTTTATATG
1 TAAGACCATAACTGGGCTATGGCACT-ATGA-ATG
* * * *
26059223 TAAGATCATAGCTGGGCTATGGCATTTTG-ATG
1 TAAGACCATAACTGGGCTATGGCACTATGAATG
* *
26059255 ATATGACCATAACTGGGTTATGGCACTATGAATG
1 -TAAGACCATAACTGGGCTATGGCACTATGAATG
26059289 TAAGACCAT
1 TAAGACCAT
26059298 GGTTGGACCA
Statistics
Matches: 82, Mismatches: 24, Indels: 8
0.72 0.21 0.07
Matches are distributed among these distances:
32 3 0.04
33 50 0.61
34 7 0.09
35 22 0.27
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.29
Consensus pattern (33 bp):
TAAGACCATAACTGGGCTATGGCACTATGAATG
Found at i:26059340 original size:101 final size:101
Alignment explanation
Indices: 26059153--26059392 Score: 381
Period size: 101 Copynumber: 2.4 Consensus size: 101
26059143 TGAATTGACG
*
26059153 GATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTT
1 GATAAGACCATAACTGGGTTATGGCACTATGAATGTAAGACCATGGTTGGACCATGGCAGTGTTT
* * *
26059218 ATATGTAAGATCATAGCTGGGCTATGGCATTTTGAT
66 ATATGTAAGACCAGAGCTGGGCTATGGCATTCTGAT
*
26059254 GATATGACCATAACTGGGTTATGGCACTATGAATGTAAGACCATGGTTGGACCATGGCAGTGTTT
1 GATAAGACCATAACTGGGTTATGGCACTATGAATGTAAGACCATGGTTGGACCATGGCAGTGTTT
* *
26059319 ATATGTAAGACCAGAGTTGGGCTATTGCATTCTGAT
66 ATATGTAAGACCAGAGCTGGGCTATGGCATTCTGAT
* * * *
26059355 GATAAAACCATAACTAGGTTATAGCACTACGAATGTAA
1 GATAAGACCATAACTGGGTTATGGCACTATGAATGTAA
26059393 AGGATGAATT
Statistics
Matches: 127, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
101 127 1.00
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (101 bp):
GATAAGACCATAACTGGGTTATGGCACTATGAATGTAAGACCATGGTTGGACCATGGCAGTGTTT
ATATGTAAGACCAGAGCTGGGCTATGGCATTCTGAT
Found at i:26063236 original size:23 final size:23
Alignment explanation
Indices: 26063198--26063241 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
26063188 GGCCACTTAT
*
26063198 TGGCTTGTTTGAATGTTTAATTA
1 TGGCTTGTTTGAATGTGTAATTA
26063221 TGGCTTG-TTGATATGTGTAAT
1 TGGCTTGTTTGA-ATGTGTAAT
26063242 GTTGATTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.20, C:0.05, G:0.25, T:0.50
Consensus pattern (23 bp):
TGGCTTGTTTGAATGTGTAATTA
Found at i:26066592 original size:21 final size:21
Alignment explanation
Indices: 26066549--26066594 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
26066539 CTCTTTAATC
**
26066549 TCTTCACTTTCTCTTCAACTT
1 TCTTCACTTTCAATTCAACTT
26066570 TCTTCACTTTCAATTCCAA-TT
1 TCTTCACTTTCAATT-CAACTT
26066591 TCTT
1 TCTT
26066595 GTTTCCAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.17, C:0.30, G:0.00, T:0.52
Consensus pattern (21 bp):
TCTTCACTTTCAATTCAACTT
Found at i:26066821 original size:13 final size:11
Alignment explanation
Indices: 26066794--26066840 Score: 58
Period size: 11 Copynumber: 4.1 Consensus size: 11
26066784 TTTTCATAGT
26066794 TAAAATATTAA
1 TAAAATATTAA
26066805 TAAAATATCTAAA
1 TAAAATAT-T-AA
*
26066818 TAAAATATTAT
1 TAAAATATTAA
*
26066829 TAAAATAATAA
1 TAAAATATTAA
26066840 T
1 T
26066841 TAACTAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
11 19 0.61
12 2 0.06
13 10 0.32
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (11 bp):
TAAAATATTAA
Found at i:26070261 original size:28 final size:28
Alignment explanation
Indices: 26070219--26070274 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
26070209 ACCAAGGCTG
*
26070219 GCTAAAAAAATTAAAATTTAACTGTCAA
1 GCTAAAAAAAGTAAAATTTAACTGTCAA
*
26070247 GCTAAACAAAGTAAAATTTAACTGTCAA
1 GCTAAAAAAAGTAAAATTTAACTGTCAA
26070275 AGCCTTAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.52, C:0.12, G:0.09, T:0.27
Consensus pattern (28 bp):
GCTAAAAAAAGTAAAATTTAACTGTCAA
Found at i:26072891 original size:21 final size:21
Alignment explanation
Indices: 26072866--26072924 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
26072856 TGGGTTTGAG
26072866 TTTGGGTGCGAATTTGGAAGA
1 TTTGGGTGCGAATTTGGAAGA
26072887 TTTGGGTGCGAATTTGGAAGA
1 TTTGGGTGCGAATTTGGAAGA
*
26072908 TTTGGGCGCGAATTTGG
1 TTTGGGTGCGAATTTGG
26072925 TGGTTCGAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.20, C:0.07, G:0.39, T:0.34
Consensus pattern (21 bp):
TTTGGGTGCGAATTTGGAAGA
Found at i:26073705 original size:3 final size:3
Alignment explanation
Indices: 26073697--26073727 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
26073687 TCATTAGTGT
*
26073697 TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
26073728 ACATATATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:26075965 original size:10 final size:11
Alignment explanation
Indices: 26075926--26075964 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
26075916 ATCAATATAT
26075926 TTTTTTCTTTC
1 TTTTTTCTTTC
*
26075937 TCTTTTTCTCTC
1 T-TTTTTCTTTC
26075949 TTTTTT-TTTC
1 TTTTTTCTTTC
26075959 TTTTTT
1 TTTTTT
26075965 TATCTAGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 9 0.36
11 6 0.24
12 10 0.40
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTTCTTTC
Found at i:26076699 original size:12 final size:12
Alignment explanation
Indices: 26076684--26076724 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
26076674 AAATTAAAGG
26076684 TAATAGTAAAAA
1 TAATAGTAAAAA
26076696 TAATAGTAAAAA
1 TAATAGTAAAAA
* *
26076708 -ATTACTAAAAA
1 TAATAGTAAAAA
26076719 TAATAG
1 TAATAG
26076725 AAATAGCATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.27
Consensus pattern (12 bp):
TAATAGTAAAAA
Found at i:26076863 original size:11 final size:11
Alignment explanation
Indices: 26076844--26076873 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
26076834 TAATAATGAG
26076844 AAAAT-AAATC
1 AAAATAAAATC
26076854 AAAATAAAATC
1 AAAATAAAATC
26076865 AAAATAAAA
1 AAAATAAAA
26076874 AAATAAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.26
11 14 0.74
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAATAAAATC
Found at i:26077736 original size:19 final size:19
Alignment explanation
Indices: 26077709--26077745 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
26077699 ATTTTCAGAA
*
26077709 TCCATACGGCCTGGGCATT
1 TCCACACGGCCTGGGCATT
*
26077728 TCCACACGGGCTGGGCAT
1 TCCACACGGCCTGGGCAT
26077746 ACACCTGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.32, G:0.30, T:0.22
Consensus pattern (19 bp):
TCCACACGGCCTGGGCATT
Found at i:26083797 original size:42 final size:41
Alignment explanation
Indices: 26083697--26083816 Score: 125
Period size: 42 Copynumber: 2.9 Consensus size: 41
26083687 AGAAGCACAT
* * * * *
26083697 AAGAGCTAAACAGAAACCCGTAAAGGTTGAACGGAAGCTCGT
1 AAGAGCTAAACTGAAACCCATAAGGGTT-AACTGAAGCTCGG
* *
26083739 AAGAGTTGAA-TAGAAACCCATAAGGGTTAATCTGAAGCTCGG
1 AAGAGCTAAACT-GAAACCCATAAGGGTTAA-CTGAAGCTCGG
*
26083781 AAGAGCTAAACTGAAACCCAGAAGGGTTAAACTGAA
1 AAGAGCTAAACTGAAACCCATAAGGGTT-AACTGAA
26083817 ACTCATATGA
Statistics
Matches: 64, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
41 2 0.03
42 59 0.92
43 3 0.05
ACGTcount: A:0.42, C:0.17, G:0.25, T:0.17
Consensus pattern (41 bp):
AAGAGCTAAACTGAAACCCATAAGGGTTAACTGAAGCTCGG
Found at i:26090048 original size:44 final size:45
Alignment explanation
Indices: 26089993--26090097 Score: 133
Period size: 44 Copynumber: 2.4 Consensus size: 45
26089983 TGGTATAGTG
26089993 CCATAGTATCTTTCAACTAGGGT-ATTTCCTGTTCCGATT-TAATA
1 CCATAGTATCTTTCAACTAGGGTCATTTCCT-TTCCGATTATAATA
* * * *
26090037 CCATAGTATCTTTCAACTATGGTCTTTTCCTTTTCGATTATAATG
1 CCATAGTATCTTTCAACTAGGGTCATTTCCTTTCCGATTATAATA
* *
26090082 TCATAATATCTTTCAA
1 CCATAGTATCTTTCAA
26090098 TCATGGTGTT
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
44 29 0.55
45 24 0.45
ACGTcount: A:0.26, C:0.20, G:0.10, T:0.44
Consensus pattern (45 bp):
CCATAGTATCTTTCAACTAGGGTCATTTCCTTTCCGATTATAATA
Found at i:26090093 original size:45 final size:45
Alignment explanation
Indices: 26089944--26090116 Score: 165
Period size: 45 Copynumber: 3.8 Consensus size: 45
26089934 TCCCGACATG
* * * *
26089944 ATGCCATAATATCTTTTAACTATGGTCTTGATCATTTTCTG-GTATA
1 ATGCCATAATATCTTTCAACTATGGTCTT-TTCCTTTTC-GATTATA
* * * * *
26089990 GTGCCATAGTATCTTTCAACTAGGGT-ATTTCCTGTTCCGATT-TA
1 ATGCCATAATATCTTTCAACTATGGTCTTTTCCT-TTTCGATTATA
* *
26090034 ATACCATAGTATCTTTCAACTATGGTCTTTTCCTTTTCGATTATA
1 ATGCCATAATATCTTTCAACTATGGTCTTTTCCTTTTCGATTATA
* *
26090079 ATGTCATAATATCTTTCAA-TCATGGTGTTTTCCTTTTC
1 ATGCCATAATATCTTTCAACT-ATGGTCTTTTCCTTTTC
26090117 TAAAATCAAT
Statistics
Matches: 104, Mismatches: 18, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
44 37 0.36
45 45 0.43
46 22 0.21
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.46
Consensus pattern (45 bp):
ATGCCATAATATCTTTCAACTATGGTCTTTTCCTTTTCGATTATA
Found at i:26096247 original size:28 final size:28
Alignment explanation
Indices: 26096216--26096333 Score: 139
Period size: 28 Copynumber: 4.2 Consensus size: 28
26096206 TTAGTGTGGG
*
26096216 AGACATTGATTATGTAACTTAGTGTATA
1 AGACATTGATTATGGAACTTAGTGTATA
* * * *
26096244 AGACATCGATTATGGCACTTAGTGTGTG
1 AGACATTGATTATGGAACTTAGTGTATA
*
26096272 AGACATTGATTATGGAACTTAGTGT-TCG
1 AGACATTGATTATGGAACTTAGTGTAT-A
* * *
26096300 AGACATTGATTGTGGCACTTAGTGTACA
1 AGACATTGATTATGGAACTTAGTGTATA
26096328 AGACAT
1 AGACAT
26096334 CGAGTATGCG
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
27 1 0.01
28 76 0.99
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.34
Consensus pattern (28 bp):
AGACATTGATTATGGAACTTAGTGTATA
Found at i:26096291 original size:56 final size:56
Alignment explanation
Indices: 26096203--26096324 Score: 183
Period size: 56 Copynumber: 2.2 Consensus size: 56
26096193 CTATGTACGA
*
26096203 CACTTAGTGTGGGAGACATTGATTATGTAACTTAGTGTAT-AAGACATCGATTATGG
1 CACTTAGTGTGGGAGACATTGATTATGGAACTTAGTGT-TCAAGACATCGATTATGG
* * * *
26096259 CACTTAGTGTGTGAGACATTGATTATGGAACTTAGTGTTCGAGACATTGATTGTGG
1 CACTTAGTGTGGGAGACATTGATTATGGAACTTAGTGTTCAAGACATCGATTATGG
26096315 CACTTAGTGT
1 CACTTAGTGT
26096325 ACAAGACATC
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
55 1 0.02
56 59 0.98
ACGTcount: A:0.27, C:0.11, G:0.26, T:0.35
Consensus pattern (56 bp):
CACTTAGTGTGGGAGACATTGATTATGGAACTTAGTGTTCAAGACATCGATTATGG
Found at i:26108588 original size:40 final size:40
Alignment explanation
Indices: 26108514--26108617 Score: 113
Period size: 40 Copynumber: 2.6 Consensus size: 40
26108504 GACATATCGA
* *
26108514 CTAAATGTGGCACTTAGTGTGCGGTTCAATATAGCTTCGG
1 CTAAATGTGGCACTTAGTGTGCGATTCAAGATAGCTTCGG
* ** *
26108554 CTAAATTTGGCACTTAGTGTGCGATTTGAGATAGCTTTGG
1 CTAAATGTGGCACTTAGTGTGCGATTCAAGATAGCTTCGG
*
26108594 CT--ATGTACGACACTTAGTGTGCGA
1 CTAAATGT--GGCACTTAGTGTGCGA
26108618 GACATTGATT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
38 3 0.06
40 51 0.94
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (40 bp):
CTAAATGTGGCACTTAGTGTGCGATTCAAGATAGCTTCGG
Found at i:26108644 original size:28 final size:28
Alignment explanation
Indices: 26108604--26108706 Score: 188
Period size: 28 Copynumber: 3.7 Consensus size: 28
26108594 CTATGTACGA
26108604 CACTTAGTGTGCGAGACATTGATTATGG
1 CACTTAGTGTGCGAGACATTGATTATGG
26108632 CACTTAGTGTGCGAGACATTGATTATGG
1 CACTTAGTGTGCGAGACATTGATTATGG
*
26108660 CACTTAGTGTGCGAGACATTGATTGTGG
1 CACTTAGTGTGCGAGACATTGATTATGG
*
26108688 CACTTAGTTTGCGAGACAT
1 CACTTAGTGTGCGAGACAT
26108707 CAAGTATGCG
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 73 1.00
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (28 bp):
CACTTAGTGTGCGAGACATTGATTATGG
Found at i:26121466 original size:16 final size:17
Alignment explanation
Indices: 26121421--26121472 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
26121411 GTATTAATAA
*
26121421 TTATGTTATTATATAAGAT
1 TTAT-TTATTATATAA-AC
*
26121440 TTATTTTTTATATAAAC
1 TTATTTATTATATAAAC
26121457 TT-TTTATTATGATAAA
1 TTATTTATTAT-ATAAA
26121473 TATATTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 7 0.24
17 8 0.28
18 10 0.34
19 4 0.14
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.56
Consensus pattern (17 bp):
TTATTTATTATATAAAC
Found at i:26121583 original size:16 final size:17
Alignment explanation
Indices: 26121554--26121587 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
26121544 AATACGATTT
*
26121554 TATTTTTTTAAAATGAA
1 TATTTTATTAAAATGAA
26121571 TATTTTATT-AAATGAA
1 TATTTTATTAAAATGAA
26121587 T
1 T
26121588 TTATAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
TATTTTATTAAAATGAA
Found at i:26133849 original size:30 final size:30
Alignment explanation
Indices: 26133814--26133882 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
26133804 ACCCCAGGGG
* *
26133814 ACACACGGCCATGTAACATAGC-CGTGTGTC
1 ACACACGGCCAAGTAACATAGCGC-TATGTC
*
26133844 ACACACGGCCAAGTAACATAGTGCTATGTC
1 ACACACGGCCAAGTAACATAGCGCTATGTC
26133874 ACACACGGC
1 ACACACGGC
26133883 TGAGACACAC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
30 34 0.97
31 1 0.03
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.17
Consensus pattern (30 bp):
ACACACGGCCAAGTAACATAGCGCTATGTC
Found at i:26134967 original size:40 final size:40
Alignment explanation
Indices: 26134850--26134968 Score: 123
Period size: 40 Copynumber: 3.0 Consensus size: 40
26134840 ACATTAAACC
* * * *
26134850 GAAGCTATCTCAGTATCGCACACTTAGTGCCACATAAAGCT
1 GAAGCTATCTC-GAATCGCACACTAAGTGCCAAATATAGCT
* * ***
26134891 CAAGCTAT-TCTAATTCGCACACTAAGTGCTGTATATAGCT
1 GAAGCTATCTCGAA-TCGCACACTAAGTGCCAAATATAGCT
*
26134931 GAAGCTATCTCGAAACGCACACTAAGTGCCAAATATAG
1 GAAGCTATCTCGAATCGCACACTAAGTGCCAAATATAG
26134969 TAGATTTGTC
Statistics
Matches: 62, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
39 1 0.02
40 50 0.81
41 11 0.18
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (40 bp):
GAAGCTATCTCGAATCGCACACTAAGTGCCAAATATAGCT
Found at i:26136946 original size:20 final size:20
Alignment explanation
Indices: 26136921--26136961 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
26136911 CCGAGTTTAT
26136921 GAGAGCAATTGTCATTAAAA
1 GAGAGCAATTGTCATTAAAA
26136941 GAGAGCAATTGTCATTAAAA
1 GAGAGCAATTGTCATTAAAA
26136961 G
1 G
26136962 GGATTTAGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.10, G:0.22, T:0.24
Consensus pattern (20 bp):
GAGAGCAATTGTCATTAAAA
Found at i:26153089 original size:30 final size:30
Alignment explanation
Indices: 26153053--26153121 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
26153043 CACACGGGTA
*
26153053 GACACACGGGCATGTGTCTAGGCTGTGTGT
1 GACACACGGGCATGTGTCTAGGCCGTGTGT
26153083 GACACACGGGCATGTGTCTAGGCCGTGTGT
1 GACACACGGGCATGTGTCTAGGCCGTGTGT
26153113 GACACACGG
1 GACACACGG
26153122 TCAGCCCCAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.19, C:0.23, G:0.36, T:0.22
Consensus pattern (30 bp):
GACACACGGGCATGTGTCTAGGCCGTGTGT
Found at i:26156616 original size:57 final size:55
Alignment explanation
Indices: 26156478--26156608 Score: 133
Period size: 56 Copynumber: 2.3 Consensus size: 55
26156468 CTCATTACAG
* * *
26156478 AAAGGATTTAGCCAT-GACGGGTAATCTTGATGCAAGTCCTCTCGAGCATATGATAG
1 AAAGGATTTAGCC-TGGAC-GGTAATCTAGATGCAAGTCCTCTAGAGCATATGATAA
** *
26156534 ATTGGATTTAGCCCGGACGGATAATCTAGAT-CAAGCTCCT-TAGAGCATATGTCATAA
1 AAAGGATTTAGCCTGGACGG-TAATCTAGATGCAAG-TCCTCTAGAGCATATG--ATAA
26156591 AAAGGATTTAGCCTGGAC
1 AAAGGATTTAGCCTGGAC
26156609 TAGTAATCCT
Statistics
Matches: 61, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
55 16 0.26
56 27 0.44
57 18 0.30
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (55 bp):
AAAGGATTTAGCCTGGACGGTAATCTAGATGCAAGTCCTCTAGAGCATATGATAA
Found at i:26157307 original size:16 final size:17
Alignment explanation
Indices: 26157275--26157307 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
26157265 GTTACACGAA
26157275 CTTACTTAGCATTTTATG
1 CTTACTTAG-ATTTTATG
26157293 CTTACTTAG-TTTTAT
1 CTTACTTAGATTTTAT
26157308 TTCCCTGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.21, C:0.15, G:0.09, T:0.55
Consensus pattern (17 bp):
CTTACTTAGATTTTATG
Found at i:26163572 original size:40 final size:40
Alignment explanation
Indices: 26163505--26163676 Score: 213
Period size: 40 Copynumber: 4.3 Consensus size: 40
26163495 ACCCAAGTAT
*
26163505 CTTCGGGAT-TTAGC-CGGATATAACAACTCGCACCAATGC
1 CTTCGGG-TCTTAGCTCGGATATAACAACTCGCACAAATGC
*
26163544 CTTCGGGTCTTAGCTCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCTCGGATATAACAACTCGCACAAATGC
* * * * *
26163584 CTTCGGGTCTTAGCCCGAATATAACCACTAGCATAAATGC
1 CTTCGGGTCTTAGCTCGGATATAACAACTCGCACAAATGC
* * * *
26163624 CTTCGGGACATAGCTCGGATATAGCAACTCGCACGAATGC
1 CTTCGGGTCTTAGCTCGGATATAACAACTCGCACAAATGC
*
26163664 CTTCGGATCTTAG
1 CTTCGGGTCTTAG
26163677 TCCGGTTATC
Statistics
Matches: 111, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
38 1 0.01
39 12 0.11
40 98 0.88
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CTTCGGGTCTTAGCTCGGATATAACAACTCGCACAAATGC
Found at i:26163638 original size:80 final size:79
Alignment explanation
Indices: 26163505--26163676 Score: 238
Period size: 80 Copynumber: 2.2 Consensus size: 79
26163495 ACCCAAGTAT
* * * * *
26163505 CTTCGGGAT-TTAGCCGGATATAACAACTCGCACCAATGCCTTCGGGTCTTAGCTCGGATATAGC
1 CTTCGGG-TCTTAGCCGAATATAACAACTAGCACAAATGCCTTCGGGACATAGCTCGGATATAGC
26163569 AACTCGCACAAATGC
65 AACTCGCACAAATGC
* *
26163584 CTTCGGGTCTTAGCCCGAATATAACCACTAGCATAAATGCCTTCGGGACATAGCTCGGATATAGC
1 CTTCGGGTCTTAG-CCGAATATAACAACTAGCACAAATGCCTTCGGGACATAGCTCGGATATAGC
*
26163649 AACTCGCACGAATGC
65 AACTCGCACAAATGC
*
26163664 CTTCGGATCTTAG
1 CTTCGGGTCTTAG
26163677 TCCGGTTATC
Statistics
Matches: 82, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
78 1 0.01
79 11 0.13
80 70 0.85
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (79 bp):
CTTCGGGTCTTAGCCGAATATAACAACTAGCACAAATGCCTTCGGGACATAGCTCGGATATAGCA
ACTCGCACAAATGC
Found at i:26168251 original size:43 final size:43
Alignment explanation
Indices: 26168186--26168268 Score: 123
Period size: 43 Copynumber: 1.9 Consensus size: 43
26168176 ATTAATTAAC
26168186 GATGCCAATGTCTCAAACATGGTCTTACACATAATCACATAAT
1 GATGCCAATGTCTCAAACATGGTCTTACACATAATCACATAAT
* * *
26168229 GATGCCAATGTC-CTAGATATGGTCTTACACATAATTACAT
1 GATGCCAATGTCTC-AAACATGGTCTTACACATAATCACAT
26168269 CTCGATAATC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 1 0.03
43 35 0.97
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (43 bp):
GATGCCAATGTCTCAAACATGGTCTTACACATAATCACATAAT
Done.