Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 186 of 210
Found at i:55035352 original size:50 final size:50
Alignment explanation
Indices: 55035226--55035620 Score: 233
Period size: 50 Copynumber: 7.9 Consensus size: 50
55035216 ATTACAGTGG
* * * **** * **
55035226 AAAATATTGAAGCCACAACGGTAAATCTTACTTCCCTGGTGGTGCAGTGG
1 AAAAGATTGAAGCCACAACGGTGAATCTTGCTTCCCTGACATTGCAATTA
* * * * *
55035276 AACAG-TTAAAGCTACAACAGTGAATCTTGCTTCCCTGACATTACAATTA
1 AAAAGATTGAAGCCACAACGGTGAATCTTGCTTCCCTGACATTGCAATTA
* ** * **
55035325 AAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCT-AGCGGTGCAGTGG
1 AAAAGATTGAAGCCACAACGGTGAATCTTGCTTCCCTGA-CATTGCAATTA
* * **
55035375 AAAAGATTGAAGCTACAATGGCAAATCTTGCTTACCC-GACATTGCAATTA
1 AAAAGATTGAAGCCACAACGGTGAATCTTGCTT-CCCTGACATTGCAATTA
* * ** * **
55035425 AAAAGATTGAAGCCGCAACGGTGAATCTTACTTCCCT-AGCGGTGCAGTGG
1 AAAAGATTGAAGCCACAACGGTGAATCTTGCTTCCCTGA-CATTGCAATTA
* * * * *
55035475 AACAGATTGAAGCTACAACAGTGAATCTTGATTCCCCGACATTGCAATTA
1 AAAAGATTGAAGCCACAACGGTGAATCTTGCTTCCCTGACATTGCAATTA
* * * ** * * * * **
55035525 AAAGGATTGAAGCCACCACAGAAAATCTTACTTCCCTGGCGA-TGTAGTGG
1 AAAAGATTGAAGCCACAACGGTGAATCTTGCTTCCCTGAC-ATTGCAATTA
* * * * * *
55035575 AACAGATTGAAGCTACGACGGCGAATCTTGTTTCCCCGACATTGCA
1 AAAAGATTGAAGCCACAACGGTGAATCTTGCTTCCCTGACATTGCA
55035621 GCTAAGCAGA
Statistics
Matches: 251, Mismatches: 85, Indels: 18
0.71 0.24 0.05
Matches are distributed among these distances:
49 41 0.16
50 204 0.81
51 6 0.02
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (50 bp):
AAAAGATTGAAGCCACAACGGTGAATCTTGCTTCCCTGACATTGCAATTA
Found at i:55035640 original size:100 final size:100
Alignment explanation
Indices: 55035226--55035620 Score: 540
Period size: 100 Copynumber: 4.0 Consensus size: 100
55035216 ATTACAGTGG
* * * *
55035226 AAAATATTGAAGCCACAACGGTAAATCTTACTTCCCTGGTGGTGCAGTGGAACAG-TTAAAGCTA
1 AAAAGATTGAAGCCACAACGGTAAATCTTACTTCCCTAGCGGTGCAGTGGAACAGATTGAAGCTA
* * *
55035290 CAACAGTGAATCTTGCTTCCCTGACATTACAATTA
66 CAACAGCGAATCTTGCTTCCCCGACATTGCAATTA
* *
55035325 AAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCTAGCGGTGCAGTGGAAAAGATTGAAGCTA
1 AAAAGATTGAAGCCACAACGGTAAATCTTACTTCCCTAGCGGTGCAGTGGAACAGATTGAAGCTA
** * *
55035390 CAATGGCAAATCTTGCTTACCCGACATTGCAATTA
66 CAACAGCGAATCTTGCTTCCCCGACATTGCAATTA
* *
55035425 AAAAGATTGAAGCCGCAACGGTGAATCTTACTTCCCTAGCGGTGCAGTGGAACAGATTGAAGCTA
1 AAAAGATTGAAGCCACAACGGTAAATCTTACTTCCCTAGCGGTGCAGTGGAACAGATTGAAGCTA
* *
55035490 CAACAGTGAATCTTGATTCCCCGACATTGCAATTA
66 CAACAGCGAATCTTGCTTCCCCGACATTGCAATTA
* * * * * * *
55035525 AAAGGATTGAAGCCACCACAGAAAATCTTACTTCCCTGGCGATGTAGTGGAACAGATTGAAGCTA
1 AAAAGATTGAAGCCACAACGGTAAATCTTACTTCCCTAGCGGTGCAGTGGAACAGATTGAAGCTA
* * *
55035590 CGACGGCGAATCTTGTTTCCCCGACATTGCA
66 CAACAGCGAATCTTGCTTCCCCGACATTGCA
55035621 GCTAAGCAGA
Statistics
Matches: 261, Mismatches: 34, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
99 50 0.19
100 211 0.81
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (100 bp):
AAAAGATTGAAGCCACAACGGTAAATCTTACTTCCCTAGCGGTGCAGTGGAACAGATTGAAGCTA
CAACAGCGAATCTTGCTTCCCCGACATTGCAATTA
Found at i:55035688 original size:44 final size:45
Alignment explanation
Indices: 55035639--55035756 Score: 143
Period size: 44 Copynumber: 2.6 Consensus size: 45
55035629 GATTAAAGCC
*
55035639 ACAAACCTTATCTCTCTAAAGTTGCAGT-AGATCAGGTTGAAG-TA
1 ACAAACCTTATCTCTCTGAAGTTGCAGTGAGAT-AGGTTGAAGATA
* *
55035683 ACAAACCTTATCCCTCTGAAGTTGCAGTGGGATAGGTTGAAGATA
1 ACAAACCTTATCTCTCTGAAGTTGCAGTGAGATAGGTTGAAGATA
* * *
55035728 GCTAATCC-TATCTCCCTGAAGTTGCAGTG
1 AC-AAACCTTATCTCTCTGAAGTTGCAGTG
55035757 GAGCGAATTA
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
44 35 0.55
45 25 0.39
46 4 0.06
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (45 bp):
ACAAACCTTATCTCTCTGAAGTTGCAGTGAGATAGGTTGAAGATA
Found at i:55036687 original size:20 final size:22
Alignment explanation
Indices: 55036633--55036680 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
55036623 TTTTACATTT
55036633 TTCGATTGGCTTTTTCTCTCGG
1 TTCGATTGGCTTTTTCTCTCGG
*
55036655 TTCGATTGGCTTTTTCTCTTGG
1 TTCGATTGGCTTTTTCTCTCGG
55036677 TTCG
1 TTCG
55036681 TTTCTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.04, C:0.21, G:0.23, T:0.52
Consensus pattern (22 bp):
TTCGATTGGCTTTTTCTCTCGG
Found at i:55037620 original size:34 final size:34
Alignment explanation
Indices: 55037546--55037636 Score: 123
Period size: 34 Copynumber: 2.7 Consensus size: 34
55037536 CATACATGCG
* * *
55037546 ATATATTTTTATAATTTAT-ATATATGTATATAC
1 ATATATTTTTATATTTTATAATTTATGTACATAC
*
55037579 A-AGTATTTTTATATTTTATAATTTATGTACATAT
1 ATA-TATTTTTATATTTTATAATTTATGTACATAC
55037613 ATATATTTTTATATTTTATAATTT
1 ATATATTTTTATATTTTATAATTT
55037637 TTATCTATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
32 1 0.02
33 16 0.31
34 33 0.65
35 1 0.02
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.58
Consensus pattern (34 bp):
ATATATTTTTATATTTTATAATTTATGTACATAC
Found at i:55037711 original size:3 final size:3
Alignment explanation
Indices: 55037703--55037742 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
55037693 TTACATGTCC
55037703 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
55037743 AATGCTTTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:55040125 original size:50 final size:48
Alignment explanation
Indices: 55039992--55040140 Score: 183
Period size: 47 Copynumber: 3.0 Consensus size: 48
55039982 GTGGAACTAT
* *
55039992 GTGGTAGTTTATCTACAAATTAGTGGTAGCTTGTCCATAAAGTGTTTCA
1 GTGGTAGTTTATCTACAAA-TAGTGGTGGCTTGTCCACAAAGTGTTTCA
* * *
55040041 GTGGTAGTATATCTGCATAT-GTGGTGGCTTGTCCACAAAGTGTTATCA
1 GTGGTAGTTTATCTACAAATAGTGGTGGCTTGTCCACAAAGTGTT-TCA
* *
55040089 GTGGCAGTTTATCTACAAATCAGTTGTGGCTTGTCCACAAATGGTGTTTCA
1 GTGGTAGTTTATCTACAAAT-AGTGGTGGCTTGTCCACAAA--GTGTTTCA
55040140 G
1 G
55040141 ATGGACAAGT
Statistics
Matches: 85, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
47 22 0.26
48 20 0.24
49 16 0.19
50 18 0.21
51 4 0.05
52 5 0.06
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.36
Consensus pattern (48 bp):
GTGGTAGTTTATCTACAAATAGTGGTGGCTTGTCCACAAAGTGTTTCA
Found at i:55061307 original size:20 final size:21
Alignment explanation
Indices: 55061277--55061317 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
55061267 AAATTTAATT
* *
55061277 TTTATGGTTGATGTTTTAAGG
1 TTTATGGTTGAGGGTTTAAGG
55061298 TTTA-GGTTGAGGGTTTAAGG
1 TTTATGGTTGAGGGTTTAAGG
55061318 ATTTGGGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.20, C:0.00, G:0.34, T:0.46
Consensus pattern (21 bp):
TTTATGGTTGAGGGTTTAAGG
Found at i:55061381 original size:15 final size:15
Alignment explanation
Indices: 55061307--55061384 Score: 56
Period size: 14 Copynumber: 5.4 Consensus size: 15
55061297 GTTTAGGTTG
55061307 AGGGTTTAAGGATTT
1 AGGGTTTAAGGATTT
*
55061322 -GGGATTT-AGGGTTT
1 AGGG-TTTAAGGATTT
* * **
55061336 -GAGTTTAAAGATCA
1 AGGGTTTAAGGATTT
* *
55061350 AGAGTTTGAGG-TTT
1 AGGGTTTAAGGATTT
55061364 AGGGTTTAAGGATTT
1 AGGGTTTAAGGATTT
55061379 AGGGTT
1 AGGGTT
55061385 ATGGGTTCGA
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
13 3 0.06
14 24 0.51
15 20 0.43
ACGTcount: A:0.26, C:0.01, G:0.35, T:0.38
Consensus pattern (15 bp):
AGGGTTTAAGGATTT
Found at i:55066664 original size:11 final size:11
Alignment explanation
Indices: 55066650--55066683 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
55066640 TCAATTATTT
55066650 TCTCAATTTCC
1 TCTCAATTTCC
* *
55066661 TCTCAAATTGC
1 TCTCAATTTCC
55066672 TCTCAATTTCC
1 TCTCAATTTCC
55066683 T
1 T
55066684 TCCAAATTTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.21, C:0.32, G:0.03, T:0.44
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:55066677 original size:22 final size:22
Alignment explanation
Indices: 55066650--55066699 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
55066640 TCAATTATTT
55066650 TCTCAATTTCC-TCTCAAATTGC
1 TCTCAATTTCCTTC-CAAATTGC
*
55066672 TCTCAATTTCCTTCCAAATTTC
1 TCTCAATTTCCTTCCAAATTGC
55066694 TCTCAA
1 TCTCAA
55066700 ATCCATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 24 0.92
23 2 0.08
ACGTcount: A:0.24, C:0.32, G:0.02, T:0.42
Consensus pattern (22 bp):
TCTCAATTTCCTTCCAAATTGC
Found at i:55066724 original size:51 final size:51
Alignment explanation
Indices: 55066661--55066760 Score: 141
Period size: 51 Copynumber: 2.0 Consensus size: 51
55066651 CTCAATTTCC
55066661 TCTCAAATTGCTCTCAATTTCCT-TCCAAATTTCTCTCAAATCCATATTTAA
1 TCTCAAATTGCTCTCAATTTCCTCT-CAAATTTCTCTCAAATCCATATTTAA
* * *
55066712 TCTC-AATCTGCTCTCAATTTCCTCTTAAATTTCTCTTAAATCCCTATTT
1 TCTCAAAT-TGCTCTCAATTTCCTCTCAAATTTCTCTCAAATCCATATTT
55066761 TTAATTATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
50 3 0.07
51 40 0.91
52 1 0.02
ACGTcount: A:0.26, C:0.28, G:0.02, T:0.44
Consensus pattern (51 bp):
TCTCAAATTGCTCTCAATTTCCTCTCAAATTTCTCTCAAATCCATATTTAA
Found at i:55067852 original size:78 final size:78
Alignment explanation
Indices: 55067738--55067890 Score: 281
Period size: 78 Copynumber: 2.0 Consensus size: 78
55067728 AATAATAGTA
55067738 TGCTAAAAATTTATTTAATTAGGTGGAACCATCCGGCAAGTTATGCTCT-ATTACCTACCTCTCT
1 TGCTAAAAATTTATTTAATTAGGTGGAACCATCCGGCAAGTTATGCT-TGATTACCTACCTCTCT
55067802 TGAAGATATACAGC
65 TGAAGATATACAGC
*
55067816 TGCTAAAAATTTATTTAATTAGGTGGAACCATCCGGCAAGTTATGCTTGATTACTTACCTCTCTT
1 TGCTAAAAATTTATTTAATTAGGTGGAACCATCCGGCAAGTTATGCTTGATTACCTACCTCTCTT
55067881 GAAGATATAC
66 GAAGATATAC
55067891 GGCTTCTATT
Statistics
Matches: 73, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
77 1 0.01
78 72 0.99
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.35
Consensus pattern (78 bp):
TGCTAAAAATTTATTTAATTAGGTGGAACCATCCGGCAAGTTATGCTTGATTACCTACCTCTCTT
GAAGATATACAGC
Found at i:55067982 original size:7 final size:7
Alignment explanation
Indices: 55067970--55067995 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
55067960 TAGTCGATTG
55067970 GTATTTA
1 GTATTTA
55067977 GTATTTA
1 GTATTTA
55067984 GTATTTA
1 GTATTTA
55067991 GTATT
1 GTATT
55067996 ATGTATTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:55068664 original size:18 final size:18
Alignment explanation
Indices: 55068641--55068683 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
55068631 TGCCAGGTGC
* *
55068641 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
*
55068659 GTATCCCAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
55068677 GTTTCCT
1 GTATCCT
55068684 TTTCCTAGTC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.19, C:0.30, G:0.09, T:0.42
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:55068970 original size:21 final size:21
Alignment explanation
Indices: 55068924--55068971 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
55068914 CCAACACCGA
*
55068924 CAACCAGATACCCTACTAGAG
1 CAACCAGATACCCCACTAGAG
* *
55068945 GAACCAGA-ATCCCCACTGGAG
1 CAACCAGATA-CCCCACTAGAG
55068966 CAACCA
1 CAACCA
55068972 CAACCCCCGC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.38, C:0.35, G:0.17, T:0.10
Consensus pattern (21 bp):
CAACCAGATACCCCACTAGAG
Found at i:55069198 original size:7 final size:7
Alignment explanation
Indices: 55069178--55069217 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
55069168 ATTTATTAAA
55069178 AATTTAT
1 AATTTAT
55069185 AATTTTAT
1 AA-TTTAT
55069193 AATTTAT
1 AATTTAT
55069200 AA-TT-T
1 AATTTAT
55069205 AATTTAT
1 AATTTAT
55069212 AATTTA
1 AATTTA
55069218 ATTGACAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 3 0.10
6 4 0.13
7 16 0.53
8 7 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
AATTTAT
Found at i:55069209 original size:12 final size:12
Alignment explanation
Indices: 55069178--55069220 Score: 59
Period size: 12 Copynumber: 3.3 Consensus size: 12
55069168 ATTTATTAAA
55069178 AATTTATAATTTTAT
1 AATTTATAA--TT-T
55069193 AATTTATAATTT
1 AATTTATAATTT
55069205 AATTTATAATTT
1 AATTTATAATTT
55069217 AATT
1 AATT
55069221 GACAAACCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 17 0.61
13 2 0.07
15 9 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
AATTTATAATTT
Found at i:55069278 original size:27 final size:27
Alignment explanation
Indices: 55069243--55069302 Score: 120
Period size: 27 Copynumber: 2.2 Consensus size: 27
55069233 CAAAAACCCT
55069243 AACCCTAACCCTAACCTTTAACTTAAA
1 AACCCTAACCCTAACCTTTAACTTAAA
55069270 AACCCTAACCCTAACCTTTAACTTAAA
1 AACCCTAACCCTAACCTTTAACTTAAA
55069297 AACCCT
1 AACCCT
55069303 TAACTTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.40, C:0.35, G:0.00, T:0.25
Consensus pattern (27 bp):
AACCCTAACCCTAACCTTTAACTTAAA
Found at i:55069313 original size:16 final size:15
Alignment explanation
Indices: 55069282--55069314 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
55069272 CCCTAACCCT
*
55069282 AACCTTTAACTTAAA
1 AACCCTTAACTTAAA
55069297 AACCCTTAACTTAAA
1 AACCCTTAACTTAAA
55069312 AAC
1 AAC
55069315 ACCAAAACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.27
Consensus pattern (15 bp):
AACCCTTAACTTAAA
Found at i:55069353 original size:21 final size:21
Alignment explanation
Indices: 55069299--55069362 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
55069289 AACTTAAAAA
* *
55069299 CCCTTAACTTAAAAACACCAAAA
1 CCCTTAACTTAAAAAC-CC-TAG
55069322 CCC-TAAC--AAAAACCCTAG
1 CCCTTAACTTAAAAACCCTAG
55069340 CCCTTAACTTAAAAACCCTAG
1 CCCTTAACTTAAAAACCCTAG
55069361 CC
1 CC
55069363 ATAACCCTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
18 4 0.11
19 6 0.17
20 6 0.17
21 13 0.36
22 4 0.11
23 3 0.08
ACGTcount: A:0.44, C:0.36, G:0.03, T:0.17
Consensus pattern (21 bp):
CCCTTAACTTAAAAACCCTAG
Found at i:55069359 original size:33 final size:33
Alignment explanation
Indices: 55069318--55069394 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 33
55069308 TAAAAACACC
* *
55069318 AAAACCCTAACAAAAACCCTAGCCCTTAACTTA
1 AAAACCCTAACAAAAACCCTAACACTTAACTTA
* * * * *
55069351 AAAACCCTAGCCATAACCCTAACATTTAACTTC
1 AAAACCCTAACAAAAACCCTAACACTTAACTTA
55069384 AAAACCCTAAC
1 AAAACCCTAAC
55069395 CCTAACCCTT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.34, G:0.03, T:0.19
Consensus pattern (33 bp):
AAAACCCTAACAAAAACCCTAACACTTAACTTA
Found at i:55069367 original size:20 final size:21
Alignment explanation
Indices: 55069329--55069367 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
55069319 AAACCCTAAC
*
55069329 AAAAACCCTAGCCCTTAACTT
1 AAAAACCCTAGCCCATAACTT
55069350 AAAAACCCTAG-CCATAAC
1 AAAAACCCTAGCCCATAAC
55069368 CCTAACATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.44, C:0.33, G:0.05, T:0.18
Consensus pattern (21 bp):
AAAAACCCTAGCCCATAACTT
Found at i:55069394 original size:27 final size:27
Alignment explanation
Indices: 55069364--55069415 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
55069354 ACCCTAGCCA
* *
55069364 TAACCCTAACATTTAACTTCAAAACCC
1 TAACCCTAACACTTAACTTAAAAACCC
*
55069391 TAACCCTAACCCTTAACTTAAAAAC
1 TAACCCTAACACTTAACTTAAAAAC
55069416 ACCAAAACCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.42, C:0.33, G:0.00, T:0.25
Consensus pattern (27 bp):
TAACCCTAACACTTAACTTAAAAACCC
Found at i:55069449 original size:6 final size:6
Alignment explanation
Indices: 55069438--55069469 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
55069428 ATGCTAACAA
*
55069438 AACCCT AACCCT AACCTT AACCCT AACCCT AA
1 AACCCT AACCCT AACCCT AACCCT AACCCT AA
55069470 TCTGATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.38, C:0.44, G:0.00, T:0.19
Consensus pattern (6 bp):
AACCCT
Found at i:55069523 original size:35 final size:36
Alignment explanation
Indices: 55069484--55069645 Score: 114
Period size: 35 Copynumber: 4.4 Consensus size: 36
55069474 ATATAATTTG
55069484 ATAATTTTACTAACAATTAATACAATTA-ACAATTA
1 ATAATTTTACTAACAATTAATACAATTACACAATTA
* * ** * * * *
55069519 ATAATTTGACTAACAAAATGTTAGATTTTACAAAATGTT
1 ATAATTTTACTAAC-AATTAATACA-ATTACACAAT-TA
* * * * * * * *
55069558 TTGACTGTACTAACAATTAATA-ATTTGATATAATTTG
1 ATAATTTTACTAACAATTAATACAATT-ACACAA-TTA
55069595 ATAATTTTACTAACAATTAATACAATTA-ACAATTA
1 ATAATTTTACTAACAATTAATACAATTACACAATTA
55069630 ATAATTTTACTAACAA
1 ATAATTTTACTAACAA
55069646 AATGTTAGAT
Statistics
Matches: 94, Mismatches: 26, Indels: 14
0.70 0.19 0.10
Matches are distributed among these distances:
35 31 0.33
36 12 0.13
37 28 0.30
38 13 0.14
39 10 0.11
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (36 bp):
ATAATTTTACTAACAATTAATACAATTACACAATTA
Found at i:55069615 original size:111 final size:112
Alignment explanation
Indices: 55069467--55069705 Score: 401
Period size: 111 Copynumber: 2.1 Consensus size: 112
55069457 ACCCTAACCC
*
55069467 TAATCTGATATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATAATTTGACTAA
1 TAATTTGATATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATAATTTGACTAA
* *
55069532 CAAAATGTTAGATTTTACAAAATGTTTTGACT-GTACTAACAAT-TAA
66 CAAAATGTTAGATTTTACAAAATGTTTTGACTGGTACAAAAAATAT-A
*
55069578 TAATTTGATATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATAATTTTACTAA
1 TAATTTGATATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATAATTTGACTAA
* *
55069643 CAAAATGTTAGATTTTACAAAATGTTTTTATTGGTACAAAAAATATA
66 CAAAATGTTAGATTTTACAAAATGTTTTGACTGGTACAAAAAATATA
55069690 TAATTTGATATAATTT
1 TAATTTGATATAATTT
55069706 TAATAACAAT
Statistics
Matches: 120, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
111 93 0.77
112 26 0.22
113 1 0.01
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41
Consensus pattern (112 bp):
TAATTTGATATAATTTGATAATTTTACTAACAATTAATACAATTAACAATTAATAATTTGACTAA
CAAAATGTTAGATTTTACAAAATGTTTTGACTGGTACAAAAAATATA
Found at i:55069719 original size:16 final size:16
Alignment explanation
Indices: 55069700--55069741 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
55069690 TAATTTGATA
55069700 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
55069716 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
55069732 TAGTTTTAAT
1 TAATTTTAAT
55069742 TTTAATAACC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:55086880 original size:28 final size:28
Alignment explanation
Indices: 55086847--55086907 Score: 122
Period size: 28 Copynumber: 2.2 Consensus size: 28
55086837 AATCCTATAA
55086847 AAGTTGAATTTCTAGTCTGCACATGATT
1 AAGTTGAATTTCTAGTCTGCACATGATT
55086875 AAGTTGAATTTCTAGTCTGCACATGATT
1 AAGTTGAATTTCTAGTCTGCACATGATT
55086903 AAGTT
1 AAGTT
55086908 TGTTGATCGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.39
Consensus pattern (28 bp):
AAGTTGAATTTCTAGTCTGCACATGATT
Found at i:55088805 original size:6 final size:6
Alignment explanation
Indices: 55088794--55088819 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
55088784 CTCGGCTCTG
55088794 GGTACT GGTACT GGTACT GGTACT GG
1 GGTACT GGTACT GGTACT GGTACT GG
55088820 ATACCCACTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.38, T:0.31
Consensus pattern (6 bp):
GGTACT
Found at i:55091777 original size:51 final size:50
Alignment explanation
Indices: 55091731--55091830 Score: 121
Period size: 53 Copynumber: 1.9 Consensus size: 50
55091721 TACAAATTTC
**
55091731 ACAAAAAATATAAGATATATAACTAAGCTTTAAAAAAGA-TTCACAAAAATGAT
1 ACAAAAAATATAAGATATATAACTAA-CGAT-AAAAAGATTTCAC--AAATGAT
* *
55091784 ACAAAAATTATAAGATTTATAACTAACGATAAAAAGATTTCACAAAT
1 ACAAAAAATATAAGATATATAACTAACGATAAAAAGATTTCACAAAT
55091831 ATATAAGACT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
50 4 0.10
51 7 0.17
52 7 0.17
53 24 0.57
ACGTcount: A:0.57, C:0.10, G:0.07, T:0.26
Consensus pattern (50 bp):
ACAAAAAATATAAGATATATAACTAACGATAAAAAGATTTCACAAATGAT
Found at i:55091798 original size:92 final size:92
Alignment explanation
Indices: 55091673--55091873 Score: 268
Period size: 92 Copynumber: 2.2 Consensus size: 92
55091663 CTAACACTAT
* * * *
55091673 AAAATATTCAC-AAAATGAAACAAAAATTATAAGATTTGTAACTAATAAT-ACAA-ATTTCACAA
1 AAAAGATTCACAAAAATGAAACAAAAATTATAAGATTTATAACTAACAATAAAAAGATTTCAC-A
55091735 AAAATATAAGA-TATATAACT-AAGCTTTAA
65 AAAATATAAGACT-TATAA-TGAAGC-TTAA
* *
55091764 AAAAGATTCACAAAAATGATACAAAAATTATAAGATTTATAACTAACGATAAAAAGATTTCACAA
1 AAAAGATTCACAAAAATGAAACAAAAATTATAAGATTTATAACTAACAATAAAAAGATTTCACAA
*
55091829 ATATATAAGACTTATAATGAAGCTTAA
66 AAATATAAGACTTATAATGAAGCTTAA
55091856 AAAAGATTCACAAAAATG
1 AAAAGATTCACAAAAATG
55091874 CCAACAAGCT
Statistics
Matches: 98, Mismatches: 7, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
91 10 0.10
92 57 0.58
93 23 0.23
94 8 0.08
ACGTcount: A:0.56, C:0.10, G:0.07, T:0.27
Consensus pattern (92 bp):
AAAAGATTCACAAAAATGAAACAAAAATTATAAGATTTATAACTAACAATAAAAAGATTTCACAA
AAATATAAGACTTATAATGAAGCTTAA
Found at i:55094917 original size:31 final size:28
Alignment explanation
Indices: 55094854--55094909 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
55094844 ATAAAACAAG
55094854 ACATACCTCTCTTGAACAAAGCTAAGTT
1 ACATACCTCTCTTGAACAAAGCTAAGTT
*
55094882 ACATACCTCTCTTGAGCAAAGCTAAGTT
1 ACATACCTCTCTTGAACAAAGCTAAGTT
55094910 GTTACATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.34, C:0.25, G:0.12, T:0.29
Consensus pattern (28 bp):
ACATACCTCTCTTGAACAAAGCTAAGTT
Found at i:55100560 original size:3 final size:3
Alignment explanation
Indices: 55100552--55100590 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
55100542 TCTTAATCAG
55100552 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
55100591 CATCATCATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:55100595 original size:3 final size:3
Alignment explanation
Indices: 55100589--55100620 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
55100579 TATTATTATT
55100589 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
55100621 TTTAATACTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:55101916 original size:138 final size:138
Alignment explanation
Indices: 55101721--55102115 Score: 598
Period size: 138 Copynumber: 2.9 Consensus size: 138
55101711 TAGAAAAAGG
* * ** *
55101721 AATTATATTCTTTCCAAGAGAATACTAATTTAAATGTCTTTTATATTTTGACTAAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCAAAATTAATTAA
* * * *
55101786 TATAATTATTTATATTAAAAAATTCGGTAAAATATAAACAGTTAATATTTTGTATAAATCAAATT
66 TATAATTATTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATAAATCAAATT
*
55101851 CATATGTT
131 CATATATT
*
55101859 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTTACCAAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCAAAATTAATTAA
* *
55101924 TATAATTATTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGCATGAATCAAATT
66 TATAATTATTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATAAATCAAATT
55101989 CATATATT
131 CATATATT
* *
55101997 AATTATATTCTTT---AAAGAATATTAATTTTCATATCTTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCAAAATTAATTAA
*** *
55102059 TATAACCGTTTATATTAATAAATTTAGTAAAATATATACAATTAATATTTTGTATAA
66 TATAATTATTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATAA
55102116 CTTTGTCAAA
Statistics
Matches: 235, Mismatches: 22, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
135 97 0.41
138 138 0.59
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.45
Consensus pattern (138 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCAAAATTAATTAA
TATAATTATTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATAAATCAAATT
CATATATT
Found at i:55102062 original size:68 final size:68
Alignment explanation
Indices: 55101847--55102062 Score: 147
Period size: 68 Copynumber: 3.1 Consensus size: 68
55101837 GTATAAATCA
* * * *
55101847 AATTCATATGTTAATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTTACC
1 AATTAATATATTAATTATATTCTTT---AAAGAATATTAATTTTCATATCTTTTATATTTTGACC
*
55101912 AAAATT
63 GAAATT
* ** ** ** ** * *
55101918 AATTAATATAATTATTTATATT-AATAAA-TTTGGTAA-AAT-ATATACAATTAATATTTTG-CA
1 AATTAATAT-ATTAATTATATTCTTTAAAGAATATTAATTTTCATAT-C-TTTTATATTTTGAC-
* *
55101978 TG-AATCA
62 CGAAAT-T
*
55101985 AATTCATATATTAATTATATTCTTTAAAGAATATTAATTTTCATATCTTTTATATTTTGACCGAA
1 AATTAATATATTAATTATATTCTTTAAAGAATATTAATTTTCATATCTTTTATATTTTGACCGAA
55102050 ATT
66 ATT
55102053 AATTAATATA
1 AATTAATATA
55102063 ACCGTTTATA
Statistics
Matches: 101, Mismatches: 33, Indels: 25
0.64 0.21 0.16
Matches are distributed among these distances:
65 3 0.03
66 17 0.17
67 25 0.25
68 27 0.27
69 6 0.06
70 4 0.04
71 9 0.09
72 10 0.10
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.47
Consensus pattern (68 bp):
AATTAATATATTAATTATATTCTTTAAAGAATATTAATTTTCATATCTTTTATATTTTGACCGAA
ATT
Found at i:55117486 original size:18 final size:19
Alignment explanation
Indices: 55117439--55117488 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
55117429 TGTTTTATAA
*
55117439 TTTAATAATCTTTTACAATT
1 TTTAATAA-ATTTTACAATT
55117459 TTTAATAAATTTTA-AATAT
1 TTTAATAAATTTTACAAT-T
55117478 TTT-ATAAATTT
1 TTTAATAAATTT
55117489 AAAAATTATG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 11 0.39
19 9 0.32
20 8 0.29
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTAATAAATTTTACAATT
Found at i:55117657 original size:21 final size:19
Alignment explanation
Indices: 55117615--55117651 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
55117605 TATTCCTCGT
55117615 TTTCTATATATATTTTTAA
1 TTTCTATATATATTTTTAA
*
55117634 TTTCTATATATTTTTTTA
1 TTTCTATATATATTTTTA
55117652 TAATTTAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTCTATATATATTTTTAA
Found at i:55118189 original size:40 final size:41
Alignment explanation
Indices: 55118115--55118197 Score: 116
Period size: 40 Copynumber: 2.0 Consensus size: 41
55118105 TATTTAGTAA
* **
55118115 AATAAAATTTTTATTATATTTATTTGTGT-TTTTTTAATAT
1 AATAAAATATTTATTATATTTATAGGTGTGTTTTTTAATAT
55118155 AATAAAATATTTATTATATTTA-AGGTAGTGTTTTTTAATAT
1 AATAAAATATTTATTATATTTATAGGT-GTGTTTTTTAATAT
55118196 AA
1 AA
55118198 ATATTTTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
39 2 0.05
40 23 0.61
41 13 0.34
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.55
Consensus pattern (41 bp):
AATAAAATATTTATTATATTTATAGGTGTGTTTTTTAATAT
Found at i:55120789 original size:9 final size:9
Alignment explanation
Indices: 55120775--55120812 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
55120765 GATAGTTTGA
55120775 TATTCGAAT
1 TATTCGAAT
55120784 TATTCGAAT
1 TATTCGAAT
*
55120793 TATTCGAGT
1 TATTCGAAT
*
55120802 TATTCAAAT
1 TATTCGAAT
55120811 TA
1 TA
55120813 AAAAACTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.45
Consensus pattern (9 bp):
TATTCGAAT
Found at i:55120883 original size:9 final size:9
Alignment explanation
Indices: 55120869--55120914 Score: 74
Period size: 9 Copynumber: 5.1 Consensus size: 9
55120859 TTGATTAGAA
55120869 TAACTCGAT
1 TAACTCGAT
*
55120878 TAACTCGAA
1 TAACTCGAT
55120887 TAACTCGAT
1 TAACTCGAT
*
55120896 TAACTCGAA
1 TAACTCGAT
55120905 TAACTCGAT
1 TAACTCGAT
55120914 T
1 T
55120915 TGTTTAACTC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (9 bp):
TAACTCGAT
Found at i:55120889 original size:18 final size:18
Alignment explanation
Indices: 55120866--55120914 Score: 98
Period size: 18 Copynumber: 2.7 Consensus size: 18
55120856 GAGTTGATTA
55120866 GAATAACTCGATTAACTC
1 GAATAACTCGATTAACTC
55120884 GAATAACTCGATTAACTC
1 GAATAACTCGATTAACTC
55120902 GAATAACTCGATT
1 GAATAACTCGATT
55120915 TGTTTAACTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (18 bp):
GAATAACTCGATTAACTC
Found at i:55121113 original size:13 final size:13
Alignment explanation
Indices: 55121095--55121119 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55121085 TTTTATTTGT
55121095 TTATTCCCACCGA
1 TTATTCCCACCGA
55121108 TTATTCCCACCG
1 TTATTCCCACCG
55121120 GCCGAATGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.40, G:0.08, T:0.32
Consensus pattern (13 bp):
TTATTCCCACCGA
Found at i:55122676 original size:12 final size:12
Alignment explanation
Indices: 55122659--55122692 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
55122649 GTTCTTTCTT
55122659 TTCTTTTGCTCG
1 TTCTTTTGCTCG
55122671 TTCTTTTGCTCG
1 TTCTTTTGCTCG
55122683 TTCTTTTGCT
1 TTCTTTTGCT
55122693 TAAAATGCGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.24, G:0.15, T:0.62
Consensus pattern (12 bp):
TTCTTTTGCTCG
Found at i:55123176 original size:32 final size:32
Alignment explanation
Indices: 55123131--55123214 Score: 141
Period size: 32 Copynumber: 2.6 Consensus size: 32
55123121 TTACGAGACT
*
55123131 TATACAACGCATTAATTAAATGTGTATATTCA
1 TATACAACTCATTAATTAAATGTGTATATTCA
55123163 TATACAACTCATTAATTAAATGTGTATATTCA
1 TATACAACTCATTAATTAAATGTGTATATTCA
* *
55123195 TATACTACTTATTAATTAAA
1 TATACAACTCATTAATTAAA
55123215 AATATTTCTA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.40
Consensus pattern (32 bp):
TATACAACTCATTAATTAAATGTGTATATTCA
Found at i:55123397 original size:64 final size:64
Alignment explanation
Indices: 55123329--55123606 Score: 474
Period size: 64 Copynumber: 4.4 Consensus size: 64
55123319 AAATAAAATA
*
55123329 AAAATTGGATCATTACATATAATCAAGTAAACAAATTGATTAAAAAACATATGGATAATATATT
1 AAAATTGGATCATTAGATATAATCAAGTAAACAAATTGATTAAAAAACATATGGATAATATATT
*
55123393 AAAATTGGATCATTACATATAATCAAGTAAACAAATTGATTAAAAAACATATGGATAATATATT
1 AAAATTGGATCATTAGATATAATCAAGTAAACAAATTGATTAAAAAACATATGGATAATATATT
* * *
55123457 AAAATTGAATAATTAGATATAATCAAGTAAACAACTTGATTAAAAAACATATGGATAATATATT
1 AAAATTGGATCATTAGATATAATCAAGTAAACAAATTGATTAAAAAACATATGGATAATATATT
*
55123521 --AATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACATATGGATAATATATT
1 AAAATTGGATCATTAGATATAATCAAGTAAACAAATTGATTAAAAAACATATGGATAATATATT
55123583 --AATTGGATCATTAGATATAATCAA
1 AAAATTGGATCATTAGATATAATCAA
55123607 CTTGATTCTA
Statistics
Matches: 208, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
62 84 0.40
64 124 0.60
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.32
Consensus pattern (64 bp):
AAAATTGGATCATTAGATATAATCAAGTAAACAAATTGATTAAAAAACATATGGATAATATATT
Found at i:55123578 original size:126 final size:127
Alignment explanation
Indices: 55123329--55123606 Score: 472
Period size: 126 Copynumber: 2.2 Consensus size: 127
55123319 AAATAAAATA
*
55123329 AAAATTGGATCATTACATATAATCAAGTAAACAAATTGATTAAAAAACATATGGATAATATATTA
1 AAAATTGGATCATTAGATATAATCAAGTAAACAAATTGATTAAAAAACATATGGATAATATATT-
55123394 AAATTGGATCATTACATATAATCAAGTAAACAAATTGATTAAAAAACATATGGATAATATATT
65 AAATTGGATCATTACATATAATCAAGTAAACAAATTGATTAAAAAACATATGGATAATATATT
* * *
55123457 AAAATTGAATAATTAGATATAATCAAGTAAACAACTTGATTAAAAAACATATGGATAATATATT-
1 AAAATTGGATCATTAGATATAATCAAGTAAACAAATTGATTAAAAAACATATGGATAATATATTA
* *
55123521 AATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACATATGGATAATATATT
66 AATTGGATCATTACATATAATCAAGTAAACAAATTGATTAAAAAACATATGGATAATATATT
55123583 --AATTGGATCATTAGATATAATCAA
1 AAAATTGGATCATTAGATATAATCAA
55123607 CTTGATTCTA
Statistics
Matches: 142, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
124 22 0.15
126 60 0.42
128 60 0.42
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.32
Consensus pattern (127 bp):
AAAATTGGATCATTAGATATAATCAAGTAAACAAATTGATTAAAAAACATATGGATAATATATTA
AATTGGATCATTACATATAATCAAGTAAACAAATTGATTAAAAAACATATGGATAATATATT
Found at i:55123937 original size:44 final size:41
Alignment explanation
Indices: 55123889--55123997 Score: 98
Period size: 44 Copynumber: 2.6 Consensus size: 41
55123879 AGTATTATAT
55123889 ATTATGATTTTAGTAAATTCATATAAGAATAAGAATT-TTATTAA
1 ATTAT-ATTTTAGTAAATT-ATAT-AGAATAAGAATTATT-TTAA
* ** *
55123933 ATTATATATTATTATTAAATTATATTTAATAATAATTATTTTAA
1 A-T-TATATT-TTAGTAAATTATATAGAATAAGAATTATTTTAA
55123977 ATTATATTTTAGT--ATTATATA
1 ATTATATTTTAGTAAATTATATA
55123998 TTATGATTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
39 7 0.13
41 4 0.07
42 6 0.11
43 1 0.02
44 15 0.27
45 10 0.18
46 12 0.22
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.50
Consensus pattern (41 bp):
ATTATATTTTAGTAAATTATATAGAATAAGAATTATTTTAA
Found at i:55123976 original size:26 final size:28
Alignment explanation
Indices: 55123922--55123985 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
55123912 TAAGAATAAG
* * *
55123922 AATTTTATTAAATTATATATTATTATTA
1 AATTATATTTAATAATATATTATTATTA
55123950 AATTATATTTAATAATA-ATTATT-TTA
1 AATTATATTTAATAATATATTATTATTA
55123976 AATTATATTT
1 AATTATATTT
55123986 TAGTATTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 13 0.39
27 6 0.18
28 14 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
AATTATATTTAATAATATATTATTATTA
Found at i:55124055 original size:108 final size:106
Alignment explanation
Indices: 55123835--55124077 Score: 310
Period size: 100 Copynumber: 2.3 Consensus size: 106
55123825 AATAAAGTAG
55123835 ATTA-TAAATTATATTTAATAATAATTATTTAAATTATATTTTATAGTATTATATATTATGATTT
1 ATTATTAAATTATATTTAATAATAATTATTTAAATTATATTTTATAGTATTATATATTATGATTT
55123899 TAGTAAATTCATATAAGAATAAGAATTTTATTAAATTATATATT
66 TAGTAAATTCATATAAGAAT---AATTTTATTAAATTATATATT
55123943 ATTATTAAATTATATTTAATAATAATTATTTTAAATTATA-TTT-TAGTATTATATATTATGATT
1 ATTATTAAATTATATTTAATAATAATTA-TTTAAATTATATTTTATAGTATTATATATTATGA--
*
55124006 TTATTAGTAAATTCATATAAGAAT-A-TTTATT--A--ACA-ATT
63 TT-TTAGTAAATTCATATAAGAATAATTTTATTAAATTATATATT
* *
55124044 -TTATTAAATTATATTTTATAACAATTATGTTAAA
1 ATTATTAAATTATATTTAATAATAATTAT-TTAAA
55124078 ATATGATTAA
Statistics
Matches: 126, Mismatches: 3, Indels: 20
0.85 0.02 0.13
Matches are distributed among these distances:
99 1 0.01
100 30 0.24
101 3 0.02
102 2 0.02
104 1 0.01
106 6 0.05
107 1 0.01
108 22 0.17
109 26 0.21
110 13 0.10
111 21 0.17
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.51
Consensus pattern (106 bp):
ATTATTAAATTATATTTAATAATAATTATTTAAATTATATTTTATAGTATTATATATTATGATTT
TAGTAAATTCATATAAGAATAATTTTATTAAATTATATATT
Found at i:55124081 original size:24 final size:25
Alignment explanation
Indices: 55124027--55124081 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
55124017 TTCATATAAG
*
55124027 AATA-TTTATTAACAATTTTATTAA
1 AATATTTTATTAACAATTATATTAA
*
55124051 ATTATATTTTA-TAACAATTATGTTAA
1 A--ATATTTTATTAACAATTATATTAA
55124077 AATAT
1 AATAT
55124082 GATTAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
24 5 0.19
26 17 0.65
27 4 0.15
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (25 bp):
AATATTTTATTAACAATTATATTAA
Found at i:55124291 original size:44 final size:46
Alignment explanation
Indices: 55124228--55124318 Score: 141
Period size: 46 Copynumber: 2.0 Consensus size: 46
55124218 ACATCTATTC
* * *
55124228 CATTCAACCAAATACAAGAA-TACC-ATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATTACCTATTAAGCCTCTATTCCATTA
55124272 CATTCAACCAAACAAAAGAATTACCTATTAAGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATTACCTATTAAGCCTCTATTCCATTA
55124318 C
1 C
55124319 GCCTCTATTC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
44 18 0.43
45 4 0.10
46 20 0.48
ACGTcount: A:0.40, C:0.29, G:0.04, T:0.27
Consensus pattern (46 bp):
CATTCAACCAAACAAAAGAATTACCTATTAAGCCTCTATTCCATTA
Found at i:55124322 original size:16 final size:16
Alignment explanation
Indices: 55124298--55124334 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
55124288 AGAATTACCT
*
55124298 ATTAAGCCTCTATTCC
1 ATTACGCCTCTATTCC
55124314 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
55124330 ATTAC
1 ATTAC
55124335 AGCGAACCAA
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:0.24, C:0.32, G:0.05, T:0.38
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:55130489 original size:15 final size:16
Alignment explanation
Indices: 55130463--55130493 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
55130453 TATCGATACT
55130463 AATCGAGCTAAGACTC
1 AATCGAGCTAAGACTC
55130479 AATCG-GCTAAGACTC
1 AATCGAGCTAAGACTC
55130494 TTTGAATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (16 bp):
AATCGAGCTAAGACTC
Found at i:55132209 original size:52 final size:52
Alignment explanation
Indices: 55132123--55132223 Score: 139
Period size: 52 Copynumber: 1.9 Consensus size: 52
55132113 AGGTGTAAAA
* * * ** *
55132123 ACATAATGCATGAAATACAACAAAGGTTGGGCCTGTTTTTGCCCCTATGCGT
1 ACATAACGCATGAAATACAACAAAAGCTAAGCCTGTTTCTGCCCCTATGCGT
*
55132175 ACATAACGCATGAAATACAACAAAAGCTAAGCCTGTTTCTGTCCCTATG
1 ACATAACGCATGAAATACAACAAAAGCTAAGCCTGTTTCTGCCCCTATG
55132224 TGTAGGCCTA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 42 1.00
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.27
Consensus pattern (52 bp):
ACATAACGCATGAAATACAACAAAAGCTAAGCCTGTTTCTGCCCCTATGCGT
Found at i:55136612 original size:16 final size:16
Alignment explanation
Indices: 55136591--55136678 Score: 110
Period size: 15 Copynumber: 5.7 Consensus size: 16
55136581 ATTATTTGTT
*
55136591 TAACCTTTTTAATCAA
1 TAACCTTTTCAATCAA
*
55136607 TAACCTTTTCAATTAA
1 TAACCTTTTCAATCAA
*
55136623 TAACCTTTTC-ATCGA
1 TAACCTTTTCAATCAA
*
55136638 TAGCCTTTTCAA-CAA
1 TAACCTTTTCAATCAA
*
55136653 TAACCTTTTCAAT-GA
1 TAACCTTTTCAATCAA
55136668 TAACCTTTTCA
1 TAACCTTTTCA
55136679 CGGATAACCT
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
15 37 0.60
16 25 0.40
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.41
Consensus pattern (16 bp):
TAACCTTTTCAATCAA
Found at i:55136646 original size:15 final size:15
Alignment explanation
Indices: 55136591--55136695 Score: 97
Period size: 15 Copynumber: 6.9 Consensus size: 15
55136581 ATTATTTGTT
* *
55136591 TAACCTTTTTAATCAA
1 TAACC-TTTTCATCGA
**
55136607 TAACCTTTTCAATTAA
1 TAACCTTTTC-ATCGA
55136623 TAACCTTTTCATCGA
1 TAACCTTTTCATCGA
* * *
55136638 TAGCCTTTTCAACAA
1 TAACCTTTTCATCGA
55136653 TAACCTTTTCAAT-GA
1 TAACCTTTTC-ATCGA
55136668 TAACCTTTTCA-CGGA
1 TAACCTTTTCATC-GA
55136683 TAACCTTTTCATC
1 TAACCTTTTCATC
55136696 ATTTTCATTG
Statistics
Matches: 74, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
14 1 0.01
15 52 0.70
16 21 0.28
ACGTcount: A:0.31, C:0.24, G:0.05, T:0.40
Consensus pattern (15 bp):
TAACCTTTTCATCGA
Found at i:55136657 original size:30 final size:30
Alignment explanation
Indices: 55136591--55136695 Score: 115
Period size: 30 Copynumber: 3.4 Consensus size: 30
55136581 ATTATTTGTT
* * *
55136591 TAACCTTTTTAATCAATAACCTTTTCAATTAA
1 TAACC-TTTTCATCGATAACCTTTTCAA-CAA
*
55136623 TAACCTTTTCATCGATAGCCTTTTCAACAA
1 TAACCTTTTCATCGATAACCTTTTCAACAA
*
55136653 TAACCTTTTCAAT-GATAACCTTTTC-ACGGA
1 TAACCTTTTC-ATCGATAACCTTTTCAAC-AA
55136683 TAACCTTTTCATC
1 TAACCTTTTCATC
55136696 ATTTTCATTG
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
29 4 0.06
30 34 0.53
31 21 0.33
32 5 0.08
ACGTcount: A:0.31, C:0.24, G:0.05, T:0.40
Consensus pattern (30 bp):
TAACCTTTTCATCGATAACCTTTTCAACAA
Found at i:55139317 original size:2 final size:2
Alignment explanation
Indices: 55139310--55139342 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
55139300 CTTAAAATTG
55139310 AT AT AT AT AT AT AT 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 A
55139343 NNNNNNNNNN
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55141829 original size:26 final size:27
Alignment explanation
Indices: 55141796--55141846 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
55141786 TCTCTATATG
55141796 AATTATTTATATATAAAT-TCCCTATT
1 AATTATTTATATATAAATCTCCCTATT
*
55141822 AATTATTTATATGTAAATCTCCCTA
1 AATTATTTATATATAAATCTCCCTA
55141847 AATAGAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 17 0.74
27 6 0.26
ACGTcount: A:0.37, C:0.14, G:0.02, T:0.47
Consensus pattern (27 bp):
AATTATTTATATATAAATCTCCCTATT
Found at i:55143554 original size:18 final size:18
Alignment explanation
Indices: 55143531--55143565 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
55143521 AAAAATAAAT
*
55143531 AAATATGTATATATATAA
1 AAATATGTACATATATAA
55143549 AAATATGTACATATATA
1 AAATATGTACATATATA
55143566 TAGGTGTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.37
Consensus pattern (18 bp):
AAATATGTACATATATAA
Found at i:55144026 original size:3 final size:3
Alignment explanation
Indices: 55144018--55144074 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
55144008 TAAAAGAGGA
55144018 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
55144066 AAT AAT AAT
1 AAT AAT AAT
55144075 GCTAAAAATA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:55144690 original size:17 final size:16
Alignment explanation
Indices: 55144668--55144699 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
55144658 ACATATATTT
55144668 TAAAAATAAAAGAAAAA
1 TAAAAAT-AAAGAAAAA
55144685 TAAAAATAAAGAAAA
1 TAAAAATAAAGAAAA
55144700 CAAACAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.12
Consensus pattern (16 bp):
TAAAAATAAAGAAAAA
Found at i:55145341 original size:23 final size:23
Alignment explanation
Indices: 55145315--55145369 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
55145305 ACTTCAAGGG
*
55145315 TTGACACTTATCATTCTCTTATA
1 TTGACACTTATCATCCTCTTATA
55145338 TTGACA-TCTATCATCCTCTTATA
1 TTGACACT-TATCATCCTCTTATA
*
55145361 TCGACACTT
1 TTGACACTT
55145370 GTTGAATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 1 0.04
23 26 0.93
24 1 0.04
ACGTcount: A:0.25, C:0.25, G:0.05, T:0.44
Consensus pattern (23 bp):
TTGACACTTATCATCCTCTTATA
Found at i:55145961 original size:74 final size:74
Alignment explanation
Indices: 55145876--55146013 Score: 267
Period size: 74 Copynumber: 1.9 Consensus size: 74
55145866 TATTATAATA
*
55145876 AATATTAATTTTTTAAAAACTAGAATTTTTAATTTTTAATATTATAAATTTTGATATTACTAAAC
1 AATATTAATTTTTTAAAAACTAGAATTTTTAATTTTTAATATTATAAATTTTGATATTAATAAAC
55145941 ATATATTTT
66 ATATATTTT
55145950 AATATTAATTTTTTAAAAACTAGAATTTTTAATTTTTAATATTATAAATTTTGATATTAATAAA
1 AATATTAATTTTTTAAAAACTAGAATTTTTAATTTTTAATATTATAAATTTTGATATTAATAAA
55146014 TTTGTGTTTC
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
74 63 1.00
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (74 bp):
AATATTAATTTTTTAAAAACTAGAATTTTTAATTTTTAATATTATAAATTTTGATATTAATAAAC
ATATATTTT
Found at i:55145987 original size:37 final size:37
Alignment explanation
Indices: 55145876--55145993 Score: 125
Period size: 37 Copynumber: 3.2 Consensus size: 37
55145866 TATTATAATA
55145876 AATATTAATTTTTTAAAAACTAGAATTTTTAATTTTT
1 AATATTAATTTTTTAAAAACTAGAATTTTTAATTTTT
* * ** ** *
55145913 AATATTATAAATTTTGATATTACTA-AACATAT-A-TTTT
1 AATA-T-TAATTTTTTA-AAAACTAGAATTTTTAATTTTT
55145950 AATATTAATTTTTTAAAAACTAGAATTTTTAATTTTT
1 AATATTAATTTTTTAAAAACTAGAATTTTTAATTTTT
55145987 AATATTA
1 AATATTA
55145994 TAAATTTTGA
Statistics
Matches: 61, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
34 5 0.08
35 12 0.20
36 2 0.03
37 23 0.38
38 2 0.03
39 12 0.20
40 5 0.08
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (37 bp):
AATATTAATTTTTTAAAAACTAGAATTTTTAATTTTT
Found at i:55146006 original size:15 final size:16
Alignment explanation
Indices: 55145983--55146016 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
55145973 AATTTTTAAT
55145983 TTTTAATATT-ATAAA
1 TTTTAATATTAATAAA
*
55145998 TTTTGATATTAATAAA
1 TTTTAATATTAATAAA
55146014 TTT
1 TTT
55146017 GTGTTTCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
TTTTAATATTAATAAA
Found at i:55148799 original size:54 final size:54
Alignment explanation
Indices: 55148683--55148801 Score: 139
Period size: 54 Copynumber: 2.2 Consensus size: 54
55148673 AGCAGACATG
* * * * * *
55148683 GTGTTACGGGCCGAGACTTTAGCTTCATTAACGCGCAATTTTAGTCGAGAGATA
1 GTGTTACGGGCCGACACTTTAGCCTCATCAACACGCAAGTTTAGTCGAAAGATA
* * * * *
55148737 ATGCTACGGGCTGACACTTTAGCCTCATCAACATGCAAGTTTAGTCGAAAGATT
1 GTGTTACGGGCCGACACTTTAGCCTCATCAACACGCAAGTTTAGTCGAAAGATA
55148791 GTGTTACGGGC
1 GTGTTACGGGC
55148802 AAAGACTTCA
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (54 bp):
GTGTTACGGGCCGACACTTTAGCCTCATCAACACGCAAGTTTAGTCGAAAGATA
Found at i:55151833 original size:3 final size:3
Alignment explanation
Indices: 55151825--55151887 Score: 64
Period size: 3 Copynumber: 22.0 Consensus size: 3
55151815 GGTTAGTGCA
*
55151825 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T-T GTCGT TCT AC- TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT -TC-T TCT TCT TCT
55151870 TC- TCT TC- TCT TC- TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT
55151888 CTGATGTTAA
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
2 8 0.16
3 40 0.78
4 2 0.04
5 1 0.02
ACGTcount: A:0.02, C:0.33, G:0.03, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:55153237 original size:20 final size:19
Alignment explanation
Indices: 55153212--55153253 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
55153202 AAAAGAAAAA
*
55153212 TTCATAATTTTTGGAAATTT
1 TTCATAATGTTT-GAAATTT
*
55153232 TTCATAATGTTTGTAATTT
1 TTCATAATGTTTGAAATTT
55153251 TTC
1 TTC
55153254 TTTTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.26, C:0.07, G:0.10, T:0.57
Consensus pattern (19 bp):
TTCATAATGTTTGAAATTT
Found at i:55158074 original size:7 final size:7
Alignment explanation
Indices: 55158062--55158086 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
55158052 GGTTCTTTTC
55158062 TTTTCTT
1 TTTTCTT
55158069 TTTTCTT
1 TTTTCTT
55158076 TTTTCTT
1 TTTTCTT
55158083 TTTT
1 TTTT
55158087 GAATTTCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTCTT
Found at i:55160792 original size:18 final size:17
Alignment explanation
Indices: 55160769--55160812 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
55160759 TTTTAAAAAA
55160769 TATAAATTTTAGAATTTT
1 TATAAATTTTAGAA-TTT
**
55160787 TATAAATATTTTTAATTT
1 TATAAAT-TTTAGAATTT
55160805 TATAAATT
1 TATAAATT
55160813 ATTTTAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.04
18 17 0.74
19 5 0.22
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TATAAATTTTAGAATTT
Found at i:55160831 original size:20 final size:20
Alignment explanation
Indices: 55160731--55160845 Score: 101
Period size: 20 Copynumber: 5.5 Consensus size: 20
55160721 TTATATATTC
55160731 TTTAGAATTTTTAAAAAATTAT
1 TTTA-AATTTTT-AAAAATTAT
*
55160753 TAT-AATTTTTAAAAAATATAAAT
1 TTTAAATTTTT-AAAAAT-T--AT
*
55160776 TTTAGAATTTTTATAAA-TAT
1 TTTA-AATTTTTAAAAATTAT
* *
55160796 TTTTAA-TTTTATAAATTAT
1 TTTAAATTTTTAAAAATTAT
55160815 TTTAAATTTTTAAAAATTAT
1 TTTAAATTTTTAAAAATTAT
*
55160835 TTTAAGTTTTT
1 TTTAAATTTTT
55160846 TTATAATTTT
Statistics
Matches: 79, Mismatches: 7, Indels: 16
0.77 0.07 0.16
Matches are distributed among these distances:
18 9 0.11
19 10 0.13
20 41 0.52
21 1 0.01
22 3 0.04
23 4 0.05
24 4 0.05
25 7 0.09
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
TTTAAATTTTTAAAAATTAT
Found at i:55160855 original size:38 final size:39
Alignment explanation
Indices: 55160731--55160837 Score: 101
Period size: 45 Copynumber: 2.6 Consensus size: 39
55160721 TTATATATTC
*
55160731 TTTAGAATTTTTAAAAA-ATTATTATAATTTTTAAAAAATATAAAT
1 TTTAGAATTTTTAAAAATATT-TT-TAA-TTTT--ATAA-AT-AAT
* *
55160776 TTTAGAATTTTTATAAATATTTTTAATTTTATAAATTAT
1 TTTAGAATTTTTAAAAATATTTTTAATTTTATAAATAAT
55160815 TTTA-AATTTTTAAAAATTATTTT
1 TTTAGAATTTTTAAAAA-TATTTT
55160838 AAGTTTTTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
38 11 0.20
39 12 0.21
40 2 0.04
41 3 0.05
43 4 0.07
44 3 0.05
45 18 0.32
46 3 0.05
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (39 bp):
TTTAGAATTTTTAAAAATATTTTTAATTTTATAAATAAT
Found at i:55161946 original size:20 final size:18
Alignment explanation
Indices: 55161911--55161947 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
55161901 TGAAACATGT
55161911 AATAAAATTAATTTTTAA
1 AATAAAATTAATTTTTAA
55161929 AATAATAATTATATTTTTA
1 AATAA-AATTA-ATTTTTA
55161948 TCACTAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 5 0.29
20 7 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AATAAAATTAATTTTTAA
Found at i:55164030 original size:21 final size:21
Alignment explanation
Indices: 55163989--55164029 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
55163979 ATTTTTTAAA
*
55163989 AAAATTTAAAAAAAGTATTTT
1 AAAATATAAAAAAAGTATTTT
*
55164010 AAAATATAAAAATA-TATTTT
1 AAAATATAAAAAAAGTATTTT
55164030 TTATTATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
AAAATATAAAAAAAGTATTTT
Found at i:55164708 original size:31 final size:31
Alignment explanation
Indices: 55164646--55164708 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
55164636 AATTTTAAAA
* *
55164646 TTTGAAAAGTACAATGACTAAATCAATAATT
1 TTTGAAAAGTACAAGGACTAAAACAATAATT
* *
55164677 TTTGTAAAGTACAAGGATTAATAACAA-AATT
1 TTTGAAAAGTACAAGGACTAA-AACAATAATT
55164708 T
1 T
55164709 AAACCTTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 23 0.85
32 4 0.15
ACGTcount: A:0.48, C:0.08, G:0.11, T:0.33
Consensus pattern (31 bp):
TTTGAAAAGTACAAGGACTAAAACAATAATT
Found at i:55169971 original size:2 final size:2
Alignment explanation
Indices: 55169964--55170000 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
55169954 TTGATAATTG
55169964 AT AT AT AT AT AT AT AT AT 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
55170001 GGCATGTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:55193128 original size:40 final size:41
Alignment explanation
Indices: 55193052--55193128 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
55193042 GGGCATGCGG
* * * *
55193052 GGATTTAGCGGCGTTTTTTATTAAGCGCCGCTAAAGATCAA
1 GGATTTAGCGGCATTTTTGATAAAGAGCCGCTAAAGATCAA
*
55193093 GGATTTAGCGGCATTTTTGATAAATAGCCGC-AAAGA
1 GGATTTAGCGGCATTTTTGATAAAGAGCCGCTAAAGA
55193129 AACCTAAGAC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
40 5 0.16
41 26 0.84
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (41 bp):
GGATTTAGCGGCATTTTTGATAAAGAGCCGCTAAAGATCAA
Found at i:55193295 original size:114 final size:114
Alignment explanation
Indices: 55193044--55193309 Score: 263
Period size: 114 Copynumber: 2.3 Consensus size: 114
55193034 CGTTTTCCGG
* * *
55193044 GCATGCGGGGATTTAGCGGCGTTTTTTATTAAGCGCCGCTAAAGATCAAGGATTTAGCGGCATTT
1 GCATTCGGGGATTTAGCGGCGTTTTTGAGTAAGCGCCGCTAAAGATCAAGGATTTAGCGGCATTT
* * * * *
55193109 TTGATAAATAGCCGCAAAGAAACCTAAGACCAACGACGCCGTTTTCTGA
66 GTGATAAAGAGCCGCAAAGAAACATAAGACCAACGACACCGTTCTCTGA
** ** * * * * * *
55193158 GCATTCGGTAACCTAGTGACGTTTTTGAGGT-AGCGCCGCTAATGTTC-AGTACTTTAGCGGCGT
1 GCATTCGGGGATTTAGCGGCGTTTTTGA-GTAAGCGCCGCTAAAGATCAAGGA-TTTAGCGGCAT
* * *
55193221 TTGT-ATGGAAGCGCCGCAAATAAACATAAG-CCGAACGACACCGTTCTCTGA
64 TTGTGAT-AAAGAGCCGCAAAGAAACATAAGACC-AACGACACCGTTCTCTGA
*
55193272 GTATTCGGGGATTTAGCGGCGTTTTTG-GTAAGCGCCGC
1 GCATTCGGGGATTTAGCGGCGTTTTTGAGTAAGCGCCGC
55193310 CAATAACCTA
Statistics
Matches: 119, Mismatches: 28, Indels: 11
0.75 0.18 0.07
Matches are distributed among these distances:
112 2 0.02
113 15 0.13
114 101 0.85
115 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (114 bp):
GCATTCGGGGATTTAGCGGCGTTTTTGAGTAAGCGCCGCTAAAGATCAAGGATTTAGCGGCATTT
GTGATAAAGAGCCGCAAAGAAACATAAGACCAACGACACCGTTCTCTGA
Found at i:55194902 original size:147 final size:146
Alignment explanation
Indices: 55194683--55195148 Score: 399
Period size: 147 Copynumber: 3.2 Consensus size: 146
55194673 TTGCTATTAC
* * ** * *** * *
55194683 TGGCGCTTTACATAAAACGCCGCAAAATTGTATTTATGTTTATCGAAATGTTGTCGTTTTGTCAA
1 TGGCGCTTTACTTAAAACGCCGCAAAATTGT-TTAACATTTATAGAAACACTGCCGTTTTGTAAA
* * *
55194748 TGGTATTAGTGGCG-TTTTTTTAGAAACGCCACAAGCTTGAGTTAAATGTTGGGGAAACGACTTC
65 TGGTATTAGTGGCGATTTTTTTA-AAACGCCACAAGCTTGAGGTAAATGTTGAGGAAACGACTGC
*
55194812 G-TTTGATCTTATATTTAG
129 GTTTTGAT-TTATAGTTAG
* *
55194830 TGGCGCTTTACTTAAAACGCCGCAACATTGTTCTAACATTTATAGAAACACTGCCGTTTTTTAAA
1 TGGCGCTTTACTTAAAACGCCGCAAAATTGTT-TAACATTTATAGAAACACTGCCGTTTTGTAAA
* ** * * * *
55194895 TGTTATTAGTGGCGATTTTTTTAAAACGCCACGGGTTTGAGGTAAGTGTTGATGAAGCGACTGCG
65 TGGTATTAGTGGCGATTTTTTTAAAACGCCACAAGCTTGAGGTAAATGTTGAGGAAACGACTGCG
55194960 TTTTGATTTATAGTTAG
130 TTTTGATTTATAGTTAG
* * * * * *
55194977 TGGCGCTTTAATTAAAACGCCGCAAAAATGTTTTAACATTTATTGATACGA-GGCCGTTTTGCTG
1 TGGCGCTTTACTTAAAACGCCGCAAAATTG-TTTAACATTTATAGAAAC-ACTGCCGTTTTG-TA
* * ** * * * ** *
55195041 TAT--TATTAGTGGTG-TTTATTCAAAAACGCCAC-AGGTGTGCGCTATTTGTTGATGAAACGAC
63 AATGGTATTAGTGGCGATTT-TTTTAAAACGCCACAAGCT-TGAGGTAAATGTTGAGGAAACGAC
* *
55195102 TGCGTTTCGACTTATAGTTAG
126 TGCGTTTTGATTTATAGTTAG
* *
55195123 TGGCGC-TTATTTATAAACGCCACAAA
1 TGGCGCTTTACTTA-AAACGCCGCAAA
55195149 TGGTTAATTT
Statistics
Matches: 264, Mismatches: 46, Indels: 19
0.80 0.14 0.06
Matches are distributed among these distances:
145 11 0.04
146 78 0.30
147 155 0.59
148 20 0.08
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.36
Consensus pattern (146 bp):
TGGCGCTTTACTTAAAACGCCGCAAAATTGTTTAACATTTATAGAAACACTGCCGTTTTGTAAAT
GGTATTAGTGGCGATTTTTTTAAAACGCCACAAGCTTGAGGTAAATGTTGAGGAAACGACTGCGT
TTTGATTTATAGTTAG
Found at i:55197712 original size:36 final size:36
Alignment explanation
Indices: 55197670--55197791 Score: 129
Period size: 36 Copynumber: 3.6 Consensus size: 36
55197660 TACTTATATG
55197670 TAAAATTTAAGTATGTTACTTAAATACATTACTTAC
1 TAAAATTTAAGTATGTTACTTAAATACATTACTTAC
* *
55197706 TAAAATTTAAGTA----AGTT---TAC-TTA--TATG
1 TAAAATTTAAGTATGTTACTTAAATACATTACTTA-C
55197733 TAAAATTTAAGTATGTTACTTAAATACATTACTTAC
1 TAAAATTTAAGTATGTTACTTAAATACATTACTTAC
*
55197769 TAAAATTTAAGTAAGTTTACTTA
1 TAAAATTTAAGTATG-TTACTTA
55197792 TATGTAAACT
Statistics
Matches: 69, Mismatches: 5, Indels: 23
0.71 0.05 0.24
Matches are distributed among these distances:
26 2 0.03
27 13 0.19
28 3 0.04
29 3 0.04
31 3 0.04
32 3 0.04
34 3 0.04
35 3 0.04
36 27 0.39
37 9 0.13
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.43
Consensus pattern (36 bp):
TAAAATTTAAGTATGTTACTTAAATACATTACTTAC
Found at i:55197726 original size:63 final size:63
Alignment explanation
Indices: 55197627--55197799 Score: 346
Period size: 63 Copynumber: 2.7 Consensus size: 63
55197617 NNNNNNNNCA
55197627 TAAATACATTACTTACTAAAATTTAAGTAAGTTTACTTATATGTAAAATTTAAGTATGTTACT
1 TAAATACATTACTTACTAAAATTTAAGTAAGTTTACTTATATGTAAAATTTAAGTATGTTACT
55197690 TAAATACATTACTTACTAAAATTTAAGTAAGTTTACTTATATGTAAAATTTAAGTATGTTACT
1 TAAATACATTACTTACTAAAATTTAAGTAAGTTTACTTATATGTAAAATTTAAGTATGTTACT
55197753 TAAATACATTACTTACTAAAATTTAAGTAAGTTTACTTATATGTAAA
1 TAAATACATTACTTACTAAAATTTAAGTAAGTTTACTTATATGTAAA
55197800 CTTACATAAT
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 110 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (63 bp):
TAAATACATTACTTACTAAAATTTAAGTAAGTTTACTTATATGTAAAATTTAAGTATGTTACT
Found at i:55197828 original size:23 final size:23
Alignment explanation
Indices: 55197798--55197841 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
55197788 CTTATATGTA
*
55197798 AACTTACATAATACATTACTTTT
1 AACTTACATAATACATAACTTTT
55197821 AACTTACATAATACATAACTT
1 AACTTACATAATACATAACTT
55197842 ATAAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.43, C:0.18, G:0.00, T:0.39
Consensus pattern (23 bp):
AACTTACATAATACATAACTTTT
Found at i:55197930 original size:9 final size:9
Alignment explanation
Indices: 55197899--55198326 Score: 413
Period size: 9 Copynumber: 48.0 Consensus size: 9
55197889 TTTTTATATA
55197899 AACTTACAT
1 AACTTACAT
55197908 AA--TACATTT
1 AACTTACA--T
55197917 AACTTACAT
1 AACTTACAT
*
55197926 AACTTACAC
1 AACTTACAT
55197935 AACTTACAT
1 AACTTACAT
55197944 AACCTT-CAT
1 AA-CTTACAT
55197953 AA--TACATTT
1 AACTTACA--T
55197962 AACTTACAT
1 AACTTACAT
55197971 AACTTACAT
1 AACTTACAT
55197980 AACTTACAT
1 AACTTACAT
55197989 AACTTACAT
1 AACTTACAT
55197998 AACTTACAT
1 AACTTACAT
*
55198007 AACATACAT
1 AACTTACAT
* **
55198016 TACTTTGAT
1 AACTTACAT
55198025 AACTTACAT
1 AACTTACAT
55198034 AACTTACAT
1 AACTTACAT
* *
55198043 AA--TGCAA
1 AACTTACAT
55198050 AACTTACAT
1 AACTTACAT
*
55198059 AAC-AAC-T
1 AACTTACAT
*
55198066 TACTTACAT
1 AACTTACAT
*
55198075 AACATACAT
1 AACTTACAT
* *
55198084 TACTTAAAT
1 AACTTACAT
* *
55198093 TATTTACAT
1 AACTTACAT
55198102 AA--TACAT
1 AACTTACAT
55198109 AACTTAGTACAT
1 AAC-T--TACAT
*
55198121 AATTTACAT
1 AACTTACAT
*
55198130 -A-GTACAT
1 AACTTACAT
55198137 AACTTAGTACAT
1 AAC-T--TACAT
55198149 AACTTACATT
1 AACTTACA-T
*
55198159 AA-TTAAAT
1 AACTTACAT
55198167 AACTTACAT
1 AACTTACAT
55198176 AACTTACAT
1 AACTTACAT
55198185 AACTTACAT
1 AACTTACAT
*
55198194 AACTTAAAT
1 AACTTACAT
55198203 AACTTACAT
1 AACTTACAT
55198212 AACTTACAT
1 AACTTACAT
*
55198221 ATCTTACAT
1 AACTTACAT
55198230 AACTTACAT
1 AACTTACAT
* *
55198239 AAATTAAAT
1 AACTTACAT
55198248 AACTTACAT
1 AACTTACAT
55198257 AACTTACAT
1 AACTTACAT
*
55198266 AAATTACAT
1 AACTTACAT
55198275 AACTTACAT
1 AACTTACAT
55198284 AACTTACAT
1 AACTTACAT
55198293 AACTTACAT
1 AACTTACAT
55198302 AA--TACAT
1 AACTTACAT
*
55198309 AACCTT-CCT
1 AA-CTTACAT
55198318 AACTTACAT
1 AACTTACAT
55198327 TATTGTTTAA
Statistics
Matches: 347, Mismatches: 42, Indels: 60
0.77 0.09 0.13
Matches are distributed among these distances:
6 1 0.00
7 33 0.10
8 12 0.03
9 269 0.78
10 7 0.02
11 10 0.03
12 15 0.04
ACGTcount: A:0.45, C:0.20, G:0.01, T:0.34
Consensus pattern (9 bp):
AACTTACAT
Found at i:55198121 original size:12 final size:12
Alignment explanation
Indices: 55198104--55198154 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 12
55198094 ATTTACATAA
55198104 TACATAACTTAG
1 TACATAACTTAG
*
55198116 TACATAATTTACATAG
1 TACAT-A---ACTTAG
55198132 TACATAACTTAG
1 TACATAACTTAG
55198144 TACATAACTTA
1 TACATAACTTA
55198155 CATTAATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
12 21 0.64
13 1 0.03
15 1 0.03
16 10 0.30
ACGTcount: A:0.43, C:0.16, G:0.06, T:0.35
Consensus pattern (12 bp):
TACATAACTTAG
Found at i:55200619 original size:29 final size:28
Alignment explanation
Indices: 55200589--55200792 Score: 207
Period size: 29 Copynumber: 7.0 Consensus size: 28
55200579 CCCCTGTACT
55200589 TTTC-AAAATTTACATTTTGACCCCAAAC
1 TTTCTAAAA-TTACATTTTGACCCCAAAC
55200617 TTTTCTAAAATTTACATTTTGACCCCAAAAC
1 -TTTCTAAAA-TTACATTTTGACCCC-AAAC
55200648 TTTCTAAAATTACATTTTGACCCCAAAAC
1 TTTCTAAAATTACATTTTGACCCC-AAAC
* *
55200677 TTTCTAAAATTACATTTTGACCCTTAGAC
1 TTTCTAAAATTACATTTTGACCC-CAAAC
*
55200706 TTTCTCAAAATTACATTTTGGAGCCCTTAAAC
1 TTTCT-AAAATTACATTTT-GA-CCC-CAAAC
* * * *
55200738 TTTCAAGAAATTACATTTTG-GCCCATAT
1 TTTCTA-AAATTACATTTTGACCCCAAAC
*
55200766 TTTCTAAAATTACGCTTTTG-CCCCAAA
1 TTTCTAAAATTAC-ATTTTGACCCCAAA
55200793 AGTTTTACGC
Statistics
Matches: 155, Mismatches: 12, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
27 7 0.05
28 17 0.11
29 57 0.37
30 42 0.27
31 8 0.05
32 24 0.15
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.38
Consensus pattern (28 bp):
TTTCTAAAATTACATTTTGACCCCAAAC
Found at i:55200687 original size:59 final size:57
Alignment explanation
Indices: 55200589--55200793 Score: 211
Period size: 59 Copynumber: 3.5 Consensus size: 57
55200579 CCCCTGTACT
55200589 TTTC-AAAATTTACATTTTGACCCC-AAACTTTTCTAAAATTTACATTTTGACCCCAAAAC
1 TTTCTAAAA-TTACATTTTGACCCCAAAAC-TTTCTAAAA-TTACATTTTGACCCC-AAAC
* *
55200648 TTTCTAAAATTACATTTTGACCCCAAAACTTTCTAAAATTACATTTTGACCCTTAGAC
1 TTTCTAAAATTACATTTTGACCCCAAAACTTTCTAAAATTACATTTTGACCC-CAAAC
** * * * *
55200706 TTTCTCAAAATTACATTTTGGAGCCCTTAAACTTTCAAGAAATTACATTTTG-GCCCATAT
1 TTTCT-AAAATTACATTTT-GA-CCCCAAAACTTTCTA-AAATTACATTTTGACCCCAAAC
*
55200766 TTTCTAAAATTACGCTTTTG-CCCCAAAA
1 TTTCTAAAATTAC-ATTTTGACCCCAAAA
55200794 GTTTTACGCC
Statistics
Matches: 126, Mismatches: 12, Indels: 18
0.81 0.08 0.12
Matches are distributed among these distances:
57 6 0.05
58 22 0.17
59 50 0.40
60 21 0.17
61 14 0.11
62 13 0.10
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.38
Consensus pattern (57 bp):
TTTCTAAAATTACATTTTGACCCCAAAACTTTCTAAAATTACATTTTGACCCCAAAC
Found at i:55201346 original size:12 final size:11
Alignment explanation
Indices: 55201329--55201387 Score: 66
Period size: 12 Copynumber: 5.2 Consensus size: 11
55201319 AGCCCCGAAG
55201329 AGGAAGGAAAAA
1 AGGAA-GAAAAA
55201341 AGGAAGAAAAA
1 AGGAAGAAAAA
*
55201352 A-GAAGAAAAG
1 AGGAAGAAAAA
55201362 AGAGAAGAAAAA
1 AG-GAAGAAAAA
*
55201374 GAGAAAGAAAAA
1 -AGGAAGAAAAA
55201386 AG
1 AG
55201388 AAAAAAAGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
10 9 0.22
11 9 0.22
12 21 0.51
13 2 0.05
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (11 bp):
AGGAAGAAAAA
Found at i:55201386 original size:13 final size:13
Alignment explanation
Indices: 55201350--55201388 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
55201340 AAGGAAGAAA
55201350 AAAGAAGAAAAGAG
1 AAAGAA-AAAAGAG
55201364 AGAAG-AAAAAGAG
1 A-AAGAAAAAAGAG
55201377 AAAGAAAAAAGA
1 AAAGAAAAAAGA
55201389 AAAAAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 3 0.13
13 15 0.65
14 2 0.09
15 3 0.13
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAAGAG
Found at i:55201387 original size:7 final size:7
Alignment explanation
Indices: 55201344--55201401 Score: 57
Period size: 7 Copynumber: 8.3 Consensus size: 7
55201334 GGAAAAAAGG
55201344 AAGAAAA
1 AAGAAAA
55201351 AAGAAGAA
1 AAGAA-AA
* *
55201359 AAGAGAG
1 AAGAAAA
55201366 AAG-AAA
1 AAGAAAA
*
55201372 AAG-AGA
1 AAGAAAA
55201378 AAGAAAA
1 AAGAAAA
55201385 AAGAAAAA
1 AAG-AAAA
55201393 AAGAAAA
1 AAGAAAA
55201400 AA
1 AA
55201402 TATCTTACAC
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
6 9 0.21
7 20 0.48
8 13 0.31
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:55201387 original size:34 final size:33
Alignment explanation
Indices: 55201326--55201396 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 33
55201316 TTCAGCCCCG
* *
55201326 AAGAGGAAGGAAAAAAGGAAGAAAAAAGAAGAA
1 AAGAGGAAGGAAAAAAGAAAGAAAAAAGAAAAA
55201359 AAGAGAGAA-GAAAAAGAGAAAGAAAAAAGAAAAA
1 AAGAG-GAAGGAAAAA-AGAAAGAAAAAAGAAAAA
55201393 AAGA
1 AAGA
55201397 AAAAATATCT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
33 11 0.32
34 23 0.68
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (33 bp):
AAGAGGAAGGAAAAAAGAAAGAAAAAAGAAAAA
Found at i:55201389 original size:11 final size:11
Alignment explanation
Indices: 55201335--55201394 Score: 70
Period size: 12 Copynumber: 5.5 Consensus size: 11
55201325 GAAGAGGAAG
*
55201335 GAAAAAAGGAA
1 GAAAAAAGAAA
55201346 GAAAAAAG-AA
1 GAAAAAAGAAA
*
55201356 GAAAAGAGAGAA
1 GAAAAAAGA-AA
55201368 GAAAAAGAGAAA
1 GAAAAA-AGAAA
55201380 GAAAAAAGAAA
1 GAAAAAAGAAA
55201391 -AAAA
1 GAAAA
55201395 GAAAAAATAT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
10 13 0.30
11 13 0.30
12 15 0.34
13 3 0.07
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (11 bp):
GAAAAAAGAAA
Found at i:55201395 original size:15 final size:16
Alignment explanation
Indices: 55201344--55201401 Score: 66
Period size: 15 Copynumber: 3.6 Consensus size: 16
55201334 GGAAAAAAGG
55201344 AAGAAAAAAGAAGAAA
1 AAGAAAAAAGAAGAAA
*
55201360 AGAGAGAAGAAA-AAGAGA
1 A-AGA-AA-AAAGAAGAAA
55201378 AAGAAAAAAGAA-AAA
1 AAGAAAAAAGAAGAAA
55201393 AAGAAAAAA
1 AAGAAAAAA
55201402 TATCTTACAC
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
15 14 0.39
16 5 0.14
17 6 0.17
18 8 0.22
19 3 0.08
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AAGAAAAAAGAAGAAA
Found at i:55202322 original size:15 final size:16
Alignment explanation
Indices: 55202304--55202354 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 16
55202294 AAAATAAAAA
55202304 TTCGTATTTCAAAT-T
1 TTCGTATTTCAAATAT
55202319 TTCGTATTTTCAAATAT
1 TTCGTA-TTTCAAATAT
55202336 TACTCGTATTTCAAA-AT
1 T--TCGTATTTCAAATAT
55202353 TT
1 TT
55202355 ACGACTTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
15 7 0.22
16 8 0.25
17 5 0.16
18 7 0.22
19 5 0.16
ACGTcount: A:0.29, C:0.14, G:0.06, T:0.51
Consensus pattern (16 bp):
TTCGTATTTCAAATAT
Found at i:55202356 original size:18 final size:17
Alignment explanation
Indices: 55202305--55202356 Score: 63
Period size: 19 Copynumber: 3.0 Consensus size: 17
55202295 AAATAAAAAT
55202305 TCGTATTTCAAATTT--
1 TCGTATTTCAAATTTAC
55202320 TCGTATTTTCAAATATTAC
1 TCGTA-TTTCAAAT-TTAC
55202339 TCGTATTTCAAAATTTAC
1 TCGTATTTC-AAATTTAC
55202357 GACTTTTCGC
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
15 5 0.16
16 8 0.25
17 2 0.06
18 8 0.25
19 9 0.28
ACGTcount: A:0.31, C:0.15, G:0.06, T:0.48
Consensus pattern (17 bp):
TCGTATTTCAAATTTAC
Found at i:55202439 original size:17 final size:17
Alignment explanation
Indices: 55202417--55202572 Score: 91
Period size: 17 Copynumber: 8.4 Consensus size: 17
55202407 TGTTTTAAAA
*
55202417 AAAAATTCTCGTATTTC
1 AAAAATTCTCGTGTTTC
* *
55202434 AAAAATTATCATGTCTT-
1 AAAAATTCTCGTGT-TTC
*
55202451 GAAAATTCTCGTGTTTC
1 AAAAATTCTCGTGTTTC
*
55202468 AAAAATTTTCGTGTTTTC
1 AAAAATTCTCGTG-TTTC
* *
55202486 AAAATTTTCATGTTTTCGGGTTTTC
1 AAAA-----A--TTCTCGTG-TTTC
55202511 AAAAAATTCTCGTGTGTTC
1 -AAAAATTCTCGTGT-TTC
*
55202530 AAAAAATTTTCGTGTTTC
1 -AAAAATTCTCGTGTTTC
55202548 AAAAA-TCTTCGTGTTTTC
1 AAAAATTC-TCGTG-TTTC
55202566 AAAAATT
1 AAAAATT
55202573 ATTATTTTGT
Statistics
Matches: 111, Mismatches: 13, Indels: 28
0.73 0.09 0.18
Matches are distributed among these distances:
16 3 0.03
17 43 0.39
18 23 0.21
19 24 0.22
21 1 0.01
23 1 0.01
25 12 0.11
26 4 0.04
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.44
Consensus pattern (17 bp):
AAAAATTCTCGTGTTTC
Found at i:55202490 original size:34 final size:34
Alignment explanation
Indices: 55202418--55202569 Score: 106
Period size: 34 Copynumber: 4.1 Consensus size: 34
55202408 GTTTTAAAAA
* * * * *
55202418 AAAATTCTCGTATTTCAAAAATTATCATGTCTTG
1 AAAATTCTCGTGTTTCAAAAATTTTCGTGTTTTC
55202452 AAAATTCTCGTGTTTCAAAAATTTTCGTGTTTTC
1 AAAATTCTCGTGTTTCAAAAATTTTCGTGTTTTC
* * *
55202486 AAAATTTTCATGTTTTCGGGTTTTCAAAAAATTCTCGTGTGTTC
1 AAAA--TTC------TCGTG-TTTC-AAAAATTTTCGTGTTTTC
* *
55202530 AAAAAATTTTCGTGTTTCAAAAATCTTCGTGTTTTC
1 --AAAATTCTCGTGTTTCAAAAATTTTCGTGTTTTC
55202566 AAAA
1 AAAA
55202570 ATTATTATTT
Statistics
Matches: 93, Mismatches: 13, Indels: 24
0.72 0.10 0.18
Matches are distributed among these distances:
34 37 0.40
36 18 0.19
37 4 0.04
38 4 0.04
42 4 0.04
43 4 0.04
44 18 0.19
46 4 0.04
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (34 bp):
AAAATTCTCGTGTTTCAAAAATTTTCGTGTTTTC
Found at i:55202532 original size:19 final size:18
Alignment explanation
Indices: 55202507--55202570 Score: 78
Period size: 19 Copynumber: 3.5 Consensus size: 18
55202497 GTTTTCGGGT
55202507 TTTCAAAAAATTCTCGTG
1 TTTCAAAAAATTCTCGTG
*
55202525 TGTTCAAAAAATTTTCGTG
1 T-TTCAAAAAATTCTCGTG
55202544 TTTC-AAAAA-TCTTCGTG
1 TTTCAAAAAATTC-TCGTG
55202561 TTTTCAAAAA
1 -TTTCAAAAA
55202571 TTATTATTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
16 1 0.03
17 10 0.25
18 8 0.20
19 21 0.52
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (18 bp):
TTTCAAAAAATTCTCGTG
Found at i:55204322 original size:4 final size:4
Alignment explanation
Indices: 55204313--55204341 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
55204303 CATCCATTGG
55204313 TCAT TCAT TCAT TCAT TCAT TCAT TCAT T
1 TCAT TCAT TCAT TCAT TCAT TCAT TCAT T
55204342 GCATATACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (4 bp):
TCAT
Found at i:55208430 original size:20 final size:19
Alignment explanation
Indices: 55208385--55208455 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 19
55208375 TATGCTTAAA
*
55208385 AAAAACAAACAAAAAAAATAG
1 AAAAA-AAAC-AAAAAAACAG
55208406 AAAAAAAACAAAAAAACAG
1 AAAAAAAACAAAAAAACAG
* * *
55208425 ATAAAAAA-AAAAAGAGA-
1 AAAAAAAACAAAAAAACAG
*
55208442 AAAAAAAAGAAAAA
1 AAAAAAAACAAAAA
55208456 TCAAGATGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
17 7 0.16
18 12 0.27
19 16 0.36
20 4 0.09
21 5 0.11
ACGTcount: A:0.85, C:0.06, G:0.07, T:0.03
Consensus pattern (19 bp):
AAAAAAAACAAAAAAACAG
Found at i:55208434 original size:16 final size:15
Alignment explanation
Indices: 55208382--55208449 Score: 61
Period size: 14 Copynumber: 4.6 Consensus size: 15
55208372 TATTATGCTT
*
55208382 AAAAAAAACAAACA-
1 AAAAAAAAAAAACAG
*
55208396 AAAAAAATAGAAA-A-
1 AAAAAAA-AAAAACAG
*
55208410 AAAACAAAAAAACAG
1 AAAAAAAAAAAACAG
*
55208425 ATAAAAAAAAAAAGAG
1 A-AAAAAAAAAAACAG
55208441 AAAAAAAAA
1 AAAAAAAAA
55208450 GAAAAATCAA
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
13 4 0.09
14 15 0.33
15 13 0.29
16 13 0.29
ACGTcount: A:0.85, C:0.06, G:0.06, T:0.03
Consensus pattern (15 bp):
AAAAAAAAAAAACAG
Found at i:55208444 original size:12 final size:11
Alignment explanation
Indices: 55208383--55208455 Score: 60
Period size: 11 Copynumber: 6.5 Consensus size: 11
55208373 ATTATGCTTA
*
55208383 AAAAAAACAAAC
1 AAAAAAA-AAAG
*
55208395 AAAAAAAATAG
1 AAAAAAAAAAG
55208406 AAAAAAAACAA-
1 AAAAAAAA-AAG
* *
55208417 AAAAACAGATA-
1 AAAAA-AAAAAG
55208428 AAAAAAAAAAG
1 AAAAAAAAAAG
55208439 AGAAAAAAAAAG
1 A-AAAAAAAAAG
55208451 AAAAA
1 AAAAA
55208456 TCAAGATGAA
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
10 3 0.06
11 26 0.52
12 21 0.42
ACGTcount: A:0.85, C:0.05, G:0.07, T:0.03
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:55208445 original size:32 final size:31
Alignment explanation
Indices: 55208382--55208455 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 31
55208372 TATTATGCTT
*
55208382 AAAAAAAACAAACAAAAAAAATAGAAAAAAA
1 AAAAAAAACAAACAAAAAAAAAAGAAAAAAA
55208413 ACAAAAAAACAGATA-AAAAAAAAAAGAGAAAAAA
1 A-AAAAAAACA-A-ACAAAAAAAAAAGA-AAAAAA
55208447 AAAGAAAAA
1 AAA-AAAAA
55208456 TCAAGATGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
31 1 0.03
32 9 0.24
33 14 0.38
34 13 0.35
ACGTcount: A:0.85, C:0.05, G:0.07, T:0.03
Consensus pattern (31 bp):
AAAAAAAACAAACAAAAAAAAAAGAAAAAAA
Found at i:55209654 original size:76 final size:75
Alignment explanation
Indices: 55209339--55209876 Score: 628
Period size: 77 Copynumber: 7.1 Consensus size: 75
55209329 TTTCAAGAAA
* *
55209339 TATTTTTAAAATTCTGTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGG
1 TATTTTTAAATTTCTG-TTTTTTCAAAAAATCAACTCATATTACAGAGGTGAGTTGAGCCTCGGG
*
55209404 TCACACTGAGG
65 TCACGCTGAGG
* * * *
55209415 TATTTTTTTTAATTTCTG-TTTTTCTAAAAATACAACTCATAATACAGAAGTGAGTTGAGCCTCG
1 TA--TTTTTAAATTTCTGTTTTTTCAAAAAAT-CAACTCATATTACAGAGGTGAGTTGAGCCTCG
55209479 GGTCACGCTGAGG
63 GGTCACGCTGAGG
*
55209492 TATTTTTTAAATTTCTGCTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGG
1 TA-TTTTTAAATTTCTG-TTTTTTCAAAAAATCAACTCATATTACAGAGGTGAGTTGAGCCTCGG
55209557 GTCACGCTGAGG
64 GTCACGCTGAGG
* *
55209569 TATTTTTTTAATTTCTGTTTTTTCAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGGCTCGG
1 TA-TTTTTAAATTTCTGTTTTTTCAAAAAATCAACTCATATTAC-AGAGGTGAGTTGAGCCTCGG
55209634 GTCACTCGCTGAGG
64 GTCA--CGCTGAGG
* *
55209648 TA-TTTTAAATTTCTG-TTTTTC-AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGAG
1 TATTTTTAAATTTCTGTTTTTTCAAAAAATCAACTCATATTAC-AGAGGTGAGTTGAGCCTCGGG
55209710 TCACG-TCGAGG
65 TCACGCT-GAGG
* * * * * *
55209721 TGTTTTTCAATTTCT-ATTTTTC-CAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAG
1 TATTTTTAAATTTCTGTTTTTTCAAAAAATCAACTCATATTAC-AGAGGTGAGTTGAGCCTCGGG
55209784 TCACG-TCGAGG
65 TCACGCT-GAGG
* * * *
55209795 TATTTTTCAA-TTCT-TGCTTTTCAAAAAAATCAACTCATATTGCTAGAGGTGAGTTGGGCCTCG
1 TATTTTTAAATTTCTGT-TTTTTC-AAAAAATCAACTCATATTAC-AGAGGTGAGTTGAGCCTCG
*
55209858 GGTTTCACGCTGAGC
63 GG--TCACGCTGAGG
55209873 TATT
1 TATT
55209877 CTCGATTTCT
Statistics
Matches: 417, Mismatches: 28, Indels: 32
0.87 0.06 0.07
Matches are distributed among these distances:
72 1 0.00
73 11 0.03
74 81 0.19
75 40 0.10
76 97 0.23
77 140 0.34
78 36 0.09
79 11 0.03
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (75 bp):
TATTTTTAAATTTCTGTTTTTTCAAAAAATCAACTCATATTACAGAGGTGAGTTGAGCCTCGGGT
CACGCTGAGG
Found at i:55210163 original size:29 final size:29
Alignment explanation
Indices: 55210065--55210212 Score: 152
Period size: 30 Copynumber: 5.0 Consensus size: 29
55210055 TTTTTTTTGC
* **
55210065 ATTTTGACCCCTAAGCTTTTCTAAAATTGC
1 ATTTTGACCCCTAAACTTTTCT-AAATTAT
* *
55210095 ATTTTAACCCCTAAACTTTCTCAAAATTAT
1 ATTTTGACCCCTAAACTTT-TCTAAATTAT
* *
55210125 AGTTTAACCCCTAAACTTTTCTAAATTAT
1 ATTTTGACCCCTAAACTTTTCTAAATTAT
* *
55210154 ATTTTGACCCCTAAACTTTTTTAAAATTAG
1 ATTTTGACCCCTAAACTTTTCT-AAATTAT
* * *
55210184 ATTTGGACCCTTAAACTTTCTCAAAATTA
1 ATTTTGACCCCTAAACTTT-TCTAAATTA
55210213 CGTTTCGGCC
Statistics
Matches: 100, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
29 28 0.28
30 69 0.69
31 3 0.03
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.41
Consensus pattern (29 bp):
ATTTTGACCCCTAAACTTTTCTAAATTAT
Found at i:55210795 original size:10 final size:10
Alignment explanation
Indices: 55210782--55210855 Score: 78
Period size: 12 Copynumber: 6.9 Consensus size: 10
55210772 GAGAAGAAGG
55210782 AAGAAAAAGA
1 AAGAAAAAGA
55210792 AAGAAAAAGA
1 AAGAAAAAGA
55210802 AGGAGAAAAAGA
1 A--AGAAAAAGA
*
55210814 GAGAAAAAAAGA
1 -A-AGAAAAAGA
55210826 AAGAAAAAAGA
1 AAG-AAAAAGA
55210837 AA-AAAAAGA
1 AAGAAAAAGA
55210846 AGAGAAAAAG
1 A-AGAAAAAG
55210856 CAAAATCAAC
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
9 8 0.14
10 13 0.23
11 16 0.29
12 18 0.32
13 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (10 bp):
AAGAAAAAGA
Found at i:55210822 original size:12 final size:12
Alignment explanation
Indices: 55210785--55210854 Score: 55
Period size: 10 Copynumber: 6.2 Consensus size: 12
55210775 AAGAAGGAAG
*
55210785 AAAAAGAAAGAA
1 AAAAAGAGAGAA
55210797 AAAGAAG-GAG--
1 AAA-AAGAGAGAA
55210807 AAAAAGAGAGAA
1 AAAAAGAGAGAA
*
55210819 AAAAAGA-A-AG
1 AAAAAGAGAGAA
55210829 AAAAA-AGA-AA
1 AAAAAGAGAGAA
55210839 AAAAAGAAGAGAA
1 AAAAAG-AGAGAA
55210852 AAA
1 AAA
55210855 GCAAAATCAA
Statistics
Matches: 47, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
9 4 0.09
10 19 0.40
11 1 0.02
12 15 0.32
13 8 0.17
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (12 bp):
AAAAAGAGAGAA
Found at i:55210860 original size:19 final size:20
Alignment explanation
Indices: 55210785--55210854 Score: 86
Period size: 24 Copynumber: 3.2 Consensus size: 20
55210775 AAGAAGGAAG
55210785 AAAAAGAAAGAAAAAGAAGGAGA
1 AAAAAGAAA-AAAAAGAA--AGA
55210808 AAAAGAGAGAAAAAAAGAAAGA
1 AAAA-AGA-AAAAAAAGAAAGA
55210830 AAAAAGAAAAAAAAGAAGAGA
1 AAAAAGAAAAAAAAGAA-AGA
55210851 AAAA
1 AAAA
55210855 GCAAAATCAA
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
20 10 0.23
21 10 0.23
22 7 0.16
23 4 0.09
24 11 0.25
25 2 0.05
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAAAGAAAAAAAAGAAAGA
Found at i:55210975 original size:14 final size:14
Alignment explanation
Indices: 55210948--55210990 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
55210938 AGGCCCGAAA
55210948 AAAAAAATAGCAAAGC
1 AAAAAAA-A-CAAAGC
55210964 AAAAAAAACAAAGC
1 AAAAAAAACAAAGC
* *
55210978 AGAAAAAAGAAAG
1 AAAAAAAACAAAG
55210991 AAGCAGCAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 17 0.68
15 1 0.04
16 7 0.28
ACGTcount: A:0.74, C:0.09, G:0.14, T:0.02
Consensus pattern (14 bp):
AAAAAAAACAAAGC
Found at i:55211000 original size:20 final size:21
Alignment explanation
Indices: 55210975--55211018 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
55210965 AAAAAAACAA
*
55210975 AGCAG-AAAAAAGAAAGAAGC
1 AGCAGAAAAAAAAAAAGAAGC
55210995 AGCAGAAAAAAAAAAAGAAGC
1 AGCAGAAAAAAAAAAAGAAGC
55211016 AGC
1 AGC
55211019 CCAGCGGCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.66, C:0.11, G:0.23, T:0.00
Consensus pattern (21 bp):
AGCAGAAAAAAAAAAAGAAGC
Found at i:55211126 original size:15 final size:14
Alignment explanation
Indices: 55211106--55211164 Score: 66
Period size: 15 Copynumber: 4.1 Consensus size: 14
55211096 GGCCCAGCAG
55211106 AGAAGAAAAAAAAA
1 AGAAGAAAAAAAAA
*
55211120 CAGAAGAAAAAAAGA
1 -AGAAGAAAAAAAAA
*
55211135 AGAAAGAAAAAAGAA
1 AG-AAGAAAAAAAAA
*
55211150 AGAA-AAAAAGAAA
1 AGAAGAAAAAAAAA
55211163 AG
1 AG
55211165 GGTTCAATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
13 9 0.24
14 4 0.11
15 25 0.66
ACGTcount: A:0.80, C:0.02, G:0.19, T:0.00
Consensus pattern (14 bp):
AGAAGAAAAAAAAA
Found at i:55211135 original size:11 final size:11
Alignment explanation
Indices: 55211108--55211163 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
55211098 CCCAGCAGAG
*
55211108 AAGAAAAAAAA
1 AAGAAGAAAAA
55211119 ACAGAAGAAAAA
1 A-AGAAGAAAAA
55211131 AAGAAGAAAGAA
1 AAGAAGAAA-AA
55211143 AA-AAGAAAGAA
1 AAGAAGAAA-AA
*
55211154 AAAAAGAAAA
1 AAGAAGAAAA
55211164 GGGTTCAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
11 21 0.51
12 20 0.49
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (11 bp):
AAGAAGAAAAA
Found at i:55211142 original size:18 final size:18
Alignment explanation
Indices: 55211116--55211164 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
55211106 AGAAGAAAAA
55211116 AAAACAGAAGAAAA-AAAG
1 AAAA-AGAAGAAAAGAAAG
55211134 AAGAAAGAA-AAAAGAAAG
1 AA-AAAGAAGAAAAGAAAG
55211152 AAAAA-AAGAAAAG
1 AAAAAGAAGAAAAG
55211165 GGTTCAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
16 2 0.07
17 12 0.43
18 12 0.43
19 2 0.07
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (18 bp):
AAAAAGAAGAAAAGAAAG
Found at i:55211144 original size:26 final size:26
Alignment explanation
Indices: 55211106--55211161 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
55211096 GGCCCAGCAG
55211106 AGAAGAAAAAAAAACAG-AAGAAAAAA
1 AGAAGAAAAAAAAA-AGAAAGAAAAAA
*
55211132 AGAAGAAAGAAAAAAGAAAGAAAAAA
1 AGAAGAAAAAAAAAAGAAAGAAAAAA
55211158 AGAA
1 AGAA
55211162 AAGGGTTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 2 0.07
26 26 0.93
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (26 bp):
AGAAGAAAAAAAAAAGAAAGAAAAAA
Found at i:55211749 original size:19 final size:19
Alignment explanation
Indices: 55211725--55211761 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
55211715 TTCAAAAATT
*
55211725 TCGTGTTTTCAAAATTCTA
1 TCGTGTTTACAAAATTCTA
*
55211744 TCGTGTTTACAAATTTCT
1 TCGTGTTTACAAAATTCT
55211762 CGACTTTTCG
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:0.24, C:0.16, G:0.11, T:0.49
Consensus pattern (19 bp):
TCGTGTTTACAAAATTCTA
Found at i:55211855 original size:18 final size:18
Alignment explanation
Indices: 55211827--55211863 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
55211817 TGTTTCTAAT
55211827 ATTCTCATATTTCAAAAAA
1 ATTCTCATATTT-AAAAAA
55211846 ATTC-CATATTTAAAAAA
1 ATTCTCATATTTAAAAAA
55211863 A
1 A
55211864 AATCTTTCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
18 7 0.39
19 4 0.22
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (18 bp):
ATTCTCATATTTAAAAAA
Found at i:55211866 original size:19 final size:19
Alignment explanation
Indices: 55211827--55211864 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
55211817 TGTTTCTAAT
*
55211827 ATTCTCATATTTCAAAAAA
1 ATTCTCATATTTAAAAAAA
55211846 ATTC-CATATTTAAAAAAA
1 ATTCTCATATTTAAAAAAA
55211864 A
1 A
55211865 ATCTTTCTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (19 bp):
ATTCTCATATTTAAAAAAA
Found at i:55211969 original size:21 final size:22
Alignment explanation
Indices: 55211932--55211973 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
55211922 TCGTCTTTCG
55211932 AAATTCTCATGTTTTCAAAATA
1 AAATTCTCATGTTTTCAAAATA
*
55211954 AAATTC-CATTTTTTCAAAAT
1 AAATTCTCATGTTTTCAAAAT
55211974 TTTTCGTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.40, C:0.14, G:0.02, T:0.43
Consensus pattern (22 bp):
AAATTCTCATGTTTTCAAAATA
Done.