Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr12
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: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4026412 characters in sequence are not A, C, G, or T
File 87 of 297
Found at i:31517505 original size:50 final size:49
Alignment explanation
Indices: 31517361--31517507 Score: 177
Period size: 50 Copynumber: 3.0 Consensus size: 49
31517351 ATCTATTGTG
* *
31517361 AGGTCACGTGTGTAGTACTAAGTGCAGGCTATTATGTGTACCGGATAAT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAAT
* * * ** * **
31517410 CGGTCGCATGTGTAGTACTAAGTGCAGGCTACTACATGTATCAGATGGTT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGAT-AAT
* *
31517460 AGGTCACGTATGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAA
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAA
31517508 CCTTGTCTAC
Statistics
Matches: 77, Mismatches: 20, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
49 38 0.49
50 39 0.51
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (49 bp):
AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAAT
Found at i:31518738 original size:17 final size:17
Alignment explanation
Indices: 31518716--31518751 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
31518706 ATGTTTAAGT
*
31518716 CCGTTAACGCCTCGAAC
1 CCGTTAACGCCTCAAAC
31518733 CCGTTAACGCCTCAAAC
1 CCGTTAACGCCTCAAAC
31518750 CC
1 CC
31518752 AGTCCCGACG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.25, C:0.44, G:0.14, T:0.17
Consensus pattern (17 bp):
CCGTTAACGCCTCAAAC
Found at i:31521306 original size:24 final size:24
Alignment explanation
Indices: 31521270--31521317 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
31521260 AGACACACCA
*
31521270 TAGCTCTTACGAGCATCCTGTTAT
1 TAGCCCTTACGAGCATCCTGTTAT
* *
31521294 TAGCCCTTTCGAGCTTCCTGTTAT
1 TAGCCCTTACGAGCATCCTGTTAT
31521318 ATGGTTCTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.17, C:0.27, G:0.17, T:0.40
Consensus pattern (24 bp):
TAGCCCTTACGAGCATCCTGTTAT
Found at i:31521443 original size:26 final size:25
Alignment explanation
Indices: 31521407--31521471 Score: 67
Period size: 27 Copynumber: 2.5 Consensus size: 25
31521397 TTAGCTCTTA
* * *
31521407 TGAGCATCCTGAGTATAGGCTTTTTG
1 TGAGCTTCCTGA-AATAGGCTCTTTG
*
31521433 TGAGCTTCCTGTTAAATTGGCTCTTTG
1 TGAGCTTCCTG--AAATAGGCTCTTTG
31521460 TGAGCTTCCTGA
1 TGAGCTTCCTGA
31521472 TAGTGCTAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
25 1 0.03
26 10 0.30
27 21 0.64
28 1 0.03
ACGTcount: A:0.17, C:0.18, G:0.25, T:0.40
Consensus pattern (25 bp):
TGAGCTTCCTGAAATAGGCTCTTTG
Found at i:31521538 original size:25 final size:25
Alignment explanation
Indices: 31521510--31521602 Score: 77
Period size: 24 Copynumber: 3.8 Consensus size: 25
31521500 GTCTATCTGA
31521510 AGCTTCCGTTATATGGCTCTTTGTG
1 AGCTTCCGTTATATGGCTCTTTGTG
* *
31521535 AGCTTCACG--ATACGGTTCTTTGTG
1 AGCTTC-CGTTATATGGCTCTTTGTG
* * *
31521559 AACTTCC-TAATTATGGCTC-TTATG
1 AGCTTCCGTTA-TATGGCTCTTTGTG
*
31521583 AGCTTCCTGTTATATAGCTC
1 AGCTTCC-GTTATATGGCTC
31521603 GAATAAGCTT
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
23 1 0.02
24 29 0.55
25 19 0.36
26 4 0.08
ACGTcount: A:0.18, C:0.22, G:0.19, T:0.41
Consensus pattern (25 bp):
AGCTTCCGTTATATGGCTCTTTGTG
Found at i:31521637 original size:24 final size:24
Alignment explanation
Indices: 31521520--31521639 Score: 68
Period size: 24 Copynumber: 5.0 Consensus size: 24
31521510 AGCTTCCGTT
* *
31521520 ATATGGCTCTTTGTGAGCTTCACG
1 ATATGGCTCTTTGTAAGCTTCCCG
* * **
31521544 ATACGGTTCTTTGTGAA-CTTCCTA
1 ATATGGCTCTTTGT-AAGCTTCCCG
*
31521568 ATTATGGCTCTTATG--AGCTTCCTG
1 A-TATGGCTCTT-TGTAAGCTTCCCG
* ***
31521592 TTATATAGCTC-GAATAAGCTTCCCG
1 --ATATGGCTCTTTGTAAGCTTCCCG
31521617 ATATGGCTCTTTGTAAGCTTCCC
1 ATATGGCTCTTTGTAAGCTTCCC
31521640 ATGATAAGGC
Statistics
Matches: 69, Mismatches: 18, Indels: 18
0.66 0.17 0.17
Matches are distributed among these distances:
23 9 0.13
24 33 0.48
25 24 0.35
26 3 0.04
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.38
Consensus pattern (24 bp):
ATATGGCTCTTTGTAAGCTTCCCG
Found at i:31522616 original size:21 final size:22
Alignment explanation
Indices: 31522574--31522616 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
31522564 TAAACGAAGT
*
31522574 ACAATATTATTTAACTACATAA
1 ACAATATTATTTAACTAAATAA
31522596 ACAATA-TAGTTT-ACTAAATAA
1 ACAATATTA-TTTAACTAAATAA
31522617 TTATATGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.51, C:0.12, G:0.02, T:0.35
Consensus pattern (22 bp):
ACAATATTATTTAACTAAATAA
Found at i:31533485 original size:62 final size:62
Alignment explanation
Indices: 31533388--31533511 Score: 212
Period size: 62 Copynumber: 2.0 Consensus size: 62
31533378 TTCTCATGGC
* * *
31533388 TTCCTCCGGTTCCCATGTAGCTTCTTCTACTCCATGTCTTTGCCATAACACTTTCACTAAAG
1 TTCCTCCGATTCCCACGTAGCTTATTCTACTCCATGTCTTTGCCATAACACTTTCACTAAAG
*
31533450 TTCCTCCGATTCCCACGTAGCTTATTCTACTCCATGTCTTTGCCATATCACTTTCACTAAAG
1 TTCCTCCGATTCCCACGTAGCTTATTCTACTCCATGTCTTTGCCATAACACTTTCACTAAAG
31533512 CTATGCTTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.20, C:0.32, G:0.10, T:0.37
Consensus pattern (62 bp):
TTCCTCCGATTCCCACGTAGCTTATTCTACTCCATGTCTTTGCCATAACACTTTCACTAAAG
Found at i:31534113 original size:277 final size:277
Alignment explanation
Indices: 31533619--31534172 Score: 1099
Period size: 277 Copynumber: 2.0 Consensus size: 277
31533609 AGAAATCACA
31533619 TGTGAAGGATCAGAACGGTAACGTCGCAACATTGATACATGAAACACGTTATGAATTCTTTATAA
1 TGTGAAGGATCAGAACGGTAACGTCGCAACATTGATACATGAAACACGTTATGAATTCTTTATAA
31533684 CTCTGCCGGTAAAGCCAACCGATATGCCACTGGTCCAATCCTTTCAATAATCTTGTACGGCCCAA
66 CTCTGCCGGTAAAGCCAACCGATATGCCACTGGTCCAATCCTTTCAATAATCTTGTACGGCCCAA
31533749 TAAAATGCGGACTCAACTTGCCTTTTCGGCCAAACCTCAGAATCTTCTTCCATGGTGACACCTTT
131 TAAAATGCGGACTCAACTTGCCTTTTCGGCCAAACCTCAGAATCTTCTTCCATGGTGACACCTTT
31533814 AAGAACACTTTATCACCCACCTGAAATTCAATCTCTTTTCTTTTTAAATCTGCATATGACTTTTG
196 AAGAACACTTTATCACCCACCTGAAATTCAATCTCTTTTCTTTTTAAATCTGCATATGACTTTTG
31533879 TCGATCTGAAGCTGCTT
261 TCGATCTGAAGCTGCTT
31533896 TGTGAAGGATCAGAACGGTAACGTCGCAACATTGATACATGAAACACGTTATGAATTCTTTATAA
1 TGTGAAGGATCAGAACGGTAACGTCGCAACATTGATACATGAAACACGTTATGAATTCTTTATAA
31533961 CTCTGCCGGTAAAGCCAACCGATATGCCACTGGTCCAATCCTTTCAATAATCTTGTACGGCCCAA
66 CTCTGCCGGTAAAGCCAACCGATATGCCACTGGTCCAATCCTTTCAATAATCTTGTACGGCCCAA
31534026 TAAAATGCGGACTCAACTTGCCTTTTCGGCCAAACCTCAGAATCTTCTTCCATGGTGACACCTTT
131 TAAAATGCGGACTCAACTTGCCTTTTCGGCCAAACCTCAGAATCTTCTTCCATGGTGACACCTTT
31534091 AAGAACACTTTATCACCCACCTGAAATTCAATCTCTTTTCTTTTTAAATCTGCATATGACTTTTG
196 AAGAACACTTTATCACCCACCTGAAATTCAATCTCTTTTCTTTTTAAATCTGCATATGACTTTTG
*
31534156 TTGATCTGAAGCTGCTT
261 TCGATCTGAAGCTGCTT
31534173 GAAAGAAATC
Statistics
Matches: 276, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
277 276 1.00
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.31
Consensus pattern (277 bp):
TGTGAAGGATCAGAACGGTAACGTCGCAACATTGATACATGAAACACGTTATGAATTCTTTATAA
CTCTGCCGGTAAAGCCAACCGATATGCCACTGGTCCAATCCTTTCAATAATCTTGTACGGCCCAA
TAAAATGCGGACTCAACTTGCCTTTTCGGCCAAACCTCAGAATCTTCTTCCATGGTGACACCTTT
AAGAACACTTTATCACCCACCTGAAATTCAATCTCTTTTCTTTTTAAATCTGCATATGACTTTTG
TCGATCTGAAGCTGCTT
Found at i:31557765 original size:22 final size:22
Alignment explanation
Indices: 31557737--31557784 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
31557727 TTGATGTGAA
31557737 TGATTTATCTATTTTAGGTTTC
1 TGATTTATCTATTTTAGGTTTC
31557759 TGATTTATCTATTTTAGGTTTC
1 TGATTTATCTATTTTAGGTTTC
31557781 TGAT
1 TGAT
31557785 ATCTCTTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.19, C:0.08, G:0.15, T:0.58
Consensus pattern (22 bp):
TGATTTATCTATTTTAGGTTTC
Found at i:31562381 original size:2 final size:2
Alignment explanation
Indices: 31562374--31562430 Score: 69
Period size: 2 Copynumber: 28.5 Consensus size: 2
31562364 CATTCTTTAA
* * *
31562374 AG AG AG AG AG AG AG AG GG AG AG AG AG GG AG AG AG AG GG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* *
31562416 AG GG AG AG AG GG AG A
1 AG AG AG AG AG AG AG A
31562431 AGGAGCATTA
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (2 bp):
AG
Found at i:31562699 original size:24 final size:23
Alignment explanation
Indices: 31562653--31562700 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
31562643 ATTGAAAGCC
* *
31562653 AATAAAAAAAAAACTTGATTTCA
1 AATAAAAAAAAAACTTAAATTCA
*
31562676 AATAAAAAAAGAACTCTAAATTCA
1 AATAAAAAAAAAACT-TAAATTCA
31562700 A
1 A
31562701 CTAGAAGCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.62, C:0.10, G:0.04, T:0.23
Consensus pattern (23 bp):
AATAAAAAAAAAACTTAAATTCA
Found at i:31566628 original size:46 final size:44
Alignment explanation
Indices: 31566534--31566742 Score: 147
Period size: 46 Copynumber: 4.5 Consensus size: 44
31566524 ATGCTAATGC
*
31566534 CATGTCCCAGACATGGTCTTACACTGGCTCATCTCGTAGCCGGTG
1 CATGTCCCAGACAT-GTCTTACACTGGCTCATCTCGTAGCCGATG
** *
31566579 CATGTCTTAGACATGTTTTACACTGGCTTACATCTCG-AGGCCGATG
1 CATGTCCCAGACATGTCTTACACTGGC-T-CATCTCGTA-GCCGATG
* * * *
31566625 CATGTCCCAGATATGTCTTACACTAGCTC-TCGTC-TCAATGTCGATAC
1 CATGTCCCAGACATGTCTTACACTGGCTCATC-TCGT--A-GCCGAT-G
* * * * *
31566672 CATGTCCCAAACATGGTCTCACACTGTCTC-TCATAATGTGGCCGATG
1 CATGTCCCAGACAT-GTCTTACACTGGCTCATC-T--CGTAGCCGATG
*
31566719 CATGTCCTAGACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
31566743 AGCTTACAAT
Statistics
Matches: 127, Mismatches: 25, Indels: 23
0.73 0.14 0.13
Matches are distributed among these distances:
43 2 0.02
44 15 0.12
45 15 0.12
46 50 0.39
47 24 0.19
48 20 0.16
51 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.19, T:0.30
Consensus pattern (44 bp):
CATGTCCCAGACATGTCTTACACTGGCTCATCTCGTAGCCGATG
Found at i:31569656 original size:23 final size:23
Alignment explanation
Indices: 31569567--31569650 Score: 150
Period size: 23 Copynumber: 3.7 Consensus size: 23
31569557 ATTAACATTT
31569567 TTCGTGAACATGTTCATCTAATG
1 TTCGTGAACATGTTCATCTAATG
31569590 TTCGTGAACATGTTCATCTAATG
1 TTCGTGAACATGTTCATCTAATG
* *
31569613 TTCGTGAACATATTCATTTAATG
1 TTCGTGAACATGTTCATCTAATG
31569636 TTCGTGAACATGTTC
1 TTCGTGAACATGTTC
31569651 GATTAAGTTA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 58 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (23 bp):
TTCGTGAACATGTTCATCTAATG
Found at i:31571806 original size:22 final size:21
Alignment explanation
Indices: 31571778--31571818 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
31571768 TAACGAATTA
*
31571778 AATGTTTAATATGAGAAAAGGT
1 AATGTTTAATA-GACAAAAGGT
31571800 AATGTTTAATAGACAAAAG
1 AATGTTTAATAGACAAAAG
31571819 ACCTAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.49, C:0.02, G:0.20, T:0.29
Consensus pattern (21 bp):
AATGTTTAATAGACAAAAGGT
Found at i:31574817 original size:19 final size:19
Alignment explanation
Indices: 31574793--31574837 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
31574783 AGATCAACTC
31574793 ACTTCAATGATCCTAATTA
1 ACTTCAATGATCCTAATTA
31574812 ACTTCAATGATCCTAATTA
1 ACTTCAATGATCCTAATTA
31574831 ACTTCAA
1 ACTTCAA
31574838 AATTTGGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.38, C:0.22, G:0.04, T:0.36
Consensus pattern (19 bp):
ACTTCAATGATCCTAATTA
Found at i:31575191 original size:16 final size:18
Alignment explanation
Indices: 31575172--31575204 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
31575162 CATACAAATT
31575172 CCAAAAC-ATA-ATAGTA
1 CCAAAACGATAGATAGTA
31575188 CCAAAACGATAGATAGT
1 CCAAAACGATAGATAGT
31575205 GTGACGAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.52, C:0.18, G:0.12, T:0.18
Consensus pattern (18 bp):
CCAAAACGATAGATAGTA
Found at i:31581493 original size:46 final size:46
Alignment explanation
Indices: 31581443--31581536 Score: 118
Period size: 46 Copynumber: 2.0 Consensus size: 46
31581433 GTCATCATAT
* *
31581443 AATATGCCACAAAGAATTTATA-GAACATGCCATAAAAGCTTTACAG
1 AATATGCCACAAAGAATTTA-ACGAACAAGCCACAAAAGCTTTACAG
* * * *
31581489 AATATGCCACACAGACTTTAACGAACAAGTCACAAAGGCTTTACAG
1 AATATGCCACAAAGAATTTAACGAACAAGCCACAAAAGCTTTACAG
31581535 AA
1 AA
31581537 CATTACGTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
45 1 0.02
46 40 0.98
ACGTcount: A:0.45, C:0.20, G:0.14, T:0.21
Consensus pattern (46 bp):
AATATGCCACAAAGAATTTAACGAACAAGCCACAAAAGCTTTACAG
Found at i:31581537 original size:23 final size:23
Alignment explanation
Indices: 31581448--31581538 Score: 67
Period size: 23 Copynumber: 4.0 Consensus size: 23
31581438 CATATAATAT
** * *
31581448 GCCACAAAGAATTTATAGAACAT
1 GCCACAAAGGCTTTACAGAACAA
* * * *
31581471 GCCATAAAAGCTTTACAGAATAT
1 GCCACAAAGGCTTTACAGAACAA
* *
31581494 GCCACACAGACTTTA-ACGAACAA
1 GCCACAAAGGCTTTACA-GAACAA
*
31581517 GTCACAAAGGCTTTACAGAACA
1 GCCACAAAGGCTTTACAGAACA
31581539 TTACGTGTTT
Statistics
Matches: 51, Mismatches: 15, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
22 1 0.02
23 49 0.96
24 1 0.02
ACGTcount: A:0.44, C:0.22, G:0.14, T:0.20
Consensus pattern (23 bp):
GCCACAAAGGCTTTACAGAACAA
Found at i:31587994 original size:20 final size:20
Alignment explanation
Indices: 31587969--31588014 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
31587959 AGGAATGTCA
* * *
31587969 ATACCTTAGGAAATATATCG
1 ATACCTTAAGAAAAAAATCG
31587989 ATACCTTAAGAAAAAAATCG
1 ATACCTTAAGAAAAAAATCG
31588009 ATACCT
1 ATACCT
31588015 ACCGAGGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.26
Consensus pattern (20 bp):
ATACCTTAAGAAAAAAATCG
Found at i:31591850 original size:13 final size:13
Alignment explanation
Indices: 31591829--31591892 Score: 92
Period size: 13 Copynumber: 4.9 Consensus size: 13
31591819 TAAACCAAAT
*
31591829 TTTTTAAAAGCAC
1 TTTTCAAAAGCAC
*
31591842 TTCTCAAAAGCAC
1 TTTTCAAAAGCAC
* *
31591855 TTTTCCATAGCAC
1 TTTTCAAAAGCAC
31591868 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
31591881 TTTTCAAAAGCA
1 TTTTCAAAAGCA
31591893 TTGCCAAACT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 44 1.00
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:31604261 original size:20 final size:19
Alignment explanation
Indices: 31604198--31604261 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 19
31604188 TAAGAAAATA
31604198 TTATTATATATATTTTAT-T
1 TTATTA-ATATATTTTATAT
*
31604217 TTAATTAATATCATTATTA-AG
1 TT-ATTAATAT-ATT-TTATAT
31604238 TTATTAATACTATTTTATAT
1 TTATTAATA-TATTTTATAT
31604258 TTAT
1 TTAT
31604262 AAAATCAGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
19 9 0.24
20 22 0.59
21 6 0.16
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (19 bp):
TTATTAATATATTTTATAT
Found at i:31609118 original size:16 final size:16
Alignment explanation
Indices: 31609097--31609127 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31609087 CCTAAGGATG
31609097 AAATAAAAAGAAAATT
1 AAATAAAAAGAAAATT
*
31609113 AAATAAAAATAAAAT
1 AAATAAAAAGAAAAT
31609128 AAAAAGTAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (16 bp):
AAATAAAAAGAAAATT
Found at i:31611637 original size:34 final size:34
Alignment explanation
Indices: 31611594--31611662 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
31611584 AGGGTCTGCT
31611594 GTATCTAATAGTACTTTGTCTCCAACCTTAAGTA
1 GTATCTAATAGTACTTTGTCTCCAACCTTAAGTA
31611628 GTATCTAATAGTACTTTGTCTCCAACCTTAAGTA
1 GTATCTAATAGTACTTTGTCTCCAACCTTAAGTA
31611662 G
1 G
31611663 CTTTGGTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (34 bp):
GTATCTAATAGTACTTTGTCTCCAACCTTAAGTA
Found at i:31615851 original size:18 final size:17
Alignment explanation
Indices: 31615806--31615867 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 17
31615796 CCGAGATAAT
*
31615806 AAAAATAATAAATTTAAA
1 AAAAATAATTAA-TTAAA
31615824 AATAAA-AATTAATTAAA
1 AA-AAATAATTAATTAAA
* *
31615841 GAAAAATAATTTAGTAAA
1 -AAAAATAATTAATTAAA
31615859 TAAAAATAA
1 -AAAAATAA
31615868 ACTAGAAAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
17 8 0.22
18 26 0.70
19 3 0.08
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.27
Consensus pattern (17 bp):
AAAAATAATTAATTAAA
Found at i:31619409 original size:32 final size:33
Alignment explanation
Indices: 31619373--31619441 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
31619363 GAGCTCAGAA
31619373 ATGAT-AAAATCTATCTTTAAATTGTCTATTTC
1 ATGATAAAAATCTATCTTTAAATTGTCTATTTC
31619405 ATGATAAAAATCTATCTTTAAATTGTCTATTTC
1 ATGATAAAAATCTATCTTTAAATTGTCTATTTC
31619438 ATGA
1 ATGA
31619442 AACCTATGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 5 0.14
33 31 0.86
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (33 bp):
ATGATAAAAATCTATCTTTAAATTGTCTATTTC
Found at i:31623295 original size:25 final size:25
Alignment explanation
Indices: 31623258--31623306 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
31623248 CTATCGAAGA
*
31623258 AAATAAAGAATATATCAATGAATGC
1 AAATAAAGAATATATCAAAGAATGC
* * *
31623283 AAATAATGTATATATTAAAGAATG
1 AAATAAAGAATATATCAAAGAATG
31623307 ATATATAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.55, C:0.04, G:0.12, T:0.29
Consensus pattern (25 bp):
AAATAAAGAATATATCAAAGAATGC
Found at i:31624513 original size:22 final size:22
Alignment explanation
Indices: 31624470--31624517 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
31624460 TCCTAATTAG
*
31624470 TTTTTTTTATTTCATTTGTTTA
1 TTTTTTTTATTTCATTTCTTTA
*
31624492 TTTTTCTTTCTTTC-TTTCTTTA
1 TTTTT-TTTATTTCATTTCTTTA
31624514 TTTT
1 TTTT
31624518 CATTATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.08, C:0.10, G:0.02, T:0.79
Consensus pattern (22 bp):
TTTTTTTTATTTCATTTCTTTA
Found at i:31627941 original size:22 final size:22
Alignment explanation
Indices: 31627902--31627943 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
31627892 GGCAGTAATG
*
31627902 GTGGTGGTTCGGAGGTGGTGCA
1 GTGGTGGTCCGGAGGTGGTGCA
31627924 GTGGTGGTCCGGTA-GTGGTG
1 GTGGTGGTCCGG-AGGTGGTG
31627944 TGGTTAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.07, C:0.10, G:0.55, T:0.29
Consensus pattern (22 bp):
GTGGTGGTCCGGAGGTGGTGCA
Found at i:31637183 original size:17 final size:17
Alignment explanation
Indices: 31637161--31637194 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
31637151 TGATTGATTT
31637161 CTGAAAATAAATAGTAA
1 CTGAAAATAAATAGTAA
* *
31637178 CTGAAATTAAATGGTAA
1 CTGAAAATAAATAGTAA
31637195 ACTCTAGTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.06, G:0.15, T:0.26
Consensus pattern (17 bp):
CTGAAAATAAATAGTAA
Found at i:31643289 original size:53 final size:53
Alignment explanation
Indices: 31643232--31643346 Score: 169
Period size: 53 Copynumber: 2.2 Consensus size: 53
31643222 TATCTCAGAC
*
31643232 ATGGTCTTATACGGCA-TCACATTATCACAATATACCAATGCCATAGCCCAGCT
1 ATGGTCTTATACGG-AGTCACATTATCACAATACACCAATGCCATAGCCCAGCT
* * * *
31643285 ATGGTCTTATACGGAGTCACATTATCACATTGCACCGATGCCATAGCCCATCT
1 ATGGTCTTATACGGAGTCACATTATCACAATACACCAATGCCATAGCCCAGCT
31643338 ATGGTCTTA
1 ATGGTCTTA
31643347 AACGAGCGCA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
52 1 0.02
53 55 0.98
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (53 bp):
ATGGTCTTATACGGAGTCACATTATCACAATACACCAATGCCATAGCCCAGCT
Found at i:31646150 original size:24 final size:25
Alignment explanation
Indices: 31646108--31646155 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
31646098 ACACAAACAC
*
31646108 AGCTCTTCATGAGCGTCCTGATATA
1 AGCTCTTCATGAGCGTCCTAATATA
*
31646133 AGCTCTT-ATGAGCTTCCTAATAT
1 AGCTCTTCATGAGCGTCCTAATAT
31646156 GGCTCGCTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (25 bp):
AGCTCTTCATGAGCGTCCTAATATA
Found at i:31659166 original size:41 final size:42
Alignment explanation
Indices: 31659109--31659262 Score: 177
Period size: 41 Copynumber: 3.7 Consensus size: 42
31659099 ACTAAGACTA
31659109 CGTGTAAGACCATATCTGGGATATGGCATC-ATATGAGATTT
1 CGTGTAAGACCATATCTGGGATATGGCATCAATATGAGATTT
* * *
31659150 CGTGTAAGACCATATCTGTGATATGGCGTCAACATGAGATTT
1 CGTGTAAGACCATATCTGGGATATGGCATCAATATGAGATTT
* * * * * *
31659192 C-AGTAAGACCATAACTGGGCTATTGGCATCGATATAAGATTA
1 CGTGTAAGACCATATCTGGGATA-TGGCATCAATATGAGATTT
* * *
31659234 CATGTAAGACCATATCTAGGATGTGGCAT
1 CGTGTAAGACCATATCTGGGATATGGCAT
31659263 TGGTATGGTA
Statistics
Matches: 93, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
41 45 0.48
42 32 0.34
43 16 0.17
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.29
Consensus pattern (42 bp):
CGTGTAAGACCATATCTGGGATATGGCATCAATATGAGATTT
Found at i:31666688 original size:41 final size:42
Alignment explanation
Indices: 31666631--31666785 Score: 134
Period size: 43 Copynumber: 3.7 Consensus size: 42
31666621 ACTAAGACTA
* *
31666631 CGTGTAAGATCATATCTGGGATATGGCATCG-TATGAGATTT
1 CGTGTAAGACCATATCTAGGATATGGCATCGATATGAGATTT
* * ** *
31666672 CGTGTAAGATCATATCT-GTGATGTGGTGTCGACATGAGATTT
1 CGTGTAAGACCATATCTAG-GATATGGCATCGATATGAGATTT
* * * * * * * *
31666714 CTTATAAGACCATAGCTAGGCTATTAGTATCGATAAGAGATTA
1 CGTGTAAGACCATATCTAGGATA-TGGCATCGATATGAGATTT
*
31666757 CATGTAAGACCATATCTAGGATATGGCAT
1 CGTGTAAGACCATATCTAGGATATGGCAT
31666786 TGGTATGGTA
Statistics
Matches: 89, Mismatches: 21, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
40 1 0.01
41 26 0.29
42 28 0.31
43 34 0.38
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (42 bp):
CGTGTAAGACCATATCTAGGATATGGCATCGATATGAGATTT
Found at i:31666722 original size:42 final size:41
Alignment explanation
Indices: 31666635--31666727 Score: 105
Period size: 41 Copynumber: 2.2 Consensus size: 41
31666625 AGACTACGTG
* *
31666635 TAAGATCATATCTGGGATATGGCATCGTATGAGATTTCGTG
1 TAAGATCATATCTGGGATATGGCATCGCATGAGATTTCGTA
* * ** *
31666676 TAAGATCATATCTGTGATGTGGTGTCGACATGAGATTTCTTA
1 TAAGATCATATCTGGGATATGGCATCG-CATGAGATTTCGTA
*
31666718 TAAGACCATA
1 TAAGATCATA
31666728 GCTAGGCTAT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 23 0.53
42 20 0.47
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.34
Consensus pattern (41 bp):
TAAGATCATATCTGGGATATGGCATCGCATGAGATTTCGTA
Found at i:31670755 original size:4 final size:4
Alignment explanation
Indices: 31670746--31670770 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
31670736 CACTACTCTT
31670746 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
31670771 CCTTCATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:31671508 original size:18 final size:17
Alignment explanation
Indices: 31671485--31671526 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
31671475 TATATATTAG
31671485 ATTAAATGTAA-ATTTAT
1 ATTAAAT-TAATATTTAT
31671502 CATTAAATTAATTATTTAT
1 -ATTAAATTAA-TATTTAT
31671521 ATTAAA
1 ATTAAA
31671527 AATTTTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.14
18 13 0.59
19 6 0.27
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (17 bp):
ATTAAATTAATATTTAT
Found at i:31671563 original size:25 final size:23
Alignment explanation
Indices: 31671512--31671564 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
31671502 CATTAAATTA
* *
31671512 ATTATTTATATTAAAAATTTTAT
1 ATTATTTATATTAAAAAATTAAT
31671535 -TTATTTATATTATTAAAAATTAAT
1 ATTATTTATATTA--AAAAATTAAT
31671559 ATTATT
1 ATTATT
31671565 AGCGGAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 12 0.48
24 8 0.32
25 5 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
ATTATTTATATTAAAAAATTAAT
Found at i:31671941 original size:2 final size:2
Alignment explanation
Indices: 31671936--31671972 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
31671926 TTCTTTAATT
31671936 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
31671973 GTTTTTTAGT
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:31674875 original size:2 final size:2
Alignment explanation
Indices: 31674868--31674894 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31674858 AAGGTGCTGT
31674868 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
31674895 GGGTGTTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:31676997 original size:70 final size:70
Alignment explanation
Indices: 31676884--31677021 Score: 249
Period size: 70 Copynumber: 2.0 Consensus size: 70
31676874 TTCAATGCCA
31676884 TCACATCTAATGATATTTTGGCATTTAGTATCAGGTGCTTTTGGATTTAATGTTGGCTTTTGTTA
1 TCACATCTAATGATATTTTGGCATTTAGTATCAGGTGCTTTTGGATTTAATGTTGGCTTTTGTTA
31676949 AAGCC
66 AAGCC
* * *
31676954 TCACATCTAATGATATTTTGGCCTTTCGTATCTGGTGCTTTTGGATTTAATGTTGGCTTTTGTTA
1 TCACATCTAATGATATTTTGGCATTTAGTATCAGGTGCTTTTGGATTTAATGTTGGCTTTTGTTA
31677019 AAG
66 AAG
31677022 TTTATTTTAA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.21, C:0.13, G:0.20, T:0.46
Consensus pattern (70 bp):
TCACATCTAATGATATTTTGGCATTTAGTATCAGGTGCTTTTGGATTTAATGTTGGCTTTTGTTA
AAGCC
Found at i:31688949 original size:16 final size:18
Alignment explanation
Indices: 31688910--31688951 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
31688900 TAAATTCATA
31688910 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
31688927 ATTTTTATATATTATG-T
1 ATATTTATATATTATGTT
31688944 A-ATTTATA
1 ATATTTATA
31688952 ATACATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 6 0.27
17 7 0.32
18 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:31690939 original size:26 final size:25
Alignment explanation
Indices: 31690909--31690996 Score: 79
Period size: 26 Copynumber: 3.4 Consensus size: 25
31690899 TTGTTATTAA
31690909 ATTTTAATAAGATTATTATTAAATAT
1 ATTTTAATAA-ATTATTATTAAATAT
** * *
31690935 ATTTTAATAAAAAATAATTTAATCAT
1 ATTTTAATAAATTATTATTAAAT-AT
* *
31690961 A-TTTAACATAATTGTTATTAAATAT
1 ATTTTAATA-AATTATTATTAAATAT
*
31690986 AATTTAATAAA
1 ATTTTAATAAA
31690997 ATAATATATA
Statistics
Matches: 48, Mismatches: 11, Indels: 7
0.73 0.17 0.11
Matches are distributed among these distances:
25 20 0.42
26 28 0.58
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (25 bp):
ATTTTAATAAATTATTATTAAATAT
Found at i:31696450 original size:79 final size:79
Alignment explanation
Indices: 31696317--31696625 Score: 458
Period size: 79 Copynumber: 3.9 Consensus size: 79
31696307 GAGTCACATC
* * * *
31696317 TCATGTAACTGTAGGGAATCAGGATTA-CCTTTTCAGGTCAAATCCTACCCACCTTAAGTTATCA
1 TCATGTAACCGTAGCGAATCAGGATTACCCTTTTCAGGTCAAATCCTATCCACCTTAAGTTACCA
* *
31696381 TAAGGAATTATATA
66 TAATGAATCATATA
* * * *
31696395 TCGTGTAATCGTAGCGAATCAGGATTACCCTTTTTAGGTCAAATCCTATCCACCTTAGGTTACCA
1 TCATGTAACCGTAGCGAATCAGGATTACCCTTTTCAGGTCAAATCCTATCCACCTTAAGTTACCA
31696460 TAATGAATCATATA
66 TAATGAATCATATA
* *
31696474 TCATGTAACCGTAGCGAATCAGGATTACCCTTTTTAGGTCAAATCCTATCCACCTTAGGTTACCA
1 TCATGTAACCGTAGCGAATCAGGATTACCCTTTTCAGGTCAAATCCTATCCACCTTAAGTTACCA
31696539 TAATGAATCATATA
66 TAATGAATCATATA
* ** *
31696553 TCATGTAACCGTAGCGAATCAGGATTACTCTTTTCAGGTCAAATCCTATCTGCCTTAAGTTACCG
1 TCATGTAACCGTAGCGAATCAGGATTACCCTTTTCAGGTCAAATCCTATCCACCTTAAGTTACCA
*
31696618 TAGTGAAT
66 TAATGAAT
31696626 TAGGAATAAA
Statistics
Matches: 211, Mismatches: 19, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
78 23 0.11
79 188 0.89
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (79 bp):
TCATGTAACCGTAGCGAATCAGGATTACCCTTTTCAGGTCAAATCCTATCCACCTTAAGTTACCA
TAATGAATCATATA
Found at i:31696656 original size:40 final size:40
Alignment explanation
Indices: 31696592--31696729 Score: 141
Period size: 40 Copynumber: 3.5 Consensus size: 40
31696582 CTTTTCAGGT
** * * * *
31696592 CAAATCCTATCTGCCTTAAGTTACCGTAGTGAATTAGGAA
1 CAAATCCTATCCACTTTAAATTACCATAGTGAATCAGGAA
* * *
31696632 TAAATCCTATTCACTTTAAATTACCATAGTGAATCAGGAG
1 CAAATCCTATCCACTTTAAATTACCATAGTGAATCAGGAA
* ** **
31696672 CAAATCCTATCCACTTTGAGGTATTATAGTGAATCAGGAA
1 CAAATCCTATCCACTTTAAATTACCATAGTGAATCAGGAA
*
31696712 CGAATCCTATCCACTTTA
1 CAAATCCTATCCACTTTA
31696730 TATTCTCAAG
Statistics
Matches: 79, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 79 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (40 bp):
CAAATCCTATCCACTTTAAATTACCATAGTGAATCAGGAA
Found at i:31698386 original size:18 final size:18
Alignment explanation
Indices: 31698363--31698399 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
31698353 TTATATATTA
*
31698363 AATAATTAATAATAAAAT
1 AATAATAAATAATAAAAT
*
31698381 AATAATAAATAGTAAAAT
1 AATAATAAATAATAAAAT
31698399 A
1 A
31698400 TCTCATTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (18 bp):
AATAATAAATAATAAAAT
Found at i:31699546 original size:28 final size:27
Alignment explanation
Indices: 31699497--31699550 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
31699487 AACCCCCAAA
31699497 ATCAGATACAGAACATGCATATCAAACT
1 ATCAGATACAGAACATGCATAT-AAACT
31699525 ATCAGATA-A-AACATGCTTATATAAAC
1 ATCAGATACAGAACATGC--ATATAAAC
31699551 AGATATCAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 7 0.29
27 5 0.21
28 12 0.50
ACGTcount: A:0.48, C:0.19, G:0.09, T:0.24
Consensus pattern (27 bp):
ATCAGATACAGAACATGCATATAAACT
Found at i:31700778 original size:9 final size:9
Alignment explanation
Indices: 31700750--31700843 Score: 93
Period size: 9 Copynumber: 10.6 Consensus size: 9
31700740 ATAAGTATAA
31700750 AATTAACCG
1 AATTAACCG
*
31700759 -ATTAACTG
1 AATTAACCG
*
31700767 AATTAATCG
1 AATTAACCG
31700776 AATTAACCG
1 AATTAACCG
*
31700785 AATTACCCG
1 AATTAACCG
31700794 AATT-ACTCG
1 AATTAAC-CG
*
31700803 AATTACCCG
1 AATTAACCG
** *
31700812 AATTAGTCA
1 AATTAACCG
*
31700821 AATTAACTG
1 AATTAACCG
31700830 AATTAACCG
1 AATTAACCG
31700839 AATTA
1 AATTA
31700844 TTTGTATAAA
Statistics
Matches: 67, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
8 8 0.12
9 58 0.87
10 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (9 bp):
AATTAACCG
Found at i:31712736 original size:27 final size:26
Alignment explanation
Indices: 31712706--31712762 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
31712696 AATACCTTTA
* *
31712706 TAGGTGAAAAATTTACAGATTTACCCC
1 TAGGAGAAAAA-TTACAGATATACCCC
* *
31712733 TAGGAGCAAAATTACTGATATACCCC
1 TAGGAGAAAAATTACAGATATACCCC
31712759 TAGG
1 TAGG
31712763 GTTAAGGTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 17 0.65
27 9 0.35
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (26 bp):
TAGGAGAAAAATTACAGATATACCCC
Found at i:31719863 original size:36 final size:35
Alignment explanation
Indices: 31719757--31719854 Score: 124
Period size: 35 Copynumber: 2.8 Consensus size: 35
31719747 TCGGTTGGAC
* *
31719757 TAGCTTTTACGAGCATTGGTGTGTTTTTGAGGGAT
1 TAGCTCTTACGAGCATTGGTGTGTTTTAGAGGGAT
* *
31719792 TAGCTCTTACGAGCGTTGGTGTGTTTTAGATGGAT
1 TAGCTCTTACGAGCATTGGTGTGTTTTAGAGGGAT
* * *
31719827 TGGCTCTTATGAGCATCTGGTTTGTTTT
1 TAGCTCTTACGAGCAT-TGGTGTGTTTT
31719855 GGTAGGATTT
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
35 44 0.81
36 10 0.19
ACGTcount: A:0.15, C:0.11, G:0.30, T:0.44
Consensus pattern (35 bp):
TAGCTCTTACGAGCATTGGTGTGTTTTAGAGGGAT
Found at i:31723259 original size:28 final size:28
Alignment explanation
Indices: 31723227--31723282 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
31723217 AACTCACACA
*
31723227 ACACAACAGTTCTCATAACATAAGCAGT
1 ACACAACAGTTCTCATAAAATAAGCAGT
31723255 ACACAACAGTTCTCATAAAATAAGCAGT
1 ACACAACAGTTCTCATAAAATAAGCAGT
31723283 GTACATATAA
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:0.45, C:0.23, G:0.11, T:0.21
Consensus pattern (28 bp):
ACACAACAGTTCTCATAAAATAAGCAGT
Found at i:31726072 original size:42 final size:42
Alignment explanation
Indices: 31726017--31726125 Score: 119
Period size: 42 Copynumber: 2.6 Consensus size: 42
31726007 CCCTAATGGA
* * * * * *
31726017 TTTCAGTTTAGCTCTTTTGAGCTTTAGTTCAACCCTTATGTGT
1 TTTC-GTTCAGCTCTTATGAGCTTCAGTTCAACCCTCACGGGT
*
31726060 TTTCGTTCAGCTCTTATGAGCTTCCGTTCAACCCTCACGGGT
1 TTTCGTTCAGCTCTTATGAGCTTCAGTTCAACCCTCACGGGT
* * *
31726102 TTTCGTTTAGCACTTATGTGCTTC
1 TTTCGTTCAGCTCTTATGAGCTTC
31726126 TGTGCAGCCT
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
42 52 0.93
43 4 0.07
ACGTcount: A:0.15, C:0.24, G:0.17, T:0.44
Consensus pattern (42 bp):
TTTCGTTCAGCTCTTATGAGCTTCAGTTCAACCCTCACGGGT
Found at i:31726087 original size:21 final size:21
Alignment explanation
Indices: 31726017--31726089 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
31726007 CCCTAATGGA
* *
31726017 TTTCAGTTTAGCTCTTTTGAGC
1 TTTC-GTTCAGCTCTTATGAGC
* * * * *
31726039 TTTAGTTCAACCCTTATGTGT
1 TTTCGTTCAGCTCTTATGAGC
31726060 TTTCGTTCAGCTCTTATGAGC
1 TTTCGTTCAGCTCTTATGAGC
*
31726081 TTCCGTTCA
1 TTTCGTTCA
31726090 ACCCTCACGG
Statistics
Matches: 38, Mismatches: 13, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
21 35 0.92
22 3 0.08
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.47
Consensus pattern (21 bp):
TTTCGTTCAGCTCTTATGAGC
Found at i:31727336 original size:85 final size:85
Alignment explanation
Indices: 31727193--31727371 Score: 358
Period size: 85 Copynumber: 2.1 Consensus size: 85
31727183 GGCCGGCCAT
31727193 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
31727258 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
31727278 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
31727343 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
31727363 GAGCATGGG
1 GAGCATGGG
31727372 CAATAAAATA
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 94 1.00
ACGTcount: A:0.38, C:0.08, G:0.27, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:31728780 original size:47 final size:47
Alignment explanation
Indices: 31728656--31728907 Score: 391
Period size: 47 Copynumber: 5.3 Consensus size: 47
31728646 NNNNNNNNNN
31728656 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
31728703 TATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TG
1 --TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-AGTG
* *
31728752 TGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-AGTG
* *
31728799 CATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
* *
31728846 TATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGGAAGTG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
*
31728893 TATAAATGTGATAAG
1 TATATATGTGATAAG
31728908 TCCCGAAGGG
Statistics
Matches: 190, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
46 1 0.01
47 143 0.75
49 45 0.24
50 1 0.01
ACGTcount: A:0.34, C:0.09, G:0.30, T:0.27
Consensus pattern (47 bp):
TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
Found at i:31732142 original size:38 final size:38
Alignment explanation
Indices: 31732092--31732187 Score: 111
Period size: 40 Copynumber: 2.5 Consensus size: 38
31732082 CCAACTCCGT
* * *
31732092 CCAACCCAACACACCATGTGGGGATAAAATCGACCCAC
1 CCAACCCTACACACCATATGGGGATAAAATCAACCCAC
* * * *
31732130 CCATCTCTACACACCAAACATGGGGATAAAATCAACCCAT
1 CCAACCCTACACACC--ATATGGGGATAAAATCAACCCAC
31732170 CCAACCCTACACACCATA
1 CCAACCCTACACACCATA
31732188 GTGTACCGTA
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
38 14 0.30
40 32 0.70
ACGTcount: A:0.39, C:0.38, G:0.10, T:0.14
Consensus pattern (38 bp):
CCAACCCTACACACCATATGGGGATAAAATCAACCCAC
Found at i:31732157 original size:40 final size:40
Alignment explanation
Indices: 31732110--31732185 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
31732100 ACACACCATG
* * *
31732110 TGGGGATAAAATCGACCCACCCATCTCTACACACCAAACA
1 TGGGGATAAAATCAACCCACCCAACCCTACACACCAAACA
*
31732150 TGGGGATAAAATCAACCCATCCAACCCTACACACCA
1 TGGGGATAAAATCAACCCACCCAACCCTACACACCA
31732186 TAGTGTACCG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.38, C:0.36, G:0.12, T:0.14
Consensus pattern (40 bp):
TGGGGATAAAATCAACCCACCCAACCCTACACACCAAACA
Found at i:31739695 original size:40 final size:40
Alignment explanation
Indices: 31739650--31739725 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
31739640 ACACACTATG
* *
31739650 TAGGGATAAAATCGACCCACCCATCCCTACACACCAAACA
1 TAGGGATAAAATCAACCCACCCAACCCTACACACCAAACA
*
31739690 TAGGGATAAAATCAACCCATCCAACCCTACACACCA
1 TAGGGATAAAATCAACCCACCCAACCCTACACACCA
31739726 TAGTGTACCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.41, C:0.37, G:0.09, T:0.13
Consensus pattern (40 bp):
TAGGGATAAAATCAACCCACCCAACCCTACACACCAAACA
Found at i:31745507 original size:40 final size:40
Alignment explanation
Indices: 31745463--31745558 Score: 115
Period size: 40 Copynumber: 2.4 Consensus size: 40
31745453 TGTTTGAATG
*
31745463 AAAAACGCCACTATAG-ATCAAGCATTAGCGACA-TTTTTCA
1 AAAAACGCCGCTATAGCA-CAAGCATTAGCGACACTTTTT-A
* * *
31745503 AAAAACGCCGCTAAAGCACGAGCATTAGCGGCACTTTTTA
1 AAAAACGCCGCTATAGCACAAGCATTAGCGACACTTTTTA
*
31745543 ACAAACGCCGCTATAG
1 AAAAACGCCGCTATAG
31745559 GTTCACCTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
40 42 0.88
41 6 0.12
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.21
Consensus pattern (40 bp):
AAAAACGCCGCTATAGCACAAGCATTAGCGACACTTTTTA
Found at i:31745872 original size:135 final size:135
Alignment explanation
Indices: 31745617--31745875 Score: 321
Period size: 135 Copynumber: 1.9 Consensus size: 135
31745607 AACGCCATCG
* * * **
31745617 TTTTAATTGAGCTTCAGTGGCGTTAGCGGCACTTTTTTAACAAGGCCGCTATAGATCAAGTATTA
1 TTTTAATTGAGCTTCAGTGGCGTTAACGGCACTTTTTTAAAAACGCAACTATAGATCAAGTATTA
31745682 GCGGCGCTTTTTAAAAAACGCCGCTAATGCTCGACCTTTAGTGGCGCTTTCAAAAAAACGCTGCA
66 GCGGCGCTTTTTAAAAAACGCCGCTAATGCTCGACCTTTAGTGGCGCTTTCAAAAAAACGCTGCA
31745747 AAAAA
131 AAAAA
* * *
31745752 TTTT-ATTGAGCTTTTAGTGGCTTTAACGGCGCTTTTTTAAAAACGCAACTATAGATCAAGTATT
1 TTTTAATTGAGC-TTCAGTGGCGTTAACGGCACTTTTTTAAAAACGCAACTATAGATCAAGTATT
** * * **
31745816 AGCGTTGTTTTTTAAAAAGCGTCC-CT-ATAG-TAC-ACCTTTAGTGGCGCTTTTTAAAAAACG
65 AGCGGCGCTTTTTAAAAAACG-CCGCTAAT-GCT-CGACCTTTAGTGGCGCTTTCAAAAAAACG
31745876 ACACTAATGC
Statistics
Matches: 106, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
134 35 0.33
135 69 0.65
136 2 0.02
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (135 bp):
TTTTAATTGAGCTTCAGTGGCGTTAACGGCACTTTTTTAAAAACGCAACTATAGATCAAGTATTA
GCGGCGCTTTTTAAAAAACGCCGCTAATGCTCGACCTTTAGTGGCGCTTTCAAAAAAACGCTGCA
AAAAA
Found at i:31746391 original size:15 final size:15
Alignment explanation
Indices: 31746371--31746432 Score: 65
Period size: 14 Copynumber: 4.3 Consensus size: 15
31746361 ACTATTTTAA
*
31746371 GGTTTATGGATTATG
1 GGTTTATGGATTAGG
* *
31746386 GGTTTAGGGATTA-T
1 GGTTTATGGATTAGG
*
31746400 GGTTTAAGGATT-GG
1 GGTTTATGGATTAGG
*
31746414 GGTTTATGGCTTAGG
1 GGTTTATGGATTAGG
31746429 GGTT
1 GGTT
31746433 AGGGGTTAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
14 21 0.54
15 18 0.46
ACGTcount: A:0.18, C:0.02, G:0.39, T:0.42
Consensus pattern (15 bp):
GGTTTATGGATTAGG
Found at i:31746391 original size:22 final size:22
Alignment explanation
Indices: 31746332--31746401 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
31746322 GTTTAGGGCA
*
31746332 TATGG-TTAAGGGTTTAAGGTT
1 TATGGATTATGGGTTTAAGGTT
**
31746353 TAT-GAGTTACT-ATTTTAAGGTT
1 TATGGA-TTA-TGGGTTTAAGGTT
* *
31746375 TATGGATTATGGGTTTAGGGAT
1 TATGGATTATGGGTTTAAGGTT
31746397 TATGG
1 TATGG
31746402 TTTAAGGATT
Statistics
Matches: 37, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
20 1 0.03
21 4 0.11
22 30 0.81
23 2 0.05
ACGTcount: A:0.24, C:0.01, G:0.30, T:0.44
Consensus pattern (22 bp):
TATGGATTATGGGTTTAAGGTT
Found at i:31746405 original size:14 final size:15
Alignment explanation
Indices: 31746371--31746411 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
31746361 ACTATTTTAA
*
31746371 GGTTTATGGATTATG
1 GGTTTAAGGATTATG
*
31746386 GGTTTAGGGATTAT-
1 GGTTTAAGGATTATG
31746400 GGTTTAAGGATT
1 GGTTTAAGGATT
31746412 GGGGTTTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.22, C:0.00, G:0.34, T:0.44
Consensus pattern (15 bp):
GGTTTAAGGATTATG
Found at i:31746555 original size:15 final size:15
Alignment explanation
Indices: 31746535--31746596 Score: 65
Period size: 14 Copynumber: 4.3 Consensus size: 15
31746525 ACTATTTTAA
*
31746535 GGTTTATGGATTATG
1 GGTTTATGGATTAGG
* *
31746550 GGTTTAGGGATTA-T
1 GGTTTATGGATTAGG
*
31746564 GGTTTAAGGATT-GG
1 GGTTTATGGATTAGG
*
31746578 GGTTTATGGCTTAGG
1 GGTTTATGGATTAGG
31746593 GGTT
1 GGTT
31746597 AGGGGTTAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
14 21 0.54
15 18 0.46
ACGTcount: A:0.18, C:0.02, G:0.39, T:0.42
Consensus pattern (15 bp):
GGTTTATGGATTAGG
Found at i:31746555 original size:22 final size:22
Alignment explanation
Indices: 31746496--31746565 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
31746486 GTTTAGGGCA
*
31746496 TATGG-TTAAGGGTTTAAGGTT
1 TATGGATTATGGGTTTAAGGTT
**
31746517 TAT-GAGTTACT-ATTTTAAGGTT
1 TATGGA-TTA-TGGGTTTAAGGTT
* *
31746539 TATGGATTATGGGTTTAGGGAT
1 TATGGATTATGGGTTTAAGGTT
31746561 TATGG
1 TATGG
31746566 TTTAAGGATT
Statistics
Matches: 37, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
20 1 0.03
21 4 0.11
22 30 0.81
23 2 0.05
ACGTcount: A:0.24, C:0.01, G:0.30, T:0.44
Consensus pattern (22 bp):
TATGGATTATGGGTTTAAGGTT
Found at i:31746569 original size:14 final size:15
Alignment explanation
Indices: 31746535--31746575 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
31746525 ACTATTTTAA
*
31746535 GGTTTATGGATTATG
1 GGTTTAAGGATTATG
*
31746550 GGTTTAGGGATTAT-
1 GGTTTAAGGATTATG
31746564 GGTTTAAGGATT
1 GGTTTAAGGATT
31746576 GGGGTTTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.22, C:0.00, G:0.34, T:0.44
Consensus pattern (15 bp):
GGTTTAAGGATTATG
Found at i:31746585 original size:164 final size:164
Alignment explanation
Indices: 31746309--31746683 Score: 691
Period size: 164 Copynumber: 2.3 Consensus size: 164
31746299 ATCATTATAG
*
31746309 TTTACGGTTTACGGTTTAGGGCATATGGTTAAGGGTTTAAGGTTTATGAGTTACTATTTTAAGGT
1 TTTAGGGTTTACGGTTTAGGGCATATGGTTAAGGGTTTAAGGTTTATGAGTTACTATTTTAAGGT
31746374 TTATGGATTATGGGTTTAGGGATTATGGTTTAAGGATTGGGGTTTATGGCTTAGGGGTTAGGGGT
66 TTATGGATTATGGGTTTAGGGATTATGGTTTAAGGATTGGGGTTTATGGCTTAGGGGTTAGGGGT
31746439 TAAAGATTAGGGGTTCAGGGTTTTTGTTTTAGGA
131 TAAAGATTAGGGGTTCAGGGTTTTTGTTTTAGGA
31746473 TTTAGGGTTTACGGTTTAGGGCATATGGTTAAGGGTTTAAGGTTTATGAGTTACTATTTTAAGGT
1 TTTAGGGTTTACGGTTTAGGGCATATGGTTAAGGGTTTAAGGTTTATGAGTTACTATTTTAAGGT
31746538 TTATGGATTATGGGTTTAGGGATTATGGTTTAAGGATTGGGGTTTATGGCTTAGGGGTTAGGGGT
66 TTATGGATTATGGGTTTAGGGATTATGGTTTAAGGATTGGGGTTTATGGCTTAGGGGTTAGGGGT
31746603 TAAAGATTAGGGGTTCAGGGTTTTTGTTTTAGGA
131 TAAAGATTAGGGGTTCAGGGTTTTTGTTTTAGGA
*
31746637 TTTAGGGTTTACGGTTTAGGG-AT-TAGAGATTAAGGGTTTAGGGTTTA
1 TTTAGGGTTTACGGTTTAGGGCATAT-G-G-TTAAGGGTTTAAGGTTTA
31746684 GATTAATTAG
Statistics
Matches: 206, Mismatches: 2, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
162 1 0.00
163 3 0.01
164 185 0.90
165 17 0.08
ACGTcount: A:0.22, C:0.03, G:0.34, T:0.41
Consensus pattern (164 bp):
TTTAGGGTTTACGGTTTAGGGCATATGGTTAAGGGTTTAAGGTTTATGAGTTACTATTTTAAGGT
TTATGGATTATGGGTTTAGGGATTATGGTTTAAGGATTGGGGTTTATGGCTTAGGGGTTAGGGGT
TAAAGATTAGGGGTTCAGGGTTTTTGTTTTAGGA
Found at i:31746662 original size:21 final size:21
Alignment explanation
Indices: 31746535--31746662 Score: 87
Period size: 21 Copynumber: 6.0 Consensus size: 21
31746525 ACTATTTTAA
* *
31746535 GGTTTATGGATTATGGGTTTAG
1 GGTTTATGGTTTA-GGGATTAG
* * *
31746557 GGATTATGGTTTAAGGATTGG
1 GGTTTATGGTTTAGGGATTAG
* *
31746578 GGTTTATGGCTTAGGGGTTAG
1 GGTTTATGGTTTAGGGATTAG
* ** * *
31746599 GGGTTAAAGATTAGGGGTTCAG
1 GGTTTATGGTTTAGGGATT-AG
* *
31746621 GGTTTTTGTTTTA-GGATTTAG
1 GGTTTATGGTTTAGGGA-TTAG
*
31746642 GGTTTACGGTTTAGGGATTAG
1 GGTTTATGGTTTAGGGATTAG
31746663 AGATTAAGGG
Statistics
Matches: 79, Mismatches: 24, Indels: 7
0.72 0.22 0.06
Matches are distributed among these distances:
21 54 0.68
22 25 0.32
ACGTcount: A:0.20, C:0.02, G:0.38, T:0.41
Consensus pattern (21 bp):
GGTTTATGGTTTAGGGATTAG
Found at i:31746884 original size:21 final size:22
Alignment explanation
Indices: 31746860--31746906 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
31746850 TATGGATTAT
*
31746860 GGTTTAAGGGTT-GGGGTTTAA
1 GGTTTAAGGGTTAGGGGTTCAA
31746881 GGTTTAAGGGTTAGGGGTTCAA
1 GGTTTAAGGGTTAGGGGTTCAA
31746903 GGTT
1 GGTT
31746907 AATGGTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.19, C:0.02, G:0.43, T:0.36
Consensus pattern (22 bp):
GGTTTAAGGGTTAGGGGTTCAA
Found at i:31746967 original size:7 final size:7
Alignment explanation
Indices: 31746841--31746967 Score: 51
Period size: 7 Copynumber: 17.7 Consensus size: 7
31746831 GAGTTACTAT
*
31746841 TTTAAGG
1 TTTAGGG
*
31746848 TTTATGG
1 TTTAGGG
* *
31746855 ATTATGG
1 TTTAGGG
31746862 TTTAAGGG
1 TTT-AGGG
*
31746870 -TTGGGG
1 TTTAGGG
*
31746876 TTTAAGG
1 TTTAGGG
31746883 TTTAAGGG
1 TTT-AGGG
31746891 -TTAGGGG
1 TTTA-GGG
* *
31746898 TTCAAGG
1 TTTAGGG
* *
31746905 TTAATGG
1 TTTAGGG
* *
31746912 TTTATGT
1 TTTAGGG
*
31746919 TTTAGGAT
1 TTTAGG-G
31746927 TTTAGGG
1 TTTAGGG
**
31746934 TTTAAAG
1 TTTAGGG
31746941 TTTAGGG
1 TTTAGGG
*
31746948 ATTAAGGG
1 -TTTAGGG
31746956 TTTAGGG
1 TTTAGGG
31746963 TTTAG
1 TTTAG
31746968 ATTAATTAGT
Statistics
Matches: 91, Mismatches: 22, Indels: 14
0.72 0.17 0.11
Matches are distributed among these distances:
6 4 0.04
7 66 0.73
8 21 0.23
ACGTcount: A:0.23, C:0.01, G:0.34, T:0.43
Consensus pattern (7 bp):
TTTAGGG
Found at i:31746967 original size:22 final size:22
Alignment explanation
Indices: 31746863--31746966 Score: 72
Period size: 22 Copynumber: 4.8 Consensus size: 22
31746853 GGATTATGGT
* *
31746863 TTAAGGG-TTGGGGTTTAAGGT
1 TTAAGGGTTTAGGGTTTAAGGA
*
31746884 TTAAGGG-TTAGGGGTTCAAGG-
1 TTAAGGGTTTA-GGGTTTAAGGA
* * *
31746905 TTAATGGTTTA-TGTTTTAGGA
1 TTAAGGGTTTAGGGTTTAAGGA
* ** *
31746926 TTTTAGGGTTTAAAGTTTAGGGA
1 -TTAAGGGTTTAGGGTTTAAGGA
31746949 TTAAGGGTTTAGGGTTTA
1 TTAAGGGTTTAGGGTTTA
31746967 GATTAATTAG
Statistics
Matches: 64, Mismatches: 14, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
20 6 0.09
21 15 0.23
22 36 0.56
23 7 0.11
ACGTcount: A:0.23, C:0.01, G:0.35, T:0.41
Consensus pattern (22 bp):
TTAAGGGTTTAGGGTTTAAGGA
Found at i:31747998 original size:14 final size:15
Alignment explanation
Indices: 31747979--31748034 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 15
31747969 AATCTTCAAT
31747979 GATATG-CAATCTTA
1 GATATGACAATCTTA
31747993 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
31748010 GATATGATTGCAATCTTA
1 GATATGA---CAATCTTA
31748028 GATATGA
1 GATATGA
31748035 TATGCAATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
14 6 0.17
15 1 0.03
17 14 0.39
18 15 0.42
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:31748023 original size:35 final size:37
Alignment explanation
Indices: 31747977--31748055 Score: 121
Period size: 35 Copynumber: 2.2 Consensus size: 37
31747967 ATAATCTTCA
31747977 ATGATATGCAATCTTAGATATGATA-CAATCTTAGAT
1 ATGATATGCAATCTTAGATATGATAGCAATCTTAGAT
31748013 ATGAT-TGCAATCTTAGATATGATATGCAATCTTAGA-
1 ATGATATGCAATCTTAGATATGATA-GCAATCTTAGAT
31748049 A-GATATG
1 ATGATATG
31748056 ATTTTGTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
35 22 0.55
36 8 0.20
37 10 0.25
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (37 bp):
ATGATATGCAATCTTAGATATGATAGCAATCTTAGAT
Found at i:31748055 original size:17 final size:19
Alignment explanation
Indices: 31747977--31748048 Score: 123
Period size: 19 Copynumber: 3.9 Consensus size: 19
31747967 ATAATCTTCA
31747977 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
31747996 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
31748013 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
31748031 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
31748049 AGATATGATT
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.32
18 16 0.32
19 18 0.36
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:31748074 original size:22 final size:22
Alignment explanation
Indices: 31747977--31748071 Score: 79
Period size: 17 Copynumber: 4.8 Consensus size: 22
31747967 ATAATCTTCA
31747977 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
31747996 ATGATA--CAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
31748013 ATGAT-TGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
31748031 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
31748053 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
31748072 GATTTAATTT
Statistics
Matches: 67, Mismatches: 2, Indels: 10
0.85 0.03 0.13
Matches are distributed among these distances:
17 16 0.24
18 16 0.24
19 15 0.22
22 8 0.12
23 12 0.18
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:31753218 original size:79 final size:78
Alignment explanation
Indices: 31753116--31753338 Score: 272
Period size: 79 Copynumber: 2.8 Consensus size: 78
31753106 GCTCCTCGTT
* *
31753116 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
31753181 ATTTAGTAACTCGCA
64 AATTAGTAACTCGCA
* *
31753196 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGG-CTTAGCCCGGA
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
*
31753260 ATTAGTATCTCGCA
65 ATTAGTAACTCGCA
* * * * *
31753274 CAAATGCCTTCGGATCTTAGTCCGGATATTGTCACTTAGCAC-AA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCG
31753337 GA
63 GA
31753339 CATCATTCAA
Statistics
Matches: 125, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
78 45 0.36
79 60 0.48
80 20 0.16
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAA
TTAGTAACTCGCA
Found at i:31753233 original size:39 final size:40
Alignment explanation
Indices: 31753116--31753338 Score: 280
Period size: 39 Copynumber: 5.7 Consensus size: 40
31753106 GCTCCTCGTT
* *
31753116 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* *
31753156 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
31753196 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
31753235 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * *
31753274 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGTAAC-TCGCA
31753315 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
31753339 CATCATTCAA
Statistics
Matches: 167, Mismatches: 10, Indels: 13
0.88 0.05 0.07
Matches are distributed among these distances:
38 2 0.01
39 88 0.53
40 67 0.40
41 10 0.06
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:31754434 original size:13 final size:13
Alignment explanation
Indices: 31754416--31754440 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31754406 AGGATGAGCA
31754416 TTTTTTTTCTTTG
1 TTTTTTTTCTTTG
31754429 TTTTTTTTCTTT
1 TTTTTTTTCTTT
31754441 CTAGTTTCGG
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:0.00, C:0.08, G:0.04, T:0.88
Consensus pattern (13 bp):
TTTTTTTTCTTTG
Found at i:31759218 original size:220 final size:220
Alignment explanation
Indices: 31758835--31759424 Score: 948
Period size: 220 Copynumber: 2.7 Consensus size: 220
31758825 CAGGATAAAG
* * * * * * ** *
31758835 CATAGCAGATTTGACCTTCAGGTGTTTACGCTGAAGCGGATCCAAGATGATTTAACATCTTTGTA
1 CATAGCAGATTTGGCTTTCACGTGTTTACGCTGAAACAGATCTAAGATGATTTGGCATCTCTGTA
*
31758900 TTGTCAGAGAACAAATCGAAGAAATAGATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAG
66 CTGTCAGAGAACAAATCGAAGAAATAGATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAG
* *
31758965 ACATAGCAGATCTAACCTTCGGATGTTTTCACATCGAAGTAGATCCAAGATGATTTGGCATCCTT
131 ACATAGCAGATCTAACCTTCGGATGTCTTCACATCGAAGTAGATCCAAGATGAGTTGGCATCCTT
31759030 GCGTTGACAAGGAGCAGATCGAAGA
196 GCGTTGACAAGGAGCAGATCGAAGA
* * *
31759055 CATAGCAGATTTGGCTTTCACGTATTTATGCTGAAACAGATCTAAGATGATTTGGTATCTCTGTA
1 CATAGCAGATTTGGCTTTCACGTGTTTACGCTGAAACAGATCTAAGATGATTTGGCATCTCTGTA
*
31759120 CTGTCAGAGAACAAATCGAAGAAATAGATTTGGCATCTCCATATTCGATGGAGAGCAGATCGAAG
66 CTGTCAGAGAACAAATCGAAGAAATAGATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAG
* *
31759185 ACATGGCAAATCTAACCTTCGGATGTCTTCACATCGAAGTAGATCCAAGATGAGTTGGCATCCTT
131 ACATAGCAGATCTAACCTTCGGATGTCTTCACATCGAAGTAGATCCAAGATGAGTTGGCATCCTT
31759250 GCGTTGACAAGGAGCAGATCGAAGA
196 GCGTTGACAAGGAGCAGATCGAAGA
* *
31759275 TATAGCAGATTTGGCTTTCACGTGTTTACCCT-AAAGCAGATCTAAGATGATTTGGCATCTCTGT
1 CATAGCAGATTTGGCTTTCACGTGTTTACGCTGAAA-CAGATCTAAGATGATTTGGCATCTCTGT
* * *
31759339 ACTGTCAAAAAACAAATCGAAGAAACAGATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAA
65 ACTGTCAGAGAACAAATCGAAGAAATAGATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAA
*
31759404 GACATAGCAGATCTGACCTTC
130 GACATAGCAGATCTAACCTTC
31759425 ATTGAAGCAG
Statistics
Matches: 339, Mismatches: 30, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
219 3 0.01
220 336 0.99
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (220 bp):
CATAGCAGATTTGGCTTTCACGTGTTTACGCTGAAACAGATCTAAGATGATTTGGCATCTCTGTA
CTGTCAGAGAACAAATCGAAGAAATAGATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAG
ACATAGCAGATCTAACCTTCGGATGTCTTCACATCGAAGTAGATCCAAGATGAGTTGGCATCCTT
GCGTTGACAAGGAGCAGATCGAAGA
Found at i:31759476 original size:78 final size:78
Alignment explanation
Indices: 31759366--31759582 Score: 380
Period size: 78 Copynumber: 2.8 Consensus size: 78
31759356 CGAAGAAACA
** * *
31759366 GATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
31759431 GCAGATCCAAGAT
66 GCAGATCCAAGAT
* *
31759444 GATTTGGCATCTCTGTATTAGAGGGGGAGCAGATCGAAGACACAGCAGATCTGACCTTCATTGAA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
31759509 GCAGATCCAAGAT
66 GCAGATCCAAGAT
31759522 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCAT
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCAT
31759583 GTGTTTACAT
Statistics
Matches: 131, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 131 1.00
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.24
Consensus pattern (78 bp):
GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
GCAGATCCAAGAT
Found at i:31760125 original size:35 final size:37
Alignment explanation
Indices: 31760054--31760151 Score: 150
Period size: 35 Copynumber: 2.7 Consensus size: 37
31760044 ATAATCTTCA
31760054 ATGATATGCAATCTTAGATATGATATGCAATCTTAGAT
1 ATGATA-GCAATCTTAGATATGATATGCAATCTTAGAT
31760092 ATGATA-CAATCTTAGATATGAT-TGCAATCTTAGAT
1 ATGATAGCAATCTTAGATATGATATGCAATCTTAGAT
31760127 ATGATATGCAATCTTAGA-A-GATATG
1 ATGATA-GCAATCTTAGATATGATATG
31760152 ATTTTGTAAT
Statistics
Matches: 57, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
35 22 0.39
36 19 0.33
37 10 0.18
38 6 0.11
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (37 bp):
ATGATAGCAATCTTAGATATGATATGCAATCTTAGAT
Found at i:31760151 original size:17 final size:19
Alignment explanation
Indices: 31760054--31760144 Score: 161
Period size: 19 Copynumber: 4.9 Consensus size: 19
31760044 ATAATCTTCA
31760054 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
31760073 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
31760092 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
31760109 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
31760127 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
31760145 AGATATGATT
Statistics
Matches: 69, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
17 16 0.23
18 16 0.23
19 37 0.54
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:31760170 original size:22 final size:22
Alignment explanation
Indices: 31760054--31760167 Score: 96
Period size: 19 Copynumber: 5.8 Consensus size: 22
31760044 ATAATCTTCA
31760054 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
31760073 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
31760092 ATGATA--CAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
31760109 ATGAT-TGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
31760127 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
31760149 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
31760168 GATTTAATTT
Statistics
Matches: 86, Mismatches: 2, Indels: 10
0.88 0.02 0.10
Matches are distributed among these distances:
17 16 0.19
18 16 0.19
19 34 0.40
22 8 0.09
23 12 0.14
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.38
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:31760457 original size:18 final size:19
Alignment explanation
Indices: 31760434--31760470 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
31760424 TGTTTCCCTG
*
31760434 ATTTTTTTATAT-ATTTTA
1 ATTTTTTTAAATAATTTTA
31760452 ATTTTTTTAAATAATTTTA
1 ATTTTTTTAAATAATTTTA
31760471 GTATCATATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
ATTTTTTTAAATAATTTTA
Found at i:31766850 original size:76 final size:76
Alignment explanation
Indices: 31766729--31766881 Score: 306
Period size: 76 Copynumber: 2.0 Consensus size: 76
31766719 ATTGAATTGA
31766729 TGAATGATATTATTTATTTAGTATATTTTTGAAAAATGAACTATTATTAAATTGTGAATTGAAAT
1 TGAATGATATTATTTATTTAGTATATTTTTGAAAAATGAACTATTATTAAATTGTGAATTGAAAT
31766794 AATTATTCGGC
66 AATTATTCGGC
31766805 TGAATGATATTATTTATTTAGTATATTTTTGAAAAATGAACTATTATTAAATTGTGAATTGAAAT
1 TGAATGATATTATTTATTTAGTATATTTTTGAAAAATGAACTATTATTAAATTGTGAATTGAAAT
31766870 AATTATTCGGC
66 AATTATTCGGC
31766881 T
1 T
31766882 AAAGTGGAAC
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 77 1.00
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.45
Consensus pattern (76 bp):
TGAATGATATTATTTATTTAGTATATTTTTGAAAAATGAACTATTATTAAATTGTGAATTGAAAT
AATTATTCGGC
Found at i:31767108 original size:42 final size:42
Alignment explanation
Indices: 31767039--31767118 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
31767029 GAGTTTCCGA
* *
31767039 TTAACCCTAATGGGTTTCTCTTTAGCTCTTTTGAGCTTTAAT
1 TTAACCCTAATGGGTTTCTCTTCAGCTCTTATGAGCTTTAAT
*
31767081 TTAACCCTTATGGGTTT-TCGTTCAGCTCTTATGAGCTT
1 TTAACCCTAATGGGTTTCTC-TTCAGCTCTTATGAGCTT
31767119 CCGTTCAACC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
41 2 0.06
42 32 0.94
ACGTcount: A:0.17, C:0.20, G:0.16, T:0.46
Consensus pattern (42 bp):
TTAACCCTAATGGGTTTCTCTTCAGCTCTTATGAGCTTTAAT
Found at i:31767113 original size:21 final size:20
Alignment explanation
Indices: 31767086--31767154 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
31767076 TTAATTTAAC
31767086 CCTTATGGGTTTTCGTTCAG
1 CCTTATGGGTTTTCGTTCAG
* * * *
31767106 CTCTTATGAGCTTCCGTTCAA
1 C-CTTATGGGTTTTCGTTCAG
* *
31767127 CCTTACGGGTTTTCGTTTAG
1 CCTTATGGGTTTTCGTTCAG
31767147 CACTTATG
1 C-CTTATG
31767155 TGCTTTTGTG
Statistics
Matches: 36, Mismatches: 11, Indels: 3
0.72 0.22 0.06
Matches are distributed among these distances:
20 15 0.42
21 21 0.58
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.42
Consensus pattern (20 bp):
CCTTATGGGTTTTCGTTCAG
Found at i:31770841 original size:42 final size:42
Alignment explanation
Indices: 31770772--31770851 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
31770762 GAGTTTCCGA
* *
31770772 TTAACCCTAATGGGTTTCTCTTTAGCTCTTTTGAGCTTTAAT
1 TTAACCCTAATGGGTTTCTCTTCAGCTCTTATGAGCTTTAAT
*
31770814 TTAACCCTTATGGGTTT-TCGTTCAGCTCTTATGAGCTT
1 TTAACCCTAATGGGTTTCTC-TTCAGCTCTTATGAGCTT
31770852 CCGTTCAACC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
41 2 0.06
42 32 0.94
ACGTcount: A:0.17, C:0.20, G:0.16, T:0.46
Consensus pattern (42 bp):
TTAACCCTAATGGGTTTCTCTTCAGCTCTTATGAGCTTTAAT
Found at i:31770846 original size:21 final size:20
Alignment explanation
Indices: 31770819--31770887 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
31770809 TTAATTTAAC
31770819 CCTTATGGGTTTTCGTTCAG
1 CCTTATGGGTTTTCGTTCAG
* * * *
31770839 CTCTTATGAGCTTCCGTTCAA
1 C-CTTATGGGTTTTCGTTCAG
* *
31770860 CCTTACGGGTTTTCGTTTAG
1 CCTTATGGGTTTTCGTTCAG
31770880 CACTTATG
1 C-CTTATG
31770888 TGCTTTTGTG
Statistics
Matches: 36, Mismatches: 11, Indels: 3
0.72 0.22 0.06
Matches are distributed among these distances:
20 15 0.42
21 21 0.58
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.42
Consensus pattern (20 bp):
CCTTATGGGTTTTCGTTCAG
Found at i:31774932 original size:893 final size:893
Alignment explanation
Indices: 31773205--31775933 Score: 3980
Period size: 893 Copynumber: 3.0 Consensus size: 893
31773195 ATTGAATACA
31773205 TTAGAAAATTTGATGGAATGGTGTACATGATGTGGAAATATGATATGGAAGAATGTTACATGGAA
1 TTAGAAAATTTGATGGAATGGTGTACATGATGTGGAAATATGATATGGAAGAATGTTACATGGAA
31773270 TGCAAGAAAACGATGATATATGACAAGTGATATAGGAAATAGGTGATATATATATATGTTTAAAT
66 TGCAAGAAAACGATGATATATGACAAGTGATATAGGAAATAGGTGATATATATATATGTTTAAAT
31773335 GTTTTATTGTTATCATGTATCATAATCTTGTTACCACGAAAGTATAAATAATGTGATAAAAGAGT
131 GTTTTATTGTTATCATGTATCATAATCTTGTTACCACGAAAGTATAAATAATGTGATAAAAGAGT
31773400 AACCTACATTATGAGCAAGTGCGACGACACCGAGTTAGATATGAAATCCCGTTGAACCTCAGGAA
196 AACCTACATTATGAGCAAGTGCGACGACACCGAGTTAGATATGAAATCCCGTTGAACCTCAGGAA
31773465 TAGTATTGGATACAAAAGGTATATCATGAGGAACTATGTGGTCTGAACTCATGAGTTGTGTCAAG
261 TAGTATTGGATACAAAAGGTATATCATGAGGAACTATGTGGTCTGAACTCATGAGTTGTGTCAAG
31773530 TTCATGAGATAAATGTTATATGTAATGTGGGTCCGGGTACTGACTTCATGACCAAACCCATGAGT
326 TTCATGAGATAAATGTTATATGTAATGTGGGTCCGGGTACTGACTTCATGACCAAACCCATGAGT
31773595 AACTCGTTGAGCGAGCATTTCATGTCAACACTATATGGGTCGGGGTGCTGCCTTTGTGTACAGAC
391 AACTCGTTGAGCGAGCATTTCATGTCAACACTATATGGGTCGGGGTGCTGCCTTTGTGTACAGAC
31773660 CCGTTAGTAGCTCAATGAGCGGGTGTTACATGATAGTGCTATGGGGTCCGGGTACTAACTGATGA
456 CCGTTAGTAGCTCAATGAGCGGGTGTTACATGATAGTGCTATGGGGTCCGGGTACTAACTGATGA
31773725 ATAGGCCAGTGAGTAGCTCAAAATGCGAGCATTACATAGTATGAGGTAGCTCTGGCTTCTTACAT
521 ATAGGCCAGTGAGTAGCTCAAAATGCGAGCATTACATAGTATGAGGTAGCTCTGGCTTCTTACAT
31773790 GGCACTTAGGTGCAAACTTCCCATGTATCCAATAGTATTCCGAGTGTTCAACGGGTATTACAATA
586 GGCACTTAGGTGCAAACTTCCCATGTATCCAATAGTATTCCGAGTGTTCAACGGGTATTACAATA
31773855 GACGTGATGAAATTCCCAATGAGGGCATGTTAAAGAGATATGGTTATATGATATATTACGATGAG
651 GACGTGATGAAATTCCCAATGAGGGCATGTTAAAGAGATATGGTTATATGATATATTACGATGAG
31773920 TACAGGTATGTACACTAAGCTTATGGCTATTGAGGCTTTAAAATGTTGAGACATCAGTGAGCTAA
716 TACAGGTATGTACACTAAGCTTATGGCTATTGAGGCTTTAAAATGTTGAGACATCAGTGAGCTAA
31773985 GATGTATGAATTATGATTATAAATTTTGTTGCAATATCATGTTAACTTATATTGTGCATTTGAAC
781 GATGTATGAATTATGATTATAAATTTTGTTGCAATATCATGTTAACTTATATTGTGCATTTGAAC
31774050 ATGGAATGCATGAAATGGTGAGTTCATGATTAGTCGGGTTTTAGGGTT
846 ATGGAATGCATGAAATGGTGAGTTCATGATTAGTCGGGTTTTAGGGTT
31774098 TTAGAAAATTTGATGGAATGGTGTACATGATGTGGAAATATGATATGGAAGAATGTTACATGGAA
1 TTAGAAAATTTGATGGAATGGTGTACATGATGTGGAAATATGATATGGAAGAATGTTACATGGAA
31774163 TGCAAGAAAACGATGATATATGACAAGTGATATAGGAAATAGGTGATATATATATATGTTTAAAT
66 TGCAAGAAAACGATGATATATGACAAGTGATATAGGAAATAGGTGATATATATATATGTTTAAAT
31774228 GTTTTATTGTTATCATGTATCATAATCTTGTTACCACGAAAGTATAAATAATGTGATAAAAGAGT
131 GTTTTATTGTTATCATGTATCATAATCTTGTTACCACGAAAGTATAAATAATGTGATAAAAGAGT
31774293 AACCTACATTATGAGCAAGTGCGACGACACCGAGTTAGATATGAAATCCCGTTGAACCTCAGGAA
196 AACCTACATTATGAGCAAGTGCGACGACACCGAGTTAGATATGAAATCCCGTTGAACCTCAGGAA
31774358 TAGTATTGGATACAAAAGGTATATCATGAGGAACTATGTGGTCTGAACTCATGAGTTGTGTCAAG
261 TAGTATTGGATACAAAAGGTATATCATGAGGAACTATGTGGTCTGAACTCATGAGTTGTGTCAAG
31774423 TTCATGAGATAAATGTTATATGTAATGTGGGTCCGGGTACTGACTTCATGACCAAACCCATGAGT
326 TTCATGAGATAAATGTTATATGTAATGTGGGTCCGGGTACTGACTTCATGACCAAACCCATGAGT
31774488 AACTCGTTGAGCGAGCATTTCATGTCAACACTATATGGGTCGGGGTGCTGCCTTTGTGTACAGAC
391 AACTCGTTGAGCGAGCATTTCATGTCAACACTATATGGGTCGGGGTGCTGCCTTTGTGTACAGAC
31774553 CCGTTAGTAGCTCAATGAGCGGGTGTTACATGATAGTGCTATGGGGTCCGGGTACTAACTGATGA
456 CCGTTAGTAGCTCAATGAGCGGGTGTTACATGATAGTGCTATGGGGTCCGGGTACTAACTGATGA
31774618 ATAGGCCAGTGAGTAGCTCAAAATGCGAGCATTACATAGTATGAGGTAGCTCTGGCTTCTTACAT
521 ATAGGCCAGTGAGTAGCTCAAAATGCGAGCATTACATAGTATGAGGTAGCTCTGGCTTCTTACAT
31774683 GGCACTTAGGTGCAAACTTCCCATGTATCCAATAGTATTCCGAGTGTTCAACGGGTATTACAATA
586 GGCACTTAGGTGCAAACTTCCCATGTATCCAATAGTATTCCGAGTGTTCAACGGGTATTACAATA
31774748 GACGTGATGAAATTCCCAATGAGGGCATGTTAAAGAGATATGGTTATATGATATATTACGATGAG
651 GACGTGATGAAATTCCCAATGAGGGCATGTTAAAGAGATATGGTTATATGATATATTACGATGAG
31774813 TACAGGTATGTACACTAAGCTTATGGCTATTGAGGCTTTAAAATGTTGAGACATCAGTGAGCTAA
716 TACAGGTATGTACACTAAGCTTATGGCTATTGAGGCTTTAAAATGTTGAGACATCAGTGAGCTAA
31774878 GATGTATGAATTATGATTATAAATTTTGTTGCAATATCATGTTAACTTATATTGTGCATTTGAAC
781 GATGTATGAATTATGATTATAAATTTTGTTGCAATATCATGTTAACTTATATTGTGCATTTGAAC
31774943 ATGGAATGCATGAAATGGTGAGTTCATGATTAGTCGGGTTTTAGGGTT
846 ATGGAATGCATGAAATGGTGAGTTCATGATTAGTCGGGTTTTAGGGTT
** * * * * ** * ** *
31774991 TTAG--GGTTT-AGGGTAAAGGAT-T--AT--TTTTGAGGT-T-ATATCAGAATTAT-TTTCATA
1 TTAGAAAATTTGATGG-AATGG-TGTACATGATGTGGAAATATGATAT-GGAAGAATGTTACAT-
* * * ** * **
31775045 GCGGAAAG-AGGAAAATG-TGATAGTGAGTAGCAAACTAAAAGAGTACAGTGAGAATCGACTTCT
62 --GGAATGCAAGAAAACGATGATA-T-A-T-G---AC-AAGTGA-TATAG-GA-AAT--A--GGT
* * * * * * *
31775108 GATAATGAATTTCAGAATATATGAGAAATTAAATAGATATATTG-GAGGCACCGCCTGAGTGA-A
110 GAT-AT--A--T----ATATAT--G--TTTAAAT-GTTTTATTGTTA-TCA-TG--T-A-TCATA
* * * ** * * * * *
31775171 AT-TTCTTCAACACTG-AA-TATGAAAT--TGAGGAATCTAAGTGAAGACC-ACTTTTCTG-GTA
155 ATCTTGTT-ACCAC-GAAAGTAT-AAATAATG-TG-ATAAAAGAGTA-ACCTAC-ATTATGAGCA
* * * ** * *
31775229 AGATTTTCGAGGACGAAAATCCCTAAAAGGGGGGAGA-ATTGTAATATCCCGAATT-ATGGCCTA
213 AG----T-G-CGACG-ACA--CC------GAGTTAGATA-TG-AA-ATCCCG--TTGA--ACCTC
* * * * ** * * * *
31775292 ATCGAAATAGTGGTTTCGTGA-CCATAAATCCG-ATAT-A-GAAATAATTAT-T-TTAT-AA-TT
256 A--GGAATAGT--ATT-G-GATACA-AAA--GGTATATCATG-AGGAACTATGTGGTCTGAACTC
* *
31775349 AT--TTTGAGGT-AAGTTCATGAGATAAATGTTATATGTAATGTGGGTCCGGGTACTGACTTCAT
311 ATGAGTTG-TGTCAAGTTCATGAGATAAATGTTATATGTAATGTGGGTCCGGGTACTGACTTCAT
31775411 GACCAAACCCATGAGTAACTCGTTGAGCGAGCATTTCATGTCAACACTATATGGGTCGGGGTGCT
375 GACCAAACCCATGAGTAACTCGTTGAGCGAGCATTTCATGTCAACACTATATGGGTCGGGGTGCT
31775476 GCCTTTGTGTACAGACCCGTTAGTAGCTCAATGAGCGGGTGTTACATGATAGTGCTATGGGGTCC
440 GCCTTTGTGTACAGACCCGTTAGTAGCTCAATGAGCGGGTGTTACATGATAGTGCTATGGGGTCC
31775541 GGGTACTAACTGATGAATAGGCCAGTGAGTAGCTCAAAATGCGAGCATTACATAGTATGAGGTAG
505 GGGTACTAACTGATGAATAGGCCAGTGAGTAGCTCAAAATGCGAGCATTACATAGTATGAGGTAG
31775606 CTCTGGCTTCTTACATGGCACTTAGGTGCAAACTTCCCATGTATCCAATAGTATTCCGAGTGTTC
570 CTCTGGCTTCTTACATGGCACTTAGGTGCAAACTTCCCATGTATCCAATAGTATTCCGAGTGTTC
31775671 AACGGGTATTACAATAGACGTGATGAAATTCCCAATGAGGGCATGTTAAAGAGATATGGTTATAT
635 AACGGGTATTACAATAGACGTGATGAAATTCCCAATGAGGGCATGTTAAAGAGATATGGTTATAT
31775736 GATATATTACGATGAGTACAGGTATGTACACTAAGCTTATGGCTATTGAGGCTTTAAAATGTTGA
700 GATATATTACGATGAGTACAGGTATGTACACTAAGCTTATGGCTATTGAGGCTTTAAAATGTTGA
31775801 GACATCAGTGAGCTAAGATGTATGAATTATGATTATAAATTTTGTTGCAATATCATGTTAACTTA
765 GACATCAGTGAGCTAAGATGTATGAATTATGATTATAAATTTTGTTGCAATATCATGTTAACTTA
31775866 TATTGTGCATTTGAACATGGAATGCATGAAATGGTGAGTTCATGATTAGTCGGGTTTTAGGGTT
830 TATTGTGCATTTGAACATGGAATGCATGAAATGGTGAGTTCATGATTAGTCGGGTTTTAGGGTT
31775930 TTAG
1 TTAG
31775934 GGTTTAGGGT
Statistics
Matches: 1699, Mismatches: 56, Indels: 116
0.91 0.03 0.06
Matches are distributed among these distances:
885 9 0.01
886 11 0.01
887 13 0.01
888 6 0.00
889 3 0.00
890 4 0.00
891 8 0.00
892 1 0.00
893 899 0.53
894 4 0.00
895 4 0.00
896 2 0.00
897 3 0.00
899 1 0.00
901 4 0.00
902 2 0.00
904 1 0.00
906 1 0.00
910 6 0.00
912 1 0.00
914 7 0.00
915 9 0.01
916 1 0.00
917 2 0.00
918 9 0.01
919 27 0.02
920 10 0.01
923 1 0.00
924 1 0.00
925 4 0.00
926 2 0.00
928 2 0.00
933 1 0.00
934 7 0.00
935 2 0.00
936 6 0.00
937 1 0.00
938 2 0.00
939 582 0.34
940 2 0.00
941 10 0.01
942 2 0.00
943 4 0.00
944 5 0.00
945 12 0.01
946 4 0.00
947 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (893 bp):
TTAGAAAATTTGATGGAATGGTGTACATGATGTGGAAATATGATATGGAAGAATGTTACATGGAA
TGCAAGAAAACGATGATATATGACAAGTGATATAGGAAATAGGTGATATATATATATGTTTAAAT
GTTTTATTGTTATCATGTATCATAATCTTGTTACCACGAAAGTATAAATAATGTGATAAAAGAGT
AACCTACATTATGAGCAAGTGCGACGACACCGAGTTAGATATGAAATCCCGTTGAACCTCAGGAA
TAGTATTGGATACAAAAGGTATATCATGAGGAACTATGTGGTCTGAACTCATGAGTTGTGTCAAG
TTCATGAGATAAATGTTATATGTAATGTGGGTCCGGGTACTGACTTCATGACCAAACCCATGAGT
AACTCGTTGAGCGAGCATTTCATGTCAACACTATATGGGTCGGGGTGCTGCCTTTGTGTACAGAC
CCGTTAGTAGCTCAATGAGCGGGTGTTACATGATAGTGCTATGGGGTCCGGGTACTAACTGATGA
ATAGGCCAGTGAGTAGCTCAAAATGCGAGCATTACATAGTATGAGGTAGCTCTGGCTTCTTACAT
GGCACTTAGGTGCAAACTTCCCATGTATCCAATAGTATTCCGAGTGTTCAACGGGTATTACAATA
GACGTGATGAAATTCCCAATGAGGGCATGTTAAAGAGATATGGTTATATGATATATTACGATGAG
TACAGGTATGTACACTAAGCTTATGGCTATTGAGGCTTTAAAATGTTGAGACATCAGTGAGCTAA
GATGTATGAATTATGATTATAAATTTTGTTGCAATATCATGTTAACTTATATTGTGCATTTGAAC
ATGGAATGCATGAAATGGTGAGTTCATGATTAGTCGGGTTTTAGGGTT
Found at i:31776238 original size:939 final size:939
Alignment explanation
Indices: 31774420--31776297 Score: 3756
Period size: 939 Copynumber: 2.0 Consensus size: 939
31774410 GAGTTGTGTC
31774420 AAGTTCATGAGATAAATGTTATATGTAATGTGGGTCCGGGTACTGACTTCATGACCAAACCCATG
1 AAGTTCATGAGATAAATGTTATATGTAATGTGGGTCCGGGTACTGACTTCATGACCAAACCCATG
31774485 AGTAACTCGTTGAGCGAGCATTTCATGTCAACACTATATGGGTCGGGGTGCTGCCTTTGTGTACA
66 AGTAACTCGTTGAGCGAGCATTTCATGTCAACACTATATGGGTCGGGGTGCTGCCTTTGTGTACA
31774550 GACCCGTTAGTAGCTCAATGAGCGGGTGTTACATGATAGTGCTATGGGGTCCGGGTACTAACTGA
131 GACCCGTTAGTAGCTCAATGAGCGGGTGTTACATGATAGTGCTATGGGGTCCGGGTACTAACTGA
31774615 TGAATAGGCCAGTGAGTAGCTCAAAATGCGAGCATTACATAGTATGAGGTAGCTCTGGCTTCTTA
196 TGAATAGGCCAGTGAGTAGCTCAAAATGCGAGCATTACATAGTATGAGGTAGCTCTGGCTTCTTA
31774680 CATGGCACTTAGGTGCAAACTTCCCATGTATCCAATAGTATTCCGAGTGTTCAACGGGTATTACA
261 CATGGCACTTAGGTGCAAACTTCCCATGTATCCAATAGTATTCCGAGTGTTCAACGGGTATTACA
31774745 ATAGACGTGATGAAATTCCCAATGAGGGCATGTTAAAGAGATATGGTTATATGATATATTACGAT
326 ATAGACGTGATGAAATTCCCAATGAGGGCATGTTAAAGAGATATGGTTATATGATATATTACGAT
31774810 GAGTACAGGTATGTACACTAAGCTTATGGCTATTGAGGCTTTAAAATGTTGAGACATCAGTGAGC
391 GAGTACAGGTATGTACACTAAGCTTATGGCTATTGAGGCTTTAAAATGTTGAGACATCAGTGAGC
31774875 TAAGATGTATGAATTATGATTATAAATTTTGTTGCAATATCATGTTAACTTATATTGTGCATTTG
456 TAAGATGTATGAATTATGATTATAAATTTTGTTGCAATATCATGTTAACTTATATTGTGCATTTG
31774940 AACATGGAATGCATGAAATGGTGAGTTCATGATTAGTCGGGTTTTAGGGTTTTAGGGTTTAGGGT
521 AACATGGAATGCATGAAATGGTGAGTTCATGATTAGTCGGGTTTTAGGGTTTTAGGGTTTAGGGT
31775005 AAAGGATTATTTTTGAGGTTATATCAGAATTATTTTCATAGCGGAAAGAGGAAAATGTGATAGTG
586 AAAGGATTATTTTTGAGGTTATATCAGAATTATTTTCATAGCGGAAAGAGGAAAATGTGATAGTG
31775070 AGTAGCAAACTAAAAGAGTACAGTGAGAATCGACTTCTGATAATGAATTTCAGAATATATGAGAA
651 AGTAGCAAACTAAAAGAGTACAGTGAGAATCGACTTCTGATAATGAATTTCAGAATATATGAGAA
31775135 ATTAAATAGATATATTGGAGGCACCGCCTGAGTGAAATTTCTTCAACACTGAATATGAAATTGAG
716 ATTAAATAGATATATTGGAGGCACCGCCTGAGTGAAATTTCTTCAACACTGAATATGAAATTGAG
31775200 GAATCTAAGTGAAGACCACTTTTCTGGTAAGATTTTCGAGGACGAAAATCCCTAAAAGGGGGGAG
781 GAATCTAAGTGAAGACCACTTTTCTGGTAAGATTTTCGAGGACGAAAATCCCTAAAAGGGGGGAG
31775265 AATTGTAATATCCCGAATTATGGCCTAATCGAAATAGTGGTTTCGTGACCATAAATCCGATATAG
846 AATTGTAATATCCCGAATTATGGCCTAATCGAAATAGTGGTTTCGTGACCATAAATCCGATATAG
31775330 AAATAATTATTTTATAATTATTTTGAGGT
911 AAATAATTATTTTATAATTATTTTGAGGT
31775359 AAGTTCATGAGATAAATGTTATATGTAATGTGGGTCCGGGTACTGACTTCATGACCAAACCCATG
1 AAGTTCATGAGATAAATGTTATATGTAATGTGGGTCCGGGTACTGACTTCATGACCAAACCCATG
31775424 AGTAACTCGTTGAGCGAGCATTTCATGTCAACACTATATGGGTCGGGGTGCTGCCTTTGTGTACA
66 AGTAACTCGTTGAGCGAGCATTTCATGTCAACACTATATGGGTCGGGGTGCTGCCTTTGTGTACA
31775489 GACCCGTTAGTAGCTCAATGAGCGGGTGTTACATGATAGTGCTATGGGGTCCGGGTACTAACTGA
131 GACCCGTTAGTAGCTCAATGAGCGGGTGTTACATGATAGTGCTATGGGGTCCGGGTACTAACTGA
31775554 TGAATAGGCCAGTGAGTAGCTCAAAATGCGAGCATTACATAGTATGAGGTAGCTCTGGCTTCTTA
196 TGAATAGGCCAGTGAGTAGCTCAAAATGCGAGCATTACATAGTATGAGGTAGCTCTGGCTTCTTA
31775619 CATGGCACTTAGGTGCAAACTTCCCATGTATCCAATAGTATTCCGAGTGTTCAACGGGTATTACA
261 CATGGCACTTAGGTGCAAACTTCCCATGTATCCAATAGTATTCCGAGTGTTCAACGGGTATTACA
31775684 ATAGACGTGATGAAATTCCCAATGAGGGCATGTTAAAGAGATATGGTTATATGATATATTACGAT
326 ATAGACGTGATGAAATTCCCAATGAGGGCATGTTAAAGAGATATGGTTATATGATATATTACGAT
31775749 GAGTACAGGTATGTACACTAAGCTTATGGCTATTGAGGCTTTAAAATGTTGAGACATCAGTGAGC
391 GAGTACAGGTATGTACACTAAGCTTATGGCTATTGAGGCTTTAAAATGTTGAGACATCAGTGAGC
31775814 TAAGATGTATGAATTATGATTATAAATTTTGTTGCAATATCATGTTAACTTATATTGTGCATTTG
456 TAAGATGTATGAATTATGATTATAAATTTTGTTGCAATATCATGTTAACTTATATTGTGCATTTG
31775879 AACATGGAATGCATGAAATGGTGAGTTCATGATTAGTCGGGTTTTAGGGTTTTAGGGTTTAGGGT
521 AACATGGAATGCATGAAATGGTGAGTTCATGATTAGTCGGGTTTTAGGGTTTTAGGGTTTAGGGT
31775944 AAAGGATTATTTTTGAGGTTATATCAGAATTATTTTCATAGCGGAAAGAGGAAAATGTGATAGTG
586 AAAGGATTATTTTTGAGGTTATATCAGAATTATTTTCATAGCGGAAAGAGGAAAATGTGATAGTG
31776009 AGTAGCAAACTAAAAGAGTACAGTGAGAATCGACTTCTGATAATGAATTTCAGAATATATGAGAA
651 AGTAGCAAACTAAAAGAGTACAGTGAGAATCGACTTCTGATAATGAATTTCAGAATATATGAGAA
31776074 ATTAAATAGATATATTGGAGGCACCGCCTGAGTGAAATTTCTTCAACACTGAATATGAAATTGAG
716 ATTAAATAGATATATTGGAGGCACCGCCTGAGTGAAATTTCTTCAACACTGAATATGAAATTGAG
31776139 GAATCTAAGTGAAGACCACTTTTCTGGTAAGATTTTCGAGGACGAAAATCCCTAAAAGGGGGGAG
781 GAATCTAAGTGAAGACCACTTTTCTGGTAAGATTTTCGAGGACGAAAATCCCTAAAAGGGGGGAG
31776204 AATTGTAATATCCCGAATTATGGCCTAATCGAAATAGTGGTTTCGTGACCATAAATCCGATATAG
846 AATTGTAATATCCCGAATTATGGCCTAATCGAAATAGTGGTTTCGTGACCATAAATCCGATATAG
31776269 AAATAATTATTTTATAATTATTTTGAGGT
911 AAATAATTATTTTATAATTATTTTGAGGT
31776298 CTATGATATG
Statistics
Matches: 939, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
939 939 1.00
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (939 bp):
AAGTTCATGAGATAAATGTTATATGTAATGTGGGTCCGGGTACTGACTTCATGACCAAACCCATG
AGTAACTCGTTGAGCGAGCATTTCATGTCAACACTATATGGGTCGGGGTGCTGCCTTTGTGTACA
GACCCGTTAGTAGCTCAATGAGCGGGTGTTACATGATAGTGCTATGGGGTCCGGGTACTAACTGA
TGAATAGGCCAGTGAGTAGCTCAAAATGCGAGCATTACATAGTATGAGGTAGCTCTGGCTTCTTA
CATGGCACTTAGGTGCAAACTTCCCATGTATCCAATAGTATTCCGAGTGTTCAACGGGTATTACA
ATAGACGTGATGAAATTCCCAATGAGGGCATGTTAAAGAGATATGGTTATATGATATATTACGAT
GAGTACAGGTATGTACACTAAGCTTATGGCTATTGAGGCTTTAAAATGTTGAGACATCAGTGAGC
TAAGATGTATGAATTATGATTATAAATTTTGTTGCAATATCATGTTAACTTATATTGTGCATTTG
AACATGGAATGCATGAAATGGTGAGTTCATGATTAGTCGGGTTTTAGGGTTTTAGGGTTTAGGGT
AAAGGATTATTTTTGAGGTTATATCAGAATTATTTTCATAGCGGAAAGAGGAAAATGTGATAGTG
AGTAGCAAACTAAAAGAGTACAGTGAGAATCGACTTCTGATAATGAATTTCAGAATATATGAGAA
ATTAAATAGATATATTGGAGGCACCGCCTGAGTGAAATTTCTTCAACACTGAATATGAAATTGAG
GAATCTAAGTGAAGACCACTTTTCTGGTAAGATTTTCGAGGACGAAAATCCCTAAAAGGGGGGAG
AATTGTAATATCCCGAATTATGGCCTAATCGAAATAGTGGTTTCGTGACCATAAATCCGATATAG
AAATAATTATTTTATAATTATTTTGAGGT
Found at i:31782469 original size:3 final size:3
Alignment explanation
Indices: 31782461--31782494 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
31782451 AATAAAGAAC
* *
31782461 TAA TAA TAA TAA TAC TAA TAA AAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
31782495 TTAATTAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:31782780 original size:23 final size:22
Alignment explanation
Indices: 31782725--31782767 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
31782715 GGAGAAAGTG
31782725 AAAGAAAG-AGGAAAGAAAGAA
1 AAAGAAAGAAGGAAAGAAAGAA
*
31782746 AAAAAAGAGAAGGAAAGAAAGA
1 AAAGAA-AGAAGGAAAGAAAGA
31782768 TAAGGGAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 2 0.11
23 12 0.63
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (22 bp):
AAAGAAAGAAGGAAAGAAAGAA
Found at i:31793024 original size:43 final size:43
Alignment explanation
Indices: 31792917--31793076 Score: 189
Period size: 43 Copynumber: 3.7 Consensus size: 43
31792907 TCGCACAATG
* * * *
31792917 CAATATCCCAGATATGGTCTTACATGTTATCAT-ATATCGATGC
1 CAATGTCCCAGACATGGTCTTACACGTAATCATAATA-CGATGC
* * * *
31792960 C-ACGTCCCAGAGAGGGTCTTACACGAAATCATAATACGATGC
1 CAATGTCCCAGACATGGTCTTACACGTAATCATAATACGATGC
* * *
31793002 CAATGTCCCAAACATGGTCTTACACGTAATCACAATACAATGC
1 CAATGTCCCAGACATGGTCTTACACGTAATCATAATACGATGC
*
31793045 CAATGTCCCAGACATGGTCTTACATGTAATCA
1 CAATGTCCCAGACATGGTCTTACACGTAATCA
31793077 CATCTCGATA
Statistics
Matches: 99, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
42 31 0.31
43 68 0.69
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (43 bp):
CAATGTCCCAGACATGGTCTTACACGTAATCATAATACGATGC
Found at i:31797175 original size:15 final size:14
Alignment explanation
Indices: 31797151--31797207 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 14
31797141 CCTAAACTAA
31797151 AATTA-TTAATTCT
1 AATTATTTAATTCT
*
31797164 AATTATTATAATATTTT
1 AATTATT-T-A-ATTCT
*
31797181 ATTTATTTAATTCCT
1 AATTATTTAATT-CT
31797196 AATTATTTAATT
1 AATTATTTAATT
31797208 ATATAATCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
13 5 0.14
14 4 0.11
15 14 0.40
16 2 0.06
17 10 0.29
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (14 bp):
AATTATTTAATTCT
Found at i:31797685 original size:85 final size:85
Alignment explanation
Indices: 31797558--31797721 Score: 258
Period size: 85 Copynumber: 1.9 Consensus size: 85
31797548 ATTCGCACAG
* * * *
31797558 TTTCATATCAACAGTAATGGAAATATGTGTATAAATTAAGCATTGGACCCTATACAAAATTAGAT
1 TTTCATATCAACAGGAATGGAAATA-GTATATAAATGAAGCATTCGACCCTATACAAAATTAGAT
*
31797623 AGGTAAGCAAGTCTCGCGCAC
65 AGGTAAACAAGTCTCGCGCAC
31797644 TTTCATATCAACATGGAATGGAAATA-TATATAAATGAAGCATTCGACCCTATACAAAATTAGAT
1 TTTCATATCAACA-GGAATGGAAATAGTATATAAATGAAGCATTCGACCCTATACAAAATTAGAT
31797708 AGGTAAACAAGTCT
65 AGGTAAACAAGTCT
31797722 TGCAAACAAG
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
85 48 0.67
86 13 0.18
87 11 0.15
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (85 bp):
TTTCATATCAACAGGAATGGAAATAGTATATAAATGAAGCATTCGACCCTATACAAAATTAGATA
GGTAAACAAGTCTCGCGCAC
Found at i:31798045 original size:55 final size:55
Alignment explanation
Indices: 31797978--31798086 Score: 182
Period size: 55 Copynumber: 2.0 Consensus size: 55
31797968 GTGATGATGT
*
31797978 AATGAACTTAGTAATATGTATAAATTATTTATTTAAATTGTAGTTGAGGCTGTGC
1 AATGAAATTAGTAATATGTATAAATTATTTATTTAAATTGTAGTTGAGGCTGTGC
* * *
31798033 AATGAAATTAGTAATATGTGTAAATTGTTTATTTAAATTGTAGTTGAGGTTGTG
1 AATGAAATTAGTAATATGTATAAATTATTTATTTAAATTGTAGTTGAGGCTGTG
31798087 TTTGCTCTGG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.34, C:0.03, G:0.20, T:0.43
Consensus pattern (55 bp):
AATGAAATTAGTAATATGTATAAATTATTTATTTAAATTGTAGTTGAGGCTGTGC
Found at i:31799494 original size:49 final size:49
Alignment explanation
Indices: 31799391--31799486 Score: 183
Period size: 49 Copynumber: 2.0 Consensus size: 49
31799381 TCGATTGGGC
*
31799391 TTTAAGGCTCTAAGGGATTGTGACAATTGTTTATTATGATGATAGTGCA
1 TTTAAGGCTCTAAGGGATTGTGAAAATTGTTTATTATGATGATAGTGCA
31799440 TTTAAGGCTCTAAGGGATTGTGAAAATTGTTTATTATGATGATAGTG
1 TTTAAGGCTCTAAGGGATTGTGAAAATTGTTTATTATGATGATAGTG
31799487 TGATTAAGAG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.29, C:0.06, G:0.25, T:0.40
Consensus pattern (49 bp):
TTTAAGGCTCTAAGGGATTGTGAAAATTGTTTATTATGATGATAGTGCA
Found at i:31800229 original size:27 final size:27
Alignment explanation
Indices: 31800189--31800281 Score: 116
Period size: 27 Copynumber: 3.4 Consensus size: 27
31800179 AGGAAGCGTC
*
31800189 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
31800216 CTGGTGGCTCTGCCACATATT-TCTGTT
1 CTGGTGGCTCTGCCACA-ATTATCTGAT
* *
31800243 CTGGTGGCTGTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
*
31800271 CTGGTGACTCT
1 CTGGTGGCTCT
31800282 ATCACCTTAT
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
26 3 0.05
27 40 0.71
28 13 0.23
ACGTcount: A:0.15, C:0.24, G:0.25, T:0.37
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:31800295 original size:54 final size:54
Alignment explanation
Indices: 31800189--31800300 Score: 145
Period size: 54 Copynumber: 2.1 Consensus size: 54
31800179 AGGAAGCGTC
* * *
31800189 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATTTCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTACCACATATATCTGTT
* * * *
31800243 CTGGTGGCTGTGCCACGATTATCTGTATCTGGTGACTCTATCACCT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTACCACATATATCTGTT
31800297 CTGG
1 CTGG
31800301 CAGCCATGCT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
54 34 0.68
55 16 0.32
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTACCACATATATCTGTT
Found at i:31807802 original size:27 final size:27
Alignment explanation
Indices: 31807762--31807845 Score: 98
Period size: 27 Copynumber: 3.1 Consensus size: 27
31807752 AGGAAGTGTC
31807762 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTATGCCACAATTATCTGAT
* * *
31807789 CTGGTGGCTTTGCCACATATT-TTTGTT
1 CTGGTGGCTATGCCACA-ATTATCTGAT
* *
31807816 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTATGCCACAATTATCTG-AT
31807844 CT
1 CT
31807846 AGTGACTCTG
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
26 3 0.06
27 38 0.81
28 6 0.13
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.39
Consensus pattern (27 bp):
CTGGTGGCTATGCCACAATTATCTGAT
Found at i:31807870 original size:54 final size:54
Alignment explanation
Indices: 31807762--31807873 Score: 127
Period size: 54 Copynumber: 2.1 Consensus size: 54
31807752 AGGAAGTGTC
* * * * *
31807762 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTTTGCCACATATTTTTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTAGTGACTCTGCCACATATATCTGTT
* * * *
31807816 CTGGTGGCTCTGCCACGATTATCTGTATCTAGTGACTCTGTCACGT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTAGTGACTCTGCCACATATATCTGTT
31807870 CTGG
1 CTGG
31807874 CAGCCATGCT
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
54 33 0.69
55 15 0.31
ACGTcount: A:0.15, C:0.22, G:0.23, T:0.39
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTAGTGACTCTGCCACATATATCTGTT
Found at i:31813623 original size:27 final size:27
Alignment explanation
Indices: 31813593--31813648 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
31813583 ATTATAAAGT
*
31813593 GATTTGCCTAACTATACATTGACGTTG
1 GATTTGCCTAACTATACATTAACGTTG
31813620 GATTTGCCTAACTATACATTAACGTTG
1 GATTTGCCTAACTATACATTAACGTTG
31813647 GA
1 GA
31813649 CTAACTAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (27 bp):
GATTTGCCTAACTATACATTAACGTTG
Found at i:31820014 original size:40 final size:40
Alignment explanation
Indices: 31819964--31820063 Score: 155
Period size: 40 Copynumber: 2.5 Consensus size: 40
31819954 TTGCCGATAC
31819964 CTGATAGCTTTGTGAGCAGCACTATGTAGCTACGTCCTGA
1 CTGATAGCTTTGTGAGCAGCACTATGTAGCTACGTCCTGA
* * *
31820004 CTGACAGCTTTGTGATCAGCACTGTGTAGCTACGTCCTGA
1 CTGATAGCTTTGTGAGCAGCACTATGTAGCTACGTCCTGA
*
31820044 CTAATAGCTTGTGTGAGCAG
1 CTGATAGCTT-TGTGAGCAG
31820064 GCCCATGAGT
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 45 0.85
41 8 0.15
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (40 bp):
CTGATAGCTTTGTGAGCAGCACTATGTAGCTACGTCCTGA
Found at i:31838997 original size:20 final size:19
Alignment explanation
Indices: 31838957--31838999 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
31838947 TTTGACCAGT
*
31838957 TTTTGGGTCTTAGTCTCAA
1 TTTTGGGTCTTAGCCTCAA
31838976 TTTTGGGTTCTTGAGCCT-AA
1 TTTTGGG-TCTT-AGCCTCAA
31838996 TTTT
1 TTTT
31839000 TTTTTTCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 7 0.33
20 10 0.48
21 4 0.19
ACGTcount: A:0.14, C:0.14, G:0.21, T:0.51
Consensus pattern (19 bp):
TTTTGGGTCTTAGCCTCAA
Found at i:31840245 original size:56 final size:56
Alignment explanation
Indices: 31840159--31840390 Score: 446
Period size: 56 Copynumber: 4.1 Consensus size: 56
31840149 ACAAGGGATG
31840159 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
31840215 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
31840271 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
* *
31840327 ATGGGCAAAACATGTCATCAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
31840383 ATGGGCAA
1 ATGGGCAA
31840391 TAAACTAATA
Statistics
Matches: 174, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 174 1.00
ACGTcount: A:0.46, C:0.09, G:0.22, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:31854723 original size:27 final size:27
Alignment explanation
Indices: 31854693--31854746 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
31854683 CCTTTCCCTA
31854693 AAAGTCTAAATTTATGTGTTTTCACTT
1 AAAGTCTAAATTTATGTGTTTTCACTT
31854720 AAAGTCTAAATTTATGTGTTTTCACTT
1 AAAGTCTAAATTTATGTGTTTTCACTT
31854747 TCCCTTCCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.48
Consensus pattern (27 bp):
AAAGTCTAAATTTATGTGTTTTCACTT
Found at i:31858598 original size:16 final size:17
Alignment explanation
Indices: 31858577--31858615 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
31858567 ATGCAAATTA
31858577 AAAGAAGAAAAGA-AAG
1 AAAGAAGAAAAGAGAAG
* *
31858593 AAAGAAGAGAAGAGGAG
1 AAAGAAGAAAAGAGAAG
31858610 AAAGAA
1 AAAGAA
31858616 ACGCAAGGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (17 bp):
AAAGAAGAAAAGAGAAG
Found at i:31859332 original size:7 final size:7
Alignment explanation
Indices: 31859320--31859355 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
31859310 ATAAAATAAA
31859320 ATATTGT
1 ATATTGT
31859327 ATATTGT
1 ATATTGT
*
31859334 ATATTTT
1 ATATTGT
*
31859341 ATATTTT
1 ATATTGT
31859348 ATATTGT
1 ATATTGT
31859355 A
1 A
31859356 CGGGATATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (7 bp):
ATATTGT
Found at i:31861788 original size:47 final size:48
Alignment explanation
Indices: 31861696--31861826 Score: 171
Period size: 47 Copynumber: 2.8 Consensus size: 48
31861686 GGTTACTTGC
* *
31861696 GTGAGCTAGTGTAAG-ACATGTCTGGGACAT-GCATCGGCTACGAGAT
1 GTGAGCCAGTGTAAGAACATGTCTGGGACATGGCATCGACTACGAGAT
* * *
31861742 GAT-AGTCAGTGTAAGAACATGTCTGGGATATGGCATCGACT-TGAGAT
1 G-TGAGCCAGTGTAAGAACATGTCTGGGACATGGCATCGACTACGAGAT
*
31861789 GTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCG
1 GTGAGCCAGTGTAAGAACATGTCTGGGACATGGCATCG
31861827 GCACCTTACC
Statistics
Matches: 73, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
46 12 0.16
47 53 0.73
48 8 0.11
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (48 bp):
GTGAGCCAGTGTAAGAACATGTCTGGGACATGGCATCGACTACGAGAT
Found at i:31862843 original size:41 final size:41
Alignment explanation
Indices: 31862777--31862868 Score: 139
Period size: 41 Copynumber: 2.2 Consensus size: 41
31862767 ATGGGCTAGG
* * *
31862777 ACACAGGCTTGTCGTGGCCGTGTGAGGGACACGGTCCATTA
1 ACACGGGCGTGTCGTGGCCGTGTGAGGGACACGGGCCATTA
*
31862818 ACACGGGCGTGTCGTGGCCGTGTGAGGGACACGGGCCATTG
1 ACACGGGCGTGTCGTGGCCGTGTGAGGGACACGGGCCATTA
*
31862859 ACATGGGCGT
1 ACACGGGCGT
31862869 ATGTCAGGCG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.17, C:0.24, G:0.39, T:0.20
Consensus pattern (41 bp):
ACACGGGCGTGTCGTGGCCGTGTGAGGGACACGGGCCATTA
Found at i:31865355 original size:49 final size:47
Alignment explanation
Indices: 31865297--31865649 Score: 589
Period size: 47 Copynumber: 7.4 Consensus size: 47
31865287 ATTGATGTAC
* * * * *
31865297 AAGTATATATATGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
31865344 AAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
1 AAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
31865393 AAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
1 AAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
31865442 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
31865489 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
31865536 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
* * *
31865583 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGA
1 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
*
31865630 AAGTGTATAAATGTGATAAG
1 AAGTGTATATATGTGATAAG
31865650 TCCCGAAGGG
Statistics
Matches: 295, Mismatches: 9, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
47 203 0.69
49 92 0.31
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
Found at i:31868030 original size:30 final size:30
Alignment explanation
Indices: 31867988--31868053 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
31867978 GTCAAATTGT
31867988 AAATAA-AAAATATCTCTAAAATTTTTTTG
1 AAATAATAAAATATCTCTAAAATTTTTTTG
31868017 AAATAATAAAATATCTCTAAAATTTTTTTG
1 AAATAATAAAATATCTCTAAAATTTTTTTG
31868047 AAATAAT
1 AAATAAT
31868054 TTCTTTAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 6 0.17
30 30 0.83
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (30 bp):
AAATAATAAAATATCTCTAAAATTTTTTTG
Found at i:31868290 original size:6 final size:6
Alignment explanation
Indices: 31868266--31868374 Score: 52
Period size: 6 Copynumber: 18.2 Consensus size: 6
31868256 TTTTATCTAC
* * *
31868266 AATATA AATATT AA-ATT AATTTT AATATT AACA-T AATCACTTT AATATT
1 AATATT AATATT AATATT AATATT AATATT AATATT AAT-A--TT AATATT
* *
31868315 AA-ATT AATAAT -ATACTTT CAATATA AATATT AA-ATTT AAT-TT AATATT
1 AATATT AATATT AATA--TT -AATATT AATATT AATA-TT AATATT AATATT
*
31868363 AA-AAT AATATT A
1 AATATT AATATT A
31868375 TTTTTTGAAT
Statistics
Matches: 78, Mismatches: 11, Indels: 28
0.67 0.09 0.24
Matches are distributed among these distances:
5 26 0.33
6 42 0.54
7 2 0.03
8 1 0.01
9 7 0.09
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (6 bp):
AATATT
Found at i:31868322 original size:20 final size:17
Alignment explanation
Indices: 31868272--31868322 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 17
31868262 CTACAATATA
31868272 AATATTAAATTAATTTT
1 AATATTAAATTAATTTT
31868289 AATATTAACA-TAATCACTTT
1 AATATTAA-ATTAAT---TTT
31868309 AATATTAAATTAAT
1 AATATTAAATTAAT
31868323 AATATACTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 12 0.41
18 1 0.03
19 1 0.03
20 15 0.52
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (17 bp):
AATATTAAATTAATTTT
Found at i:31868360 original size:17 final size:17
Alignment explanation
Indices: 31868272--31868365 Score: 56
Period size: 17 Copynumber: 5.5 Consensus size: 17
31868262 CTACAATATA
31868272 AATATTAAA-TTAATTTT
1 AATATTAAATTTAA-TTT
* *
31868289 AATATTAACATAATCACTTT
1 AATATTAA-AT--TTAATTT
31868309 AATATTAAA-TTAA--T
1 AATATTAAATTTAATTT
* *
31868323 AATA-T-ACTTTCAATATA
1 AATATTAAATTT-AAT-TT
31868340 AATATTAAATTTAATTT
1 AATATTAAATTTAATTT
31868357 AATATTAAA
1 AATATTAAA
31868366 ATAATATTAT
Statistics
Matches: 58, Mismatches: 8, Indels: 22
0.66 0.09 0.25
Matches are distributed among these distances:
12 1 0.02
13 3 0.05
14 7 0.12
16 2 0.03
17 22 0.38
18 5 0.09
19 5 0.09
20 11 0.19
21 2 0.03
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (17 bp):
AATATTAAATTTAATTT
Found at i:31871006 original size:243 final size:243
Alignment explanation
Indices: 31870578--31871310 Score: 1403
Period size: 243 Copynumber: 3.0 Consensus size: 243
31870568 ATAAAAATTC
*
31870578 ATATAAATTATCACCAAAGTATTTTACATTATCATTGACTTGGGATGTTTTAACCAGTCATTCCA
1 ATATAAATTATCATCAAAGTATTTTACATTATCATTGACTTGGGATGTTTTAACCAGTCATTCCA
*
31870643 ACACTAGTGAACTTCTTGTTTCTATTTTATACATCAATCATACAAGTGTAATGTATTCTTTCAAG
66 ACACTAGTGAACTTCTTGTTTCTATTTCATACATCAATCATACAAGTGTAATGTATTCTTTCAAG
*
31870708 GAATATCGATAATCCAATGACATGCGTATCTTATTTCGGTTTTATCCATGGTTATAATGTAAAAC
131 GAATATCGATAATGCAATGACATGCGTATCTTATTTCGGTTTTATCCATGGTTATAATGTAAAAC
*
31870773 GCTTAAAGATTTCCTTCAACATATATCTTATTGATCTAAATAATAATA
196 GCTTAAAGATTTCCTTCAACATATATCTTATTGATCTAAAAAATAATA
31870821 ATATAAATTATCATCAAAGTATTTTACATTATCATTGACTTGGGATGTTTTAACCAGTCATTCCA
1 ATATAAATTATCATCAAAGTATTTTACATTATCATTGACTTGGGATGTTTTAACCAGTCATTCCA
31870886 ACACTAGTGAACTTCTTGTTTCTATTTCATACATCAATCATACAAGTGTAATGTATTCTTTCAAG
66 ACACTAGTGAACTTCTTGTTTCTATTTCATACATCAATCATACAAGTGTAATGTATTCTTTCAAG
31870951 GAATATCGATAATGCAATGACATGCGTATCTTATTTCGGTTTTATCCATGGTTATAATGTAAAAC
131 GAATATCGATAATGCAATGACATGCGTATCTTATTTCGGTTTTATCCATGGTTATAATGTAAAAC
31871016 GCTTAAAGATTTCCTTCAACATATATCTTATTGATCTAAAAAATAATA
196 GCTTAAAGATTTCCTTCAACATATATCTTATTGATCTAAAAAATAATA
*
31871064 ATATAAATTATCATCAAAGTATTTAACATTATCATTGACTTGGGATGTTTTAACCAGTCATTCCA
1 ATATAAATTATCATCAAAGTATTTTACATTATCATTGACTTGGGATGTTTTAACCAGTCATTCCA
31871129 ACACTAGTGAACTTCTTGTTTCTATTTCATACATCAATCATACAAGTGTAATGTATTCTTTCAAG
66 ACACTAGTGAACTTCTTGTTTCTATTTCATACATCAATCATACAAGTGTAATGTATTCTTTCAAG
* *
31871194 GAATATCGATAATGCAATGACATGTGTATCTTATTTCAGTTTTATCCATGGTTATAATGTAAAAC
131 GAATATCGATAATGCAATGACATGCGTATCTTATTTCGGTTTTATCCATGGTTATAATGTAAAAC
31871259 GCTTAAAGATTTCCTTCAACATATATCTTATTGATCTAAAAAATAATA
196 GCTTAAAGATTTCCTTCAACATATATCTTATTGATCTAAAAAATAATA
31871307 ATAT
1 ATAT
31871311 TATGTTCTAC
Statistics
Matches: 483, Mismatches: 7, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
243 483 1.00
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (243 bp):
ATATAAATTATCATCAAAGTATTTTACATTATCATTGACTTGGGATGTTTTAACCAGTCATTCCA
ACACTAGTGAACTTCTTGTTTCTATTTCATACATCAATCATACAAGTGTAATGTATTCTTTCAAG
GAATATCGATAATGCAATGACATGCGTATCTTATTTCGGTTTTATCCATGGTTATAATGTAAAAC
GCTTAAAGATTTCCTTCAACATATATCTTATTGATCTAAAAAATAATA
Found at i:31873249 original size:46 final size:49
Alignment explanation
Indices: 31873066--31873383 Score: 271
Period size: 46 Copynumber: 6.7 Consensus size: 49
31873056 GGTAAAGTGT
* * *
31873066 CGATGCCATGTCCCAGACATGGTTTTACACTGGC-TACCATCTTCG-AGGA
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTTA-CATC-TCGTAGGC
31873115 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACATAAC-CGT--GC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCT-T-ACAT--CTCGTAGGC
*
31873165 CGATGCCATGTCCCAGACATGGTCTTACACTAAC--ACATCTCGTA-GC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTTACATCTCGTAGGC
* * *
31873211 CGATG-CATGTCCCAGACAT-GTCTTATACTGGCTTACATCCCG-AGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTTACATCTCGTAGGC
* * * * * *
31873257 TGATG-CATGTCCCAAACAT-GTCTTACACTAGCACT-CTTCTC-AATGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGC-TTACATCTCGTAGGC
* *
31873303 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-CATAAT-GT-GGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCT-TACAT-CTCGTAGGC
*
31873351 CGAT-ACATGTCCCAGACAT-GTCTTACACTAGCT
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCT
31873384 CACACAAACG
Statistics
Matches: 225, Mismatches: 26, Indels: 39
0.78 0.09 0.13
Matches are distributed among these distances:
44 11 0.05
45 18 0.08
46 72 0.32
47 28 0.12
48 21 0.09
49 33 0.15
50 34 0.15
51 6 0.03
52 1 0.00
53 1 0.00
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (49 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTAGCTTACATCTCGTAGGC
Found at i:31873360 original size:94 final size:93
Alignment explanation
Indices: 31873072--31873382 Score: 323
Period size: 94 Copynumber: 3.3 Consensus size: 93
31873062 GTGTCGATGC
* * *
31873072 CATGTCCCAGACATGGTTTTACACTGGCTACCATCTTCG-AGGACGATGCCATGTCCCAGACATG
1 CATGTCCCAGACAT-GTCTTACACTAGC-A-CATC-TCGTA-GCCGATGCCATGTCCCAGACATG
* *
31873136 GTCTTACACTAGCTCTCACATAACCGT-GCCGATGC
61 GTCTTACACTGGCTCT-ACATAA-CGTGGCCGAT-A
*
31873171 CATGTCCCAGACATGGTCTTACACTAACACATCTCGTAGCCGATG-CATGTCCCAGACAT-GTCT
1 CATGTCCCAGACAT-GTCTTACACTAGCACATCTCGTAGCCGATGCCATGTCCCAGACATGGTCT
* ** * * *
31873234 TATACTGGCT-TACATCCCGAGGCTGATG
65 TACACTGGCTCTACATAACGTGGCCGATA
*
31873262 CATGTCCCAAACATGTCTTACACTAGCAC-TCTTC-TCAATGCCGATGCCATGTCCCAGACATGG
1 CATGTCCCAGACATGTCTTACACTAGCACATC-TCGT--A-GCCGATGCCATGTCCCAGACATGG
*
31873325 TCTTACACTGGCTCT-CATAATGTGGCCGATA
62 TCTTACACTGGCTCTACATAACGTGGCCGATA
31873356 CATGTCCCAGACATGTCTTACACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
31873383 TCACACAAAC
Statistics
Matches: 182, Mismatches: 21, Indels: 23
0.81 0.09 0.10
Matches are distributed among these distances:
89 3 0.02
90 16 0.09
91 16 0.09
92 16 0.09
93 15 0.08
94 61 0.34
95 15 0.08
96 9 0.05
97 5 0.03
98 1 0.01
99 25 0.14
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (93 bp):
CATGTCCCAGACATGTCTTACACTAGCACATCTCGTAGCCGATGCCATGTCCCAGACATGGTCTT
ACACTGGCTCTACATAACGTGGCCGATA
Found at i:31873370 original size:140 final size:141
Alignment explanation
Indices: 31873072--31873379 Score: 362
Period size: 140 Copynumber: 2.2 Consensus size: 141
31873062 GTGTCGATGC
* * *
31873072 CATGTCCCAGACATGGTTTTACACTGGCTACCATCTTCGAGGACGATGCCATGTCCCAGACATGG
1 CATGTCCCAGACAT-GTCTTACACTGGCTACCATCTCCGAGGACGATGCCATGTCCCAAACATGG
*
31873137 TCTTACACTAGCTCTCACATAACCGTGCCGATGCCATGTCCCAGACATGGTCTTACACTAACACA
65 TCTTACACTAGCACTCACATAA-C-TGCCGATGCCATGTCCCAGACATGGTCTTACACTAACACA
*
31873202 TCTCGTAGCCGATG
128 TCTCGTAGCCGATA
*
31873216 CATGTCCCAGACATGTCTTATACTGGCTTA-CATC-CCGAGG-CTGATG-CATGTCCCAAACAT-
1 CATGTCCCAGACATGTCTTACACTGGC-TACCATCTCCGAGGAC-GATGCCATGTCCCAAACATG
* ** *
31873276 GTCTTACACTAGCACTCTTC-TCAA-TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTC
64 GTCTTACACTAGCACTC-ACAT-AACTGCCGATGCCATGTCCCAGACATGGTCTTACACTAACAC
* *
31873339 -TCATAATGTGGCCGATA
127 ATC-T--CGTAGCCGATA
31873356 CATGTCCCAGACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
31873380 AGCTCACACA
Statistics
Matches: 144, Mismatches: 13, Indels: 18
0.82 0.07 0.10
Matches are distributed among these distances:
137 2 0.01
138 37 0.26
140 48 0.33
141 17 0.12
142 9 0.06
143 15 0.10
144 16 0.11
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.27
Consensus pattern (141 bp):
CATGTCCCAGACATGTCTTACACTGGCTACCATCTCCGAGGACGATGCCATGTCCCAAACATGGT
CTTACACTAGCACTCACATAACTGCCGATGCCATGTCCCAGACATGGTCTTACACTAACACATCT
CGTAGCCGATA
Done.