Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 4 of 292
Found at i:1051342 original size:9 final size:9
Alignment explanation
Indices: 1051311--1051411 Score: 55
Period size: 9 Copynumber: 10.9 Consensus size: 9
1051301 TAAAAAGAAT
*
1051311 AAAATTTTA
1 AAAATTATA
*
1051320 TAAATTTATAA
1 -AAAATTAT-A
1051331 AAAATTATA
1 AAAATTATA
1051340 AAAA-TATTA
1 AAAATTA-TA
* *
1051349 GAAATTTATTT
1 -AAAATTA-TA
* *
1051360 CAAATCATAA
1 AAAATTAT-A
1051370 AAAATT-TA
1 AAAATTATA
*
1051378 AAATTTATA
1 AAAATTATA
1051387 AAAATT-TA
1 AAAATTATA
*
1051395 AAATTTATA
1 AAAATTATA
1051404 AAAATTAT
1 AAAATTAT
1051412 TAGAAATTAA
Statistics
Matches: 69, Mismatches: 15, Indels: 15
0.70 0.15 0.15
Matches are distributed among these distances:
8 15 0.22
9 25 0.36
10 24 0.35
11 5 0.07
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (9 bp):
AAAATTATA
Found at i:1051390 original size:10 final size:10
Alignment explanation
Indices: 1051311--1051464 Score: 62
Period size: 10 Copynumber: 16.2 Consensus size: 10
1051301 TAAAAAGAAT
1051311 AAAATTT-TA
1 AAAATTTATA
*
1051320 TAAATTTATA
1 AAAATTTATA
*
1051330 AAAAATTATA
1 AAAATTTATA
*
1051340 AAAATAT-TA
1 AAAATTTATA
* *
1051349 GAAATTTATTT
1 AAAATTTA-TA
* *
1051360 CAAA-TCATA
1 AAAATTTATA
*
1051369 AAAAATT-T-
1 AAAATTTATA
1051377 AAAATTTATA
1 AAAATTTATA
1051387 AAAA-TT-T-
1 AAAATTTATA
1051394 AAAATTTATA
1 AAAATTTATA
1051404 AAAA-TTATTA
1 AAAATTTA-TA
* * *
1051414 GAAATTAATTT
1 AAAATTTA-TA
*
1051425 AAAA-TCAT-
1 AAAATTTATA
1051433 AAAATTT-TA
1 AAAATTTATA
*
1051442 GAAAATTTAGA
1 -AAAATTTATA
*
1051453 AAATTTTATA
1 AAAATTTATA
1051463 AA
1 AA
1051465 CTATTAGAAA
Statistics
Matches: 107, Mismatches: 23, Indels: 29
0.67 0.14 0.18
Matches are distributed among these distances:
7 4 0.04
8 14 0.13
9 27 0.25
10 50 0.47
11 12 0.11
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (10 bp):
AAAATTTATA
Found at i:1051455 original size:19 final size:20
Alignment explanation
Indices: 1051433--1051474 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1051423 TTAAAATCAT
1051433 AAAATTTTAGAAAAT-TTAG
1 AAAATTTTAGAAAATATTAG
* *
1051452 AAAATTTTATAAACTATTAG
1 AAAATTTTAGAAAATATTAG
1051472 AAA
1 AAA
1051475 CTAATTGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (20 bp):
AAAATTTTAGAAAATATTAG
Found at i:1053064 original size:59 final size:62
Alignment explanation
Indices: 1052995--1053112 Score: 170
Period size: 62 Copynumber: 2.0 Consensus size: 62
1052985 ATCACTCTAA
* *
1052995 TATTAAATTAATATAATATTT-T-T-CAAGATAAATATTAGATTAAATTTAAAATTAAATCT
1 TATTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTAAATTTAAAATTAAATCT
* * *
1053054 TATTAAATTAATAGAATGTTTATCTACAAGATTAATATTAAATTAAATTTAATATTAAA
1 TATTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTAAATTTAAAATTAAA
1053113 ATAATCACCT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
59 19 0.37
60 1 0.02
61 1 0.02
62 30 0.59
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.43
Consensus pattern (62 bp):
TATTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTAAATTTAAAATTAAATCT
Found at i:1055678 original size:59 final size:61
Alignment explanation
Indices: 1055607--1055723 Score: 166
Period size: 62 Copynumber: 1.9 Consensus size: 61
1055597 ACCACTTTAA
* * * * *
1055607 TATTAAATTAATATAATATTTA-T-CAAGATAAATATTAGATTAAATTTAATATTAAATCT
1 TATTAAAATAATAAAATATTTACTACAAAATAAACATTAAATTAAATTTAATATTAAATCT
1055666 TATTAAAATAATAAAATATTTATCTACAAAATAAACATTAAATTAAATTTAATATTAA
1 TATTAAAATAATAAAATATTTA-CTACAAAATAAACATTAAATTAAATTTAATATTAA
1055724 GATATCACTT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 20 0.40
61 1 0.02
62 29 0.58
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (61 bp):
TATTAAAATAATAAAATATTTACTACAAAATAAACATTAAATTAAATTTAATATTAAATCT
Found at i:1055760 original size:18 final size:17
Alignment explanation
Indices: 1055739--1055772 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1055729 CACTTTAATA
1055739 TTAATATAAGTATTAAAT
1 TTAATATAA-TATTAAAT
*
1055757 TTAATTTAATATTAAA
1 TTAATATAATATTAAA
1055773 CTATTCTCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
TTAATATAATATTAAAT
Found at i:1061614 original size:47 final size:47
Alignment explanation
Indices: 1061544--1061909 Score: 254
Period size: 47 Copynumber: 7.7 Consensus size: 47
1061534 GGGTTATGTG
* *
1061544 AGAGCCAGTGTAAGATCATGTCTGGGACATGGCATCGGCATTGAGACA
1 AGAGCTAGTGTAAGA-CATGTCTGGGACATGGCATCGGCATCGAGACA
* * *
1061592 AGGGCTAGTGTAATG-CATGTCTGGGACAT-GCATCAGCCA-C-ATTATC-
1 AGAGCTAGTGTAA-GACATGTCTGGGACATGGCATC-GGCATCGA-GA-CA
* * * * **
1061638 ATAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTAGAGAGG
1 AGAGCTAGTGTAAGA-CATGTCTGGGACATGGCATCGGCATCGAGACA
* * **
1061686 AGTGCTAGTGTAAGACATGTCTGGGACATGG-ATCGGCAACGATGATG
1 AGAGCTAGTGTAAGACATGTCTGGGACATGGCATCGGCATCGA-GACA
* * * * * *
1061733 ATAGCCAGTGTAAGACGTGTCTGGGACAT-GCATCGAC-T-AAG-CTT
1 AGAGCTAGTGTAAGACATGTCTGGGACATGGCATCGGCATCGAGAC-A
* * * *
1061777 CGTGCTAGTGTAAGACATGTCTGGGACAT-GCATCAGCA-CGTATACAA
1 AGAGCTAGTGTAAGACATGTCTGGGACATGGCATCGGCATCG-AGAC-A
*
1061824 GAGAGCTAGTGTAAGACTATGTCTGGGACATGGCATCGGCCTCGATGA-A
1 -AGAGCTAGTGTAAGAC-ATGTCTGGGACATGGCATCGGCATCGA-GACA
* *
1061873 GATAGCTAGTGTAATACCATGTCTGGGACATGGCATC
1 -AGAGCTAGTGTAAGA-CATGTCTGGGACATGGCATC
1061910 AGAAACTTAA
Statistics
Matches: 248, Mismatches: 47, Indels: 45
0.73 0.14 0.13
Matches are distributed among these distances:
44 31 0.12
45 3 0.01
46 26 0.10
47 84 0.34
48 43 0.17
49 49 0.20
50 9 0.04
51 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (47 bp):
AGAGCTAGTGTAAGACATGTCTGGGACATGGCATCGGCATCGAGACA
Found at i:1061666 original size:94 final size:94
Alignment explanation
Indices: 1061546--1061911 Score: 347
Period size: 94 Copynumber: 3.9 Consensus size: 94
1061536 GTTATGTGAG
* *
1061546 AGCCAGTGTAAGATCATGTCTGGGACATGGCATCGGCATTGAGACAAGGGCTAGTGTAATG-CAT
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACAAGTGCTAGTGTAA-GACAT
1061610 GTCTGGGACATGCATCAGCCACATTATCAT
65 GTCTGGGACATGCATCAGCCACATTATCAT
* * **
1061640 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTAGAGAGGAGTGCTAGTGTAAGACATG
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACAAGTGCTAGTGTAAGACATG
* * * * *
1061705 TCTGGGACATGGATCGGCAACGATGATGAT
66 TCTGGGACATGCATCAGCCAC-ATTATCAT
* * * **
1061735 AGCCAGTGTAAGA-CGTGTCTGGGACAT-GCATC-G-ACTAAG-CTTCGTGCTAGTGTAAGACAT
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGAC-AAGTGCTAGTGTAAGACAT
* *
1061795 GTCTGGGACATGCATCAG-CAC-GTATACAAGAG
65 GTCTGGGACATGCATCAGCCACATTAT-C---AT
* * * * *
1061827 AGCTAGTGTAAGACTATGTCTGGGACATGGCATCGGCCTCGATG--AAGATAGCTAGTGTAATAC
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGA-GACAAG-T-GCTAGTGTAAGA-
1061890 CATGTCTGGGACATGGCATCAG
62 CATGTCTGGGACAT-GCATCAG
1061912 AAACTTAACC
Statistics
Matches: 220, Mismatches: 36, Indels: 27
0.78 0.13 0.10
Matches are distributed among these distances:
88 2 0.01
90 2 0.01
91 35 0.16
92 14 0.06
93 18 0.08
94 93 0.42
95 21 0.10
96 2 0.01
97 12 0.05
98 14 0.06
99 7 0.03
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (94 bp):
AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACAAGTGCTAGTGTAAGACATG
TCTGGGACATGCATCAGCCACATTATCAT
Found at i:1065724 original size:16 final size:17
Alignment explanation
Indices: 1065695--1065729 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1065685 AAGATATTTA
1065695 ATAAAAATAATTTAATC
1 ATAAAAATAATTTAATC
*
1065712 ATAAAAA-ATTTTAATC
1 ATAAAAATAATTTAATC
1065728 AT
1 AT
1065730 CCAAATATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (17 bp):
ATAAAAATAATTTAATC
Found at i:1066785 original size:18 final size:18
Alignment explanation
Indices: 1066759--1066797 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1066749 CCCTAGAAAC
*
1066759 TTTATATCC-TTATGGGAT
1 TTTAAATCCTTTAT-GGAT
1066777 TTTAAATCCTTTATGGAT
1 TTTAAATCCTTTATGGAT
1066795 TTT
1 TTT
1066798 CATATAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.23, C:0.10, G:0.13, T:0.54
Consensus pattern (18 bp):
TTTAAATCCTTTATGGAT
Found at i:1069460 original size:28 final size:28
Alignment explanation
Indices: 1069429--1069487 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
1069419 ATTCTGACAG
1069429 TACCGCAATATTTGTATGACAGCTCAGC
1 TACCGCAATATTTGTATGACAGCTCAGC
1069457 TACCGCAATATTTGTATGACAGCTCAGC
1 TACCGCAATATTTGTATGACAGCTCAGC
1069485 TAC
1 TAC
1069488 ACCATTATGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (28 bp):
TACCGCAATATTTGTATGACAGCTCAGC
Found at i:1069659 original size:34 final size:34
Alignment explanation
Indices: 1069616--1069739 Score: 149
Period size: 34 Copynumber: 3.6 Consensus size: 34
1069606 TTCTGATATG
* * **
1069616 ATATGACATTTTGATATGATATATGCTTCTAAAA
1 ATATGACATTCTGATATGATATATGTTTCTGGAA
* * *
1069650 ATATGACATTCTAATCTGGTATATGTTTCTGGAA
1 ATATGACATTCTGATATGATATATGTTTCTGGAA
* * *
1069684 ATATGACATTTTGATCTGATATATGTTTCTGGTA
1 ATATGACATTCTGATATGATATATGTTTCTGGAA
*
1069718 ATGTGACATTCTGATATGATAT
1 ATATGACATTCTGATATGATAT
1069740 TTGTATATGT
Statistics
Matches: 76, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 76 1.00
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (34 bp):
ATATGACATTCTGATATGATATATGTTTCTGGAA
Found at i:1070607 original size:14 final size:15
Alignment explanation
Indices: 1070579--1070607 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1070569 CAGTTAACTG
1070579 TACTTTAGTTACTTT
1 TACTTTAGTTACTTT
1070594 TACTTTAG-TACTTT
1 TACTTTAGTTACTTT
1070608 AGTAAAACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.59
Consensus pattern (15 bp):
TACTTTAGTTACTTT
Found at i:1075606 original size:77 final size:77
Alignment explanation
Indices: 1075515--1075691 Score: 241
Period size: 77 Copynumber: 2.3 Consensus size: 77
1075505 GATGAACTAT
* *
1075515 TATCATGGCCCGAAGCCAAATT-ATCCAATATGCATGGCCTGAAGTCAAATCAATAATATACACA
1 TATCATGGCCCGAAGCC-AATTCATCCAATATGCATGGCCCGAAGCCAAATCAATAATATACACA
*
1075579 CCCAAAGTGTTGA
65 CCCAAAGTGCTGA
* ** *
1075592 TATCATGGCCCGAAGCCAATTCATCCGATATGCATGGCCCGAAGCCAAATCGGTAATATACGCAC
1 TATCATGGCCCGAAGCCAATTCATCCAATATGCATGGCCCGAAGCCAAATCAATAATATACACAC
*
1075657 CCGAAGTGCTGA
66 CCAAAGTGCTGA
*
1075669 TATCATGGCTCGATA-CCAATTCA
1 TATCATGGCCCGA-AGCCAATTCA
1075692 ACGTATCACT
Statistics
Matches: 89, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
76 4 0.04
77 84 0.94
78 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (77 bp):
TATCATGGCCCGAAGCCAATTCATCCAATATGCATGGCCCGAAGCCAAATCAATAATATACACAC
CCAAAGTGCTGA
Found at i:1089378 original size:14 final size:14
Alignment explanation
Indices: 1089359--1089387 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1089349 ATTTGAGAAT
1089359 GAAATAACTAACTG
1 GAAATAACTAACTG
1089373 GAAATAACTAACTG
1 GAAATAACTAACTG
1089387 G
1 G
1089388 TGAGTGTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.14, G:0.17, T:0.21
Consensus pattern (14 bp):
GAAATAACTAACTG
Found at i:1092845 original size:21 final size:22
Alignment explanation
Indices: 1092802--1092847 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
1092792 GTATTCAATT
*
1092802 TTAGTTTTTTTGTCTAGAGAAA
1 TTAGTTTTTTCGTCTAGAGAAA
1092824 TTAGTTTTTATCGT-TAGA-AAA
1 TTAGTTTTT-TCGTCTAGAGAAA
1092845 TTA
1 TTA
1092848 AAGTTTTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 6 0.27
22 13 0.59
23 3 0.14
ACGTcount: A:0.30, C:0.04, G:0.15, T:0.50
Consensus pattern (22 bp):
TTAGTTTTTTCGTCTAGAGAAA
Found at i:1093074 original size:18 final size:19
Alignment explanation
Indices: 1093039--1093076 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1093029 TATTAATTTT
* *
1093039 AAATTTTATTTTTGAAATA
1 AAATTTTAATATTGAAATA
1093058 AAATTTTAATATT-AAATA
1 AAATTTTAATATTGAAATA
1093076 A
1 A
1093077 TAAATTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
AAATTTTAATATTGAAATA
Found at i:1094309 original size:169 final size:168
Alignment explanation
Indices: 1094020--1094362 Score: 454
Period size: 169 Copynumber: 2.0 Consensus size: 168
1094010 CACTTTCCAA
*
1094020 GAAAAACTATTGGTGACCGACGGAGTTTTAGCGAACAACAGACACCGTCATCTGTCCATCACAAC
1 GAAAAACTATTGGTGACCGACGAAGTTTTAGCGAACAACAGACACCGTCATCTGTCCATCACAAC
* * * * *
1094085 TTGTGAAGACAACAAAAATGCCTACAAAATAGATCTGCAAGCTGAAAATAGAGAAGACGAGTAGT
66 TTGTGAAGACAACAAAAATACCCACAAAATAGATCTGCAAACTGAAAAGAGAGAAGACGAGCAGT
* *
1094150 AAATGAGAAGAAGAAAGCAAGAAATGGTTAATAGGAGGG
131 AAATGAGAAGAAGAAAGAAAGAAATGGTTAAT-GGAAGG
** ** *
1094189 GAAAAACTATTGGTGACCGGTGAAGTTTTAGCGAATGACATG-CACCGTCATCTGTCCATTACAA
1 GAAAAACTATTGGTGACCGACGAAGTTTTAGCGAACAACA-GACACCGTCATCTGTCCATCACAA
* * * * * * *
1094253 CTTGTGAAGATAACAAAGATACCCACAATATAGATCTGTAAATTGAAACGAGAGAAGACGTGCAG
65 CTTGTGAAGACAACAAAAATACCCACAAAATAGATCTGCAAACTGAAAAGAGAGAAGACGAGCAG
* * *
1094318 TGAATGAGAAGAAGAAATAAAGAAATGGTTGATGGAAGG
130 TAAATGAGAAGAAGAAAGAAAGAAATGGTTAATGGAAGG
1094357 GAAAAA
1 GAAAAA
1094363 ATGCAGGCGA
Statistics
Matches: 150, Mismatches: 23, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
168 11 0.07
169 138 0.92
170 1 0.01
ACGTcount: A:0.42, C:0.15, G:0.24, T:0.20
Consensus pattern (168 bp):
GAAAAACTATTGGTGACCGACGAAGTTTTAGCGAACAACAGACACCGTCATCTGTCCATCACAAC
TTGTGAAGACAACAAAAATACCCACAAAATAGATCTGCAAACTGAAAAGAGAGAAGACGAGCAGT
AAATGAGAAGAAGAAAGAAAGAAATGGTTAATGGAAGG
Found at i:1094483 original size:28 final size:27
Alignment explanation
Indices: 1094428--1094482 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
1094418 AAGAAGTAAA
1094428 TGGCTTAGAAAAAAAGTAGAAAATTTT
1 TGGCTTAGAAAAAAAGTAGAAAATTTT
1094455 TGGCTTAGAAAAAAAGTAGAAAATTTT
1 TGGCTTAGAAAAAAAGTAGAAAATTTT
1094482 T
1 T
1094483 TAGGATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.47, C:0.04, G:0.18, T:0.31
Consensus pattern (27 bp):
TGGCTTAGAAAAAAAGTAGAAAATTTT
Found at i:1095240 original size:19 final size:20
Alignment explanation
Indices: 1095197--1095240 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
1095187 AAATACATTT
*
1095197 AAAAACATAAAAACAAATAT
1 AAAAACATAAAAACAAATAA
* *
1095217 TAAAACA-AGAAACAAATAA
1 AAAAACATAAAAACAAATAA
1095236 AAAAA
1 AAAAA
1095241 TGATACTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.77, C:0.09, G:0.02, T:0.11
Consensus pattern (20 bp):
AAAAACATAAAAACAAATAA
Found at i:1102019 original size:24 final size:24
Alignment explanation
Indices: 1101991--1102039 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1101981 TGAAGAATGC
1101991 TGGTCCATAATTAAAGAACGAGCA
1 TGGTCCATAATTAAAGAACGAGCA
1102015 TGGTCCATAATTAAAGAACGAGCA
1 TGGTCCATAATTAAAGAACGAGCA
1102039 T
1 T
1102040 TGATGGCCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.22
Consensus pattern (24 bp):
TGGTCCATAATTAAAGAACGAGCA
Found at i:1104043 original size:210 final size:210
Alignment explanation
Indices: 1103771--1104162 Score: 608
Period size: 210 Copynumber: 1.9 Consensus size: 210
1103761 GATTGAAAAG
* *
1103771 ATTGTCCTAATTTAAGTTGGATTCCGGATTTGGAAGGATTTTCCTCTCTTCAAAATCTGTCAATT
1 ATTGTCCTAATTTAAGTTCGATTCCAGATTTGGAAGGATTTTCCTCTCTTCAAAATCTGTCAATT
* ** * * * *
1103836 GATAGCTGCAAGGAATTGGAAGTTCTTCCTATAACCGGAGGTTGTTCATCTCTTGAAAAGCTTAG
66 AATAGCTGCAACAAATTGGAAGTTCTTCCGATAACAGGAAGATGTTCATCTCTTGAAAAGCTTAG
* ** * *
1103901 GATTTTGGGTTGTGAAAAATTAAGCAAGATCGGAGACGGATTATTTAGCTCCACTTGTCTCAAAG
131 CATTTCCGGTTGCGAAAAATTAAGCAAGATCGGAGACGGATTATTTACCTCCACTTGTCTCAAAG
1103966 AATTATATCTATGTC
196 AATTATATCTATGTC
*
1103981 ATTGTTCTAATTTAAGTTCGATTCCAGATTTGGAAGGATGTTT-CTCTCTT-AAAATTCTGTCAA
1 ATTGTCCTAATTTAAGTTCGATTCCAGATTTGGAAGGAT-TTTCCTCTCTTCAAAA-TCTGTCAA
*
1104044 TTAATAGCTGCAACAAATTGGAAGTTCTTCCGGTAACAGGAAGATGTTCATCTCTTGAAAAGCTT
64 TTAATAGCTGCAACAAATTGGAAGTTCTTCCGATAACAGGAAGATGTTCATCTCTTGAAAAGCTT
1104109 AGCATTTCCGGTTGCGAAAAATTAAGCAAGATCGGAGACGGATTATTTACCTCC
129 AGCATTTCCGGTTGCGAAAAATTAAGCAAGATCGGAGACGGATTATTTACCTCC
1104163 TCTCTTCAAA
Statistics
Matches: 164, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
209 4 0.02
210 157 0.96
211 3 0.02
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.34
Consensus pattern (210 bp):
ATTGTCCTAATTTAAGTTCGATTCCAGATTTGGAAGGATTTTCCTCTCTTCAAAATCTGTCAATT
AATAGCTGCAACAAATTGGAAGTTCTTCCGATAACAGGAAGATGTTCATCTCTTGAAAAGCTTAG
CATTTCCGGTTGCGAAAAATTAAGCAAGATCGGAGACGGATTATTTACCTCCACTTGTCTCAAAG
AATTATATCTATGTC
Found at i:1104240 original size:138 final size:138
Alignment explanation
Indices: 1104024--1104292 Score: 396
Period size: 138 Copynumber: 1.9 Consensus size: 138
1104014 AAGGATGTTT
* *
1104024 CTCTCTTAAAATTCTGTCAATTAATAGCTGCAACAAATTGGAAGTTCTTCCGGTAACAGGAAGAT
1 CTCTCTTAAAATTCTGTCAATTAATAGCTGCAACAAATTAGAAGTTCTTCCAGTAACAGGAAGAT
1104089 GTTCATCTCTTGAAAAGCTTAGCATTTCCGGTTGCGAAAAATTAAGCAAGATCGGAGACGGATTA
66 GTTCATCTCTTGAAAAGCTTAGCATTTCCGGTTGCGAAAAATTAAGCAAGATCGGAGACGGATTA
1104154 TTTACCTC
131 TTTACCTC
* * * * * * * *
1104162 CTCTCTTCAAAA-TCTGTCAATTGATAGTTGCAACGAATTAGAAGTTCTTTCATTACCCGGAAGG
1 CTCTCTT-AAAATTCTGTCAATTAATAGCTGCAACAAATTAGAAGTTCTTCCAGTAACAGGAAGA
* ** *
1104226 TGTTCATCTCTTGAAAAGTTTAGCATTTTTGGTTGCGAAAAATTAAGCAAGATTGGAGACGGATT
65 TGTTCATCTCTTGAAAAGCTTAGCATTTCCGGTTGCGAAAAATTAAGCAAGATCGGAGACGGATT
1104291 AT
130 AT
1104293 CTGCCTGCGC
Statistics
Matches: 116, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
138 112 0.97
139 4 0.03
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Consensus pattern (138 bp):
CTCTCTTAAAATTCTGTCAATTAATAGCTGCAACAAATTAGAAGTTCTTCCAGTAACAGGAAGAT
GTTCATCTCTTGAAAAGCTTAGCATTTCCGGTTGCGAAAAATTAAGCAAGATCGGAGACGGATTA
TTTACCTC
Found at i:1104452 original size:348 final size:348
Alignment explanation
Indices: 1103812--1104510 Score: 1012
Period size: 348 Copynumber: 2.0 Consensus size: 348
1103802 GGAAGGATTT
* * *
1103812 TCCTCTCTTCAAAATCTGTCAATTGATAGCTGCAAGGAATTGGAAGTTCTTCCTATAACCGGAGG
1 TCCTCTCTTCAAAATCTGTCAATTGATAGCTGCAACGAATTAGAAGTTCTTCATATAACCGGAGG
* *
1103877 TTGTTCATCTCTTGAAAAGCTTAGGATTTTGGGTTGTGAAAAATTAAGCAAGATCGGAGACGGAT
66 TTGTTCATCTCTTGAAAAGCTTAGCATTTTGGGTTGCGAAAAATTAAGCAAGATCGGAGACGGAT
* * * * *
1103942 TATTTAGCTCCACTTGTCTCAAAGAATTATATCTATGTCATTGTTCTAATTTAAGTTCGATTCCA
131 TATCTAGCTCCACTTGTCTCAAAGAATTAGATCTATATAATTGTCCTAATTTAAGTTCGATTCCA
* **
1104007 GATTTGGAAGGATGTTTCTCTCTTAAAATTCTGTCAATTAATAGCTGCAACAAATTGGAAGTTCT
196 AATTTGGAAGGATGTTTCTCTCTTAAAAGCCTGTCAATTAATAGCTGCAACAAATTGGAAGTTCT
** * * *
1104072 TCCGGTAACAGGAAGATGTTCATCTCTTGAAAAGCTTAGCATTTCCGGTTGCGAAAAAT-TAAGC
261 TCCAATAACAGGAAGATGTTCATCTATTGAAAAGCTTAGAATTTCCAGTTGC-AAAAATATAAGC
*
1104136 AAGATCGGAGACGGATTATTTACC
325 AAGATCGGAGACGGATTATCTACC
* *
1104160 TCCTCTCTTCAAAATCTGTCAATTGATAGTTGCAACGAATTAGAAGTTCTTTCAT-TACCCGGAA
1 TCCTCTCTTCAAAATCTGTCAATTGATAGCTGCAACGAATTAGAAGTTC-TTCATATAACCGG-A
* * *
1104224 GG-TGTTCATCTCTTGAAAAGTTTAGCATTTTTGGTTGCGAAAAATTAAGCAAGATTGGAGACGG
64 GGTTGTTCATCTCTTGAAAAGCTTAGCATTTTGGGTTGCGAAAAATTAAGCAAGATCGGAGACGG
* * * *
1104288 ATTATCT-GCCTGCGCTTGTCTCAATGAATTAGGTCTATATAATTGTCCTAATTTAAGTTCGATT
129 ATTATCTAG-CTCCACTTGTCTCAAAGAATTAGATCTATATAATTGTCCTAATTTAAGTTCGATT
* * * **
1104352 CCAAATTTGGAAGGAT-TTTCCTCTCTTCAGAGCCTGTCAATTAATAGGTGCAATGAATTGGAAG
193 CCAAATTTGGAAGGATGTTT-CTCTCTTAAAAGCCTGTCAATTAATAGCTGCAACAAATTGGAAG
*
1104416 TTCTTCCAATAACTGGAAGATGTTCATCTATTGAAAAGCTTAGAATTTCCAGTTGCAAAAATATA
257 TTCTTCCAATAACAGGAAGATGTTCATCTATTGAAAAGCTTAGAATTTCCAGTTGCAAAAATATA
1104481 AGCAAGATCGGAGACGGATTATCTACC
322 AGCAAGATCGGAGACGGATTATCTACC
1104508 TCC
1 TCC
1104511 ACTTGTCTCA
Statistics
Matches: 312, Mismatches: 34, Indels: 10
0.88 0.10 0.03
Matches are distributed among these distances:
347 10 0.03
348 295 0.95
349 7 0.02
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (348 bp):
TCCTCTCTTCAAAATCTGTCAATTGATAGCTGCAACGAATTAGAAGTTCTTCATATAACCGGAGG
TTGTTCATCTCTTGAAAAGCTTAGCATTTTGGGTTGCGAAAAATTAAGCAAGATCGGAGACGGAT
TATCTAGCTCCACTTGTCTCAAAGAATTAGATCTATATAATTGTCCTAATTTAAGTTCGATTCCA
AATTTGGAAGGATGTTTCTCTCTTAAAAGCCTGTCAATTAATAGCTGCAACAAATTGGAAGTTCT
TCCAATAACAGGAAGATGTTCATCTATTGAAAAGCTTAGAATTTCCAGTTGCAAAAATATAAGCA
AGATCGGAGACGGATTATCTACC
Found at i:1104537 original size:210 final size:210
Alignment explanation
Indices: 1104160--1105042 Score: 1336
Period size: 210 Copynumber: 4.2 Consensus size: 210
1104150 ATTATTTACC
* * * * * *
1104160 TCCTCTCTTCAAAATCTGTCAATTGATAGTTGCAACGAATTAGAAGTTCTTTCATTACCCGGAAG
1 TCCTCTCTTCAAAATCTGTCAATTGATAGCTGCAACGAATTGGAAGTTCTTCCAATAACAGGAAG
* * * *** * *
1104225 GTGTTCATCTCTTGAAAAGTTTAGCATTTTTGGTTGCGAAAAAT-TAAGCAAGATTGGAGACGGA
66 ATGTTCATCTCTTGAAAAGCTTAGAATTTCCAGTTGC-AAAAATATAACCAAGATCGGAGACGGA
* * * * * * ** * *
1104289 TTATCTGCCTGCGCTTGTCTCAATGAATTAGGTCTATATAATTGTCCTAATTTAAGTTCGATTCC
130 TTATCTACCTCCACTTATCTCAAAGAATTAGATCTATATCTTTGTTCTAATTTAAGTTTGATTCC
*
1104354 AAATTTGGAAGGATTT
195 AGATTTGGAAGGATTT
* ** * * * *
1104370 TCCTCTCTTCAGAGCCTGTCAATTAATAGGTGCAATGAATTGGAAGTTCTTCCAATAACTGGAAG
1 TCCTCTCTTCAAAATCTGTCAATTGATAGCTGCAACGAATTGGAAGTTCTTCCAATAACAGGAAG
* *
1104435 ATGTTCATCTATTGAAAAGCTTAGAATTTCCAGTTGCAAAAATATAAGCAAGATCGGAGACGGAT
66 ATGTTCATCTCTTGAAAAGCTTAGAATTTCCAGTTGCAAAAATATAACCAAGATCGGAGACGGAT
* *
1104500 TATCTACCTCCACTTGTCTCAAAGAATTATATCTATATCTTTGTTCTAATTTAAGTTTGATTCCA
131 TATCTACCTCCACTTATCTCAAAGAATTAGATCTATATCTTTGTTCTAATTTAAGTTTGATTCCA
1104565 GATTTGGAAGGATTT
196 GATTTGGAAGGATTT
* *
1104580 TCCTCTCTTCAAAATCTATCAATTGATAGCTGCAACGAATTGGAAGTTCTTCCCATAACAGGAAG
1 TCCTCTCTTCAAAATCTGTCAATTGATAGCTGCAACGAATTGGAAGTTCTTCCAATAACAGGAAG
*
1104645 ATGTTCATCTCTTGAAAAGCTTAGAATTTCCAGTTGCAAAAATATGACCAAGATCGGAGACGGAT
66 ATGTTCATCTCTTGAAAAGCTTAGAATTTCCAGTTGCAAAAATATAACCAAGATCGGAGACGGAT
*
1104710 TATCTACCTCCACTTATCTTAAAGAATTAGATCTATATCTTTGTTCTAATTTAAGTTTGATTCCA
131 TATCTACCTCCACTTATCTCAAAGAATTAGATCTATATCTTTGTTCTAATTTAAGTTTGATTCCA
1104775 GATTTGGAAGGATTT
196 GATTTGGAAGGATTT
* *
1104790 TCCTCTCTTCAAAATCTATCAATTGATAGCTGCAACGAATTGGAAGTTCTTCCCATAACAGGAAG
1 TCCTCTCTTCAAAATCTGTCAATTGATAGCTGCAACGAATTGGAAGTTCTTCCAATAACAGGAAG
*
1104855 ATGTTCATCTCTTGAAAAGCTTAGAATTTCCAGTTGCAAAAATATGACCAAGATCGGAGACGGAT
66 ATGTTCATCTCTTGAAAAGCTTAGAATTTCCAGTTGCAAAAATATAACCAAGATCGGAGACGGAT
* *
1104920 TATCTACCTCCACTTATCTTAAAGAATTAGATCTATATCTTTGTTCTAATTTAAGTTGGATTCCA
131 TATCTACCTCCACTTATCTCAAAGAATTAGATCTATATCTTTGTTCTAATTTAAGTTTGATTCCA
1104985 GATTTGGAAGGATTT
196 GATTTGGAAGGATTT
*
1105000 TCCTCTCTTCAAAATCTGTCAATTGATAGCTGCAAGGAATTGG
1 TCCTCTCTTCAAAATCTGTCAATTGATAGCTGCAACGAATTGG
1105043 CGAGTTTTCC
Statistics
Matches: 624, Mismatches: 48, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
209 6 0.01
210 618 0.99
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (210 bp):
TCCTCTCTTCAAAATCTGTCAATTGATAGCTGCAACGAATTGGAAGTTCTTCCAATAACAGGAAG
ATGTTCATCTCTTGAAAAGCTTAGAATTTCCAGTTGCAAAAATATAACCAAGATCGGAGACGGAT
TATCTACCTCCACTTATCTCAAAGAATTAGATCTATATCTTTGTTCTAATTTAAGTTTGATTCCA
GATTTGGAAGGATTT
Found at i:1105661 original size:144 final size:144
Alignment explanation
Indices: 1105410--1105674 Score: 343
Period size: 144 Copynumber: 1.8 Consensus size: 144
1105400 CTGGTTGGGA
* * * * * *
1105410 AAAGCTTAAGAGTCTTCCTCCGCAACTTCAATTCCTCTCTGCCCTTGAAGAATTGACGATATTAG
1 AAAGCTAAAGAGTCTTCCTCCGCAACTCCAACTCCCCACTGCCCTTGAAGAATTGACGATATGAG
* * * * ** *
1105475 AGTTTCAAGGAATAGAAGCCTTTCCAGAGTGGTTGGGAAATCTCTCTTCTTTAAGGCATCTATAT
66 AGTTTCAAGAAATAGAAGCCTTGCCAGACTCGTTCAGAAATCTCTCTTCTCTAAGGCATCTATAT
1105540 TTAAGTGGTTTTGG
131 TTAAGTGGTTTTGG
* * * *
1105554 AAAGCTAAAGAGTCTTCCTCAC-CAACTCCAACTCCCCACTGCCCTTGAAGATTTGACTATGTGG
1 AAAGCTAAAGAGTCTTCCTC-CGCAACTCCAACTCCCCACTGCCCTTGAAGAATTGACGATATGA
* *
1105618 GGGTTTCATGAAATAGAAGCCTTGCCAGACTCGTTCAGAAATCTCTCTTCTCTAAGG
65 GAGTTTCAAGAAATAGAAGCCTTGCCAGACTCGTTCAGAAATCTCTCTTCTCTAAGG
1105675 TGTCTGCGTA
Statistics
Matches: 101, Mismatches: 19, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
144 100 0.99
145 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (144 bp):
AAAGCTAAAGAGTCTTCCTCCGCAACTCCAACTCCCCACTGCCCTTGAAGAATTGACGATATGAG
AGTTTCAAGAAATAGAAGCCTTGCCAGACTCGTTCAGAAATCTCTCTTCTCTAAGGCATCTATAT
TTAAGTGGTTTTGG
Found at i:1109056 original size:17 final size:17
Alignment explanation
Indices: 1109036--1109106 Score: 70
Period size: 17 Copynumber: 3.9 Consensus size: 17
1109026 AATTTTATTT
1109036 TTTATAATTTTTATAAA
1 TTTATAATTTTTATAAA
*
1109053 TTTATAAATTTTATAAA
1 TTTATAATTTTTATAAA
* *
1109070 TTTTATGATTTTTAATTAAT
1 -TTTATAATTTTT-A-TAAA
1109090 TTCTAATAATTTTTATA
1 TT-T-ATAATTTTTATA
1109107 TTTTTTATAC
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
17 16 0.36
18 10 0.23
19 5 0.11
20 5 0.11
21 8 0.18
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (17 bp):
TTTATAATTTTTATAAA
Found at i:1109064 original size:26 final size:26
Alignment explanation
Indices: 1109000--1109075 Score: 82
Period size: 26 Copynumber: 2.9 Consensus size: 26
1108990 TTTATGATTG
* *
1109000 TTTATTAATTTCTAATACTTTTTATAAA
1 TTTATAAATTT-T-ATAATTTTTATAAA
**
1109028 TTT-TATTTTTTATAATTTTTATAAA
1 TTTATAAATTTTATAATTTTTATAAA
*
1109053 TTTATAAATTTTATAAATTTTAT
1 TTTATAAATTTTATAATTTTTAT
1109076 GATTTTTAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
25 16 0.40
26 17 0.43
27 4 0.10
28 3 0.08
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (26 bp):
TTTATAAATTTTATAATTTTTATAAA
Found at i:1109113 original size:9 final size:9
Alignment explanation
Indices: 1108979--1109122 Score: 96
Period size: 9 Copynumber: 15.6 Consensus size: 9
1108969 TTACCCTTAA
*
1108979 TTTTATAAAA
1 TTTTAT-AAT
*
1108989 TTTTATGAT
1 TTTTATAAT
1108998 TGTTTATTAAT
1 T-TTTA-TAAT
* *
1109009 TTCTAATACT
1 TT-TTATAAT
*
1109019 TTTTATAAA
1 TTTTATAAT
1109028 TTTTAT--T
1 TTTTATAAT
1109035 TTTTATAAT
1 TTTTATAAT
1109044 TTTTATAA-
1 TTTTATAAT
* *
1109052 ATTTATAAA
1 TTTTATAAT
*
1109061 TTTTATAAA
1 TTTTATAAT
*
1109070 TTTTATGAT
1 TTTTATAAT
1109079 TTTTAATTAAT
1 TTTT-A-TAAT
*
1109090 TTCTAATAAT
1 TT-TTATAAT
*
1109100 TTTTATATT
1 TTTTATAAT
*
1109109 TTTTATACT
1 TTTTATAAT
1109118 TTTTA
1 TTTTA
1109123 GAATGAACCT
Statistics
Matches: 107, Mismatches: 18, Indels: 19
0.74 0.12 0.13
Matches are distributed among these distances:
7 6 0.06
8 7 0.07
9 58 0.54
10 23 0.21
11 12 0.11
12 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (9 bp):
TTTTATAAT
Found at i:1114074 original size:69 final size:69
Alignment explanation
Indices: 1113963--1114101 Score: 269
Period size: 69 Copynumber: 2.0 Consensus size: 69
1113953 GATAGGAAAA
*
1113963 ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTTGTGGTAGG
1 ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTGGTGGTAGG
1114028 GCTG
66 GCTG
1114032 ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTGGTGGTAGG
1 ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTGGTGGTAGG
1114097 GCTG
66 GCTG
1114101 A
1 A
1114102 TAGAGTCTTG
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.27, C:0.13, G:0.32, T:0.28
Consensus pattern (69 bp):
ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTGGTGGTAGG
GCTG
Found at i:1124109 original size:21 final size:21
Alignment explanation
Indices: 1124076--1124122 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
1124066 ATCATGTTCC
*
1124076 ACAAAAAA--AAAAAAAAA-G
1 ACAAAAAAGCAAAAAAAAACA
1124094 ACAAAAAAGCAAAAAAAAACA
1 ACAAAAAAGCAAAAAAAAACA
1124115 ACAAAAAA
1 ACAAAAAA
1124123 AAGAAGAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 8 0.32
20 9 0.36
21 8 0.32
ACGTcount: A:0.85, C:0.11, G:0.04, T:0.00
Consensus pattern (21 bp):
ACAAAAAAGCAAAAAAAAACA
Found at i:1124110 original size:22 final size:21
Alignment explanation
Indices: 1124082--1124122 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1124072 TTCCACAAAA
1124082 AAAAAAAAAAAGACAAAAAAGC
1 AAAAAAAAAAA-ACAAAAAAGC
*
1124104 AAAAAAAAACAACAAAAAA
1 AAAAAAAAAAAACAAAAAA
1124123 AAGAAGAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.85, C:0.10, G:0.05, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAAAACAAAAAAGC
Found at i:1124122 original size:23 final size:23
Alignment explanation
Indices: 1124081--1124125 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1124071 GTTCCACAAA
* *
1124081 AAAAAAAAAAAAGACAAAAAAGC
1 AAAAAAAAAAAACAAAAAAAAGC
*
1124104 AAAAAAAAACAACAAAAAAAAG
1 AAAAAAAAAAAACAAAAAAAAG
1124126 AAGAAGAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.84, C:0.09, G:0.07, T:0.00
Consensus pattern (23 bp):
AAAAAAAAAAAACAAAAAAAAGC
Found at i:1124157 original size:9 final size:9
Alignment explanation
Indices: 1124078--1124192 Score: 67
Period size: 9 Copynumber: 12.3 Consensus size: 9
1124068 CATGTTCCAC
1124078 AAAAAAA-A
1 AAAAAAAGA
1124086 AAAAAAAGA
1 AAAAAAAGA
*
1124095 CAAAAAAGCA
1 AAAAAAAG-A
1124105 AAAAAAA-A
1 AAAAAAAGA
1124113 CAACAAAAA-A
1 -AA-AAAAAGA
*
1124123 AAGAAGAAGA
1 AA-AAAAAGA
***
1124133 AATAATTCGA
1 AA-AAAAAGA
1124143 AAAAAAA-A
1 AAAAAAAGA
1124151 GAAAAAAAGA
1 -AAAAAAAGA
*
1124161 AAAGAAAGA
1 AAAAAAAGA
1124170 AAAAAAAGTTA
1 AAAAAAAG--A
*
1124181 AAAAAAATA
1 AAAAAAAGA
1124190 AAA
1 AAA
1124193 GTTTGATGAT
Statistics
Matches: 84, Mismatches: 14, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
8 9 0.11
9 44 0.52
10 23 0.27
11 8 0.10
ACGTcount: A:0.81, C:0.04, G:0.10, T:0.05
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:1124163 original size:13 final size:12
Alignment explanation
Indices: 1124142--1124187 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 12
1124132 AAATAATTCG
1124142 AAAAAAAAAGAA
1 AAAAAAAAAGAA
1124154 AAAAAGAAAAGAA
1 AAAAA-AAAAGAA
1124167 AGAAAAAAAAGTTAA
1 A-AAAAAAAAG--AA
1124182 AAAAAA
1 AAAAAA
1124188 TAAAAGTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 5 0.17
13 13 0.43
14 9 0.30
15 3 0.10
ACGTcount: A:0.85, C:0.00, G:0.11, T:0.04
Consensus pattern (12 bp):
AAAAAAAAAGAA
Found at i:1124192 original size:8 final size:8
Alignment explanation
Indices: 1124078--1124175 Score: 58
Period size: 8 Copynumber: 11.9 Consensus size: 8
1124068 CATGTTCCAC
*
1124078 AAAAAAAA
1 AAAAAAAG
1124086 AAAAAAAG
1 AAAAAAAG
1124094 ACAAAAAAG
1 A-AAAAAAG
1124103 CAAAAAAA-
1 -AAAAAAAG
* *
1124111 AACAACA-
1 AAAAAAAG
1124118 AAAAAAAG
1 AAAAAAAG
*
1124126 AAGAAGAAAT
1 AA-AA-AAAG
***
1124136 AATTCGAA-
1 AA-AAAAAG
1124144 AAAAAAAG
1 AAAAAAAG
1124152 AAAAAAAG
1 AAAAAAAG
1124160 AAAAGAAAG
1 AAAA-AAAG
1124169 AAAAAAA
1 AAAAAAA
1124176 AGTTAAAAAA
Statistics
Matches: 70, Mismatches: 13, Indels: 14
0.72 0.13 0.14
Matches are distributed among these distances:
7 12 0.17
8 27 0.39
9 25 0.36
10 6 0.09
ACGTcount: A:0.82, C:0.05, G:0.10, T:0.03
Consensus pattern (8 bp):
AAAAAAAG
Found at i:1132384 original size:23 final size:23
Alignment explanation
Indices: 1132341--1132383 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1132331 TGTTCCACAA
1132341 AAAAAAAAAAAAAGCAAAAAAGC
1 AAAAAAAAAAAAAGCAAAAAAGC
*
1132364 AAAAAAAAAACAA-CAAAAAA
1 AAAAAAAAAAAAAGCAAAAAA
1132384 AAAGAAGAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.86, C:0.09, G:0.05, T:0.00
Consensus pattern (23 bp):
AAAAAAAAAAAAAGCAAAAAAGC
Found at i:1132384 original size:25 final size:24
Alignment explanation
Indices: 1132338--1132387 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
1132328 TCATGTTCCA
1132338 CAAAAAAAAAAAAAAAGCAAAAAAG
1 CAAAAAAAAAAAAAAA-CAAAAAAG
1132363 CAAAAAAAAAACAACAAA-AAAAAAG
1 CAAAAAAAAAA-AA-AAACAAAAAAG
1132388 AAGAAGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 18 0.78
26 2 0.09
27 3 0.13
ACGTcount: A:0.84, C:0.10, G:0.06, T:0.00
Consensus pattern (24 bp):
CAAAAAAAAAAAAAAACAAAAAAG
Found at i:1132406 original size:39 final size:37
Alignment explanation
Indices: 1132365--1132454 Score: 94
Period size: 39 Copynumber: 2.4 Consensus size: 37
1132355 CAAAAAAGCA
1132365 AAAAAAAA-ACAACAAAAAAAAAGAAGAAGAAATAATTC
1 AAAAAAAAAACAACAAAAAAAAAGAA-AAGAAA-AATTC
* * *
1132403 AAAAAGAAAAGAAAAAAAAGAAAAGAAAAGAAAAAGTT-
1 AAAAAAAAAACAACAAAAA-AAAAGAAAAGAAAAA-TTC
1132441 AAAAAAAAATACAA
1 AAAAAAAAA-ACAA
1132455 GTTTGATGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
38 17 0.40
39 19 0.44
40 7 0.16
ACGTcount: A:0.79, C:0.04, G:0.10, T:0.07
Consensus pattern (37 bp):
AAAAAAAAAACAACAAAAAAAAAGAAAAGAAAAATTC
Found at i:1132414 original size:5 final size:5
Alignment explanation
Indices: 1132404--1132436 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
1132394 AAATAATTCA
1132404 AAAAG AAAAG AAAA- AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
1132437 AGTTAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:1132445 original size:19 final size:18
Alignment explanation
Indices: 1132382--1132449 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 18
1132372 AACAACAAAA
1132382 AAAAAGAAGAAGAAATAATT
1 AAAAAGAA-AAGAAA-AATT
**
1132402 CAAAAAGAAAAGAAAAAAA
1 -AAAAAGAAAAGAAAAATT
1132421 AGAAAAGAAAAGAAAAAGTT
1 A-AAAAGAAAAGAAAAA-TT
1132441 AAAAA-AAAA
1 AAAAAGAAAA
1132450 TACAAGTTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
18 5 0.12
19 21 0.51
20 7 0.17
21 8 0.20
ACGTcount: A:0.78, C:0.01, G:0.13, T:0.07
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAATT
Found at i:1136575 original size:24 final size:24
Alignment explanation
Indices: 1136548--1136599 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1136538 TTCGTAGGTC
*
1136548 AAATAAATTATACTAATAAATGTT
1 AAATAAATTATACTAATAAATATT
* *
1136572 AAATATATTATACTAATGAATATT
1 AAATAAATTATACTAATAAATATT
1136596 AAAT
1 AAAT
1136600 CTTCTAGAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATATT
Found at i:1141367 original size:6 final size:6
Alignment explanation
Indices: 1141353--1141420 Score: 82
Period size: 6 Copynumber: 11.3 Consensus size: 6
1141343 ATAATTTTGG
* * * *
1141353 GAGAAA GAGAGA GAGAGA GAAAGA GAAAGA GAGAGA GAGAGA GAAAGA
1 GAGAGA GAGAGA GAGAGA GAGAGA GAGAGA GAGAGA GAGAGA GAGAGA
* *
1141401 GAAAGA GAAAGA GAGAGA GA
1 GAGAGA GAGAGA GAGAGA GA
1141421 TAGACGTGTT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 57 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (6 bp):
GAGAGA
Found at i:1141377 original size:12 final size:12
Alignment explanation
Indices: 1141362--1141420 Score: 91
Period size: 12 Copynumber: 4.9 Consensus size: 12
1141352 GGAGAAAGAG
1141362 AGAGAGAGAGAA
1 AGAGAGAGAGAA
* *
1141374 AGAGAAAGAGAG
1 AGAGAGAGAGAA
1141386 AGAGAGAGAGAA
1 AGAGAGAGAGAA
*
1141398 AGAGAAAGAGAA
1 AGAGAGAGAGAA
1141410 AGAGAGAGAGA
1 AGAGAGAGAGA
1141421 TAGACGTGTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 41 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (12 bp):
AGAGAGAGAGAA
Found at i:1141385 original size:24 final size:24
Alignment explanation
Indices: 1141358--1141420 Score: 117
Period size: 24 Copynumber: 2.6 Consensus size: 24
1141348 TTTGGGAGAA
1141358 AGAGAGAGAGAGAGAAAGAGAAAG
1 AGAGAGAGAGAGAGAAAGAGAAAG
1141382 AGAGAGAGAGAGAGAAAGAGAAAG
1 AGAGAGAGAGAGAGAAAGAGAAAG
*
1141406 AGAAAGAGAGAGAGA
1 AGAGAGAGAGAGAGA
1141421 TAGACGTGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (24 bp):
AGAGAGAGAGAGAGAAAGAGAAAG
Found at i:1141392 original size:30 final size:30
Alignment explanation
Indices: 1141353--1141420 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 30
1141343 ATAATTTTGG
* *
1141353 GAGAAAGAGAGAGAGAGAGAAAGAGAAAGA
1 GAGAGAGAGAGAGAAAGAGAAAGAGAAAGA
1141383 GAGAGAGAGAGAGAAAGAGAAAGAGAAAGA
1 GAGAGAGAGAGAGAAAGAGAAAGAGAAAGA
1141413 GAGAGAGA
1 GAGAGAGA
1141421 TAGACGTGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (30 bp):
GAGAGAGAGAGAGAAAGAGAAAGAGAAAGA
Found at i:1142033 original size:124 final size:124
Alignment explanation
Indices: 1141812--1142059 Score: 460
Period size: 124 Copynumber: 2.0 Consensus size: 124
1141802 TCGGCCACCA
*
1141812 ATCCGGTTTAAAAAACATTGAGATTAATATTTTATGCATTAATATTTTATATAGGATGGAAATTT
1 ATCCGGTTTAAAAAACATTGAGATTAATATTTTATGCATTAATATTTTATATAAGATGGAAATTT
1141877 GAAGTGTATAATTCTATGTACCATCAAACAATTTGATTATTCCCAATCACTAAGGCTTT
66 GAAGTGTATAATTCTATGTACCATCAAACAATTTGATTATTCCCAATCACTAAGGCTTT
1141936 ATCCGGTTTAAAAAACATTGAGATTAATATTTTATGCATTAATATTTTATATAAGATGGAAATTT
1 ATCCGGTTTAAAAAACATTGAGATTAATATTTTATGCATTAATATTTTATATAAGATGGAAATTT
* * *
1142001 GAAGTGTATAATTCTATGTACCATCAATCAATTTGATTATTCTCAATCATTAAGGCTTT
66 GAAGTGTATAATTCTATGTACCATCAAACAATTTGATTATTCCCAATCACTAAGGCTTT
1142060 GCTTGGTAGA
Statistics
Matches: 120, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
124 120 1.00
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.40
Consensus pattern (124 bp):
ATCCGGTTTAAAAAACATTGAGATTAATATTTTATGCATTAATATTTTATATAAGATGGAAATTT
GAAGTGTATAATTCTATGTACCATCAAACAATTTGATTATTCCCAATCACTAAGGCTTT
Found at i:1149582 original size:77 final size:77
Alignment explanation
Indices: 1149455--1149608 Score: 290
Period size: 77 Copynumber: 2.0 Consensus size: 77
1149445 TAGACGGTTT
1149455 GAAATTGGGGTTATTCTGTTGGCTAGGTCTAAGAATTCAATCTGCCATCCATGCTTGAGTTCAAG
1 GAAATTGGGGTTATTCTGTTGGCTAGGTCTAAGAATTCAATCTGCCATCCATGCTTGAGTTCAAG
1149520 ATTATTAGCTTC
66 ATTATTAGCTTC
* *
1149532 GAAATTGGGGTTGTTCTGTTGGCTAGGTCTAAGGATTCAATCTGCCATCCATGCTTGAGTTCAAG
1 GAAATTGGGGTTATTCTGTTGGCTAGGTCTAAGAATTCAATCTGCCATCCATGCTTGAGTTCAAG
1149597 ATTATTAGCTTC
66 ATTATTAGCTTC
1149609 AACCATGCTG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 75 1.00
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (77 bp):
GAAATTGGGGTTATTCTGTTGGCTAGGTCTAAGAATTCAATCTGCCATCCATGCTTGAGTTCAAG
ATTATTAGCTTC
Found at i:1150963 original size:21 final size:21
Alignment explanation
Indices: 1150939--1150981 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1150929 TGTGGATGCA
1150939 TTTG-AGTATGCTGATTGTAAT
1 TTTGTAGT-TGCTGATTGTAAT
* *
1150960 TTTGTTGTTGTTGATTGTAAT
1 TTTGTAGTTGCTGATTGTAAT
1150981 T
1 T
1150982 CCCTTATCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.19, C:0.02, G:0.23, T:0.56
Consensus pattern (21 bp):
TTTGTAGTTGCTGATTGTAAT
Found at i:1161561 original size:13 final size:13
Alignment explanation
Indices: 1161543--1161604 Score: 88
Period size: 13 Copynumber: 4.8 Consensus size: 13
1161533 TTTGGCAATA
1161543 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
*
1161556 CTTTTGAGAAGTG
1 CTTTTGAAAAGTG
* *
1161569 CTGTGGAAAAGTG
1 CTTTTGAAAAGTG
*
1161582 CTTTTGAGAAGTG
1 CTTTTGAAAAGTG
1161595 CTTTTGAAAA
1 CTTTTGAAAA
1161605 TTTGGTTTAA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.29, C:0.08, G:0.27, T:0.35
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:1161603 original size:26 final size:26
Alignment explanation
Indices: 1161543--1161604 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
1161533 TTTGGCAATA
1161543 CTTTTGAAAAGTGCTTTTGAGAAGTG
1 CTTTTGAAAAGTGCTTTTGAGAAGTG
* *
1161569 CTGTGGAAAAGTGCTTTTGAGAAGTG
1 CTTTTGAAAAGTGCTTTTGAGAAGTG
1161595 CTTTTGAAAA
1 CTTTTGAAAA
1161605 TTTGGTTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.29, C:0.08, G:0.27, T:0.35
Consensus pattern (26 bp):
CTTTTGAAAAGTGCTTTTGAGAAGTG
Found at i:1162108 original size:13 final size:13
Alignment explanation
Indices: 1162090--1162114 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1162080 TTCAGAAGTG
1162090 CTTTTGAAAAGCA
1 CTTTTGAAAAGCA
1162103 CTTTTGAAAAGC
1 CTTTTGAAAAGC
1162115 TAAAAATTTC
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
CTTTTGAAAAGCA
Found at i:1176822 original size:21 final size:21
Alignment explanation
Indices: 1176796--1176844 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
1176786 TGGAGATAGG
1176796 AAAACAGGTTCCAAAACAGGA
1 AAAACAGGTTCCAAAACAGGA
*
1176817 AAAACAGGTTCCAAAATAGGA
1 AAAACAGGTTCCAAAACAGGA
*
1176838 ATAACAG
1 AAAACAG
1176845 TGGCTGTAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.53, C:0.16, G:0.18, T:0.12
Consensus pattern (21 bp):
AAAACAGGTTCCAAAACAGGA
Found at i:1188649 original size:9 final size:9
Alignment explanation
Indices: 1188630--1188674 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
1188620 ATCACGTCAA
1188630 TAAATAATTT
1 TAAA-AATTT
1188640 TAAAAATTT
1 TAAAAATTT
*
1188649 TAAAAATAT
1 TAAAAATTT
1188658 TAGAAAATTT
1 TA-AAAATTT
*
1188668 TCAAAAT
1 TAAAAAT
1188675 GAAAAACATG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
9 20 0.65
10 11 0.35
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (9 bp):
TAAAAATTT
Found at i:1190388 original size:29 final size:29
Alignment explanation
Indices: 1190324--1190389 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
1190314 ATTCGAACTT
* *
1190324 ATTTGATTCATTTTAATAATATAGGGACTG
1 ATTTGA-TCATTTTAATAATAGAAGGACTG
* *
1190354 AATTGATCATTTTAATAATAGAATGACT-
1 ATTTGATCATTTTAATAATAGAAGGACTG
1190382 AGTTTGAT
1 A-TTTGAT
1190390 ACAGTCCCTA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 1 0.03
29 24 0.80
30 5 0.17
ACGTcount: A:0.36, C:0.06, G:0.15, T:0.42
Consensus pattern (29 bp):
ATTTGATCATTTTAATAATAGAAGGACTG
Found at i:1190602 original size:12 final size:12
Alignment explanation
Indices: 1190585--1190614 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1190575 TTTTAATCAT
1190585 CACATGGCAACC
1 CACATGGCAACC
*
1190597 CACATGGCAATC
1 CACATGGCAACC
1190609 CACATG
1 CACATG
1190615 TATTTTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.37, G:0.17, T:0.13
Consensus pattern (12 bp):
CACATGGCAACC
Found at i:1190857 original size:31 final size:31
Alignment explanation
Indices: 1190822--1190891 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 31
1190812 TTAAAACAAC
* * *
1190822 AATTTAACCTTTTCTGAAAGGTTGATGGTCA
1 AATTTAACCTTTTCTAAAAGGTAGAGGGTCA
* * * *
1190853 AATTTGACTTTTTTTAAAAGGTAGAGGGTTA
1 AATTTAACCTTTTCTAAAAGGTAGAGGGTCA
1190884 AATTTAAC
1 AATTTAAC
1190892 TCAAAAAAAG
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.40
Consensus pattern (31 bp):
AATTTAACCTTTTCTAAAAGGTAGAGGGTCA
Found at i:1193347 original size:31 final size:30
Alignment explanation
Indices: 1193309--1193417 Score: 98
Period size: 31 Copynumber: 3.6 Consensus size: 30
1193299 ATATTGTCTC
*
1193309 AATTTAGTACCTAAACTTGATGCTTTTTCCT
1 AATTTAATACCTAAACTTGAT-CTTTTTCCT
* * * * *
1193340 AATTTAGTACTTAAGCTT--TTTTTATTTC-
1 AATTTAATACCTAAACTTGATCTTT-TTCCT
* *
1193368 AATTTAATACCTAAACTTGACACTTTTTCTT
1 AATTTAATACCTAAACTTGA-TCTTTTTCCT
1193399 AATTTAATACCTAAACTTG
1 AATTTAATACCTAAACTTG
1193418 TTTTACGTTT
Statistics
Matches: 62, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
28 18 0.29
29 4 0.06
30 2 0.03
31 38 0.61
ACGTcount: A:0.30, C:0.17, G:0.06, T:0.47
Consensus pattern (30 bp):
AATTTAATACCTAAACTTGATCTTTTTCCT
Found at i:1193379 original size:59 final size:59
Alignment explanation
Indices: 1193307--1193422 Score: 160
Period size: 59 Copynumber: 2.0 Consensus size: 59
1193297 AAATATTGTC
* ** * * * *
1193307 TCAATTTAGTACCTAAACTTGATGCTTTTTCCTAATTTAGTACTTAAGCTTTTTTTATT
1 TCAATTTAATACCTAAACTTGACACTTTTTCCTAATTTAATACCTAAACTTGTTTTATT
*
1193366 TCAATTTAATACCTAAACTTGACACTTTTTCTTAATTTAATACCTAAACTTGTTTTA
1 TCAATTTAATACCTAAACTTGACACTTTTTCCTAATTTAATACCTAAACTTGTTTTA
1193423 CGTTTAATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
59 49 1.00
ACGTcount: A:0.29, C:0.16, G:0.06, T:0.48
Consensus pattern (59 bp):
TCAATTTAATACCTAAACTTGACACTTTTTCCTAATTTAATACCTAAACTTGTTTTATT
Found at i:1194307 original size:46 final size:46
Alignment explanation
Indices: 1194255--1194350 Score: 156
Period size: 46 Copynumber: 2.1 Consensus size: 46
1194245 AAAGCTAGAT
*
1194255 TAAAATGTTGATTAAGCTCAAAGAATTTATGCAAACCCCTACACAA
1 TAAAATGTTGATTAAGCTCAAAGAACTTATGCAAACCCCTACACAA
* * *
1194301 TAAAATGTTGATTCAGCTCAAAGAACTTATGCAATCCCCTACTCAA
1 TAAAATGTTGATTAAGCTCAAAGAACTTATGCAAACCCCTACACAA
1194347 TAAA
1 TAAA
1194351 GCCAAGACCC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.42, C:0.21, G:0.10, T:0.27
Consensus pattern (46 bp):
TAAAATGTTGATTAAGCTCAAAGAACTTATGCAAACCCCTACACAA
Found at i:1195088 original size:3 final size:3
Alignment explanation
Indices: 1195080--1195112 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1195070 TGCTTGGACA
1195080 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1195113 CTAGTATTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1198293 original size:17 final size:16
Alignment explanation
Indices: 1198253--1198296 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
1198243 TTTTTCGGTT
1198253 TTTCTTCTTCCCTGCC
1 TTTCTTCTTCCCTGCC
* *
1198269 TTTCCTTCTTCCATTGTC
1 TTT-CTTCTTCC-CTGCC
1198287 TTTCTTCTTC
1 TTTCTTCTTC
1198297 TTTTTTCGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 3 0.12
17 15 0.62
18 6 0.25
ACGTcount: A:0.02, C:0.36, G:0.05, T:0.57
Consensus pattern (16 bp):
TTTCTTCTTCCCTGCC
Found at i:1215068 original size:20 final size:20
Alignment explanation
Indices: 1215045--1215082 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1215035 ATTTTTTAAA
1215045 ATTAAAATTAA-AATTTTATT
1 ATTAAAA-TAATAATTTTATT
*
1215065 ATTAATATAATAATTTTA
1 ATTAAAATAATAATTTTA
1215083 AACTTGATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTAAAATAATAATTTTATT
Found at i:1217370 original size:18 final size:18
Alignment explanation
Indices: 1217319--1217372 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
1217309 GATTTTATTT
*
1217319 TTATATATTA-TGTAAT-
1 TTATATATTATTATAATA
*
1217335 TTATA-AATATATATTAATA
1 TTATATATTAT-TA-TAATA
1217354 TTATATATTATTATAATA
1 TTATATATTATTATAATA
1217372 T
1 T
1217373 AAATATTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 3 0.10
16 5 0.17
17 1 0.03
18 10 0.33
19 7 0.23
20 4 0.13
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
TTATATATTATTATAATA
Found at i:1219755 original size:12 final size:11
Alignment explanation
Indices: 1219732--1219764 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
1219722 AAATTATATT
1219732 TTTTAATA-AA
1 TTTTAATATAA
1219742 TTTTAATATTAA
1 TTTTAATA-TAA
1219754 TTTTAATATAA
1 TTTTAATATAA
1219765 AAATAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.38
11 3 0.14
12 10 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TTTTAATATAA
Found at i:1221584 original size:46 final size:45
Alignment explanation
Indices: 1221534--1221709 Score: 194
Period size: 46 Copynumber: 3.8 Consensus size: 45
1221524 TGGTTGAGCA
1221534 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
1221580 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
* * *
1221627 TCCGAGCTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGGACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC-GAAG
* *
1221673 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1221710 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
43 1 0.01
44 1 0.01
45 2 0.02
46 68 0.63
47 31 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:1221690 original size:93 final size:93
Alignment explanation
Indices: 1221531--1221701 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
1221521 GGATGGTTGA
* *
1221531 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
1221596 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* * * *
1221624 GCATCCGAGCTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGGACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
1221689 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
1221702 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:1224682 original size:15 final size:15
Alignment explanation
Indices: 1224662--1224725 Score: 89
Period size: 15 Copynumber: 4.4 Consensus size: 15
1224652 GTATCTTGGG
1224662 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
1224677 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
1224692 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
1224707 TTTCTTTATTC-GG-
1 TTTCTTTATTCTGGA
1224720 TTTCTT
1 TTTCTT
1224726 GTTATCTTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
13 6 0.13
14 4 0.09
15 33 0.73
16 2 0.04
ACGTcount: A:0.11, C:0.16, G:0.12, T:0.61
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:1227145 original size:46 final size:44
Alignment explanation
Indices: 1227094--1227268 Score: 201
Period size: 46 Copynumber: 3.9 Consensus size: 44
1227084 ATGGTTGAGC
1227094 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
*** * *
1227138 ATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GC
1 A--TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGA
*
1227187 ATCCGAGCTCGTTGAGTTGAGT-CGAGTTCACTTATGGATGCGA
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
* *
1227230 CACCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 -ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1227269 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 12, Indels: 17
0.79 0.09 0.12
Matches are distributed among these distances:
42 1 0.01
43 2 0.02
44 23 0.21
45 19 0.17
46 36 0.33
47 24 0.22
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (44 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
Found at i:1229108 original size:17 final size:17
Alignment explanation
Indices: 1229069--1229111 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1229059 ACTATCAAGA
1229069 TAAATAATAAATTTAAT
1 TAAATAATAAATTTAAT
* *
1229086 TTAATATTAAATTT-AT
1 TAAATAATAAATTTAAT
1229102 TAAAATAATA
1 T-AAATAATA
1229112 TTATTTTTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATAATAAATTTAAT
Found at i:1229612 original size:29 final size:29
Alignment explanation
Indices: 1229579--1229642 Score: 128
Period size: 29 Copynumber: 2.2 Consensus size: 29
1229569 TTTAATTAAT
1229579 TTTATTAATTTAATTTTGTTTGATCAAAA
1 TTTATTAATTTAATTTTGTTTGATCAAAA
1229608 TTTATTAATTTAATTTTGTTTGATCAAAA
1 TTTATTAATTTAATTTTGTTTGATCAAAA
1229637 TTTATT
1 TTTATT
1229643 CTCTCAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (29 bp):
TTTATTAATTTAATTTTGTTTGATCAAAA
Found at i:1231741 original size:2 final size:2
Alignment explanation
Indices: 1231736--1231774 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1231726 TACTCATGTC
1231736 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1231775 GTTTGGTCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1246096 original size:18 final size:18
Alignment explanation
Indices: 1246075--1246112 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1246065 AAAAAGTAAC
*
1246075 AAAATGATAAAATTATTAA
1 AAAAT-ATAAAAATATTAA
1246094 AAAATATAAAAATATTAA
1 AAAATATAAAAATATTAA
1246112 A
1 A
1246113 TTTTATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (18 bp):
AAAATATAAAAATATTAA
Found at i:1246478 original size:10 final size:10
Alignment explanation
Indices: 1246463--1246509 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
1246453 TATTTTATTA
1246463 TTTTTATAAC
1 TTTTTATAAC
1246473 TTTTTA-ATAC
1 TTTTTATA-AC
1246483 -TTTTATTAAC
1 TTTTTA-TAAC
*
1246493 TTTTTATAAA
1 TTTTTATAAC
1246503 TTTTTAT
1 TTTTTAT
1246510 GTACAACTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
9 6 0.19
10 20 0.62
11 6 0.19
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (10 bp):
TTTTTATAAC
Found at i:1246624 original size:10 final size:10
Alignment explanation
Indices: 1246580--1246669 Score: 73
Period size: 10 Copynumber: 9.3 Consensus size: 10
1246570 TCTAAATTTA
*
1246580 TTTATAGTAT
1 TTTATAATAT
1246590 TTATATAATAT
1 TT-TATAATAT
1246601 TTTCAT-AT-T
1 TTT-ATAATAT
*
1246610 TTTATAACAT
1 TTTATAATAT
1246620 TTTATAATAT
1 TTTATAATAT
* *
1246630 TTAAAAATAT
1 TTTATAATAT
*
1246640 CTTATAATAT
1 TTTATAATAT
*
1246650 TGTAT-A-AT
1 TTTATAATAT
1246658 TTTATAA-AT
1 TTTATAATAT
1246667 TTT
1 TTT
1246670 CTTTGTAATG
Statistics
Matches: 64, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
8 8 0.12
9 12 0.19
10 33 0.52
11 11 0.17
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (10 bp):
TTTATAATAT
Found at i:1246952 original size:21 final size:20
Alignment explanation
Indices: 1246924--1246966 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
1246914 ATATAATTTA
1246924 ATAATAATTAAAATATTT-TT
1 ATAATAATTAAAAT-TTTATT
1246944 ATAACTAATTAAAATTTTATT
1 ATAA-TAATTAAAATTTTATT
1246965 AT
1 AT
1246967 CTTTAATTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
ATAATAATTAAAATTTTATT
Found at i:1248583 original size:31 final size:31
Alignment explanation
Indices: 1248547--1248615 Score: 104
Period size: 31 Copynumber: 2.2 Consensus size: 31
1248537 ATAACAGCCC
1248547 AATGACTTGAAT-AAAATTTTTTAAATAATTT
1 AATGACTTGAATGAAAA-TTTTTAAATAATTT
* *
1248578 AATGACTTTAATGATAATTTTTAAATAATTT
1 AATGACTTGAATGAAAATTTTTAAATAATTT
1248609 AATGACT
1 AATGACT
1248616 ATTTTAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 32 0.91
32 3 0.09
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.45
Consensus pattern (31 bp):
AATGACTTGAATGAAAATTTTTAAATAATTT
Found at i:1248894 original size:11 final size:11
Alignment explanation
Indices: 1248880--1248905 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1248870 TTTTCATTAC
1248880 TTTTTTTTATT
1 TTTTTTTTATT
1248891 TTTTTTTTATT
1 TTTTTTTTATT
1248902 TTTT
1 TTTT
1248906 AAATATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTTATT
Found at i:1250282 original size:21 final size:20
Alignment explanation
Indices: 1250249--1250287 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1250239 GATATAATGC
*
1250249 ATTTTAAACATATAATTTACT
1 ATTTGAAACATAT-ATTTACT
*
1250270 ATTTGAAATATATATTTA
1 ATTTGAAACATATATTTA
1250288 ATTTAGTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.49
Consensus pattern (20 bp):
ATTTGAAACATATATTTACT
Found at i:1262280 original size:136 final size:136
Alignment explanation
Indices: 1262032--1262297 Score: 444
Period size: 136 Copynumber: 2.0 Consensus size: 136
1262022 CTCAAAAATT
1262032 CCCCTTACTCATGACTTTCAAAAGAATAGTGATATAAATGCTTAGCAAATACATTCAAATAGTCA
1 CCCCTTACTCATGACTTTCAAAAGAATAGTGATATAAATGCTTAGCAAATACATTCAAATAGTCA
*
1262097 TTTGAAAGACTAGTGTTCAAGATTGAATACGTAGAATATGAGAAAGTATGTAATGTTTTCATGAG
66 TTTGAAAGACTAGTATTCAAGATTGAATACGTAGAATATGAGAAAGTATGTAATGTTTTCATGAG
1262162 GGGGAG
131 GGGGAG
* *
1262168 CCCCTTCCTCATGACTTTCAAAAGAAT-GATGATATAAATGTTTAGCAAATACATTCAAATAGTC
1 CCCCTTACTCATGACTTTCAAAAGAATAG-TGATATAAATGCTTAGCAAATACATTCAAATAGTC
* * * * *
1262232 ATTTGAAATATTAGTATTCAAGATTGAATATGTAGAATATGAGGAAGTATGTGATGTTTTCATGA
65 ATTTGAAAGACTAGTATTCAAGATTGAATACGTAGAATATGAGAAAGTATGTAATGTTTTCATGA
1262297 G
130 G
1262298 TAAGAGTAAA
Statistics
Matches: 121, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
135 1 0.01
136 120 0.99
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.32
Consensus pattern (136 bp):
CCCCTTACTCATGACTTTCAAAAGAATAGTGATATAAATGCTTAGCAAATACATTCAAATAGTCA
TTTGAAAGACTAGTATTCAAGATTGAATACGTAGAATATGAGAAAGTATGTAATGTTTTCATGAG
GGGGAG
Found at i:1263361 original size:24 final size:26
Alignment explanation
Indices: 1263334--1263384 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
1263324 TACTGTTTAA
* *
1263334 TATAGTT-AATAATTATAA-AATTTT
1 TATAGTTCAATAAATAAAATAATTTT
1263358 TATAGTTCAATAAATAAAATAATTTT
1 TATAGTTCAATAAATAAAATAATTTT
1263384 T
1 T
1263385 TGAAATTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 7 0.30
25 9 0.39
26 7 0.30
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (26 bp):
TATAGTTCAATAAATAAAATAATTTT
Found at i:1280220 original size:2 final size:2
Alignment explanation
Indices: 1280213--1280243 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1280203 ATATCTTAAT
1280213 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1280244 GTAAATGCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1280366 original size:40 final size:40
Alignment explanation
Indices: 1280298--1280446 Score: 201
Period size: 40 Copynumber: 3.7 Consensus size: 40
1280288 TACATATGTA
* * * *
1280298 ATTGTCGGTTTATCCCATTA-CTGCTGGGCGCACATTTGAT
1 ATTGTCGGTTTATCCGACTAGC-GTTGGGCACACATTTGAT
* * * *
1280338 GTTGTTGGTTTATCCGACTAGTGATGGGCACACATTTGAT
1 ATTGTCGGTTTATCCGACTAGCGTTGGGCACACATTTGAT
*
1280378 ATTATCGGTTTATCCGACTAGCGTTGGGCACACATTTGAT
1 ATTGTCGGTTTATCCGACTAGCGTTGGGCACACATTTGAT
1280418 ATTGTCGGTTTATCCGACTAGCGTTGGGC
1 ATTGTCGGTTTATCCGACTAGCGTTGGGC
1280447 GCAAAACATT
Statistics
Matches: 95, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
40 95 1.00
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (40 bp):
ATTGTCGGTTTATCCGACTAGCGTTGGGCACACATTTGAT
Found at i:1283678 original size:26 final size:28
Alignment explanation
Indices: 1283649--1283705 Score: 100
Period size: 26 Copynumber: 2.1 Consensus size: 28
1283639 AAGATCGGGG
1283649 ATAGTAAAATCAGT-A-ATATGAACTGT
1 ATAGTAAAATCAGTAATATATGAACTGT
1283675 ATAGTAAAATCAGTAATATATGAACTGT
1 ATAGTAAAATCAGTAATATATGAACTGT
1283703 ATA
1 ATA
1283706 TGAATTCCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 14 0.48
27 1 0.03
28 14 0.48
ACGTcount: A:0.47, C:0.07, G:0.14, T:0.32
Consensus pattern (28 bp):
ATAGTAAAATCAGTAATATATGAACTGT
Found at i:1284813 original size:13 final size:15
Alignment explanation
Indices: 1284779--1284812 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 15
1284769 ATGTCATGCA
1284779 AATAAACATAGAAAAT
1 AATAAACATA-AAAAT
1284795 AATAAACATAAAATAT
1 AATAAACATAAAA-AT
1284811 AA
1 AA
1284813 AATTACATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.18
16 14 0.82
ACGTcount: A:0.71, C:0.06, G:0.03, T:0.21
Consensus pattern (15 bp):
AATAAACATAAAAAT
Found at i:1284819 original size:50 final size:51
Alignment explanation
Indices: 1284721--1284821 Score: 127
Period size: 50 Copynumber: 2.0 Consensus size: 51
1284711 CATTAATACT
* * * *
1284721 TCATGCGAATATAACATAGCAAATAATAAATAACAATATTATATTTACATG
1 TCATGCAAATATAACATAGAAAATAATAAATAACAATATTAAAATTACATG
1284772 TCATGCAAATA-AACATAGAAAATAATAAACATAA-AATA-TAAAATTACATG
1 TCATGCAAATATAACATAGAAAATAAT-AA-ATAACAATATTAAAATTACATG
1284822 GTGCACACAA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
50 24 0.55
51 16 0.36
52 4 0.09
ACGTcount: A:0.54, C:0.11, G:0.07, T:0.28
Consensus pattern (51 bp):
TCATGCAAATATAACATAGAAAATAATAAATAACAATATTAAAATTACATG
Found at i:1285260 original size:22 final size:22
Alignment explanation
Indices: 1285232--1285280 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1285222 AGAATATTAC
1285232 ATAATATACT-AAATATTTAATA
1 ATAATATA-TGAAATATTTAATA
* *
1285254 ATAATATATGTATTATTTAATA
1 ATAATATATGAAATATTTAATA
1285276 ATAAT
1 ATAAT
1285281 TTAAAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (22 bp):
ATAATATATGAAATATTTAATA
Found at i:1285331 original size:5 final size:5
Alignment explanation
Indices: 1285315--1285441 Score: 60
Period size: 5 Copynumber: 24.0 Consensus size: 5
1285305 AGTAATAAAT
* * * *
1285315 AATAA AAT-- AATAA AATAA CATAA TATAT AATAA AATAAA AATAA TATAA
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AAT-AA AATAA AATAA
* * * * *
1285364 TGAATAA TATATAT AATAA AATGA TATAA TATAT AATAA AATATA TAATAA
1 --AATAA -A-ATAA AATAA AATAA AATAA AATAA AATAA AATA-A -AATAA
* *
1285415 ATATAT AATAA AATATA AATAA TATAA
1 A-ATAA AATAA AATA-A AATAA AATAA
1285442 TAAATAATAC
Statistics
Matches: 93, Mismatches: 19, Indels: 20
0.70 0.14 0.15
Matches are distributed among these distances:
3 3 0.03
5 61 0.66
6 18 0.19
7 11 0.12
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.31
Consensus pattern (5 bp):
AATAA
Found at i:1285351 original size:12 final size:12
Alignment explanation
Indices: 1285308--1285477 Score: 104
Period size: 12 Copynumber: 14.0 Consensus size: 12
1285298 TATACATAGT
*
1285308 AATAAATAATAA
1 AATATATAATAA
*
1285320 AATAATAAAATAACA
1 AAT-ATATAAT-A-A
1285335 TAATATATAATAA
1 -AATATATAATAA
*
1285348 AATA-AAAATAA
1 AATATATAATAA
*
1285359 TATA-ATGAATAA
1 AATATAT-AATAA
*
1285371 TATATATAATAA
1 AATATATAATAA
*
1285383 AAT-GAT-AT--
1 AATATATAATAA
1285391 AATATATAATAA
1 AATATATAATAA
1285403 AATATATAAT-A
1 AATATATAATAA
1285414 AATATATAATAA
1 AATATATAATAA
*
1285426 AATATAAATAATAT
1 AATAT--ATAATAA
*
1285440 AATAAATAATACA
1 AATATATAATA-A
*
1285453 TAA-ATAAAAATAA
1 -AATAT-ATAATAA
*
1285466 TATATATAATAA
1 AATATATAATAA
1285478 TTTTTTACAT
Statistics
Matches: 125, Mismatches: 16, Indels: 34
0.71 0.09 0.19
Matches are distributed among these distances:
8 3 0.02
9 2 0.02
10 4 0.03
11 23 0.18
12 52 0.42
13 12 0.10
14 19 0.15
15 7 0.06
16 3 0.02
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (12 bp):
AATATATAATAA
Found at i:1285474 original size:19 final size:19
Alignment explanation
Indices: 1285366--1285474 Score: 79
Period size: 18 Copynumber: 5.7 Consensus size: 19
1285356 TAATATAATG
1285366 AATAATATATAT-AAT-AA
1 AATAATATATATAAATAAA
*
1285383 AATGATATAATATATAAT-AA
1 AATAATAT-ATATA-AATAAA
*
1285403 AAT-ATATA-ATAAATATAT
1 AATAATATATATAAATA-AA
1285421 AATAA-A-ATATAAATAATA
1 AATAATATATATAAATAA-A
*
1285439 TAATAAATAATACATAAATAAA
1 -AAT-AAT-ATATATAAATAAA
1285461 AATAATATATATAA
1 AATAATATATATAA
1285475 TAATTTTTTA
Statistics
Matches: 74, Mismatches: 5, Indels: 24
0.72 0.05 0.23
Matches are distributed among these distances:
16 3 0.04
17 12 0.16
18 17 0.23
19 15 0.20
20 13 0.18
21 3 0.04
22 2 0.03
23 9 0.12
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (19 bp):
AATAATATATATAAATAAA
Found at i:1285478 original size:78 final size:75
Alignment explanation
Indices: 1285312--1285478 Score: 214
Period size: 78 Copynumber: 2.2 Consensus size: 75
1285302 CATAGTAATA
* * * *
1285312 AATA-ATAAAATAATAAAATAACATAATATATAATAAAATAAAAATAATATAATGAATAATATAT
1 AATATATATAATAATAAAATAAAATAATATATAATAAAATAAAAATAATATAATAAATAATACAT
1285376 ATAATAAAAT
66 ATAATAAAAT
* *
1285386 GATATA-ATATATAATAAAATATATAATAAATATATAATAAAATATAAATAATATAATAAATAAT
1 AATATATATA-ATAATAAAATA-A-AAT-AATATATAATAAAATAAAAATAATATAATAAATAAT
1285450 ACATA-AATAAAAAT
62 ACATATAAT-AAAAT
1285464 AATATATATAATAAT
1 AATATATATAATAAT
1285479 TTTTTACATA
Statistics
Matches: 79, Mismatches: 7, Indels: 10
0.82 0.07 0.10
Matches are distributed among these distances:
74 5 0.06
75 12 0.15
76 1 0.01
77 5 0.06
78 53 0.67
79 3 0.04
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (75 bp):
AATATATATAATAATAAAATAAAATAATATATAATAAAATAAAAATAATATAATAAATAATACAT
ATAATAAAAT
Found at i:1285503 original size:19 final size:21
Alignment explanation
Indices: 1285465--1285503 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1285455 AATAAAAATA
*
1285465 ATATATATAATAATTTTTTAC
1 ATATATATAATAATTGTTTAC
1285486 ATATATA-AATAA-TGTTTA
1 ATATATATAATAATTGTTTA
1285504 TAGTAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 5 0.29
21 7 0.41
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (21 bp):
ATATATATAATAATTGTTTAC
Found at i:1285543 original size:29 final size:29
Alignment explanation
Indices: 1285510--1285566 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
1285500 TTTATAGTAA
*
1285510 AAATAAATAATATATAAAATATTTAAAAT
1 AAATAAATAATATATAAAAAATTTAAAAT
*
1285539 AAATAAATTATATATAAAAAATTTAAAA
1 AAATAAATAATATATAAAAAATTTAAAA
1285567 AGGATTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (29 bp):
AAATAAATAATATATAAAAAATTTAAAAT
Found at i:1285761 original size:30 final size:30
Alignment explanation
Indices: 1285727--1285786 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1285717 ATAATGGCCA
*
1285727 TTAGGACTAAATTGA-AACAAAAATAAAATG
1 TTAGGACCAAATT-ATAACAAAAATAAAATG
* *
1285757 TTAGGGCCAAATTATAATAAAAATAAAATG
1 TTAGGACCAAATTATAACAAAAATAAAATG
1285787 AAATTATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.55, C:0.07, G:0.13, T:0.25
Consensus pattern (30 bp):
TTAGGACCAAATTATAACAAAAATAAAATG
Found at i:1294164 original size:23 final size:25
Alignment explanation
Indices: 1294106--1294168 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 25
1294096 AATCTAAAAT
1294106 TAAATATTAATAATT-TTAGTTAAAC
1 TAAATATTAATAATTATTAG-TAAAC
1294131 -ATAAT-TT-ATAATTATTA-T-AAC
1 TA-AATATTAATAATTATTAGTAAAC
1294152 TAAATATTAATAATTAT
1 TAAATATTAATAATTAT
1294169 CGGATTTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
21 6 0.18
22 4 0.12
23 14 0.42
24 6 0.18
25 3 0.09
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (25 bp):
TAAATATTAATAATTATTAGTAAAC
Found at i:1294232 original size:21 final size:21
Alignment explanation
Indices: 1294206--1294247 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1294196 TAGGATTTAA
1294206 GAGTTTAGAATCTTAG-GTTTT
1 GAGTTTAGAAT-TTAGAGTTTT
1294227 GAGTTTAGAATTTAGAGTTTT
1 GAGTTTAGAATTTAGAGTTTT
1294248 AGCATTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.26, C:0.02, G:0.24, T:0.48
Consensus pattern (21 bp):
GAGTTTAGAATTTAGAGTTTT
Found at i:1297764 original size:33 final size:33
Alignment explanation
Indices: 1297727--1297905 Score: 107
Period size: 33 Copynumber: 5.4 Consensus size: 33
1297717 TGGCCCTGTC
* *
1297727 ATGGTCTTACATTC-GTAGTGCCATAACCCAATT
1 ATGGTCTTACATTCAG-AATGCCATAACCCAACT
* *
1297760 ATGGTCTTGTCA-TCAGAATGCCATAGCCCAACT
1 ATGGTCTT-ACATTCAGAATGCCATAACCCAACT
*** *
1297793 ATGGTCTTACATAT-AGATACTGCCATGGTCCAACC
1 ATGGTCTTACAT-TCAGA-A-TGCCATAACCCAACT
* * * **
1297828 ATGGTCTTACGTTTA-AGGTGCCATAACCCAGTT
1 ATGGTCTTACATTCAGA-ATGCCATAACCCAACT
* * * *
1297861 ATGGTCTTTTCATT-AAAATGCCATAGCCCAGCT
1 ATGGTC-TTACATTCAGAATGCCATAACCCAACT
1297894 ATGGTCTTACAT
1 ATGGTCTTACAT
1297906 ATAAATACTG
Statistics
Matches: 114, Mismatches: 23, Indels: 19
0.73 0.15 0.12
Matches are distributed among these distances:
32 7 0.06
33 70 0.61
34 13 0.11
35 24 0.21
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (33 bp):
ATGGTCTTACATTCAGAATGCCATAACCCAACT
Found at i:1297826 original size:35 final size:33
Alignment explanation
Indices: 1297778--1297938 Score: 126
Period size: 35 Copynumber: 4.8 Consensus size: 33
1297768 GTCATCAGAA
1297778 TGCCATAGCCCAACTATGGTCTTACATATAGATAC
1 TGCCATAGCCCAACTATGGTCTTACATATA-A-AC
* * * * * **
1297813 TGCCATGGTCCAACCATGGTCTTACGTTTAAGG
1 TGCCATAGCCCAACTATGGTCTTACATATAAAC
* ** * *
1297846 TGCCATAACCCAGTTATGGTCTTTTCAT-TAAAA
1 TGCCATAGCCCAACTATGGTC-TTACATATAAAC
*
1297879 TGCCATAGCCCAGCTATGGTCTTACATATAAATAC
1 TGCCATAGCCCAACTATGGTCTTACATAT-AA-AC
* * *
1297914 TGCCATGGTCCAACCATGGTCTTAC
1 TGCCATAGCCCAACTATGGTCTTAC
1297939 GCTCAATTCA
Statistics
Matches: 97, Mismatches: 25, Indels: 8
0.75 0.19 0.06
Matches are distributed among these distances:
32 5 0.05
33 38 0.39
34 7 0.07
35 47 0.48
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.30
Consensus pattern (33 bp):
TGCCATAGCCCAACTATGGTCTTACATATAAAC
Found at i:1297852 original size:101 final size:101
Alignment explanation
Indices: 1297744--1297939 Score: 338
Period size: 101 Copynumber: 1.9 Consensus size: 101
1297734 TACATTCGTA
* *
1297744 GTGCCATAACCCAATTATGGTCTTGTCATCAGAATGCCATAGCCCAACTATGGTCTTACATATAG
1 GTGCCATAACCCAATTATGGTCTTGTCATCAAAATGCCATAGCCCAACTATGGTCTTACATATAA
1297809 ATACTGCCATGGTCCAACCATGGTCTTACGTTTAAG
66 ATACTGCCATGGTCCAACCATGGTCTTACGTTTAAG
* * * *
1297845 GTGCCATAACCCAGTTATGGTCTTTTCATTAAAATGCCATAGCCCAGCTATGGTCTTACATATAA
1 GTGCCATAACCCAATTATGGTCTTGTCATCAAAATGCCATAGCCCAACTATGGTCTTACATATAA
1297910 ATACTGCCATGGTCCAACCATGGTCTTACG
66 ATACTGCCATGGTCCAACCATGGTCTTACG
1297940 CTCAATTCAT
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
101 89 1.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (101 bp):
GTGCCATAACCCAATTATGGTCTTGTCATCAAAATGCCATAGCCCAACTATGGTCTTACATATAA
ATACTGCCATGGTCCAACCATGGTCTTACGTTTAAG
Found at i:1300896 original size:33 final size:32
Alignment explanation
Indices: 1300811--1301037 Score: 127
Period size: 33 Copynumber: 6.8 Consensus size: 32
1300801 ATTTTTCTTG
* * *
1300811 TGCCATAGTCCAACTATGGTCTTACACATGTAT
1 TGCCATAGCCCAACTATGGTCTTACA-TTGTAA
* ** *
1300844 TGCCATGGCCCTGCCATGGTCTTACATTCGTAA
1 TGCCATAGCCCAACTATGGTCTTACATT-GTAA
* *
1300877 TGCCATAACCCAATTATGGTCTTATC-TTCAG-AA
1 TGCCATAGCCCAACTATGGTCTTA-CATT--GTAA
* * *
1300910 TGCCATAGCCCAGCTATGGTTTTACATATAGATAC
1 TGCCATAGCCCAACTATGGTCTTACAT-T-G-TAA
* * * *
1300945 TGCCATGGTCCAACCATGGTCTTACGTT-TAA
1 TGCCATAGCCCAACTATGGTCTTACATTGTAA
* * ** * **
1300976 GGTGCCATAACCTAGTTATGGTCTTTTCATTAAAA
1 --TGCCATAGCCCAACTATGGTC-TTACATTGTAA
1301011 TGCCATAGCCCAACTATGGTCTTACAT
1 TGCCATAGCCCAACTATGGTCTTACAT
1301038 ATAAATACTG
Statistics
Matches: 142, Mismatches: 41, Indels: 23
0.69 0.20 0.11
Matches are distributed among these distances:
31 2 0.01
32 7 0.05
33 100 0.70
34 9 0.06
35 24 0.17
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.33
Consensus pattern (32 bp):
TGCCATAGCCCAACTATGGTCTTACATTGTAA
Found at i:1300950 original size:35 final size:33
Alignment explanation
Indices: 1300910--1301070 Score: 99
Period size: 35 Copynumber: 4.8 Consensus size: 33
1300900 ATCTTCAGAA
*
1300910 TGCCATAGCCCAGCTATGGTTTTACATATAGATAC
1 TGCCATAGCCCAACTATGGTTTTACATATA-A-AC
* * * * * * **
1300945 TGCCATGGTCCAACCATGGTCTTACGTTTAAGG
1 TGCCATAGCCCAACTATGGTTTTACATATAAAC
* * ** * *
1300978 TGCCATAACCTAGTTATGGTCTTTTCAT-TAAAA
1 TGCCATAGCCCAACTATGGT-TTTACATATAAAC
*
1301011 TGCCATAGCCCAACTATGGTCTTACATATAAATAC
1 TGCCATAGCCCAACTATGGTTTTACATAT-AA-AC
* * *
1301046 TGCCATGGTCCAACCATGGTTTTAC
1 TGCCATAGCCCAACTATGGTTTTAC
1301071 GTTCAATTCA
Statistics
Matches: 90, Mismatches: 32, Indels: 8
0.69 0.25 0.06
Matches are distributed among these distances:
32 5 0.06
33 33 0.37
34 7 0.08
35 45 0.50
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (33 bp):
TGCCATAGCCCAACTATGGTTTTACATATAAAC
Found at i:1300984 original size:101 final size:100
Alignment explanation
Indices: 1300811--1301074 Score: 329
Period size: 101 Copynumber: 2.6 Consensus size: 100
1300801 ATTTTTCTTG
* * * * ** *
1300811 TGCCATAGTCCAACTATGGTCTTACACAT-G-TATTGCCATGGCCCTGCCATGGTCTTACATTCG
1 TGCCATAGCCCAACTATGGTCTTACATATAGATACTGCCATGGTCCAACCATGGTCTTACGTTC-
*
1300874 TAATGCCATAACCCAATTATGGTCTTATC-TTCAGAA
65 TAATGCCATAACCCAATTATGGTCTTATCATT-AAAA
* *
1300910 TGCCATAGCCCAGCTATGGTTTTACATATAGATACTGCCATGGTCCAACCATGGTCTTACGTT-T
1 TGCCATAGCCCAACTATGGTCTTACATATAGATACTGCCATGGTCCAACCATGGTCTTACGTTCT
* * *
1300974 AAGGTGCCATAACCTAGTTATGGTCTTTTCATTAAAA
66 AA--TGCCATAACCCAATTATGGTCTTATCATTAAAA
* *
1301011 TGCCATAGCCCAACTATGGTCTTACATATAAATACTGCCATGGTCCAACCATGGTTTTACGTTC
1 TGCCATAGCCCAACTATGGTCTTACATATAGATACTGCCATGGTCCAACCATGGTCTTACGTTC
1301075 AATTCATCCT
Statistics
Matches: 142, Mismatches: 17, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
99 28 0.20
100 1 0.01
101 111 0.78
102 2 0.01
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.33
Consensus pattern (100 bp):
TGCCATAGCCCAACTATGGTCTTACATATAGATACTGCCATGGTCCAACCATGGTCTTACGTTCT
AATGCCATAACCCAATTATGGTCTTATCATTAAAA
Found at i:1302655 original size:22 final size:21
Alignment explanation
Indices: 1302629--1302669 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1302619 TGGAAGGTGT
1302629 TTAAACTCTCTTTAAGGTTTCA
1 TTAAA-TCTCTTTAAGGTTTCA
* *
1302651 TTAAATGTTTTTAAGGTTT
1 TTAAATCTCTTTAAGGTTT
1302670 TGTTGAGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.27, C:0.10, G:0.12, T:0.51
Consensus pattern (21 bp):
TTAAATCTCTTTAAGGTTTCA
Found at i:1307832 original size:46 final size:46
Alignment explanation
Indices: 1307757--1308099 Score: 499
Period size: 46 Copynumber: 7.4 Consensus size: 46
1307747 GATGTCATAA
* * * * * *
1307757 TATCTTTCAACTATGGTTTTACTCGTTTTC-TGTCATGTTTCCATGG
1 TATCTTTCAACCATGGTCTTACTC-ATTTCATATCACGTTGCCATGG
* *** *
1307803 TATCTTTCAACCATGGTCTTATTCATTTTCCCGTCATGTTGCCATGG
1 TATCTTTCAACCATGGTCTTACTCA-TTTCATATCACGTTGCCATGG
* *
1307850 TATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGTTGCCATGG
1 TATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATGG
*
1307896 TATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATGG
1 TATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATGG
* *
1307942 TATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGG
1 TATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATGG
*
1307988 TATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATGG
1 TATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATGG
*
1308034 TATCTTTCAACCATGGTCTTACACATTTCATATCACGTTGCCATGG
1 TATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATGG
1308080 TATCTTTCAACCATGGTCTT
1 TATCTTTCAACCATGGTCTT
1308100 CCATATTCCA
Statistics
Matches: 278, Mismatches: 17, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
46 240 0.86
47 38 0.14
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.41
Consensus pattern (46 bp):
TATCTTTCAACCATGGTCTTACTCATTTCATATCACGTTGCCATGG
Found at i:1310771 original size:21 final size:21
Alignment explanation
Indices: 1310747--1310789 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1310737 GCCCAGTTCC
*
1310747 AAAGAAGACTTGGGTTAAGTT
1 AAAGAAGACTTAGGTTAAGTT
*
1310768 AAAGAATACTTAGGTTAAGTT
1 AAAGAAGACTTAGGTTAAGTT
1310789 A
1 A
1310790 GGAAAGGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.05, G:0.23, T:0.30
Consensus pattern (21 bp):
AAAGAAGACTTAGGTTAAGTT
Found at i:1314225 original size:24 final size:24
Alignment explanation
Indices: 1314174--1314285 Score: 143
Period size: 24 Copynumber: 4.7 Consensus size: 24
1314164 GATTCAACTC
* * * *
1314174 CGCACACATAGTGCCAAATAATTC
1 CGCACACATAGTGCCATACAAATA
* *
1314198 CGCACACATAGTGCCTTACATATA
1 CGCACACATAGTGCCATACAAATA
*
1314222 CGCACACATAGTGCCGTACAAATA
1 CGCACACATAGTGCCATACAAATA
*
1314246 CGCTCACATAGTGCCATACAAATA
1 CGCACACATAGTGCCATACAAATA
*
1314270 TGCACACATAGTGCCA
1 CGCACACATAGTGCCA
1314286 CTTAAATCCG
Statistics
Matches: 76, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 76 1.00
ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21
Consensus pattern (24 bp):
CGCACACATAGTGCCATACAAATA
Found at i:1316647 original size:20 final size:20
Alignment explanation
Indices: 1316581--1316649 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 20
1316571 ATATCTGAAC
1316581 TCATCGAGTTGTGGTCTGAGT
1 TCAT-GAGTTGTGGTCTGAGT
* * * **
1316602 TCATGATTCATGTGATTTGAAC
1 TCATGAGT--TGTGGTCTGAGT
1316624 TCATGAGTTGTGGTCTGAGT
1 TCATGAGTTGTGGTCTGAGT
1316644 TCATGA
1 TCATGA
1316650 TTATGAGACA
Statistics
Matches: 36, Mismatches: 10, Indels: 5
0.71 0.20 0.10
Matches are distributed among these distances:
20 17 0.47
21 4 0.11
22 15 0.42
ACGTcount: A:0.20, C:0.13, G:0.28, T:0.39
Consensus pattern (20 bp):
TCATGAGTTGTGGTCTGAGT
Found at i:1316954 original size:49 final size:49
Alignment explanation
Indices: 1316898--1316995 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
1316888 AAGCCCAATG
1316898 GGTAATGTGTAATCTTAATGAATACGACAAAGAAGCGAAAGTAAGTTAT
1 GGTAATGTGTAATCTTAATGAATACGACAAAGAAGCGAAAGTAAGTTAT
1316947 GGTAATGTGTAATCTTAATGAATACGACAAAGAAGCGAAAGTAAGTTAT
1 GGTAATGTGTAATCTTAATGAATACGACAAAGAAGCGAAAGTAAGTTAT
1316996 TTTGTGCAAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.43, C:0.08, G:0.22, T:0.27
Consensus pattern (49 bp):
GGTAATGTGTAATCTTAATGAATACGACAAAGAAGCGAAAGTAAGTTAT
Found at i:1323148 original size:30 final size:30
Alignment explanation
Indices: 1323112--1323171 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
1323102 TTCCCGAGCC
1323112 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
* *
1323142 TAGGGGCAAAAGTGTAATTTTTCAAAAGTT
1 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
1323172 CGTATTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.30
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAATTATGCAAAAGTT
Found at i:1333129 original size:30 final size:28
Alignment explanation
Indices: 1333080--1333139 Score: 93
Period size: 30 Copynumber: 2.1 Consensus size: 28
1333070 TTTTTGTGCT
1333080 TTCTTTTTTGATAAAAAACTTTTGATAC
1 TTCTTTTTTGATAAAAAACTTTTGATAC
*
1333108 TTCTGTTTTTGATGAATAAACTTTTGATAC
1 TTCT-TTTTTGAT-AAAAAACTTTTGATAC
1333138 TT
1 TT
1333140 TTTATAACCA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 4 0.14
29 8 0.28
30 17 0.59
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.52
Consensus pattern (28 bp):
TTCTTTTTTGATAAAAAACTTTTGATAC
Found at i:1341743 original size:6 final size:6
Alignment explanation
Indices: 1341732--1341760 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1341722 AAGCTTATCC
1341732 CGGTCT CGGTCT CGGTCT CGGTCT CGGTC
1 CGGTCT CGGTCT CGGTCT CGGTCT CGGTC
1341761 CCCGTCATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.34, G:0.34, T:0.31
Consensus pattern (6 bp):
CGGTCT
Found at i:1341871 original size:30 final size:30
Alignment explanation
Indices: 1341808--1341873 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
1341798 AGAGAGCACA
* *
1341808 GCCGGAGAAGCCGTTCATCCTCTCCACGTC
1 GCCGCAGAAGCCGTTCATCCTCTCCACGAC
1341838 GCCGCAGAAGCCGTTC-TCCATCT-CATCGAC
1 GCCGCAGAAGCCGTTCATCC-TCTCCA-CGAC
1341868 GCCGCA
1 GCCGCA
1341874 AAAGTCGATC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 5 0.16
30 27 0.84
ACGTcount: A:0.18, C:0.41, G:0.23, T:0.18
Consensus pattern (30 bp):
GCCGCAGAAGCCGTTCATCCTCTCCACGAC
Found at i:1343678 original size:37 final size:37
Alignment explanation
Indices: 1343623--1343701 Score: 124
Period size: 37 Copynumber: 2.1 Consensus size: 37
1343613 TTTGCTAGAG
*
1343623 ATAAAACACACCATGAACATTGTAAGTGAATTTATTT
1 ATAAAACACACCAGGAACATTGTAAGTGAATTTATTT
1343660 ATAAAA-AGCACCAGGAACATTGTAAGTGAATTTATTT
1 ATAAAACA-CACCAGGAACATTGTAAGTGAATTTATTT
*
1343697 TTAAA
1 ATAAA
1343702 CAGATTTAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
36 1 0.03
37 38 0.97
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (37 bp):
ATAAAACACACCAGGAACATTGTAAGTGAATTTATTT
Found at i:1347532 original size:27 final size:27
Alignment explanation
Indices: 1347487--1347642 Score: 194
Period size: 27 Copynumber: 5.8 Consensus size: 27
1347477 AGGCTGCCAA
* * *
1347487 ATATTGTGACAAAGTCACCAGATACAG
1 ATATTGTGGCAGAGCCACCAGATACAG
1347514 ATATTGTGGCAGAGCCACCAGA-ACAG
1 ATATTGTGGCAGAGCCACCAGATACAG
1347540 ATATATGTGGCAGAGCCACCAGAT-CAG
1 ATAT-TGTGGCAGAGCCACCAGATACAG
* *
1347567 ATAATCGTGGCATAGCCACCAGA-ACAG
1 AT-ATTGTGGCAGAGCCACCAGATACAG
1347594 ATATATGTGGCAGAGCCACCAGAT-CAG
1 ATAT-TGTGGCAGAGCCACCAGATACAG
*
1347621 ATAATTGTGGCATAGCCACCAG
1 AT-ATTGTGGCAGAGCCACCAG
1347643 GACGCTTCCT
Statistics
Matches: 114, Mismatches: 8, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
26 10 0.09
27 100 0.88
28 4 0.04
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (27 bp):
ATATTGTGGCAGAGCCACCAGATACAG
Found at i:1347584 original size:54 final size:54
Alignment explanation
Indices: 1347502--1347642 Score: 248
Period size: 54 Copynumber: 2.6 Consensus size: 54
1347492 GTGACAAAGT
*
1347502 CACCAGATACAGAT-ATTGTGGCAGAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
*
1347556 CACCAGATCAGATAATCGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
1347610 CACCAGATCAGATAATTGTGGCATAGCCACCAG
1 CACCAGATCAGATAATTGTGGCATAGCCACCAG
1347643 GACGCTTCCT
Statistics
Matches: 83, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
53 5 0.06
54 78 0.94
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
Found at i:1349178 original size:44 final size:45
Alignment explanation
Indices: 1349130--1349215 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
1349120 TCTAACTTTC
1349130 GGACAAAAATTTCAT-ATTTCACCCCTTTTTCTTTTAATAAAGAT
1 GGACAAAAATTTCATCATTTCACCCCTTTTTCTTTTAATAAAGAT
** *
1349174 GGACAAAAATTTGTTCTTTTCACCCCTTTTTCTTTTAATAAA
1 GGACAAAAATTTCATCATTTCACCCCTTTTTCTTTTAATAAA
1349216 ATTTCATATT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
44 13 0.34
45 25 0.66
ACGTcount: A:0.31, C:0.19, G:0.07, T:0.43
Consensus pattern (45 bp):
GGACAAAAATTTCATCATTTCACCCCTTTTTCTTTTAATAAAGAT
Found at i:1349298 original size:26 final size:26
Alignment explanation
Indices: 1349267--1349374 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
1349257 TGAAATGCCC
*
1349267 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
1349293 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
1349319 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
1349345 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
1349371 ATCA
1 ATCA
1349375 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:1350976 original size:34 final size:34
Alignment explanation
Indices: 1350933--1351002 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
1350923 AAAAGTAAGG
*
1350933 CACATTAACATAAATCGCATTACACACAATACAA
1 CACATTAACATAAATCACATTACACACAATACAA
1350967 CACATTAACATAAATCACATTACACACAATACAA
1 CACATTAACATAAATCACATTACACACAATACAA
1351001 CA
1 CA
1351003 TTCAATTTAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.51, C:0.27, G:0.01, T:0.20
Consensus pattern (34 bp):
CACATTAACATAAATCACATTACACACAATACAA
Found at i:1350987 original size:15 final size:15
Alignment explanation
Indices: 1350933--1350988 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
1350923 AAAAGTAAGG
1350933 CACATTAACATAAAT
1 CACATTAACATAAAT
*
1350948 CGCATTACACACAATACAA-
1 CACATT--A-AC-ATA-AAT
1350967 CACATTAACATAAAT
1 CACATTAACATAAAT
1350982 CACATTA
1 CACATTA
1350989 CACACAATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
14 2 0.06
15 15 0.45
16 2 0.06
17 2 0.06
18 2 0.06
19 8 0.24
20 2 0.06
ACGTcount: A:0.50, C:0.25, G:0.02, T:0.23
Consensus pattern (15 bp):
CACATTAACATAAAT
Found at i:1351911 original size:27 final size:26
Alignment explanation
Indices: 1351876--1351929 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 26
1351866 AGAATTCAAC
1351876 TTTTTCATTTTATGCGATTTAGTCCT
1 TTTTTCATTTTATGCGATTTAGTCCT
1351902 TTTTTGCATTTTATGCGATTTAGTCCT
1 TTTTT-CATTTTATGCGATTTAGTCCT
1351929 T
1 T
1351930 CTCGTAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 5 0.19
27 22 0.81
ACGTcount: A:0.15, C:0.15, G:0.13, T:0.57
Consensus pattern (26 bp):
TTTTTCATTTTATGCGATTTAGTCCT
Done.