Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 86 of 167
Found at i:28410869 original size:56 final size:56
Alignment explanation
Indices: 28410783--28411008 Score: 292
Period size: 56 Copynumber: 4.0 Consensus size: 56
28410773 ATTGATTTGC
* * *
28410783 ACTACGGTGCCTAGTGATTCGCAT-TTTGATGCGTACTGCTCAGCATTTTGGTGCCT
1 ACTACGGTGCCTAGTGATTCGC-TCTTCGATGCATACTGCTCAGCACTTTGGTGCCT
* *
28410839 ACTACGGTGCCTAGTGATTCGCTCTTTGATGCATACTGCTTAGCACTTTGGTGCCT
1 ACTACGGTGCCTAGTGATTCGCTCTTCGATGCATACTGCTCAGCACTTTGGTGCCT
* ** * * * *
28410895 ATTGTGGTGCCTAGTGATTCGCGCTTCGATACATACTGCTAAGCACTTTGGTGCTT
1 ACTACGGTGCCTAGTGATTCGCTCTTCGATGCATACTGCTCAGCACTTTGGTGCCT
* ** *
28410951 ATTATAGTGCCTAGTGATTCGCACTTCGATGCATACTGCTCAGCACTTTGGTGCCT
1 ACTACGGTGCCTAGTGATTCGCTCTTCGATGCATACTGCTCAGCACTTTGGTGCCT
28411007 AC
1 AC
28411009 CGTTAAAGCA
Statistics
Matches: 151, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
55 1 0.01
56 150 0.99
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (56 bp):
ACTACGGTGCCTAGTGATTCGCTCTTCGATGCATACTGCTCAGCACTTTGGTGCCT
Found at i:28413726 original size:19 final size:22
Alignment explanation
Indices: 28413687--28413726 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 22
28413677 AGAAACCCAA
28413687 CCATATCCAACCGTATACACCC
1 CCATATCCAACCGTATACACCC
28413709 CCATA-CCAACC-T-TACACC
1 CCATATCCAACCGTATACACC
28413727 GTGTGGGGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 6 0.33
22 5 0.28
ACGTcount: A:0.33, C:0.47, G:0.03, T:0.17
Consensus pattern (22 bp):
CCATATCCAACCGTATACACCC
Found at i:28413828 original size:27 final size:26
Alignment explanation
Indices: 28413788--28413902 Score: 131
Period size: 27 Copynumber: 4.3 Consensus size: 26
28413778 AGCATGGCTG
*
28413788 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGACAGAGCCA
* *
28413814 CCAGATACATATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGACAGAGCCA
28413842 CCAGAACAGATATATGTGACAGAGCCA
1 CCAGAACAGATA-ATGTGACAGAGCCA
* * * *
28413869 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGACAGAGCCA
28413896 CCAGAAC
1 CCAGAAC
28413903 GCTTCCTCCA
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
26 5 0.07
27 54 0.71
28 17 0.22
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGACAGAGCCA
Found at i:28413852 original size:54 final size:54
Alignment explanation
Indices: 28413788--28413902 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
28413778 AGCATGGCTG
* *
28413788 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACATATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * *
28413842 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
28413896 CCAGAAC
1 CCAGAAC
28413903 GCTTCCTCCA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 36 0.65
55 19 0.35
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:28415546 original size:26 final size:26
Alignment explanation
Indices: 28415510--28415619 Score: 177
Period size: 26 Copynumber: 4.2 Consensus size: 26
28415500 CATGGAATTC
28415510 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
28415536 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
28415562 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
*
28415588 TTATCATTG-AACATTTACCTAACCTA
1 TTATCA-TGAAACATTTACCTAACCCA
28415614 TTATCA
1 TTATCA
28415620 ATTTGTATCA
Statistics
Matches: 81, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
26 79 0.98
27 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:28417489 original size:148 final size:148
Alignment explanation
Indices: 28417221--28418260 Score: 1994
Period size: 148 Copynumber: 7.0 Consensus size: 148
28417211 GTTCGATAGT
28417221 TTAATTGTTGTGGAAATGTTAAGTTTTAACACTGATTTGATTAAATTGTAAAGTATGTAATATAG
1 TTAATTGTTGTGGAAATGTTAAGTTTTAACACTGATTTGATTAAATTGTAAAGTATGTAATATAG
*
28417286 TTTCTAAATAAGTAGGTGGCAAATGATGGTTGTAAAATGTTTATATAGTTAAATGAAATGTATAA
66 TTTCTAAATAAGTAGGTGGCAAATGATGGTTGTAAAATGTTTATATAGTAAAATGAAATGTATAA
28417351 ATGATTATATTAGAGAGA
131 ATGATTATATTAGAGAGA
28417369 TTAATTGTTGTGGAAATGTTAAGTTTTAACACTGATTTGATTAAATTGTAAAGTATGTAATATAG
1 TTAATTGTTGTGGAAATGTTAAGTTTTAACACTGATTTGATTAAATTGTAAAGTATGTAATATAG
28417434 TTTCTAAATAAGTAGGTGGCAAATGATGGTTGTAAAATGTTTATATAGTAAAATGAAATGTATAA
66 TTTCTAAATAAGTAGGTGGCAAATGATGGTTGTAAAATGTTTATATAGTAAAATGAAATGTATAA
28417499 ATGATTATATTAGAGAGA
131 ATGATTATATTAGAGAGA
28417517 TTAATTGTTGTGGAAATGTTAAGTTTTAACACTGATTTGATTAAATTGTAAAGTATGTAATATAG
1 TTAATTGTTGTGGAAATGTTAAGTTTTAACACTGATTTGATTAAATTGTAAAGTATGTAATATAG
28417582 TTTCTAAATAAGTAGGTGGCAAATGATGGTTGTAAAATGTTTATATAGTAAAATGAAATGTATAA
66 TTTCTAAATAAGTAGGTGGCAAATGATGGTTGTAAAATGTTTATATAGTAAAATGAAATGTATAA
28417647 ATGATTATATTAGAGAGA
131 ATGATTATATTAGAGAGA
28417665 TTAATTGTTGTGGAAATGTTAAGTTTTAACACTGATTTGATTAAATTGTAAAGTATGTAATATAG
1 TTAATTGTTGTGGAAATGTTAAGTTTTAACACTGATTTGATTAAATTGTAAAGTATGTAATATAG
28417730 TTTCTAAATAAGTAGGTGGCAAATGATGGTTGTAAAATGTTTATATAGTAAAATGAAATGTATAA
66 TTTCTAAATAAGTAGGTGGCAAATGATGGTTGTAAAATGTTTATATAGTAAAATGAAATGTATAA
28417795 ATGATTATATTAGAGAGA
131 ATGATTATATTAGAGAGA
28417813 TTAATTGTTGTGGAAATGTTAAGTTTTAACACTGATTTGATTAAATTGTAAAGTATGTAATATAG
1 TTAATTGTTGTGGAAATGTTAAGTTTTAACACTGATTTGATTAAATTGTAAAGTATGTAATATAG
28417878 TTTCTAAATAAGTAGGTGGCAAATGATGGTTGTAAAATGTTTATATAGTAAAATGAAATGTATAA
66 TTTCTAAATAAGTAGGTGGCAAATGATGGTTGTAAAATGTTTATATAGTAAAATGAAATGTATAA
28417943 ATGATTATATTAGAGAGA
131 ATGATTATATTAGAGAGA
28417961 TTAATTGTTGTGGAAATGTTAAGTTTTAACACTGATTTGATTAAATTGTAAAGTATGTAATATAG
1 TTAATTGTTGTGGAAATGTTAAGTTTTAACACTGATTTGATTAAATTGTAAAGTATGTAATATAG
*
28418026 TTTCTAAATAAGTAGGTGGCAAATGATGGTTGTAAAATGTTTATATAGTAAAATGAAATGTTTAT
66 TTTCTAAATAAGTAGGTGGCAAATGATGGTTGTAAAATGTTTATATAGTAAAATGAAATGTATA-
* * * *
28418091 AAT-A-TATTGTTCGATAGT
130 AATGATTA-TATTAGAGAGA
28418109 TTAATTGTTGTGGAAATGTTAAGTTTTAACACTGATTTGATTAAATTGTAAAGTATGTAATATAG
1 TTAATTGTTGTGGAAATGTTAAGTTTTAACACTGATTTGATTAAATTGTAAAGTATGTAATATAG
28418174 TTTCTAAATAAGTAGGTGGCAAATGATGGTTGTAAAATGTTTATATAGTAAAATGAAATGTATAA
66 TTTCTAAATAAGTAGGTGGCAAATGATGGTTGTAAAATGTTTATATAGTAAAATGAAATGTATAA
28418239 ATGATTATATTAGAGAGA
131 ATGATTATATTAGAGAGA
28418257 TTAA
1 TTAA
28418261 AATGTAAGTA
Statistics
Matches: 877, Mismatches: 11, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
147 5 0.01
148 867 0.99
149 5 0.01
ACGTcount: A:0.39, C:0.03, G:0.19, T:0.39
Consensus pattern (148 bp):
TTAATTGTTGTGGAAATGTTAAGTTTTAACACTGATTTGATTAAATTGTAAAGTATGTAATATAG
TTTCTAAATAAGTAGGTGGCAAATGATGGTTGTAAAATGTTTATATAGTAAAATGAAATGTATAA
ATGATTATATTAGAGAGA
Found at i:28420590 original size:37 final size:37
Alignment explanation
Indices: 28420531--28420632 Score: 159
Period size: 37 Copynumber: 2.8 Consensus size: 37
28420521 AGCTCAGATG
* *
28420531 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGAAA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGAAA
*
28420568 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGAAA
* *
28420605 TAATCTCCACACGTAGTCATCTGGTCTT
1 AAATCTCCACACGTAGTCATCGGGTCTT
28420633 TAATCCCAAG
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.25
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGAAA
Found at i:28420911 original size:47 final size:47
Alignment explanation
Indices: 28420851--28421092 Score: 342
Period size: 47 Copynumber: 5.1 Consensus size: 47
28420841 ACACATTTCG
* *
28420851 CATTAGCCATTCGGCCTTA-CTACATGTATACACGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCT-CATATATACACGTTCACATTCATCA
* *
28420898 CATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCTCATATATACACGTTCACATTCATCA
* *
28420945 CATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCTCATATATACACGTTCACATTCATCA
* *
28420992 CATTGGCCATTCGGCCTTATCACGCATATATATACAGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTAT--CTC--ATATATACACGTTCACATTCATCA
* *
28421043 CATTTGCCATTCGGCCTTATCTCATATATACACATTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCTCATATATACACGTTCACATTCATCA
28421090 CAT
1 CAT
28421093 AAAATCCTAA
Statistics
Matches: 179, Mismatches: 11, Indels: 10
0.89 0.05 0.05
Matches are distributed among these distances:
47 132 0.74
48 2 0.01
49 4 0.02
51 41 0.23
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.34
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCTCATATATACACGTTCACATTCATCA
Found at i:28421058 original size:98 final size:94
Alignment explanation
Indices: 28420851--28421092 Score: 351
Period size: 98 Copynumber: 2.5 Consensus size: 94
28420841 ACACATTTCG
*
28420851 CATTAGCCATTCGGCCTTA-CTACATGTATACACGTTCACATTCATCACATTGGCCATTCGGCCT
1 CATTAGCCATTCGGCCTTATCT-CATATATACACGTTCACATTCATCACATTGGCCATTCGGCCT
* * *
28420915 TATCTCATATATGCATGTTCACATTCATCA
65 TATCGCATATATACAGGTTCACATTCATCA
* * *
28420945 CATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTAGCCATTCGGCCTTATCTCATATATACACGTTCACATTCATCACATTGGCCATTCGGCCTT
28421010 ATCACGCATATATATACAGGTTCACATTCATCA
66 AT--CGC--ATATATACAGGTTCACATTCATCA
* *
28421043 CATTTGCCATTCGGCCTTATCTCATATATACACATTCACATTCATCACAT
1 CATTAGCCATTCGGCCTTATCTCATATATACACGTTCACATTCATCACAT
28421093 AAAATCCTAA
Statistics
Matches: 132, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
94 60 0.45
95 2 0.02
96 2 0.02
98 68 0.52
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.34
Consensus pattern (94 bp):
CATTAGCCATTCGGCCTTATCTCATATATACACGTTCACATTCATCACATTGGCCATTCGGCCTT
ATCGCATATATACAGGTTCACATTCATCA
Found at i:28434284 original size:40 final size:41
Alignment explanation
Indices: 28434225--28434509 Score: 372
Period size: 40 Copynumber: 7.1 Consensus size: 41
28434215 AAACCAAGTA
* * * *
28434225 CCTTCGGGATTTA-ACCGGATA-TAGTTACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATTAGTCACTCGCACAAATG
* *
28434264 CCTTCGAGACTTAGCCCGGATA-TAGT-AGTTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATTAGTCA-CTCGCACAAATG
* *
28434304 CCTTCGGGACTTAGCCCAGATA-TAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATTAGTCACTCGCACAAATG
*
28434344 CCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATTAGTCACTCGCACAAATG
* *
28434384 CCTTCGGGACTTAGCCC-GAAATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATTAGTCACTCGCACAAATG
* *
28434424 CCTTCGGGACTTAGCCC-GAAATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATTAGTCACTCGCACAAATG
*
28434464 CCTTCGGGACTTAGCCCGGA-ATTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATTAGTCACTCGCACAAATG
28434504 CCTTCG
1 CCTTCG
28434510 NNNNNNNNNN
Statistics
Matches: 227, Mismatches: 13, Indels: 11
0.90 0.05 0.04
Matches are distributed among these distances:
39 15 0.07
40 209 0.92
41 3 0.01
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (41 bp):
CCTTCGGGACTTAGCCCGGATATTAGTCACTCGCACAAATG
Found at i:28434405 original size:23 final size:23
Alignment explanation
Indices: 28434379--28434445 Score: 56
Period size: 23 Copynumber: 3.2 Consensus size: 23
28434369 TCACTAGCAC
28434379 AAATGCCTTCGGGACTTAGCCCG
1 AAATGCCTTCGGGACTTAGCCCG
* ** *
28434402 AAA----TTAGTCAC-TAGCAC-
1 AAATGCCTTCGGGACTTAGCCCG
28434419 AAATGCCTTCGGGACTTAGCCCG
1 AAATGCCTTCGGGACTTAGCCCG
28434442 AAAT
1 AAAT
28434446 TAGTCACTAG
Statistics
Matches: 30, Mismatches: 8, Indels: 12
0.60 0.16 0.24
Matches are distributed among these distances:
17 3 0.10
18 5 0.17
19 5 0.17
21 5 0.17
22 5 0.17
23 7 0.23
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (23 bp):
AAATGCCTTCGGGACTTAGCCCG
Found at i:28448434 original size:21 final size:21
Alignment explanation
Indices: 28448408--28448469 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
28448398 CCCAACCCAT
* * *
28448408 GCATATAATGTGTATATTATA
1 GCATATCATGTGCATATCATA
28448429 GCATATCATGTGCATATCATA
1 GCATATCATGTGCATATCATA
*
28448450 ACATATCATGTGCATATCAT
1 GCATATCATGTGCATATCAT
28448470 GTCCTATCAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (21 bp):
GCATATCATGTGCATATCATA
Found at i:28448477 original size:10 final size:11
Alignment explanation
Indices: 28448407--28448481 Score: 66
Period size: 11 Copynumber: 7.1 Consensus size: 11
28448397 ACCCAACCCA
*
28448407 TGCATATAATG
1 TGCATATCATG
* *
28448418 TGTATATTAT-
1 TGCATATCATG
*
28448428 AGCATATCATG
1 TGCATATCATG
28448439 TGCATATCAT-
1 TGCATATCATG
**
28448449 AACATATCATG
1 TGCATATCATG
28448460 TGCATATCATG
1 TGCATATCATG
*
28448471 T-CCTATCATG
1 TGCATATCATG
28448481 T
1 T
28448482 ATAACAATAT
Statistics
Matches: 51, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
10 24 0.47
11 27 0.53
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (11 bp):
TGCATATCATG
Found at i:28448548 original size:20 final size:20
Alignment explanation
Indices: 28448523--28448562 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
28448513 CAAATCCGTC
*
28448523 AACCACACAGTCCAAGTCAG
1 AACCACACAGTACAAGTCAG
28448543 AACCACACAGTACAAGTCAG
1 AACCACACAGTACAAGTCAG
28448563 TCACTTGCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.33, G:0.15, T:0.10
Consensus pattern (20 bp):
AACCACACAGTACAAGTCAG
Found at i:28448659 original size:54 final size:54
Alignment explanation
Indices: 28448601--28448707 Score: 126
Period size: 54 Copynumber: 2.0 Consensus size: 54
28448591 TTTAACACCC
*
28448601 TAGGGGCAAAATGGTAATTT-TACCCCACAAGGTTATCTCGGTAACTCTACCCTA
1 TAGGGGCAAAATGGT-ATTTCTACCCCACAAGGGTATCTCGGTAACTCTACCCTA
* *** * * *
28448655 TAGGGGTATTTTGGTATTTCTACCCTACAAGGGTATTTCGGTAATTCTACCCT
1 TAGGGGCAAAATGGTATTTCTACCCCACAAGGGTATCTCGGTAACTCTACCCT
28448708 GCAGGGGTAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
53 4 0.09
54 40 0.91
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (54 bp):
TAGGGGCAAAATGGTATTTCTACCCCACAAGGGTATCTCGGTAACTCTACCCTA
Found at i:28448769 original size:21 final size:21
Alignment explanation
Indices: 28448743--28448783 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28448733 GTACAGGGGT
*
28448743 ATTTTAGTAACTCTACCCTAC
1 ATTTTAATAACTCTACCCTAC
*
28448764 ATTTTAATAATTCTACCCTA
1 ATTTTAATAACTCTACCCTA
28448784 TAGGGGTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.02, T:0.41
Consensus pattern (21 bp):
ATTTTAATAACTCTACCCTAC
Found at i:28448802 original size:27 final size:27
Alignment explanation
Indices: 28448612--28448829 Score: 162
Period size: 27 Copynumber: 8.3 Consensus size: 27
28448602 AGGGGCAAAA
* * * * *
28448612 TGGTAATTTTACCCCACAAGGTTATCT
1 TGGTAATTCTACCCTACAGGGGTATTT
* * *
28448639 CGGTAACTCTACCCTATAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* *
28448666 TGGTATTTCTACCCTACAAGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* *
28448693 CGGTAATTCTACCCTGCAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
** **
28448720 CAGTAATTCTACTGTACAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* *
28448747 TAGTAACTCTACCCTAC------ATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
** *
28448768 TAATAATTCTACCCTATAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTT
* **
28448795 TGGTAATTTTA-CAAACCAGGGGTATTT
1 TGGTAATTCTACCCTA-CAGGGGTATTT
28448822 TGGTAATT
1 TGGTAATT
28448830 TTGTAAACTA
Statistics
Matches: 150, Mismatches: 34, Indels: 14
0.76 0.17 0.07
Matches are distributed among these distances:
21 18 0.12
26 2 0.01
27 130 0.87
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (27 bp):
TGGTAATTCTACCCTACAGGGGTATTT
Found at i:28448875 original size:81 final size:80
Alignment explanation
Indices: 28448787--28449236 Score: 551
Period size: 81 Copynumber: 5.6 Consensus size: 80
28448777 TACCCTATAG
* * ** *
28448787 GGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTGTAAACTAAGGGTATTTTGG
1 GGGTATTTTAGTAATTTCACAAACCAGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGG
28448852 TAATTTTACAAGGTGA
66 TAATTTTACAA-GTGA
** *
28448868 GGGTATTTTAGTAATTTCACAAATTAGGGGTATTTTGGTAATTTTACAAACAAGGGGTATTTTGG
1 GGGTATTTTAGTAATTTCACAAACCAGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGG
* ***
28448933 TAATTTCACAAACCA
66 TAATTTTACAAGTGA
* * * * * * *
28448948 GAGGTATTTTGGTAATTTTACAAACCAGGTGTGTTTTAGTAATTTTACAAACCAGGGGTATTTTA
1 G-GGTATTTTAGTAATTTCACAAACCAGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTG
*
28449013 GTAATTTTATAAGTGGA
65 GTAATTTTACAAGT-GA
* ** * *
28449030 GGGTATTTTAGTAATTTCAAAAATTAGGGGTATTTTGATAATTTCACAAACTAGGGGTATTTTGG
1 GGGTATTTTAGTAATTTCACAAACCAGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGG
28449095 TAATTTTACAAGTCGA
66 TAATTTTACAAGT-GA
* *
28449111 GGGTATTTTAGTAATTTCACAAATCAGGGGTATTTTGGTAATTTCACAAACTAGGGGTATTTTGG
1 GGGTATTTTAGTAATTTCACAAACCAGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGG
* *
28449176 TAATTTCACAAACT-A
66 TAATTTTAC-AAGTGA
* * *
28449191 GGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTAGTAATTTT
1 -GGGTATTTTAGTAATTTCACAAACCAGGGGTATTTTGGTAATTTT
28449237 GCTAATCGAG
Statistics
Matches: 315, Mismatches: 50, Indels: 8
0.84 0.13 0.02
Matches are distributed among these distances:
80 3 0.01
81 307 0.97
82 5 0.02
ACGTcount: A:0.30, C:0.08, G:0.22, T:0.40
Consensus pattern (80 bp):
GGGTATTTTAGTAATTTCACAAACCAGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGG
TAATTTTACAAGTGA
Found at i:28449250 original size:27 final size:27
Alignment explanation
Indices: 28448785--28449236 Score: 496
Period size: 27 Copynumber: 16.7 Consensus size: 27
28448775 TCTACCCTAT
28448785 AGGGGTATTTTGGTAATTTTACAAACC
1 AGGGGTATTTTGGTAATTTTACAAACC
** *
28448812 AGGGGTATTTTGGTAATTTTGTAAACT
1 AGGGGTATTTTGGTAATTTTACAAACC
* **
28448839 AAGGGTATTTTGGTAATTTTAC-AAGG
1 AGGGGTATTTTGGTAATTTTACAAACC
* * * **
28448865 TGAGGGTATTTTAGTAATTTCACAAATT
1 AG-GGGTATTTTGGTAATTTTACAAACC
*
28448893 AGGGGTATTTTGGTAATTTTACAAACA
1 AGGGGTATTTTGGTAATTTTACAAACC
*
28448920 AGGGGTATTTTGGTAATTTCACAAACC
1 AGGGGTATTTTGGTAATTTTACAAACC
*
28448947 AGAGGTATTTTGGTAATTTTACAAACC
1 AGGGGTATTTTGGTAATTTTACAAACC
* * *
28448974 AGGTGTGTTTTAGTAATTTTACAAACC
1 AGGGGTATTTTGGTAATTTTACAAACC
* * **
28449001 AGGGGTATTTTAGTAATTTTA-TAAGT
1 AGGGGTATTTTGGTAATTTTACAAACC
* * * * **
28449027 GGAGGGTATTTTAGTAATTTCAAAAATT
1 AG-GGGTATTTTGGTAATTTTACAAACC
* * *
28449055 AGGGGTATTTTGATAATTTCACAAACT
1 AGGGGTATTTTGGTAATTTTACAAACC
**
28449082 AGGGGTATTTTGGTAATTTTACAAGTC
1 AGGGGTATTTTGGTAATTTTACAAACC
* * *
28449109 -GAGGGTATTTTAGTAATTTCACAAATC
1 AG-GGGTATTTTGGTAATTTTACAAACC
* *
28449136 AGGGGTATTTTGGTAATTTCACAAACT
1 AGGGGTATTTTGGTAATTTTACAAACC
* *
28449163 AGGGGTATTTTGGTAATTTCACAAACT
1 AGGGGTATTTTGGTAATTTTACAAACC
28449190 AGGGGTATTTTGGTAATTTTACAAACC
1 AGGGGTATTTTGGTAATTTTACAAACC
*
28449217 AGGGGTATTTTAGTAATTTT
1 AGGGGTATTTTGGTAATTTT
28449237 GCTAATCGAG
Statistics
Matches: 364, Mismatches: 55, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
26 6 0.02
27 350 0.96
28 8 0.02
ACGTcount: A:0.31, C:0.08, G:0.22, T:0.39
Consensus pattern (27 bp):
AGGGGTATTTTGGTAATTTTACAAACC
Found at i:28451918 original size:14 final size:14
Alignment explanation
Indices: 28451899--28451932 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
28451889 TCCTTGAGTT
28451899 TCTATAGGCACATC
1 TCTATAGGCACATC
28451913 TCTATAGGCACATC
1 TCTATAGGCACATC
28451927 TCTATA
1 TCTATA
28451933 CAGCTTATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (14 bp):
TCTATAGGCACATC
Found at i:28454390 original size:27 final size:26
Alignment explanation
Indices: 28454342--28454393 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
28454332 GCGAGGCTGC
*
28454342 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
28454368 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
28454394 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:28461611 original size:41 final size:41
Alignment explanation
Indices: 28461560--28461861 Score: 396
Period size: 41 Copynumber: 7.3 Consensus size: 41
28461550 TATTCGGGCT
*
28461560 TTATTTCCTAGCAGGCTTTGTGCCGGTGTATTATATCAGGC
1 TTATTGCCTAGCAGGCTTTGTGCCGGTGTATTATATCAGGC
* *
28461601 TTATTGCCTAGCAGGCTTTGTGCCGGTGCATTATATTAGGC
1 TTATTGCCTAGCAGGCTTTGTGCCGGTGTATTATATCAGGC
* *
28461642 TTATTGCCTAGCAGGCTTTGTGCTGATGTA--ATATCAGGC
1 TTATTGCCTAGCAGGCTTTGTGCCGGTGTATTATATCAGGC
* * *
28461681 TTATTGCCTAGCAGACTTTATATGCCGGTGTATTAAATCAGGC
1 TTATTGCCTAGCAGGC-TT-TGTGCCGGTGTATTATATCAGGC
28461724 TTATTGCCTAGCAGGCTTTGTGCCGGTGTATTATATCAGGC
1 TTATTGCCTAGCAGGCTTTGTGCCGGTGTATTATATCAGGC
* * **
28461765 TTATTGCCTAGCAGACTTTATATGCCAATGTATTATATCAGGC
1 TTATTGCCTAGCAGGC-TT-TGTGCCGGTGTATTATATCAGGC
* *
28461808 TTATTGCCTAGTAGGCTTTGTGCTGGTGTATTATA-CTAGGC
1 TTATTGCCTAGCAGGCTTTGTGCCGGTGTATTATATC-AGGC
28461849 TT-TATGCCTAGCA
1 TTAT-TGCCTAGCA
28461862 AATTTTATGT
Statistics
Matches: 227, Mismatches: 26, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
39 23 0.10
40 4 0.02
41 137 0.60
42 6 0.03
43 57 0.25
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.37
Consensus pattern (41 bp):
TTATTGCCTAGCAGGCTTTGTGCCGGTGTATTATATCAGGC
Found at i:28461790 original size:84 final size:84
Alignment explanation
Indices: 28461560--28461861 Score: 436
Period size: 84 Copynumber: 3.6 Consensus size: 84
28461550 TATTCGGGCT
* * *
28461560 TTATTTCCTAGCAGGCTTTGTGCCGGTGTATTATATCAGGCTTATTGCCTAGCAGGC-TT-TGTG
1 TTATTGCCTAGCAGGCTTTGTGCCGGTGTATTATATCAGGCTTATTGCCTAGCAGACTTTATATG
* *
28461623 CCGGTGCATTATATTAGGC
66 CCGGTGTATTATATCAGGC
* *
28461642 TTATTGCCTAGCAGGCTTTGTGCTGATGTA--ATATCAGGCTTATTGCCTAGCAGACTTTATATG
1 TTATTGCCTAGCAGGCTTTGTGCCGGTGTATTATATCAGGCTTATTGCCTAGCAGACTTTATATG
*
28461705 CCGGTGTATTAAATCAGGC
66 CCGGTGTATTATATCAGGC
28461724 TTATTGCCTAGCAGGCTTTGTGCCGGTGTATTATATCAGGCTTATTGCCTAGCAGACTTTATATG
1 TTATTGCCTAGCAGGCTTTGTGCCGGTGTATTATATCAGGCTTATTGCCTAGCAGACTTTATATG
**
28461789 CCAATGTATTATATCAGGC
66 CCGGTGTATTATATCAGGC
* *
28461808 TTATTGCCTAGTAGGCTTTGTGCTGGTGTATTATA-CTAGGCTT-TATGCCTAGCA
1 TTATTGCCTAGCAGGCTTTGTGCCGGTGTATTATATC-AGGCTTAT-TGCCTAGCA
28461862 AATTTTATGT
Statistics
Matches: 199, Mismatches: 15, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
80 24 0.12
81 2 0.01
82 74 0.37
83 2 0.01
84 97 0.49
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.37
Consensus pattern (84 bp):
TTATTGCCTAGCAGGCTTTGTGCCGGTGTATTATATCAGGCTTATTGCCTAGCAGACTTTATATG
CCGGTGTATTATATCAGGC
Found at i:28464222 original size:26 final size:26
Alignment explanation
Indices: 28464161--28464215 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
28464151 TGAAATGGTT
28464161 GGTATTTGGTTATGAGTTTAAGTGCA
1 GGTATTTGGTTATGAGTTTAAGTGCA
28464187 GGTATTTGGTTATGAGTTTAAGTGCA
1 GGTATTTGGTTATGAGTTTAAGTGCA
28464213 GGT
1 GGT
28464216 CATTGGTGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.22, C:0.04, G:0.33, T:0.42
Consensus pattern (26 bp):
GGTATTTGGTTATGAGTTTAAGTGCA
Found at i:28475784 original size:27 final size:27
Alignment explanation
Indices: 28475746--28475888 Score: 164
Period size: 27 Copynumber: 5.3 Consensus size: 27
28475736 CAAAATAGTC
* *
28475746 ATTTTAC-CCTACAGGGGTATTTCGGTA
1 ATTTTACACC-ACAAGGGTATTTCGATA
* *
28475773 ATTTTACACTACAAGGGTATTTCGTTA
1 ATTTTACACCACAAGGGTATTTCGATA
* * *
28475800 ATTTTACACCACAAAGGTATTTTGGTA
1 ATTTTACACCACAAGGGTATTTCGATA
*
28475827 ATTTTACACCATAAGGGTATTTCGATA
1 ATTTTACACCACAAGGGTATTTCGATA
**
28475854 ATTTTA-AAAATCAAGGGTATTTCGATA
1 ATTTTACACCA-CAAGGGTATTTCGATA
28475881 ATTTTACA
1 ATTTTACA
28475889 AATTGGGGGT
Statistics
Matches: 99, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
26 2 0.02
27 95 0.96
28 2 0.02
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.38
Consensus pattern (27 bp):
ATTTTACACCACAAGGGTATTTCGATA
Found at i:28475891 original size:27 final size:27
Alignment explanation
Indices: 28475760--28475923 Score: 138
Period size: 27 Copynumber: 6.1 Consensus size: 27
28475750 TACCCTACAG
* *
28475760 GGGTATTTCGGTAATTTTAC-ACTACAA
1 GGGTATTTCGATAATTTTACAAAT-CAA
* *
28475787 GGGTATTTCGTTAATTTTACACCA-CAA
1 GGGTATTTCGATAATTTTACA-AATCAA
* * * *
28475814 AGGTATTTTGGTAATTTTACACCAT-AA
1 GGGTATTTCGATAATTTTACA-AATCAA
*
28475841 GGGTATTTCGATAATTTTAAAAATCAA
1 GGGTATTTCGATAATTTTACAAATCAA
***
28475868 GGGTATTTCGATAATTTTACAAATTGG
1 GGGTATTTCGATAATTTTACAAATCAA
* *
28475895 GGGTATTT-TAGTAATTTTACAAATTAA
1 GGGTATTTCGA-TAATTTTACAAATCAA
28475922 GG
1 GG
28475924 TCTTAACATC
Statistics
Matches: 114, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
26 3 0.03
27 111 0.97
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (27 bp):
GGGTATTTCGATAATTTTACAAATCAA
Found at i:28480188 original size:19 final size:19
Alignment explanation
Indices: 28480138--28480196 Score: 75
Period size: 19 Copynumber: 3.2 Consensus size: 19
28480128 AGTACAGTAA
*
28480138 CAGTAACCAGTGCAGTATG
1 CAGTAATCAGTGCAGTATG
*
28480157 CA-TAATCAGTGCAGTACG
1 CAGTAATCAGTGCAGTATG
* *
28480175 CAGTACTTAGTGCAGTATG
1 CAGTAATCAGTGCAGTATG
28480194 CAG
1 CAG
28480197 GTCCTACCCA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
18 16 0.47
19 18 0.53
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (19 bp):
CAGTAATCAGTGCAGTATG
Found at i:28480562 original size:27 final size:27
Alignment explanation
Indices: 28480531--28480730 Score: 258
Period size: 27 Copynumber: 7.4 Consensus size: 27
28480521 GGGCATATCG
*
28480531 GTCATCTTACCAT-ATAAGGGCAAAACA
1 GTCATTTTACC-TCATAAGGGCAAAACA
* *
28480558 ATCATTTTACCTTATAAGGGCAAAACA
1 GTCATTTTACCTCATAAGGGCAAAACA
* * *
28480585 GTCATTTTACCTCATCAGGGAAAAATA
1 GTCATTTTACCTCATAAGGGCAAAACA
28480612 GTCATTTTACCTCATAAGGGCAAAACA
1 GTCATTTTACCTCATAAGGGCAAAACA
* *
28480639 GTCATTTTACCTCAGAAGGGCAAAATA
1 GTCATTTTACCTCATAAGGGCAAAACA
* * *
28480666 GTCATTTTACCTCAAAAGCGCAAAATA
1 GTCATTTTACCTCATAAGGGCAAAACA
* * *
28480693 GTCATTTTACCTCATAAGCGAAAAATA
1 GTCATTTTACCTCATAAGGGCAAAACA
28480720 GTCATTTTACC
1 GTCATTTTACC
28480731 GATTAGGGTT
Statistics
Matches: 156, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
26 1 0.01
27 155 0.99
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (27 bp):
GTCATTTTACCTCATAAGGGCAAAACA
Found at i:28480871 original size:18 final size:17
Alignment explanation
Indices: 28480845--28480878 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
28480835 CATAATGCGG
28480845 GCCCATGTGGGCCCACAC
1 GCCCATGT-GGCCCACAC
*
28480863 GCCCGTGTGGCCCACA
1 GCCCATGTGGCCCACA
28480879 AAGCCCAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.15, C:0.44, G:0.29, T:0.12
Consensus pattern (17 bp):
GCCCATGTGGCCCACAC
Found at i:28485038 original size:26 final size:26
Alignment explanation
Indices: 28485009--28485168 Score: 311
Period size: 26 Copynumber: 6.2 Consensus size: 26
28484999 TGATAAAAAT
*
28485009 TGATAATGGGTTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
28485035 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
28485061 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
28485087 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
28485113 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
28485139 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
28485165 TGAT
1 TGAT
28485169 GGGCATTTCA
Statistics
Matches: 133, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
26 133 1.00
ACGTcount: A:0.31, C:0.07, G:0.26, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:28486568 original size:27 final size:27
Alignment explanation
Indices: 28486471--28486575 Score: 126
Period size: 27 Copynumber: 3.9 Consensus size: 27
28486461 AGGAAGTGTC
* *
28486471 CTGGTGGCTATGCCACGATTATCTG-AT
1 CTGGTGGCTCTGCCAC-AATATCTGTAT
28486498 CTGGTGGCTCTGCCACATATATCTGT-T
1 CTGGTGGCTCTGCCACA-ATATCTGTAT
28486525 CTGGTGGCTCTGCCACAATATCTGTAT
1 CTGGTGGCTCTGCCACAATATCTGTAT
* *
28486552 CTGGTGACT-TCGTCACAATATCTG
1 CTGGTGGCTCT-GCCACAATATCTG
28486576 GCAGCCTCGC
Statistics
Matches: 70, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
26 10 0.14
27 60 0.86
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.34
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATATCTGTAT
Found at i:28488090 original size:24 final size:24
Alignment explanation
Indices: 28488058--28488133 Score: 116
Period size: 24 Copynumber: 3.2 Consensus size: 24
28488048 AAGTCTATCA
*
28488058 GGAGAGGATTTAGGAGTTGGTAAG
1 GGAGAGGATTTAGGAGTTGATAAG
28488082 GGAGAGGATTTAGGAGTTGATAAG
1 GGAGAGGATTTAGGAGTTGATAAG
* **
28488106 GGATAGGATTTAGGAGCAGATAAG
1 GGAGAGGATTTAGGAGTTGATAAG
28488130 GGAG
1 GGAG
28488134 GAAATCTAGG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.33, C:0.01, G:0.43, T:0.22
Consensus pattern (24 bp):
GGAGAGGATTTAGGAGTTGATAAG
Found at i:28488302 original size:79 final size:79
Alignment explanation
Indices: 28488171--28488323 Score: 297
Period size: 79 Copynumber: 1.9 Consensus size: 79
28488161 GAGGTGGCCG
*
28488171 GCCAAGGGACTTTAGCATGGGAATTTCGGCTAGGGTTAGTGCCAGTATAAATTCGGCATTAGTGG
1 GCCAAGGGACTTTACCATGGGAATTTCGGCTAGGGTTAGTGCCAGTATAAATTCGGCATTAGTGG
28488236 TAAGTGGTGCCGTA
66 TAAGTGGTGCCGTA
28488250 GCCAAGGGACTTTACCATGGGAATTTCGGCTAGGGTTAGTGCCAGTATAAATTCGGCATTAGTGG
1 GCCAAGGGACTTTACCATGGGAATTTCGGCTAGGGTTAGTGCCAGTATAAATTCGGCATTAGTGG
28488315 TAAGTGGTG
66 TAAGTGGTG
28488324 TCGTTTTCTG
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 73 1.00
ACGTcount: A:0.24, C:0.15, G:0.33, T:0.28
Consensus pattern (79 bp):
GCCAAGGGACTTTACCATGGGAATTTCGGCTAGGGTTAGTGCCAGTATAAATTCGGCATTAGTGG
TAAGTGGTGCCGTA
Found at i:28489732 original size:28 final size:27
Alignment explanation
Indices: 28489639--28489743 Score: 115
Period size: 27 Copynumber: 3.9 Consensus size: 27
28489629 AGGAAGCGTC
* *
28489639 CTGGTGGCTATGACACAATTATCTG-AT
1 CTGGTGGCTCTGCCAC-ATTATCTGTAT
* *
28489666 CTAGTGGCTCTGCCACATATTTCTGT-T
1 CTGGTGGCTCTGCCACAT-TATCTGTAT
28489693 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTGTAT
* *
28489721 CTGGTGACTCTGTCACATTATCT
1 CTGGTGGCTCTGCCACATTATCT
28489744 ATTCTGGCAG
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
26 2 0.03
27 47 0.71
28 17 0.26
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.37
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACATTATCTGTAT
Found at i:28489749 original size:54 final size:54
Alignment explanation
Indices: 28489639--28489750 Score: 136
Period size: 54 Copynumber: 2.1 Consensus size: 54
28489629 AGGAAGCGTC
* * *
28489639 CTGGTGGCTATGACACAATTATCTGATCTAGTGGCTCTGCCACATATTTCTGTT
1 CTGGTGGCTATGACACAATTATCTGATCTAGTGACTCTGCCACATATATCTATT
* * * * *
28489693 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTATT
1 CTGGTGGCTATGACACAATTATCTG-ATCTAGTGACTCTGCCACATATATCTATT
28489747 CTGG
1 CTGG
28489751 CAGCCATGCT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
54 32 0.65
55 17 0.35
ACGTcount: A:0.18, C:0.23, G:0.21, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGACACAATTATCTGATCTAGTGACTCTGCCACATATATCTATT
Found at i:28490833 original size:11 final size:10
Alignment explanation
Indices: 28490805--28490839 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
28490795 AGCCTGTAAG
28490805 TATTCTGAAT
1 TATTCTGAAT
*
28490815 TTTTCTGAAT
1 TATTCTGAAT
28490825 ATATTCTGAAT
1 -TATTCTGAAT
28490836 TATT
1 TATT
28490840 TGTCTGTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.54
Consensus pattern (10 bp):
TATTCTGAAT
Found at i:28491791 original size:17 final size:19
Alignment explanation
Indices: 28491764--28491798 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
28491754 GTTAAGATAG
28491764 CTGAGGAGGTA-AAGCGTA
1 CTGAGGAGGTAGAAGCGTA
28491782 CTGA-GAGGTAGAAGCGT
1 CTGAGGAGGTAGAAGCGT
28491799 GAGAAAGATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.31, C:0.11, G:0.40, T:0.17
Consensus pattern (19 bp):
CTGAGGAGGTAGAAGCGTA
Found at i:28495614 original size:24 final size:24
Alignment explanation
Indices: 28495549--28495619 Score: 115
Period size: 24 Copynumber: 3.0 Consensus size: 24
28495539 CTGTCAGGAG
*
28495549 AGGATTTAGGAGTTGATAAAGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
28495573 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
**
28495597 AGGATTTAGGAGCAGATAAGGGA
1 AGGATTTAGGAGTTGATAAGGGA
28495620 GGAAATCTAG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.37, C:0.01, G:0.37, T:0.25
Consensus pattern (24 bp):
AGGATTTAGGAGTTGATAAGGGAT
Found at i:28497076 original size:27 final size:27
Alignment explanation
Indices: 28497038--28497146 Score: 132
Period size: 27 Copynumber: 4.0 Consensus size: 27
28497028 AAGCGTCCTA
*
28497038 GTGGCTATGCCACAATTATCTGATCTG
1 GTGGCTCTGCCACAATTATCTGATCTG
*
28497065 GTGGCTCTGCCACATATT-TCTGTTCTG
1 GTGGCTCTGCCACA-ATTATCTGATCTG
*
28497092 GTGGCTCTGCCACGATTATCTGTATCTG
1 GTGGCTCTGCCACAATTATCTG-ATCTG
* * *
28497120 GTGACTCTGTCAC-ATTATCTGTTCTG
1 GTGGCTCTGCCACAATTATCTGATCTG
28497146 G
1 G
28497147 CAGCCATGCT
Statistics
Matches: 72, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
26 8 0.11
27 46 0.64
28 18 0.25
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.38
Consensus pattern (27 bp):
GTGGCTCTGCCACAATTATCTGATCTG
Found at i:28497141 original size:54 final size:54
Alignment explanation
Indices: 28497038--28497146 Score: 157
Period size: 54 Copynumber: 2.0 Consensus size: 54
28497028 AAGCGTCCTA
* *
28497038 GTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATTTCTGTTCTG
1 GTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTTCTG
* * *
28497092 GTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTTCTG
1 GTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTTCTG
28497146 G
1 G
28497147 CAGCCATGCT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
54 31 0.63
55 18 0.37
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.38
Consensus pattern (54 bp):
GTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTTCTG
Found at i:28519478 original size:41 final size:41
Alignment explanation
Indices: 28519414--28519797 Score: 529
Period size: 41 Copynumber: 9.3 Consensus size: 41
28519404 ACATAAAATT
*
28519414 TGCTAGGC-ATAAAGCCT-AGTATAATACACCGGCACAGAGCC
1 TGCTAGGCAAT-AAGCCTGA-TATAATACACCGGCACAAAGCC
* * * *
28519455 TACTAGGCAATAAGCCTGATATAATACACTGAGATATAAAGCC
1 TGCTAGGCAATAAGCCTGATATAATACACCG-G-CACAAAGCC
28519498 TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCC
1 TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCC
* * * * *
28519539 TACTAGGCAATAAACCTGATTTAATACATCGACACAAAGCC
1 TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCC
* * *
28519580 TGCTAGGCAATAAGCCTGATTTAAAACACCGGAACAAAGCC
1 TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCC
* *
28519621 TGCTAGGCAATAAGCCTGATTTAATACACCGGCACAAAGCG
1 TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCC
* * * *
28519662 TGCTAGGCAATAAGCTTGATTTAAAACACCGGCACAAAGCT
1 TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCC
*
28519703 TGCTAGGCAATAAGCTTGATATAATACACCGGCACAAAGCC
1 TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCC
*
28519744 TGCTAGGCAATAAGCCTGATATAATACACCGACACAAAGCC
1 TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCC
28519785 TGCTAGGCAATAA
1 TGCTAGGCAATAA
28519798 AGCTCGAATA
Statistics
Matches: 308, Mismatches: 31, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
41 268 0.87
42 5 0.02
43 35 0.11
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.20
Consensus pattern (41 bp):
TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCC
Found at i:28523858 original size:20 final size:20
Alignment explanation
Indices: 28523829--28523866 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28523819 GTTGATTCAT
* *
28523829 TTAATTTTCTAATCACGTTA
1 TTAATCTTCTAAACACGTTA
28523849 TTAATCTTCTAAACACGT
1 TTAATCTTCTAAACACGT
28523867 ACTTTTGTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.05, T:0.45
Consensus pattern (20 bp):
TTAATCTTCTAAACACGTTA
Found at i:28526373 original size:41 final size:41
Alignment explanation
Indices: 28526316--28526658 Score: 519
Period size: 41 Copynumber: 8.3 Consensus size: 41
28526306 ACATAAAATT
*
28526316 TGCTAGGC-ATAAAGCCT-AGTATAATACACCGGCACAGAGCC
1 TGCTAGGCAAT-AAGCCTGA-TATAATACACCGGCACAAAGCC
*
28526357 TGCTAGGCAATAAGCCTGATATAATACACCGGCATATAAAGCC
1 TGCTAGGCAATAAGCCTGATATAATACACCGGC--ACAAAGCC
*
28526400 TGCTAGGCAATAAGCCTGATATAATACACCGACACAAAGCC
1 TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCC
* * *
28526441 TGCTAGGCAAAAAGCATGATTTAATACACCGGCACAAAGCC
1 TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCC
* * * *
28526482 TACTAGGTAATAAGCCTGATTTAAAACACCGGCACAAAGCC
1 TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCC
* *
28526523 TGCTAGGCAATAAGCCTGATTTAAAACACCGGCACAAAGCC
1 TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCC
*
28526564 TACTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCC
1 TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCC
28526605 TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCC
1 TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCC
28526646 TGCTAGGCAATAA
1 TGCTAGGCAATAA
28526659 AGCCCGAATA
Statistics
Matches: 279, Mismatches: 19, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
41 238 0.85
42 3 0.01
43 38 0.14
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (41 bp):
TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCC
Found at i:28527982 original size:26 final size:26
Alignment explanation
Indices: 28527953--28528030 Score: 129
Period size: 26 Copynumber: 3.0 Consensus size: 26
28527943 TGTTACATAT
*
28527953 TTATTTAGCAGGCTTTGAGCCGGTGA
1 TTATTTAGCAGGCTTTGAGCTGGTGA
* *
28527979 TTATTTAGCAGGCTTTGAGTTGGTGT
1 TTATTTAGCAGGCTTTGAGCTGGTGA
28528005 TTATTTAGCAGGCTTTGAGCTGGTGA
1 TTATTTAGCAGGCTTTGAGCTGGTGA
28528031 ATATATAGGA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 47 1.00
ACGTcount: A:0.18, C:0.12, G:0.31, T:0.40
Consensus pattern (26 bp):
TTATTTAGCAGGCTTTGAGCTGGTGA
Found at i:28528452 original size:26 final size:26
Alignment explanation
Indices: 28528416--28528469 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
28528406 ATGGGATGTT
28528416 AGTAAGGTCGTATTAAAATTTTGATA
1 AGTAAGGTCGTATTAAAATTTTGATA
28528442 AGTAAGGTCGTATTAAAATTTTGATA
1 AGTAAGGTCGTATTAAAATTTTGATA
28528468 AG
1 AG
28528470 AATTATGATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.39, C:0.04, G:0.20, T:0.37
Consensus pattern (26 bp):
AGTAAGGTCGTATTAAAATTTTGATA
Found at i:28531536 original size:12 final size:13
Alignment explanation
Indices: 28531510--28531540 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
28531500 TGCAAAATTA
28531510 AAGAAAAGAAAAG
1 AAGAAAAGAAAAG
28531523 AAGAAAAG-AAAG
1 AAGAAAAGAAAAG
28531535 AAGAAA
1 AAGAAA
28531541 GAACGCACGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
AAGAAAAGAAAAG
Found at i:28531771 original size:13 final size:13
Alignment explanation
Indices: 28531753--28531777 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28531743 AATTGATATC
28531753 TGTGAAAATTTTG
1 TGTGAAAATTTTG
28531766 TGTGAAAATTTT
1 TGTGAAAATTTT
28531778 ATCGTTTGTG
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:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (13 bp):
TGTGAAAATTTTG
Found at i:28532714 original size:28 final size:28
Alignment explanation
Indices: 28532674--28532730 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
28532664 CGTACGAGGT
28532674 AAGTCTATATACAAATAAATGTGTTTGA
1 AAGTCTATATACAAATAAATGTGTTTGA
28532702 AAGTCTATATACAAATAAATGTGTTTGA
1 AAGTCTATATACAAATAAATGTGTTTGA
28532730 A
1 A
28532731 TTGATTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.35
Consensus pattern (28 bp):
AAGTCTATATACAAATAAATGTGTTTGA
Found at i:28532995 original size:42 final size:41
Alignment explanation
Indices: 28532888--28533005 Score: 121
Period size: 44 Copynumber: 2.8 Consensus size: 41
28532878 AGGATTTTCG
* * **
28532888 ATATTTGATTTCGTGTAAGAACACATCTGGGACATTGGCAT
1 ATATTTGATTTCGTGTAAGACCATATCTGGGACATCAGCAT
* *
28532929 -TGATTTGAGATTTACGTGTAAGACCATGTCTGGGACATCAGTAT
1 AT-ATTT--GATTT-CGTGTAAGACCATATCTGGGACATCAGCAT
*
28532973 CATATTTGATTTCGTGTAAGACCCTATCTGGGA
1 -ATATTTGATTTCGTGTAAGACCATATCTGGGA
28533006 TAGTGGCATT
Statistics
Matches: 63, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
40 1 0.02
41 4 0.06
42 19 0.30
43 10 0.16
44 24 0.38
45 4 0.06
46 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (41 bp):
ATATTTGATTTCGTGTAAGACCATATCTGGGACATCAGCAT
Found at i:28533056 original size:43 final size:43
Alignment explanation
Indices: 28532887--28533059 Score: 154
Period size: 43 Copynumber: 4.0 Consensus size: 43
28532877 TAGGATTTTC
* *
28532887 GATATTTGATTTCGTGTAAGAACACATCTGGGACATTGGCATT
1 GATATTTGATTACGTGTAAGACCACATCTGGGACATTGGCATT
* ** ** *
28532930 GAT-TTGAGATTTACGTGTAAGACCATGTCTGGGACATCAGTA-T
1 GATATT-TGA-TTACGTGTAAGACCACATCTGGGACATTGGCATT
* * * *
28532973 CATATTTGATTTCGTGTAAGACC-CTATCTGGGATAGTGGCATT
1 GATATTTGATTACGTGTAAGACCAC-ATCTGGGACATTGGCATT
* * * *
28533016 GATAATTGATTACATGTAAGACCACGTCTGGGACGTTGGCATT
1 GATATTTGATTACGTGTAAGACCACATCTGGGACATTGGCATT
28533059 G
1 G
28533060 TACGAACTTT
Statistics
Matches: 98, Mismatches: 26, Indels: 12
0.72 0.19 0.09
Matches are distributed among these distances:
42 25 0.26
43 45 0.46
44 28 0.29
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.34
Consensus pattern (43 bp):
GATATTTGATTACGTGTAAGACCACATCTGGGACATTGGCATT
Found at i:28536031 original size:24 final size:24
Alignment explanation
Indices: 28536004--28536062 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 24
28535994 GTAAGGAGGG
28536004 GATAAGGGAGAAGATTTAGGAGCT
1 GATAAGGGAGAAGATTTAGGAGCT
*
28536028 GATAAGGGGAGAAGTTTTAGGAGCT
1 GATAA-GGGAGAAGATTTAGGAGCT
*
28536053 GATTAGGGAG
1 GATAAGGGAG
28536063 GGCAGTGTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 10 0.31
25 22 0.69
ACGTcount: A:0.34, C:0.03, G:0.41, T:0.22
Consensus pattern (24 bp):
GATAAGGGAGAAGATTTAGGAGCT
Found at i:28536949 original size:16 final size:15
Alignment explanation
Indices: 28536923--28536953 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
28536913 ACTAGATCGG
28536923 TAAAAGCCGAAAAGC
1 TAAAAGCCGAAAAGC
28536938 TAAAATGCCGAAAAGC
1 TAAAA-GCCGAAAAGC
28536954 CAGTATTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.52, C:0.19, G:0.19, T:0.10
Consensus pattern (15 bp):
TAAAAGCCGAAAAGC
Found at i:28537404 original size:27 final size:26
Alignment explanation
Indices: 28537372--28537477 Score: 131
Period size: 27 Copynumber: 3.9 Consensus size: 26
28537362 AGGAAGCGTC
*
28537372 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
* *
28537399 CTGGTGGCTCTGTCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
28537426 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
* *
28537454 CTGGTGACTCTGTCACATTATCTG
1 CTGGTGGCTCTGCCACATTATCTG
28537478 TTCTAGCAGC
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
26 2 0.03
27 50 0.72
28 17 0.25
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.37
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:28537476 original size:54 final size:54
Alignment explanation
Indices: 28537372--28537481 Score: 177
Period size: 54 Copynumber: 2.0 Consensus size: 54
28537362 AGGAAGCGTC
*
28537372 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGTCACATATATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGTCACATATATCTGTT
* *
28537426 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGTCACATATATCTGTT
28537480 CT
1 CT
28537482 AGCAGCTATG
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
54 33 0.63
55 19 0.37
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGTCACATATATCTGTT
Found at i:28538905 original size:628 final size:628
Alignment explanation
Indices: 28537709--28538964 Score: 2512
Period size: 628 Copynumber: 2.0 Consensus size: 628
28537699 ACCGATATAG
28537709 ACTATGGTTGGATTATTTTACACACTGAGTTTCCCCAAACTCACCCCTTTATTTTCATCCACACA
1 ACTATGGTTGGATTATTTTACACACTGAGTTTCCCCAAACTCACCCCTTTATTTTCATCCACACA
28537774 GGTAATCCCCAACCATAGTGGGCTTGGAGCCGTGAGGGATTTGGAGTGGCCATACGTTCTGCAAG
66 GGTAATCCCCAACCATAGTGGGCTTGGAGCCGTGAGGGATTTGGAGTGGCCATACGTTCTGCAAG
28537839 ATTAATTTTCTTCTGGTGAACTACACATCCTTTTTATTTACGTTTAAGGTTTTGGGTTCTTTAAT
131 ATTAATTTTCTTCTGGTGAACTACACATCCTTTTTATTTACGTTTAAGGTTTTGGGTTCTTTAAT
28537904 TGTAATAAGGCCGCTTAATTATTTTTATGGTTTTAATATGTTTTATTAATATAGGTATTACTTAT
196 TGTAATAAGGCCGCTTAATTATTTTTATGGTTTTAATATGTTTTATTAATATAGGTATTACTTAT
28537969 ATTTAACTGTCGAAATTGAATAGCTTTTAGGGCGCATTTTTTTAAAAAACAGTAATTGATTTCAA
261 ATTTAACTGTCGAAATTGAATAGCTTTTAGGGCGCATTTTTTTAAAAAACAGTAATTGATTTCAA
28538034 AAATACACGACAACAAGTAAAGCTTCTGTAATGAAAATATTTTCCAAAATTAATCACTTTTCCTA
326 AAATACACGACAACAAGTAAAGCTTCTGTAATGAAAATATTTTCCAAAATTAATCACTTTTCCTA
28538099 AAAAGGACTTAATCAAATTGGTTTCCTGGAAATATACATGACGTTAAGGTGTGGCAATGGTGGTG
391 AAAAGGACTTAATCAAATTGGTTTCCTGGAAATATACATGACGTTAAGGTGTGGCAATGGTGGTG
28538164 TGCATGTCTAGGATTGGATCCGAAGGGAGCTTGGTACTTAAGCAGTCCGATGGACTCACCTCCTC
456 TGCATGTCTAGGATTGGATCCGAAGGGAGCTTGGTACTTAAGCAGTCCGATGGACTCACCTCCTC
28538229 CTTTCTGATTTCCTACCTGGTGTTCAGCTTCTATTCACTTTAACCCGCATTAAAATTATCTTTTA
521 CTTTCTGATTTCCTACCTGGTGTTCAGCTTCTATTCACTTTAACCCGCATTAAAATTATCTTTTA
28538294 AAACACTAAGTAAGTTTTCTAGAACAACGACCTGAAATGTTTT
586 AAACACTAAGTAAGTTTTCTAGAACAACGACCTGAAATGTTTT
28538337 ACTATGGTTGGATTATTTTACACACTGAGTTTCCCCAAACTCACCCCTTTATTTTCATCCACACA
1 ACTATGGTTGGATTATTTTACACACTGAGTTTCCCCAAACTCACCCCTTTATTTTCATCCACACA
28538402 GGTAATCCCCAACCATAGTGGGCTTGGAGCCGTGAGGGATTTGGAGTGGCCATACGTTCTGCAAG
66 GGTAATCCCCAACCATAGTGGGCTTGGAGCCGTGAGGGATTTGGAGTGGCCATACGTTCTGCAAG
28538467 ATTAATTTTCTTCTGGTGAACTACACATCCTTTTTATTTACGTTTAAGGTTTTGGGTTCTTTAAT
131 ATTAATTTTCTTCTGGTGAACTACACATCCTTTTTATTTACGTTTAAGGTTTTGGGTTCTTTAAT
28538532 TGTAATAAGGCCGCTTAATTATTTTTATGGTTTTAATATGTTTTATTAATATAGGTATTACTTAT
196 TGTAATAAGGCCGCTTAATTATTTTTATGGTTTTAATATGTTTTATTAATATAGGTATTACTTAT
28538597 ATTTAACTGTCGAAATTGAATAGCTTTTAGGGCGCATTTTTTTAAAAAACAGTAATTGATTTCAA
261 ATTTAACTGTCGAAATTGAATAGCTTTTAGGGCGCATTTTTTTAAAAAACAGTAATTGATTTCAA
28538662 AAATACACGACAACAAGTAAAGCTTCTGTAATGAAAATATTTTCCAAAATTAATCACTTTTCCTA
326 AAATACACGACAACAAGTAAAGCTTCTGTAATGAAAATATTTTCCAAAATTAATCACTTTTCCTA
28538727 AAAAGGACTTAATCAAATTGGTTTCCTGGAAATATACATGACGTTAAGGTGTGGCAATGGTGGTG
391 AAAAGGACTTAATCAAATTGGTTTCCTGGAAATATACATGACGTTAAGGTGTGGCAATGGTGGTG
28538792 TGCATGTCTAGGATTGGATCCGAAGGGAGCTTGGTACTTAAGCAGTCCGATGGACTCACCTCCTC
456 TGCATGTCTAGGATTGGATCCGAAGGGAGCTTGGTACTTAAGCAGTCCGATGGACTCACCTCCTC
28538857 CTTTCTGATTTCCTACCTGGTGTTCAGCTTCTATTCACTTTAACCCGCATTAAAATTATCTTTTA
521 CTTTCTGATTTCCTACCTGGTGTTCAGCTTCTATTCACTTTAACCCGCATTAAAATTATCTTTTA
28538922 AAACACTAAGTAAGTTTTCTAGAACAACGACCTGAAATGTTTT
586 AAACACTAAGTAAGTTTTCTAGAACAACGACCTGAAATGTTTT
28538965 TGAACGCTTT
Statistics
Matches: 628, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
628 628 1.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (628 bp):
ACTATGGTTGGATTATTTTACACACTGAGTTTCCCCAAACTCACCCCTTTATTTTCATCCACACA
GGTAATCCCCAACCATAGTGGGCTTGGAGCCGTGAGGGATTTGGAGTGGCCATACGTTCTGCAAG
ATTAATTTTCTTCTGGTGAACTACACATCCTTTTTATTTACGTTTAAGGTTTTGGGTTCTTTAAT
TGTAATAAGGCCGCTTAATTATTTTTATGGTTTTAATATGTTTTATTAATATAGGTATTACTTAT
ATTTAACTGTCGAAATTGAATAGCTTTTAGGGCGCATTTTTTTAAAAAACAGTAATTGATTTCAA
AAATACACGACAACAAGTAAAGCTTCTGTAATGAAAATATTTTCCAAAATTAATCACTTTTCCTA
AAAAGGACTTAATCAAATTGGTTTCCTGGAAATATACATGACGTTAAGGTGTGGCAATGGTGGTG
TGCATGTCTAGGATTGGATCCGAAGGGAGCTTGGTACTTAAGCAGTCCGATGGACTCACCTCCTC
CTTTCTGATTTCCTACCTGGTGTTCAGCTTCTATTCACTTTAACCCGCATTAAAATTATCTTTTA
AAACACTAAGTAAGTTTTCTAGAACAACGACCTGAAATGTTTT
Found at i:28544048 original size:24 final size:24
Alignment explanation
Indices: 28544021--28544080 Score: 93
Period size: 25 Copynumber: 2.5 Consensus size: 24
28544011 GTAAGGAGGG
28544021 GATAAGGGAGAAGATTTAGGAGCT
1 GATAAGGGAGAAGATTTAGGAGCT
*
28544045 GATAAGGGGAGAAGTTTTAGGAGCT
1 GATAA-GGGAGAAGATTTAGGAGCT
*
28544070 GATTAGGGAGA
1 GATAAGGGAGA
28544081 GCAGTGTTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
24 11 0.33
25 22 0.67
ACGTcount: A:0.35, C:0.03, G:0.40, T:0.22
Consensus pattern (24 bp):
GATAAGGGAGAAGATTTAGGAGCT
Found at i:28545062 original size:27 final size:26
Alignment explanation
Indices: 28545021--28545159 Score: 152
Period size: 27 Copynumber: 5.2 Consensus size: 26
28545011 AGGAAGCATC
*
28545021 CTGGTGGCTGTGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
* *
28545048 CTAGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
* *
28545075 CTGGTGGCTCTACCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
*
28545102 CTGGTGGCTCTGCTACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
* * *
28545130 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGAT
28545156 CTGG
1 CTGG
28545160 CAGCTATGCT
Statistics
Matches: 97, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
26 7 0.07
27 74 0.76
28 16 0.16
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:28545109 original size:54 final size:55
Alignment explanation
Indices: 28545021--28545159 Score: 169
Period size: 54 Copynumber: 2.6 Consensus size: 55
28545011 AGGAAGCATC
* * *
28545021 CTGGTGGCTGTGCCACA-ATTATCTGATCTAGTGGCTCTGCCAC-ATATATCTGT-T
1 CTGGTGGCTCTGCCACATA-TATCTGTTCTGGTGGCTCTGCCACGAT-TATCTGTAT
* *
28545075 CTGGTGGCTCTACCACATATATCTGTTCTGGTGGCTCTGCTACGATTATCTGTAT
1 CTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACGATTATCTGTAT
* *
28545130 CTGGTGACTCTGTCACAT-TATCTGTTCTGG
1 CTGGTGGCTCTGCCACATATATCTGTTCTGG
28545160 CAGCTATGCT
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
54 55 0.74
55 19 0.26
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (55 bp):
CTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACGATTATCTGTAT
Found at i:28545181 original size:54 final size:54
Alignment explanation
Indices: 28545062--28545181 Score: 136
Period size: 54 Copynumber: 2.2 Consensus size: 54
28545052 TGGCTCTGCC
* ** *
28545062 ACATATATCTGTTCTGGTGGCTCTACCACATATATCTGTTCTGGTGGCTCTGCT
1 ACATATATCTGTTCTGGTGACTCTACCACATATATCTGTTCTGGCAGCTATGCT
**
28545116 ACGAT-TATCTGTATCTGGTGACTCTGTCACAT-TATCTGTTCTGGCAGCTATGCT
1 AC-ATATATCTGT-TCTGGTGACTCTACCACATATATCTGTTCTGGCAGCTATGCT
* *
28545170 GCATATTTCTGT
1 ACATATATCTGT
28545182 GGCGTGTAGC
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
53 2 0.04
54 35 0.64
55 18 0.33
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.40
Consensus pattern (54 bp):
ACATATATCTGTTCTGGTGACTCTACCACATATATCTGTTCTGGCAGCTATGCT
Found at i:28547269 original size:11 final size:10
Alignment explanation
Indices: 28547248--28547280 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 10
28547238 CCTGTAGTTG
28547248 AATTTTTCTA
1 AATTTTTCTA
28547258 AATTTTTCCTA
1 AATTTTT-CTA
28547269 AATTTTT-TA
1 AATTTTTCTA
28547278 AAT
1 AAT
28547281 GTTCCCAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.23
10 7 0.32
11 10 0.45
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (10 bp):
AATTTTTCTA
Found at i:28549894 original size:34 final size:34
Alignment explanation
Indices: 28549851--28549918 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
28549841 TAAACATATT
28549851 TACAAGCCATTTTAAAACAATTAATTCAAGTCAA
1 TACAAGCCATTTTAAAACAATTAATTCAAGTCAA
28549885 TACAAGCCATTTTAAAACAATTAATTCAAGTCAA
1 TACAAGCCATTTTAAAACAATTAATTCAAGTCAA
28549919 AACCGAGTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.47, C:0.18, G:0.06, T:0.29
Consensus pattern (34 bp):
TACAAGCCATTTTAAAACAATTAATTCAAGTCAA
Found at i:28551334 original size:49 final size:49
Alignment explanation
Indices: 28551236--28551334 Score: 112
Period size: 49 Copynumber: 2.0 Consensus size: 49
28551226 TATACCAGGC
* * * *
28551236 AACTCATAAGAGTCTATAACAGGAAGTTCACAAAGAACTTTTAATTAGGA
1 AACTCATAAGAGCCTAT-ACAGGAAGATCACAAAGAACATGTAATTAGGA
*
28551286 AACTCATGAAGAGCCTAT-CAGGAAGATCACAAAGAGCAATGTAA-TAGGA
1 AACTCAT-AAGAGCCTATACAGGAAGATCACAAAGAAC-ATGTAATTAGGA
28551335 CCTCCAATAG
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
49 22 0.52
50 11 0.26
51 9 0.21
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.21
Consensus pattern (49 bp):
AACTCATAAGAGCCTATACAGGAAGATCACAAAGAACATGTAATTAGGA
Found at i:28555360 original size:41 final size:41
Alignment explanation
Indices: 28555310--28555446 Score: 193
Period size: 41 Copynumber: 3.3 Consensus size: 41
28555300 TGTAAACAGT
* **
28555310 GGCACGTATGTGTAATTCAGGGGTACCAAAGTACAAATAGG
1 GGCACATATGTGTAATTCAGGGGTACTGAAGTACAAATAGG
** * *
28555351 GGCATGTATGTGTAATTTAGGGGTACTGAAGTACAAACAGG
1 GGCACATATGTGTAATTCAGGGGTACTGAAGTACAAATAGG
* *
28555392 GGCACAAATGTGCAATTCAGGGGTACTGAAGTACAAATAGG
1 GGCACATATGTGTAATTCAGGGGTACTGAAGTACAAATAGG
28555433 GGCACATATGTGTA
1 GGCACATATGTGTA
28555447 GTTTATAGAA
Statistics
Matches: 83, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 83 1.00
ACGTcount: A:0.34, C:0.13, G:0.30, T:0.23
Consensus pattern (41 bp):
GGCACATATGTGTAATTCAGGGGTACTGAAGTACAAATAGG
Found at i:28561139 original size:39 final size:40
Alignment explanation
Indices: 28561085--28561339 Score: 351
Period size: 39 Copynumber: 6.5 Consensus size: 40
28561075 AAACCAAGTA
* * * *
28561085 CCTTCGGAATTTAG-CCGGATATAGCT-ACTTGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
28561124 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
28561164 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
28561204 CCTTC-GGACTTATCCCGGATATAGTAACTC-CACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
28561242 CCTTCGGGACTTCGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
28561282 CCTTCGGG-CTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
28561321 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
28561340 TTATCATCCG
Statistics
Matches: 196, Mismatches: 14, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
38 14 0.07
39 91 0.46
40 91 0.46
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:28561162 original size:40 final size:40
Alignment explanation
Indices: 28561118--28561343 Score: 361
Period size: 39 Copynumber: 5.7 Consensus size: 40
28561108 GCTACTTGCT
28561118 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
28561158 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* *
28561198 CAAATGCCTTC-GGACTTATCCCGGATATAGTAACTC-CA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
28561236 CAAATGCCTTCGGGACTTCGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * *
28561276 CAAATGCCTTCGGG-CTTAGCCCGG-AATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
28561315 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
28561344 CATCCGAATA
Statistics
Matches: 171, Mismatches: 10, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
38 14 0.08
39 78 0.46
40 78 0.46
41 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:28574213 original size:28 final size:27
Alignment explanation
Indices: 28574151--28574302 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
28574141 TAAATTGTGC
* *
28574151 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAGTTGATTATGT
28574178 AGCACTAAGTGTGCGAGTATGATTATGT
1 AGCACTAAGTGTGCGAGT-TGATTATGT
*
28574206 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGATTATGT
28574233 AGCACTAAGTGTGCGAGTATGATTATGT
1 AGCACTAAGTGTGCGAGT-TGATTATGT
*
28574261 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGATTATGT
*
28574288 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28574303 GACTTAATAT
Statistics
Matches: 117, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
27 65 0.56
28 52 0.44
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGATTATGT
Found at i:28574216 original size:55 final size:55
Alignment explanation
Indices: 28574151--28574302 Score: 268
Period size: 55 Copynumber: 2.8 Consensus size: 55
28574141 TAAATTGTGC
*
28574151 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTATGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTATGATTATGT
28574206 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTATGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTATGATTATGT
* * *
28574261 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
28574303 GACTTAATAT
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 93 1.00
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.30
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTATGATTATGT
Found at i:28579235 original size:31 final size:31
Alignment explanation
Indices: 28579200--28579261 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
28579190 TTACGGTTCG
28579200 ATTGATTTTTAGTAAGGGAGTTTCATTTGTT
1 ATTGATTTTTAGTAAGGGAGTTTCATTTGTT
28579231 ATTGATTTTTAGTAAGGGAGTTTCATTTGTT
1 ATTGATTTTTAGTAAGGGAGTTTCATTTGTT
28579262 CATCGATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.03, G:0.23, T:0.52
Consensus pattern (31 bp):
ATTGATTTTTAGTAAGGGAGTTTCATTTGTT
Found at i:28580973 original size:15 final size:15
Alignment explanation
Indices: 28580953--28580984 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
28580943 CAGCACATGA
28580953 AATGATTTCCAAACT
1 AATGATTTCCAAACT
*
28580968 AATGATTTCCAAGCT
1 AATGATTTCCAAACT
28580983 AA
1 AA
28580985 GTTTGTAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (15 bp):
AATGATTTCCAAACT
Found at i:28593995 original size:16 final size:16
Alignment explanation
Indices: 28593974--28594007 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
28593964 ATTAAATATG
28593974 TAAAAATGAATTGAGT
1 TAAAAATGAATTGAGT
28593990 TAAAAATGAATTGAGT
1 TAAAAATGAATTGAGT
28594006 TA
1 TA
28594008 GCCAAGTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.18, T:0.32
Consensus pattern (16 bp):
TAAAAATGAATTGAGT
Found at i:28597232 original size:19 final size:19
Alignment explanation
Indices: 28597208--28597245 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
28597198 TTGCAGTAAG
*
28597208 GATTTAGCCCGGACGGGTA
1 GATTTAGCCCGAACGGGTA
28597227 GATTTAGCCCGAACGGGTA
1 GATTTAGCCCGAACGGGTA
28597246 ATCTGTGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.21, G:0.34, T:0.21
Consensus pattern (19 bp):
GATTTAGCCCGAACGGGTA
Found at i:28607099 original size:56 final size:56
Alignment explanation
Indices: 28607032--28607263 Score: 371
Period size: 56 Copynumber: 4.1 Consensus size: 56
28607022 TATTAGTTTA
* *
28607032 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTGATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
28607088 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
* * *
28607144 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACA-ATTTC-TTA-TTAGTTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACAT-G-TT
28607199 ATTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 -TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
28607256 TTGCCCAT
1 TTGCCCAT
28607264 CATCCCTTGT
Statistics
Matches: 162, Mismatches: 8, Indels: 12
0.89 0.04 0.07
Matches are distributed among these distances:
53 1 0.01
54 3 0.02
55 6 0.04
56 142 0.88
57 6 0.04
58 3 0.02
59 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.09, T:0.47
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:28614826 original size:40 final size:40
Alignment explanation
Indices: 28614771--28614868 Score: 137
Period size: 40 Copynumber: 2.5 Consensus size: 40
28614761 CGGATGATAA
*
28614771 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAACTA-CTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGAGCG-ACTAGCTATAT
*
28614811 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAGTAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGAGCGACTAGCTATAT
* *
28614851 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
28614869 TACTTGGTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
39 17 0.32
40 36 0.68
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.22
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGAGCGACTAGCTATAT
Found at i:28616902 original size:32 final size:32
Alignment explanation
Indices: 28616861--28616925 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
28616851 CTTGTGTGAG
28616861 ATTCATGAACTCACGCCTACGAGCATCCACAT
1 ATTCATGAACTCACGCCTACGAGCATCCACAT
* *
28616893 ATTCATGAACTCGCGCCTACGAGCATCTACAT
1 ATTCATGAACTCACGCCTACGAGCATCCACAT
28616925 A
1 A
28616926 ACTAACTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.31, C:0.32, G:0.14, T:0.23
Consensus pattern (32 bp):
ATTCATGAACTCACGCCTACGAGCATCCACAT
Found at i:28617405 original size:15 final size:15
Alignment explanation
Indices: 28617385--28617426 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
28617375 CTATGGACTC
28617385 TACCACGGCCACGAG
1 TACCACGGCCACGAG
28617400 TACCACGGCCACGAG
1 TACCACGGCCACGAG
*
28617415 TACCACGTCCAC
1 TACCACGGCCAC
28617427 ATGTTCCATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.26, C:0.43, G:0.21, T:0.10
Consensus pattern (15 bp):
TACCACGGCCACGAG
Found at i:28622092 original size:48 final size:48
Alignment explanation
Indices: 28621854--28622092 Score: 325
Period size: 48 Copynumber: 5.0 Consensus size: 48
28621844 ATGACATTAG
* *
28621854 GAGTTACATTGATTTGGCTTCGGGCCATGATATTAGCACTTCGAGTGC
1 GAGTTACATTGATTTGGCTTCGGGCCATGATATTGGCACTTCGGGTGC
* * * *
28621902 GAGTTACATTGATTTGGCTTTGGGCCATGATATTAGCACTTCGAGTGT
1 GAGTTACATTGATTTGGCTTCGGGCCATGATATTGGCACTTCGGGTGC
** *
28621950 GAGTTATTTTGATTTGGCTTCGGGCCATGATGTTGGCACTTCGGGTGC
1 GAGTTACATTGATTTGGCTTCGGGCCATGATATTGGCACTTCGGGTGC
* * *
28621998 GAGTTATATTAATTTGGCTTCGGGCCATGATTTTGGCACTTCGGGTGC
1 GAGTTACATTGATTTGGCTTCGGGCCATGATATTGGCACTTCGGGTGC
** * * *
28622046 GAAATACATTGAGTTGGCTTCGGGCCATGATATTGGAACTTAGGGTG
1 GAGTTACATTGATTTGGCTTCGGGCCATGATATTGGCACTTCGGGTG
28622093 AAAGACTCCT
Statistics
Matches: 171, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 171 1.00
ACGTcount: A:0.19, C:0.16, G:0.30, T:0.35
Consensus pattern (48 bp):
GAGTTACATTGATTTGGCTTCGGGCCATGATATTGGCACTTCGGGTGC
Found at i:28629481 original size:34 final size:34
Alignment explanation
Indices: 28629443--28629518 Score: 143
Period size: 34 Copynumber: 2.2 Consensus size: 34
28629433 AGTTACAGTC
28629443 CAGTATCAGTGTGGGCCTTAGCCCATTACAATAA
1 CAGTATCAGTGTGGGCCTTAGCCCATTACAATAA
*
28629477 CAGTATCAGTGTGGGCTTTAGCCCATTACAATAA
1 CAGTATCAGTGTGGGCCTTAGCCCATTACAATAA
28629511 CAGTATCA
1 CAGTATCA
28629519 AAAAATGCAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (34 bp):
CAGTATCAGTGTGGGCCTTAGCCCATTACAATAA
Found at i:28636878 original size:40 final size:40
Alignment explanation
Indices: 28636637--28636864 Score: 406
Period size: 40 Copynumber: 5.7 Consensus size: 40
28636627 TATTTGGATG
* *
28636637 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
28636677 A-ATTCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
28636716 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
28636756 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
28636796 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
28636836 ATAACCGGGCTAAGTCCCGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
28636865 AGCAAGTAGC
Statistics
Matches: 181, Mismatches: 4, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
39 35 0.19
40 146 0.81
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:28636878 original size:120 final size:119
Alignment explanation
Indices: 28636637--28636897 Score: 402
Period size: 119 Copynumber: 2.2 Consensus size: 119
28636627 TATTTGGATG
* *
28636637 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCGAAGGCAT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGTCCGAAGGCAT
* *
28636702 TTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
66 TTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAGTTACT
*
28636756 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTAAGTCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-ACCGGGCTAAGT-CCGAAGGC
28636820 ATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAG-TAGCT
64 ATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAGTTA-CT
* * *
28636876 ATATCC-GGCTAAATTCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGG
28636898 TACTTGGTTT
Statistics
Matches: 131, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
118 2 0.02
119 65 0.50
120 64 0.49
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (119 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGTCCGAAGGCAT
TTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTGAGCAAGTTACT
Found at i:28640921 original size:40 final size:40
Alignment explanation
Indices: 28640821--28641085 Score: 286
Period size: 40 Copynumber: 6.7 Consensus size: 40
28640811 GCTCCTCGTT
* * * *
28640821 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* **
28640861 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
28640900 CGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
28640940 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
28640980 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
28641020 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
28641061 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
28641086 CAGCATTCAA
Statistics
Matches: 197, Mismatches: 22, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
39 39 0.20
40 143 0.73
41 15 0.08
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:28641045 original size:80 final size:80
Alignment explanation
Indices: 28640788--28641085 Score: 263
Period size: 80 Copynumber: 3.7 Consensus size: 80
28640778 AAATCACGTA
* ** * * *
28640788 CCTTCGGGATTTAA-CCGGATATAGCTC-CTCGTTCAAATGCCTTCGGGACATAGCCCGG-TTTT
1 CCTTCGGGACTTAACCCGGATATAG-TCACTCGCACAAA-GCCTTCGGGACTTAACCCGGAATTT
* *
28640850 AGTAACTCACAC-AATG
64 AATAACTCGCACAAATG
* * * *
28640866 CCTTCGGGACATAACCCGGATTTA-ACAACTCGCACGAATGCCTTCGGGACTTAACCCGG-ATTT
1 CCTTCGGGACTTAACCCGGATATAGTC-ACTCGCAC-AAAGCCTTCGGGACTTAACCCGGAATTT
*
28640929 AATAACTCGCACGAATG
64 AATAACTCGCACAAATG
* *
28640946 CCTTCGGGACTTAACCCGGATTTAGT-ATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGAATTT
1 CCTTCGGGACTTAACCCGGATATAGTCA-CTCGCACAAA-GCCTTCGGGACTTAACCCGGAATTT
* *
28641010 -GTATCTCGCACAAATG
64 AATAACTCGCACAAATG
** * * *
28641026 CCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 CCTTCGGGA-CTTAACCCGGATATAGTCAC-TCGCACAAAGCCTTCGGGACTTAACCCGGA
28641086 CAGCATTCAA
Statistics
Matches: 182, Mismatches: 26, Indels: 22
0.79 0.11 0.10
Matches are distributed among these distances:
77 1 0.01
78 12 0.07
79 50 0.27
80 106 0.58
81 13 0.07
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (80 bp):
CCTTCGGGACTTAACCCGGATATAGTCACTCGCACAAAGCCTTCGGGACTTAACCCGGAATTTAA
TAACTCGCACAAATG
Found at i:28641094 original size:41 final size:41
Alignment explanation
Indices: 28641017--28641094 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
28641007 TTTGTATCTC
* * *
28641017 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
28641058 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
28641095 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:28648871 original size:40 final size:40
Alignment explanation
Indices: 28648771--28649035 Score: 286
Period size: 40 Copynumber: 6.7 Consensus size: 40
28648761 GCTCCTCGTT
* * * *
28648771 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* **
28648811 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
28648850 CGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
28648890 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
28648930 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
28648970 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
28649011 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
28649036 CAGCATTCAA
Statistics
Matches: 197, Mismatches: 22, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
39 39 0.20
40 143 0.73
41 15 0.08
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:28648995 original size:80 final size:80
Alignment explanation
Indices: 28648738--28649035 Score: 263
Period size: 80 Copynumber: 3.7 Consensus size: 80
28648728 AAATCACGTA
* ** * * *
28648738 CCTTCGGGATTTAA-CCGGATATAGCTC-CTCGTTCAAATGCCTTCGGGACATAGCCCGG-TTTT
1 CCTTCGGGACTTAACCCGGATATAG-TCACTCGCACAAA-GCCTTCGGGACTTAACCCGGAATTT
* *
28648800 AGTAACTCACAC-AATG
64 AATAACTCGCACAAATG
* * * *
28648816 CCTTCGGGACATAACCCGGATTTA-ACAACTCGCACGAATGCCTTCGGGACTTAACCCGG-ATTT
1 CCTTCGGGACTTAACCCGGATATAGTC-ACTCGCAC-AAAGCCTTCGGGACTTAACCCGGAATTT
*
28648879 AATAACTCGCACGAATG
64 AATAACTCGCACAAATG
* *
28648896 CCTTCGGGACTTAACCCGGATTTAGT-ATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGAATTT
1 CCTTCGGGACTTAACCCGGATATAGTCA-CTCGCACAAA-GCCTTCGGGACTTAACCCGGAATTT
* *
28648960 -GTATCTCGCACAAATG
64 AATAACTCGCACAAATG
** * * *
28648976 CCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 CCTTCGGGA-CTTAACCCGGATATAGTCAC-TCGCACAAAGCCTTCGGGACTTAACCCGGA
28649036 CAGCATTCAA
Statistics
Matches: 182, Mismatches: 26, Indels: 22
0.79 0.11 0.10
Matches are distributed among these distances:
77 1 0.01
78 12 0.07
79 50 0.27
80 106 0.58
81 13 0.07
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (80 bp):
CCTTCGGGACTTAACCCGGATATAGTCACTCGCACAAAGCCTTCGGGACTTAACCCGGAATTTAA
TAACTCGCACAAATG
Found at i:28649044 original size:41 final size:41
Alignment explanation
Indices: 28648967--28649044 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
28648957 TTTGTATCTC
* * *
28648967 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
28649008 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
28649045 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:28653315 original size:23 final size:23
Alignment explanation
Indices: 28653289--28653336 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
28653279 AGATGAGAAT
28653289 GTGTATGAGATTAGTACGAGATG
1 GTGTATGAGATTAGTACGAGATG
28653312 GTGTATGAGATTAGTACGAGATG
1 GTGTATGAGATTAGTACGAGATG
28653335 GT
1 GT
28653337 ATAGTAATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.31
Consensus pattern (23 bp):
GTGTATGAGATTAGTACGAGATG
Found at i:28658474 original size:44 final size:43
Alignment explanation
Indices: 28658424--28658582 Score: 207
Period size: 43 Copynumber: 3.7 Consensus size: 43
28658414 TATGTGTTAT
*
28658424 CGTGTAAGACCATGTCTGGGACTTTGGCATCG-ACTTATGATTTA
1 CGTGTAAGACCATGTCTGGGACATTGGCATCGTA-TT-TGATTTA
* *
28658468 CGTGTAAGACTACGTCTGGGACATTGGCATCGTATTTGATTT-
1 CGTGTAAGACCATGTCTGGGACATTGGCATCGTATTTGATTTA
* * *
28658510 CGTGTAAGACCCTGTCTGGGATAGTGGCATCGGTATTTGA-TTA
1 CGTGTAAGACCATGTCTGGGACATTGGCATC-GTATTTGATTTA
*
28658553 CATGTAAGACCATGTCTGGGACATTGGCAT
1 CGTGTAAGACCATGTCTGGGACATTGGCAT
28658583 TGTACGAGCT
Statistics
Matches: 100, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
42 28 0.28
43 40 0.40
44 31 0.31
45 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.33
Consensus pattern (43 bp):
CGTGTAAGACCATGTCTGGGACATTGGCATCGTATTTGATTTA
Found at i:28661392 original size:63 final size:63
Alignment explanation
Indices: 28661293--28661420 Score: 247
Period size: 63 Copynumber: 2.0 Consensus size: 63
28661283 CAAGAGATTA
*
28661293 TGCAAAATCCGAGGCCAAGTGGCAATGCATCTCGTGGTAGACCTCCCAGAAATATGGATATTG
1 TGCAAAATCCGAGGCCAAGTGGCAATGCATCTCGTGGTAGACCTCCCAGAAATATGGATAGTG
28661356 TGCAAAATCCGAGGCCAAGTGGCAATGCATCTCGTGGTAGACCTCCCAGAAATATGGATAGTG
1 TGCAAAATCCGAGGCCAAGTGGCAATGCATCTCGTGGTAGACCTCCCAGAAATATGGATAGTG
28661419 TG
1 TG
28661421 AGTGGCAGTC
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.22
Consensus pattern (63 bp):
TGCAAAATCCGAGGCCAAGTGGCAATGCATCTCGTGGTAGACCTCCCAGAAATATGGATAGTG
Found at i:28664176 original size:39 final size:40
Alignment explanation
Indices: 28664122--28664207 Score: 131
Period size: 40 Copynumber: 2.2 Consensus size: 40
28664112 AACCCAAGTA
* *
28664122 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
28664161 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
28664201 CCTTCGG
1 CCTTCGG
28664208 ATCTTTGTCC
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
39 13 0.30
40 29 0.67
41 1 0.02
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:28665605 original size:13 final size:13
Alignment explanation
Indices: 28665587--28665612 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28665577 TTATTTATTT
28665587 TTAACATAAAATA
1 TTAACATAAAATA
28665600 TTAACATAAAATA
1 TTAACATAAAATA
28665613 ATTACAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
TTAACATAAAATA
Found at i:28666047 original size:26 final size:27
Alignment explanation
Indices: 28666018--28666141 Score: 103
Period size: 27 Copynumber: 4.6 Consensus size: 27
28666008 TTAGTTTACC
*
28666018 AAATTACTGAAATACCCCCAG-TTGCA
1 AAATTACTCAAATACCCCCAGTTTGCA
* **
28666044 AAA-TAATCAAAGTACCCCCAGTTTATA
1 AAATTACTCAAA-TACCCCCAGTTTGCA
* * * *
28666071 AAATTACCCAAATATCCTC-GATTTGTA
1 AAATTACTCAAATACCCCCAG-TTTGCA
*
28666098 AAATTAC-CGAAATACCCTCAGTTTGCA
1 AAATTACTC-AAATACCCCCAGTTTGCA
*
28666125 AAATTACTAAAATACCC
1 AAATTACTCAAATACCC
28666142 TCGACATGTA
Statistics
Matches: 79, Mismatches: 12, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
25 6 0.08
26 14 0.18
27 52 0.66
28 7 0.09
ACGTcount: A:0.41, C:0.24, G:0.08, T:0.27
Consensus pattern (27 bp):
AAATTACTCAAATACCCCCAGTTTGCA
Found at i:28666099 original size:27 final size:27
Alignment explanation
Indices: 28666069--28666167 Score: 101
Period size: 27 Copynumber: 3.7 Consensus size: 27
28666059 CCCCAGTTTA
* *
28666069 TAAAATTACCCAAATATCCTCGATTTG
1 TAAAATTACCAAAATACCCTCGATTTG
*
28666096 TAAAATTACCGAAATACCCTC-AGTTTG
1 TAAAATTACCAAAATACCCTCGA-TTTG
* * **
28666123 CAAAATTACTAAAATACCCTCGACATG
1 TAAAATTACCAAAATACCCTCGATTTG
* *
28666150 TAAAATTATCAAAGTACC
1 TAAAATTACCAAAATACC
28666168 AGCAAATTAC
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
26 1 0.02
27 57 0.97
28 1 0.02
ACGTcount: A:0.41, C:0.22, G:0.08, T:0.28
Consensus pattern (27 bp):
TAAAATTACCAAAATACCCTCGATTTG
Found at i:28666204 original size:27 final size:27
Alignment explanation
Indices: 28666174--28666520 Score: 435
Period size: 27 Copynumber: 12.9 Consensus size: 27
28666164 TACCAGCAAA
* *
28666174 TTACAAAATTACTATTTTACCCTCGAT
1 TTACAGAATTACTGTTTTACCCTCGAT
*
28666201 TTACAGAATTACCGTTTTACCCTCGAT
1 TTACAGAATTACTGTTTTACCCTCGAT
*
28666228 TTACAGAATTACTGTTTTACACTCGAT
1 TTACAGAATTACTGTTTTACCCTCGAT
* * *
28666255 TTATAGAATTACGGTTTTACCCTTGAT
1 TTACAGAATTACTGTTTTACCCTCGAT
*
28666282 TTACAGAATTACTGTTTTACACTCGAT
1 TTACAGAATTACTGTTTTACCCTCGAT
*
28666309 TTACAGAATTA-TCGTTTTACCCTTGAT
1 TTACAGAATTACT-GTTTTACCCTCGAT
*
28666336 TTACAGAATTACCGTTTTACCCTCGAT
1 TTACAGAATTACTGTTTTACCCTCGAT
* *
28666363 TTATAGAATTACTGTTTTACCCTCAAT
1 TTACAGAATTACTGTTTTACCCTCGAT
* * *
28666390 TTACAAAATTACTATTTTACCATCGAT
1 TTACAGAATTACTGTTTTACCCTCGAT
* ** *
28666417 TTAAAGAATTACCATTTTAACCTCGAT
1 TTACAGAATTACTGTTTTACCCTCGAT
* *
28666444 TTACAAAATTACTATTTTACCCTCGAT
1 TTACAGAATTACTGTTTTACCCTCGAT
* *
28666471 TTACAAAATTACCGTTTTACCCTCGAT
1 TTACAGAATTACTGTTTTACCCTCGAT
* * **
28666498 TTATAAAATTACCATTTTACCCT
1 TTACAGAATTACTGTTTTACCCT
28666521 TAGGGTGTTA
Statistics
Matches: 280, Mismatches: 38, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
26 1 0.00
27 279 1.00
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.41
Consensus pattern (27 bp):
TTACAGAATTACTGTTTTACCCTCGAT
Found at i:28666799 original size:27 final size:26
Alignment explanation
Indices: 28666755--28666806 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
28666745 CTCGCTGCAA
*
28666755 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
28666782 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
28666807 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:28671183 original size:29 final size:29
Alignment explanation
Indices: 28671148--28671203 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
28671138 TGAGACATCT
*
28671148 GAGAAAGTATCGACAAAGTTTTGACATTC
1 GAGAAAGTATCGACAAAGTTCTGACATTC
28671177 GAGAAAGTATCGACAAAGTTCTGACAT
1 GAGAAAGTATCGACAAAGTTCTGACAT
28671204 CCGTAAAGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.25
Consensus pattern (29 bp):
GAGAAAGTATCGACAAAGTTCTGACATTC
Found at i:28671434 original size:43 final size:43
Alignment explanation
Indices: 28671300--28671435 Score: 109
Period size: 43 Copynumber: 3.2 Consensus size: 43
28671290 ATCTGAGACA
* * * *
28671300 TTGGCATCGACT-TATGATTTACATGTAAGACAACGT-TTACGACG
1 TTGGCATCGA-TATTTGA-TTACATGTAAGACCATGTCTTGC-ACG
* * * * * * *
28671344 TTGACATCG-TATTTGATTTCGTGTACGACCCTGTCTGGGACAG
1 TTGGCATCGATATTTGATTACATGTAAGACCATGTCTTGCAC-G
28671387 -TGGCATCGATATTTGATTACATGTAAGACCATGTCTTGCACG
1 TTGGCATCGATATTTGATTACATGTAAGACCATGTCTTGCACG
28671429 TTGGCAT
1 TTGGCAT
28671436 TGTACAAGCT
Statistics
Matches: 69, Mismatches: 18, Indels: 11
0.70 0.18 0.11
Matches are distributed among these distances:
42 23 0.33
43 38 0.55
44 8 0.12
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (43 bp):
TTGGCATCGATATTTGATTACATGTAAGACCATGTCTTGCACG
Found at i:28676961 original size:43 final size:43
Alignment explanation
Indices: 28676773--28676953 Score: 233
Period size: 43 Copynumber: 4.2 Consensus size: 43
28676763 TGATTATGTA
* * *
28676773 TAAGACTATGCCTGGGACATTGGCATCATATTGCGATTACATG
1 TAAGACCATGTCTGGGACATTGGCATCATATTGTGATTACATG
*
28676816 TAAGACCATGTCTGGGACATTGGCATCATATTGTGATTACGTG
1 TAAGACCATGTCTGGGACATTGGCATCATATTGTGATTACATG
* * * * *
28676859 TAAGACAATGTCTGGGACATTGGCATCGTCA-TATGATTTCGTG
1 TAAGACCATGTCTGGGACATTGGCATCAT-ATTGTGATTACATG
28676902 TAAGACCATGTCTGGGACATTGGCATCGATA-TGTGA-TACCATG
1 TAAGACCATGTCTGGGACATTGGCATC-ATATTGTGATTA-CATG
28676945 TAAGACCAT
1 TAAGACCAT
28676954 ATTTGGGATA
Statistics
Matches: 122, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
42 1 0.01
43 119 0.98
44 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (43 bp):
TAAGACCATGTCTGGGACATTGGCATCATATTGTGATTACATG
Found at i:28685506 original size:15 final size:16
Alignment explanation
Indices: 28685486--28685515 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28685476 TCAAACCCAA
28685486 ATCATATA-TCATCAT
1 ATCATATATTCATCAT
28685501 ATCATATATTCATCA
1 ATCATATATTCATCA
28685516 ACCTATTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (16 bp):
ATCATATATTCATCAT
Found at i:28686347 original size:44 final size:43
Alignment explanation
Indices: 28686245--28686362 Score: 123
Period size: 44 Copynumber: 2.7 Consensus size: 43
28686235 AAAGCTCGTA
* * **
28686245 CAATGCCAATGTCCCAGACGTGGTCTTACATGTAATCAAATAT
1 CAATGCCAACGTCCCAGACATGGTCTTACACATAATCAAATAT
*
28686288 CAATGCC-ACTGTCCCAGACATGGTCTTACACATAAATCATAA-GT
1 CAATGCCAAC-GTCCCAGACATGGTCTTACACAT-AATCA-AATAT
* * *
28686332 CAATGCCAACATCCCATACATGATCTTACAC
1 CAATGCCAACGTCCCAGACATGGTCTTACAC
28686363 GAAAACACAT
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
42 1 0.02
43 27 0.43
44 31 0.49
45 4 0.06
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.25
Consensus pattern (43 bp):
CAATGCCAACGTCCCAGACATGGTCTTACACATAATCAAATAT
Found at i:28699791 original size:20 final size:21
Alignment explanation
Indices: 28699766--28699804 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28699756 TTCTGTGGAC
*
28699766 TTGGGCC-GTTATGGGCCATG
1 TTGGGCCGGCTATGGGCCATG
28699786 TTGGGCCGGCTATGGGCCA
1 TTGGGCCGGCTATGGGCCA
28699805 AATGGGCTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.10, C:0.23, G:0.41, T:0.26
Consensus pattern (21 bp):
TTGGGCCGGCTATGGGCCATG
Found at i:28701342 original size:48 final size:47
Alignment explanation
Indices: 28701276--28701608 Score: 292
Period size: 48 Copynumber: 6.9 Consensus size: 47
28701266 ATAATAGGGT
* * *
28701276 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCAGCATTTA
1 TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATC-GCATCTA
* * *
28701324 TATGAGAGCTAGTGTAAGACCATGTCTAGG-ACATGGCATCGACCTCGA
1 TATGAGAGCTAGTGTAAGACCATGT-TTGGAACATGGCATCG-CATCTA
* * * *
28701372 CATGTGGGCTAGTGTCAGACCATGTTTGGAACATGGCATCG-ATACAGATA
1 TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGCAT-C---TA
* * *
28701422 TATGAGAGCCAGTGTAAAACCATGTTTGGAACATGGCATCGACATTTA
1 TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCG-CATCTA
* * * *
28701470 TATGAGAGCTAGTGTAAGACCATGTTTGGGACATGGCATTGGCCTCGA
1 TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCA-TCGCATCTA
* * * * *
28701518 CATGTGGGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGAACCGATA
1 TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATC-GCATC--TA
* ** * * *
28701568 TATGAGAACCGGTATAAGACCATGTCTGGGACATGGCATCG
1 TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCG
28701609 GTATCTTACC
Statistics
Matches: 227, Mismatches: 45, Indels: 25
0.76 0.15 0.08
Matches are distributed among these distances:
46 1 0.00
47 6 0.03
48 144 0.63
49 6 0.03
50 68 0.30
52 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.26
Consensus pattern (47 bp):
TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGCATCTA
Found at i:28701545 original size:146 final size:147
Alignment explanation
Indices: 28701276--28701608 Score: 519
Period size: 146 Copynumber: 2.3 Consensus size: 147
28701266 ATAATAGGGT
*
28701276 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATC-AGCATTTATATGAGAGCTAGTGTA
1 TATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGAGCATTTATATGAGAGCTAGTGTA
*
28701340 AGACCATGTCTAGGACATGGCATCGACCTCGACATGTGGGCTAGTGTCAGACCATGTTTGGAACA
66 AGACCATGTCTAGGACATGGCATCGACCTCGACATGTGGGCTAGTGTAAGACCATGTTTGGAACA
28701405 TGGCATC-GATACAGATA
131 TGGCATCGGA-ACAGATA
*
28701422 TATGAGAGCCAGTGTAAAACCATGTTTGGAACATGGCATCGA-CATTTATATGAGAGCTAGTGTA
1 TATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGAGCATTTATATGAGAGCTAGTGTA
* * * *
28701486 AGACCATGTTTGGGACATGGCATTGGCCTCGACATGTGGGCTAGTGTAAGACCATGTTTGGAACA
66 AGACCATGTCTAGGACATGGCATCGACCTCGACATGTGGGCTAGTGTAAGACCATGTTTGGAACA
*
28701551 TGGCATCGGAACCGATA
131 TGGCATCGGAACAGATA
* * * * *
28701568 TATGAGAACCGGTATAAGACCATGTCTGGGACATGGCATCG
1 TATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCG
28701609 GTATCTTACC
Statistics
Matches: 171, Mismatches: 14, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
146 168 0.98
147 3 0.02
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.26
Consensus pattern (147 bp):
TATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGAGCATTTATATGAGAGCTAGTGTA
AGACCATGTCTAGGACATGGCATCGACCTCGACATGTGGGCTAGTGTAAGACCATGTTTGGAACA
TGGCATCGGAACAGATA
Found at i:28701570 original size:98 final size:97
Alignment explanation
Indices: 28701276--28701606 Score: 296
Period size: 98 Copynumber: 3.4 Consensus size: 97
28701266 ATAATAGGGT
* * ** * *
28701276 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCAGCATTTATATGAGAGCTAGTGTAA
1 TATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATTAGCATCGATATGTGGGCTAGTGTAA
* * *
28701341 GACCATGTCTAGG-ACATGGCATCGACCTCGACA
66 GACCATGT-TTGGAACATGGCATCGAAC-CGATA
* * * * * *
28701374 TGTG-G-GCTAGTGTCAGACCATGTTTGGAACATGGCA-TCG-ATACAGATATATGAGAGCCAGT
1 TATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATTAGCAT-C-GATATGTG-G-GCTAGT
* ***
28701435 GTAAAACCATGTTTGGAACATGGCATCG-ACATTTA
62 GTAAGACCATGTTTGGAACATGGCATCGAACCGATA
* * * * *
28701470 TATGAGAGCTAGTGTAAGACCATGTTTGGGACATGGCATTGGCCTCGACATGTGGGCTAGTGTAA
1 TATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATTAGCATCGATATGTGGGCTAGTGTAA
28701535 GACCATGTTTGGAACATGGCATCGGAACCGATA
66 GACCATGTTTGGAACATGGCATC-GAACCGATA
* * * * *
28701568 TATGAGAACCGGTATAAGACCATGTCTGGGACATGGCAT
1 TATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCAT
28701607 CGGTATCTTA
Statistics
Matches: 187, Mismatches: 35, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
94 2 0.01
95 1 0.01
96 69 0.37
97 8 0.04
98 103 0.55
99 3 0.02
100 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (97 bp):
TATGAGAGCCAGTGTAAGACCATGTTTGGAACATGGCATTAGCATCGATATGTGGGCTAGTGTAA
GACCATGTTTGGAACATGGCATCGAACCGATA
Found at i:28703837 original size:22 final size:21
Alignment explanation
Indices: 28703812--28703875 Score: 57
Period size: 22 Copynumber: 3.2 Consensus size: 21
28703802 CATATACAGC
28703812 CATACTTCAACATCACAATACT
1 CATAC-TCAACATCACAATACT
* *
28703834 CATA-T-ACCA-C-CAAT-CA
1 CATACTCAACATCACAATACT
28703850 CATACGTCAACATCACAATACT
1 CATAC-TCAACATCACAATACT
28703872 CATA
1 CATA
28703876 TACCACCAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
16 5 0.16
17 4 0.12
18 2 0.06
19 6 0.19
20 2 0.06
21 4 0.12
22 9 0.28
ACGTcount: A:0.42, C:0.33, G:0.02, T:0.23
Consensus pattern (21 bp):
CATACTCAACATCACAATACT
Found at i:28703863 original size:38 final size:38
Alignment explanation
Indices: 28703812--28703892 Score: 153
Period size: 38 Copynumber: 2.1 Consensus size: 38
28703802 CATATACAGC
*
28703812 CATACTTCAACATCACAATACTCATATACCACCAATCA
1 CATACGTCAACATCACAATACTCATATACCACCAATCA
28703850 CATACGTCAACATCACAATACTCATATACCACCAATCA
1 CATACGTCAACATCACAATACTCATATACCACCAATCA
28703888 CATAC
1 CATAC
28703893 TTCATCTTAC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.42, C:0.35, G:0.01, T:0.22
Consensus pattern (38 bp):
CATACGTCAACATCACAATACTCATATACCACCAATCA
Found at i:28704925 original size:18 final size:18
Alignment explanation
Indices: 28704870--28704925 Score: 85
Period size: 18 Copynumber: 3.1 Consensus size: 18
28704860 GGATGTTACA
28704870 CTATGTTATTATGCGAAC
1 CTATGTTATTATGCGAAC
* *
28704888 CCATGTTATTATACGAAC
1 CTATGTTATTATGCGAAC
*
28704906 CTATGTTATTGTGCGAAC
1 CTATGTTATTATGCGAAC
28704924 CT
1 CT
28704926 TAATATTAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.38
Consensus pattern (18 bp):
CTATGTTATTATGCGAAC
Found at i:28710195 original size:13 final size:13
Alignment explanation
Indices: 28710177--28710202 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28710167 TGAGTTGGCA
28710177 TTGATATGTGATT
1 TTGATATGTGATT
28710190 TTGATATGTGATT
1 TTGATATGTGATT
28710203 ACGTGTAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (13 bp):
TTGATATGTGATT
Found at i:28710252 original size:43 final size:43
Alignment explanation
Indices: 28710190--28710411 Score: 315
Period size: 43 Copynumber: 5.2 Consensus size: 43
28710180 ATATGTGATT
28710190 TTGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCA
1 TTGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCA
* *
28710233 TTGATATGTGATTATGTGTAAGACCATGTCTGGGACGTTGGCA
1 TTGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCA
*
28710276 TTGATATGTGATTACGTGTAAGACCACGTCTGGGACATTGGCA
1 TTGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCA
* *
28710319 TCGATATGTGATTACGTGTAAGACC-CTGTCTGGGACAG-TGGTA
1 TTGATATGTGATTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCA
* * ** *
28710362 TCGATATGTGATTACATGTAAGACCATATCTGGGACATTGGCA
1 TTGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCA
28710405 TTG-TATG
1 TTGATATG
28710412 ATATATGCGA
Statistics
Matches: 161, Mismatches: 14, Indels: 9
0.88 0.08 0.05
Matches are distributed among these distances:
42 5 0.03
43 156 0.97
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.32
Consensus pattern (43 bp):
TTGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCA
Found at i:28725027 original size:16 final size:16
Alignment explanation
Indices: 28725006--28725039 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
28724996 GAATAAATTA
28725006 TTAACCCTAGCTTAGC
1 TTAACCCTAGCTTAGC
28725022 TTAACCCTAGCTTAGC
1 TTAACCCTAGCTTAGC
28725038 TT
1 TT
28725040 TCATAGATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.35
Consensus pattern (16 bp):
TTAACCCTAGCTTAGC
Found at i:28733882 original size:15 final size:16
Alignment explanation
Indices: 28733862--28733894 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28733852 TACTTTATAG
28733862 ATTTTA-ATAATTATT
1 ATTTTACATAATTATT
*
28733877 ATTTTACATATTTATT
1 ATTTTACATAATTATT
28733893 AT
1 AT
28733895 ACATATATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTTACATAATTATT
Found at i:28736526 original size:33 final size:33
Alignment explanation
Indices: 28736484--28736550 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
28736474 AATATAAATT
28736484 TGATTGACAAAATTAACGAATTAATTAAAAAAA
1 TGATTGACAAAATTAACGAATTAATTAAAAAAA
28736517 TGATTGACAAAATTAACGAATTAATTAAAAAAA
1 TGATTGACAAAATTAACGAATTAATTAAAAAAA
28736550 T
1 T
28736551 ATTTTTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.57, C:0.06, G:0.09, T:0.28
Consensus pattern (33 bp):
TGATTGACAAAATTAACGAATTAATTAAAAAAA
Found at i:28737122 original size:21 final size:21
Alignment explanation
Indices: 28737084--28737123 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
28737074 TCATTATTTG
*
28737084 TTATATGTCATTTTTATATGC
1 TTATATGTCATTTCTATATGC
28737105 TTATATGT-ATGTTCTATAT
1 TTATATGTCAT-TTCTATAT
28737124 ATGTTGCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.25, C:0.07, G:0.10, T:0.57
Consensus pattern (21 bp):
TTATATGTCATTTCTATATGC
Found at i:28737851 original size:20 final size:20
Alignment explanation
Indices: 28737826--28737869 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
28737816 AATTACTTGC
28737826 TTTATAAAACAGGTAAACTA
1 TTTATAAAACAGGTAAACTA
28737846 TTTATAAAACAGGTAAACTA
1 TTTATAAAACAGGTAAACTA
28737866 TTTA
1 TTTA
28737870 GTTGGTCACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.34
Consensus pattern (20 bp):
TTTATAAAACAGGTAAACTA
Found at i:28738428 original size:16 final size:17
Alignment explanation
Indices: 28738393--28738443 Score: 52
Period size: 16 Copynumber: 3.0 Consensus size: 17
28738383 AAAGGGAAAA
28738393 AAATTATTGCAATTAATT
1 AAATTATT-CAATTAATT
*
28738411 AAATTATT-AATTACTT
1 AAATTATTCAATTAATT
*
28738427 -AATTAATTAAATTAATT
1 AAATT-ATTCAATTAATT
28738444 GCTTGTTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 4 0.14
16 10 0.34
17 7 0.24
18 8 0.28
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (17 bp):
AAATTATTCAATTAATT
Found at i:28740460 original size:62 final size:59
Alignment explanation
Indices: 28740345--28740461 Score: 144
Period size: 62 Copynumber: 1.9 Consensus size: 59
28740335 ATCACTTTAA
* * * * *
28740345 TATTAAATTAGTATAATACTTATAAAGATAAATATTAGATTAAATTTATTATTAAATCT
1 TATTAAATTAGTAGAATACTTATAAAGATAAACATTAAAATAAATTTAATATTAAATCT
* *
28740404 TATTAAATTAGTAGAATATTTATCTACAAGTTAAACATTAAAATAAATTTAATATTAA
1 TATTAAATTAGTAGAATACTTA--TA-AAGATAAACATTAAAATAAATTTAATATTAA
28740462 GATAATCTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
59 20 0.42
61 2 0.04
62 26 0.54
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (59 bp):
TATTAAATTAGTAGAATACTTATAAAGATAAACATTAAAATAAATTTAATATTAAATCT
Found at i:28741689 original size:11 final size:11
Alignment explanation
Indices: 28741670--28741701 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
28741660 TGATTGCATG
*
28741670 ATTTTGTGAAA
1 ATTTCGTGAAA
28741681 ATTTCGTGAAA
1 ATTTCGTGAAA
28741692 ATTTCGTGAA
1 ATTTCGTGAA
28741702 GAAATTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.34, C:0.06, G:0.19, T:0.41
Consensus pattern (11 bp):
ATTTCGTGAAA
Found at i:28744169 original size:48 final size:48
Alignment explanation
Indices: 28744095--28744408 Score: 221
Period size: 46 Copynumber: 6.7 Consensus size: 48
28744085 TAAGGTGCCA
28744095 ATGCCATGTCCCAGACATGGTCTTACACTAGCTATCATCTTCGAGGCTG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTATCATC-TCGAGGCTG
* * *
28744144 ATGCCATGTCCCA-ACATGGTCTTACACTAGCTCTCA-CATAACCG-TGCAG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTATCATC-T---CGAGGCTG
** * *
28744193 ATGCCATGTTTCAGACATGGTTTTACACT-GAC-A-CATCTCGCA-GCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAG-CTATCATCTCG-AGGCTG
* *
28744239 ATG-CATGTCCCAGACAT-GTCTTACACTGGCT-TACGTCTCGAGG-TCG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTAT-CATCTCGAGGCT-G
* * *
28744285 ATG-TATGTCCCAGACAT-GTCTTACACTAGC-ACTCGTCTCGATGCTG
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTA-TCATCTCGAGGCTG
* * * * * *** **
28744331 ATGCCATGTCCCAGATATGGTCTTA-ACTGGATCTCATATTTCGGCCA
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCTATCATCTCGAGGCTG
28744378 ATG-CATGTCCCAGACAT-GTCTTACACTAGCT
1 ATGCCATGTCCCAGACATGGTCTTACACTAGCT
28744409 TACACAAGTG
Statistics
Matches: 211, Mismatches: 33, Indels: 45
0.73 0.11 0.16
Matches are distributed among these distances:
44 10 0.05
45 22 0.10
46 73 0.35
47 29 0.14
48 31 0.15
49 29 0.14
50 17 0.08
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACACTAGCTATCATCTCGAGGCTG
Found at i:28744386 original size:93 final size:94
Alignment explanation
Indices: 28744091--28744407 Score: 282
Period size: 93 Copynumber: 3.4 Consensus size: 94
28744081 TGGGTAAGGT
28744091 GCCAATGCCATGTCCCAGACATGGTCTTACACTAGCTA-TCATCTTCGAGGCTGATGCCATGTCC
1 GCCAATGCCATGTCCCAGACATGGTCTTACACTAGC-ACTCATC-TCGA-GCTGATGCCATGTCC
* *
28744155 CA-ACATGGTCTTACACTAGCTCTCACATAACCG
63 CAGACATGGTCTTACACT-GGTCTCACAT-ATCG
** * * *
28744188 TG-CAGATGCCATGTTTCAGACATGGTTTTACACT-G-ACACATCTCGCAGCCGATG-CATGTCC
1 -GCCA-ATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATCTCG-AGCTGATGCCATGTCC
* * *
28744249 CAGACAT-GTCTTACACTGG-CTTACGTCTCGAG
63 CAGACATGGTCTTACACTGGTCTCACATATC--G
* * * *
28744281 GTCGATG-TATGTCCCAGACAT-GTCTTACACTAGCACTCGTCTCGATGCTGATGCCATGTCCCA
1 GCCAATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATCTCGA-GCTGATGCCATGTCCCA
* * *
28744344 GATATGGTCTTA-ACTGGATCTCATATTTCG
65 GACATGGTCTTACACTGG-TCTCACATATCG
28744374 GCCAATG-CATGTCCCAGACAT-GTCTTACACTAGC
1 GCCAATGCCATGTCCCAGACATGGTCTTACACTAGC
28744408 TTACACAAGT
Statistics
Matches: 179, Mismatches: 26, Indels: 33
0.75 0.11 0.14
Matches are distributed among these distances:
90 9 0.05
91 14 0.08
92 23 0.13
93 53 0.30
94 25 0.14
95 20 0.11
96 5 0.03
97 3 0.02
98 27 0.15
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (94 bp):
GCCAATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATCTCGAGCTGATGCCATGTCCCAG
ACATGGTCTTACACTGGTCTCACATATCG
Found at i:28744770 original size:30 final size:30
Alignment explanation
Indices: 28744729--28744787 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
28744719 AAATTTACAC
* *
28744729 CTTTGGTAAAATGACCATTTTGTCCCTATA
1 CTTTGGCAAAATGACCATTTTGCCCCTATA
28744759 CTTTGGCAAAATGACCATTTTGCCCCTAT
1 CTTTGGCAAAATGACCATTTTGCCCCTAT
28744788 GCTCGAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (30 bp):
CTTTGGCAAAATGACCATTTTGCCCCTATA
Found at i:28745838 original size:18 final size:18
Alignment explanation
Indices: 28745805--28745839 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28745795 TATCATATTA
*
28745805 AATTTAATTAATTTGATT
1 AATTTAATTAACTTGATT
*
28745823 AATTTAATTTACTTGAT
1 AATTTAATTAACTTGAT
28745840 CAAAATTAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.03, G:0.06, T:0.54
Consensus pattern (18 bp):
AATTTAATTAACTTGATT
Done.