Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 206 of 208
Found at i:62879010 original size:2 final size:2
Alignment explanation
Indices: 62879003--62879044 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
62878993 TGTGTAAGAA
62879003 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
62879045 GATTATTCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62880939 original size:3 final size:3
Alignment explanation
Indices: 62880931--62880983 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
62880921 ATGTGTAGAT
62880931 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
62880979 ATA AT
1 ATA AT
62880984 GGTAAAATTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:62881801 original size:31 final size:31
Alignment explanation
Indices: 62881766--62881830 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
62881756 CTTTTTATAG
* *
62881766 TTGGGCAG-CCAAAAAAGAAGTTTACTAATAA
1 TTGGG-AGACCAAAAAAGAAATATACTAATAA
* *
62881797 TTGGGTGACCAAAATAGAAATATACTAATAA
1 TTGGGAGACCAAAAAAGAAATATACTAATAA
62881828 TTG
1 TTG
62881831 AGTGATTACT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 1 0.03
31 28 0.97
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.26
Consensus pattern (31 bp):
TTGGGAGACCAAAAAAGAAATATACTAATAA
Found at i:62884478 original size:54 final size:54
Alignment explanation
Indices: 62884396--62884504 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
62884386 GAAATTCACT
62884396 ATCTCCCTATTTAAGAGTTAATCTTACTGCTAATCACATACTTTTATTAAGTTG
1 ATCTCCCTATTTAAGAGTTAATCTTACTGCTAATCACATACTTTTATTAAGTTG
62884450 ATCTCCCTATTTAAGAGTTAATCTTACTGCTAATCACATACTTTTATTAAGTTG
1 ATCTCCCTATTTAAGAGTTAATCTTACTGCTAATCACATACTTTTATTAAGTTG
62884504 A
1 A
62884505 CATCTAGAAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.42
Consensus pattern (54 bp):
ATCTCCCTATTTAAGAGTTAATCTTACTGCTAATCACATACTTTTATTAAGTTG
Found at i:62886095 original size:21 final size:21
Alignment explanation
Indices: 62886071--62886111 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
62886061 TCAAATTTTT
*
62886071 TATATTTTAATTAAAGTAAAC
1 TATAATTTAATTAAAGTAAAC
*
62886092 TATAATTTAATTAAATTAAA
1 TATAATTTAATTAAAGTAAA
62886112 TTTTATATTA
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:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (21 bp):
TATAATTTAATTAAAGTAAAC
Found at i:62894483 original size:69 final size:68
Alignment explanation
Indices: 62894372--62894510 Score: 215
Period size: 69 Copynumber: 2.0 Consensus size: 68
62894362 TTTTCTATCC
* * **
62894372 AGTTATCACGTTCAAGCTCTCATATGAGAATAGTTGTCTAATTTAAGCCCCAATGTGAAGACATT
1 AGTTATCAAGTTCAAGCTCTCATATAAGAATAACTGTCTAATTTAAGCCCC-ATGTGAAGACATT
62894437 TGTA
65 TGTA
* *
62894441 AGTTATCAAGTTTAAGCTCTTATATAAGAATAACTGTCTAATTTAAGCCCCATGTGAAGACATTT
1 AGTTATCAAGTTCAAGCTCTCATATAAGAATAACTGTCTAATTTAAGCCCCATGTGAAGACATTT
62894506 GTA
66 GTA
62894509 AG
1 AG
62894511 GATTAACTTA
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
68 19 0.30
69 45 0.70
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Consensus pattern (68 bp):
AGTTATCAAGTTCAAGCTCTCATATAAGAATAACTGTCTAATTTAAGCCCCATGTGAAGACATTT
GTA
Found at i:62898220 original size:10 final size:10
Alignment explanation
Indices: 62898205--62898237 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
62898195 AATTAAATTG
62898205 ATTTTATATT
1 ATTTTATATT
62898215 ATTTTATAATT
1 ATTTTAT-ATT
62898226 -TTTTATATT
1 ATTTTATATT
62898235 ATT
1 ATT
62898238 AATATTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
9 3 0.14
10 15 0.71
11 3 0.14
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
ATTTTATATT
Found at i:62898244 original size:18 final size:20
Alignment explanation
Indices: 62898206--62898245 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
62898196 ATTAAATTGA
*
62898206 TTTTATATTATTTTATAATT
1 TTTTATATTATTTAATAATT
62898226 TTTTATATTA-TTAAT-ATT
1 TTTTATATTATTTAATAATT
62898244 TT
1 TT
62898246 AACAATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 4 0.21
20 10 0.53
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTATATTATTTAATAATT
Found at i:62900417 original size:31 final size:31
Alignment explanation
Indices: 62900382--62900503 Score: 99
Period size: 31 Copynumber: 3.9 Consensus size: 31
62900372 GAGCCTTTCA
*
62900382 AAAATTTTAATTAGACCCTCCAAAATTTTTG
1 AAAATTTTAATTAAACCCTCCAAAATTTTTG
* * *
62900413 AAAATTCTT-ATT-AATCTTCTCGAAATCTTTT-
1 AAAATT-TTAATTAAACCCTC-CAAAAT-TTTTG
*
62900444 AAAATTTTAATTAAACCC-CCTAAAGTTTTTG
1 AAAATTTTAATTAAACCCTCC-AAAATTTTTG
* * *
62900475 AAAATATTAAGTAAACCCTTCCAAGATTT
1 AAAATTTTAATTAAACCC-TCCAAAATTT
62900504 AATGTCACGT
Statistics
Matches: 70, Mismatches: 12, Indels: 17
0.71 0.12 0.17
Matches are distributed among these distances:
30 11 0.16
31 43 0.61
32 14 0.20
33 2 0.03
ACGTcount: A:0.39, C:0.16, G:0.06, T:0.39
Consensus pattern (31 bp):
AAAATTTTAATTAAACCCTCCAAAATTTTTG
Found at i:62917221 original size:18 final size:18
Alignment explanation
Indices: 62917190--62917224 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
62917180 TCTATTATTA
*
62917190 AGTGGGGAATGTGCAATG
1 AGTGGGGAAGGTGCAATG
*
62917208 AGTGGTGAAGGTGCAAT
1 AGTGGGGAAGGTGCAAT
62917225 AGCTGGGGTC
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:0.29, C:0.06, G:0.43, T:0.23
Consensus pattern (18 bp):
AGTGGGGAAGGTGCAATG
Found at i:62930046 original size:186 final size:186
Alignment explanation
Indices: 62929720--62930058 Score: 624
Period size: 186 Copynumber: 1.8 Consensus size: 186
62929710 TAGCATACTG
*
62929720 GTGGTATTTGATGAGATGTCAATGTGGAACTGGGAGAAGAAAGAACCAGAGGTAGTTTCTGAAGA
1 GTGGTATTTGATGAGATGTCAAGGTGGAACTGGGAGAAGAAAGAACCAGAGGTAGTTTCTGAAGA
62929785 CCTTGTAGCAGATCAGACTGAATCTGATCAGAATGGTCCTGAAATGGACATTGATGATGAACCAG
66 CCTTGTAGCAGATCAGACTGAATCTGATCAGAATGGTCCTGAAATGGACATTGATGATGAACCAG
62929850 TCAAGGGCACTAGACCCTTGGATCCTTCAGCAAATAAGGTGCTTGTGAGTAGAGAT
131 TCAAGGGCACTAGACCCTTGGATCCTTCAGCAAATAAGGTGCTTGTGAGTAGAGAT
*
62929906 GTGGTATTTGATGAGATGTCAAGGTGGAACTGGGAGAAGAAAGAACTAGAGGTAGTTTCTGAAGA
1 GTGGTATTTGATGAGATGTCAAGGTGGAACTGGGAGAAGAAAGAACCAGAGGTAGTTTCTGAAGA
* * *
62929971 CCTTGTAGCGGATCAGACTGAATCTGATCAGAATGGTTCTGAAATGGACATTGATGATGAATCAG
66 CCTTGTAGCAGATCAGACTGAATCTGATCAGAATGGTCCTGAAATGGACATTGATGATGAACCAG
*
62930036 TCAGGGGCACTAGACCCTTGGAT
131 TCAAGGGCACTAGACCCTTGGAT
62930059 GAGATTTATG
Statistics
Matches: 147, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
186 147 1.00
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.25
Consensus pattern (186 bp):
GTGGTATTTGATGAGATGTCAAGGTGGAACTGGGAGAAGAAAGAACCAGAGGTAGTTTCTGAAGA
CCTTGTAGCAGATCAGACTGAATCTGATCAGAATGGTCCTGAAATGGACATTGATGATGAACCAG
TCAAGGGCACTAGACCCTTGGATCCTTCAGCAAATAAGGTGCTTGTGAGTAGAGAT
Found at i:62930963 original size:11 final size:13
Alignment explanation
Indices: 62930939--62930970 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
62930929 TAGTTTATTA
62930939 ATATTTTAATATG
1 ATATTTTAATATG
62930952 AT-TTTTAA-ATG
1 ATATTTTAATATG
62930963 ATATTTTA
1 ATATTTTA
62930971 TTAATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (13 bp):
ATATTTTAATATG
Found at i:62943358 original size:172 final size:172
Alignment explanation
Indices: 62943067--62943416 Score: 673
Period size: 172 Copynumber: 2.0 Consensus size: 172
62943057 ACTTGATTCC
*
62943067 CATTGCTAGTCAGCTTCTCCCCTTGAGCCACAGGTGTGCTGACTATTTTGCAGTTCTGCATATAA
1 CATTTCTAGTCAGCTTCTCCCCTTGAGCCACAGGTGTGCTGACTATTTTGCAGTTCTGCATATAA
62943132 AGTTTATTAAGAATTTTTAAAGCAAAGGCATGTTGAATAATGAAAATACCTTGATCAGATTGATG
66 AGTTTATTAAGAATTTTTAAAGCAAAGGCATGTTGAATAATGAAAATACCTTGATCAGATTGATG
62943197 CACTTCCATACCAAGGAAGTATGTCATGACTCCCAAATCTGT
131 CACTTCCATACCAAGGAAGTATGTCATGACTCCCAAATCTGT
*
62943239 CATTTCTAGTCAGCTTCTCCCCTTGAGCCACAGGTGTGCTGACTATTTTGCAGTTCTGCATATGA
1 CATTTCTAGTCAGCTTCTCCCCTTGAGCCACAGGTGTGCTGACTATTTTGCAGTTCTGCATATAA
*
62943304 AGTTTATTAAGAATTTTTAAAGCAAAGGCATGTTGACTAATGAAAATACCTTGATCAGATTGATG
66 AGTTTATTAAGAATTTTTAAAGCAAAGGCATGTTGAATAATGAAAATACCTTGATCAGATTGATG
62943369 CACTTCCATACCAAGGAAGTATGTCATGACTCCCAAATCTGT
131 CACTTCCATACCAAGGAAGTATGTCATGACTCCCAAATCTGT
62943411 CATTTC
1 CATTTC
62943417 AAACACCTCT
Statistics
Matches: 175, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
172 175 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (172 bp):
CATTTCTAGTCAGCTTCTCCCCTTGAGCCACAGGTGTGCTGACTATTTTGCAGTTCTGCATATAA
AGTTTATTAAGAATTTTTAAAGCAAAGGCATGTTGAATAATGAAAATACCTTGATCAGATTGATG
CACTTCCATACCAAGGAAGTATGTCATGACTCCCAAATCTGT
Found at i:62946272 original size:42 final size:42
Alignment explanation
Indices: 62946222--62946319 Score: 133
Period size: 42 Copynumber: 2.3 Consensus size: 42
62946212 TCTTGGTATT
* * **
62946222 GCACACTTAGTGCTCGTTATTCGACATCGTCATTTTTGTTTC
1 GCACACTTAGTGCCCGTTATTCAACATCGTCATTTTAATTTC
* *
62946264 GCACACTTAGTGCCCGTTATTCAACGTCTTCATTTTAATTTC
1 GCACACTTAGTGCCCGTTATTCAACATCGTCATTTTAATTTC
*
62946306 TCACACTTAGTGCC
1 GCACACTTAGTGCC
62946320 ATTCGTATAG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.19, C:0.27, G:0.14, T:0.40
Consensus pattern (42 bp):
GCACACTTAGTGCCCGTTATTCAACATCGTCATTTTAATTTC
Found at i:62957639 original size:18 final size:18
Alignment explanation
Indices: 62957618--62957662 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
62957608 ACCAATATGT
* * *
62957618 GGCCCAATACCATTCTTC
1 GGCCCAATACCACTATTA
*
62957636 GGCCCAACACCACTATTA
1 GGCCCAATACCACTATTA
62957654 GGCCCAATA
1 GGCCCAATA
62957663 GTACCATCAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.38, G:0.13, T:0.20
Consensus pattern (18 bp):
GGCCCAATACCACTATTA
Found at i:62957848 original size:18 final size:17
Alignment explanation
Indices: 62957825--62957870 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
62957815 AGCATACCAC
*
62957825 TTTTGACCACAATCATAA
1 TTTTGACCACAA-AATAA
62957843 TTTTGACCAGCAAAATAA
1 TTTTGACCA-CAAAATAA
*
62957861 TTCTGACCAC
1 TTTTGACCAC
62957871 TTCCATTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 1 0.04
18 21 0.84
19 3 0.12
ACGTcount: A:0.37, C:0.24, G:0.09, T:0.30
Consensus pattern (17 bp):
TTTTGACCACAAAATAA
Found at i:62957902 original size:21 final size:21
Alignment explanation
Indices: 62957853--62957912 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
62957843 TTTTGACCAG
* *
62957853 CAAAATAATTCTGACCACTTC
1 CAAAATAATTTTGACCATTTC
** *
62957874 CATTATAATTTTGACCATTTT
1 CAAAATAATTTTGACCATTTC
62957895 CAAAATAATTTTGACCAT
1 CAAAATAATTTTGACCAT
62957913 GGTTAGAGAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.37, C:0.20, G:0.05, T:0.38
Consensus pattern (21 bp):
CAAAATAATTTTGACCATTTC
Found at i:62979551 original size:8 final size:8
Alignment explanation
Indices: 62979538--62979570 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
62979528 CTAATCCAAA
62979538 AAATTAAT
1 AAATTAAT
62979546 AAATTAAT
1 AAATTAAT
62979554 AAATTTAAT
1 AAA-TTAAT
62979563 AAATTAAT
1 AAATTAAT
62979571 TTAATTACGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
AAATTAAT
Found at i:62979694 original size:9 final size:9
Alignment explanation
Indices: 62979665--62979700 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
62979655 ATTTCTCTCC
62979665 AAAACCCTA
1 AAAACCCTA
* *
62979674 AAAATCCGA
1 AAAACCCTA
62979683 AAAACCCTA
1 AAAACCCTA
62979692 AAAACCCTA
1 AAAACCCTA
62979701 CCGCGAAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.56, C:0.31, G:0.03, T:0.11
Consensus pattern (9 bp):
AAAACCCTA
Found at i:62983947 original size:2 final size:2
Alignment explanation
Indices: 62983940--62983983 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
62983930 ACCCAAAAAC
*
62983940 TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
62983982 TA
1 TA
62983984 ATTGGTAAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:62990630 original size:25 final size:25
Alignment explanation
Indices: 62990596--62990645 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
62990586 TGGCTGGTGG
*
62990596 TGCAGCATGCTGGCTC-ACTTCATCA
1 TGCAGCATGCTAGC-CAACTTCATCA
62990621 TGCAGCATGCTAGCCAACTTCATCA
1 TGCAGCATGCTAGCCAACTTCATCA
62990646 GCTTTGCATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 1 0.04
25 22 0.96
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.26
Consensus pattern (25 bp):
TGCAGCATGCTAGCCAACTTCATCA
Found at i:63002489 original size:13 final size:13
Alignment explanation
Indices: 63002471--63002495 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
63002461 CCTCATTGGG
63002471 TTTTTCTTTCTTT
1 TTTTTCTTTCTTT
63002484 TTTTTCTTTCTT
1 TTTTTCTTTCTT
63002496 ATAATGATCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTCTTTCTTT
Found at i:63011624 original size:14 final size:12
Alignment explanation
Indices: 63011599--63011639 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
63011589 ATTGATTTTT
63011599 AAAAATTATAAA
1 AAAAATTATAAA
63011611 AAAAATTATTTAAA
1 AAAAATTA--TAAA
*
63011625 AAAAACTATAAA
1 AAAAATTATAAA
63011637 AAA
1 AAA
63011640 GTTATAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 15 0.58
14 11 0.42
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAAATTATAAA
Found at i:63013160 original size:16 final size:16
Alignment explanation
Indices: 63013141--63013184 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
63013131 CTCAATTTTG
*
63013141 AATAATCCAAATCCAA
1 AATAATCCAAACCCAA
63013157 AATAA-CTCAAACCCAA
1 AATAATC-CAAACCCAA
63013173 AATAATCCAAAC
1 AATAATCCAAAC
63013185 TTAAAACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 1 0.04
16 23 0.92
17 1 0.04
ACGTcount: A:0.57, C:0.27, G:0.00, T:0.16
Consensus pattern (16 bp):
AATAATCCAAACCCAA
Found at i:63013190 original size:16 final size:16
Alignment explanation
Indices: 63013141--63013190 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
63013131 CTCAATTTTG
63013141 AATAATCCAAA-TCCAA
1 AATAATCCAAACT-CAA
*
63013157 AATAA-CTCAAACCCAA
1 AATAATC-CAAACTCAA
*
63013173 AATAATCCAAACTTAA
1 AATAATCCAAACTCAA
63013189 AA
1 AA
63013191 CATTCAAACG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 1 0.04
16 26 0.93
17 1 0.04
ACGTcount: A:0.58, C:0.24, G:0.00, T:0.18
Consensus pattern (16 bp):
AATAATCCAAACTCAA
Found at i:63020152 original size:44 final size:44
Alignment explanation
Indices: 63020080--63020180 Score: 150
Period size: 44 Copynumber: 2.3 Consensus size: 44
63020070 ATTACTTATT
* *
63020080 TAATTTCACTTGAATCCACCATTTCTACGAATTTATGAT-AGTAC
1 TAATGTCAATTGAATCCACCATTTCTACGAATTTATGATGA-TAC
* *
63020124 TAATGTCAATTGAATCTACCATTTCTACGAATTTATGATGATAT
1 TAATGTCAATTGAATCCACCATTTCTACGAATTTATGATGATAC
63020168 TAATGTCAATTGA
1 TAATGTCAATTGA
63020181 GTAATTATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
44 51 0.98
45 1 0.02
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.40
Consensus pattern (44 bp):
TAATGTCAATTGAATCCACCATTTCTACGAATTTATGATGATAC
Found at i:63036041 original size:2 final size:2
Alignment explanation
Indices: 63036034--63036076 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
63036024 TACATTCACC
63036034 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
63036076 T
1 T
63036077 TTATTAATCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:63036272 original size:2 final size:2
Alignment explanation
Indices: 63036265--63036300 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
63036255 CTGATGTCTT
63036265 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
63036301 CGGATTTCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:63039587 original size:11 final size:12
Alignment explanation
Indices: 63039570--63039601 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
63039560 AAACACCAAT
63039570 TTTTTAAAAAAA
1 TTTTTAAAAAAA
63039582 -TTTTAAAAAAA
1 TTTTTAAAAAAA
63039593 TTTTTAAAA
1 TTTTTAAAA
63039602 TATAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TTTTTAAAAAAA
Found at i:63050284 original size:24 final size:23
Alignment explanation
Indices: 63050217--63050286 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
63050207 TTCAGGCTCG
** *
63050217 GTTCATTTAACCTTCGTGAACAT
1 GTTCATTTAATGTTCATGAACAT
** *
63050240 GTTTGTTTAATGTTCACGAACAT
1 GTTCATTTAATGTTCATGAACAT
63050263 GTTCATTTATATGTTCATGAACAT
1 GTTCATTTA-ATGTTCATGAACAT
63050287 TAAACAAACA
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
23 24 0.65
24 13 0.35
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (23 bp):
GTTCATTTAATGTTCATGAACAT
Found at i:63050331 original size:23 final size:23
Alignment explanation
Indices: 63050282--63050343 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
63050272 TATGTTCATG
** ** *
63050282 AACATTAAACAAACATGTTTGCG
1 AACATTAAACAAACACATTCACA
63050305 AACATTAAACAAACACATTCACA
1 AACATTAAACAAACACATTCACA
*
63050328 AACAGTAAACCAAACA
1 AACATTAAA-CAAACA
63050344 AACAAACAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 26 0.81
24 6 0.19
ACGTcount: A:0.53, C:0.23, G:0.06, T:0.18
Consensus pattern (23 bp):
AACATTAAACAAACACATTCACA
Found at i:63050366 original size:24 final size:23
Alignment explanation
Indices: 63050339--63050386 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 23
63050329 ACAGTAAACC
63050339 AAACAAACAAACAAAATATTAAAT
1 AAACAAACAAACAAAAT-TTAAAT
*
63050363 AAACAAACCAACAAAATTTAAAT
1 AAACAAACAAACAAAATTTAAAT
63050386 A
1 A
63050387 TAAAAATAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.69, C:0.15, G:0.00, T:0.17
Consensus pattern (23 bp):
AAACAAACAAACAAAATTTAAAT
Found at i:63052681 original size:5 final size:5
Alignment explanation
Indices: 63052671--63052698 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
63052661 AAGGCATGTA
63052671 ATAAT ATAAT ATAAT ATAAT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATA
63052699 GGCATAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:63056489 original size:25 final size:25
Alignment explanation
Indices: 63056460--63056510 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
63056450 ATTTGAATGC
63056460 TTTTATTTTTAATCTACTCTTTCCA
1 TTTTATTTTTAATCTACTCTTTCCA
63056485 TTTTATTTTTAATCTACTCTTTCCA
1 TTTTATTTTTAATCTACTCTTTCCA
63056510 T
1 T
63056511 ATAGCCATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.61
Consensus pattern (25 bp):
TTTTATTTTTAATCTACTCTTTCCA
Found at i:63067233 original size:12 final size:13
Alignment explanation
Indices: 63067216--63067253 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
63067206 TTTATTCTGT
63067216 TTAGTTAGTTAG-
1 TTAGTTAGTTAGA
63067228 TTAGTTAGTTAGAA
1 TTAGTTAGTTAG-A
63067242 TTGAGTTAGTTA
1 TT-AGTTAGTTA
63067254 TTCAGTTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 12 0.52
14 2 0.09
15 9 0.39
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (13 bp):
TTAGTTAGTTAGA
Found at i:63071600 original size:98 final size:98
Alignment explanation
Indices: 63071430--63071624 Score: 266
Period size: 98 Copynumber: 2.0 Consensus size: 98
63071420 ACCCTAAAGG
* * * **
63071430 TTTGTTCGATTAGCTGAAGTTTGGTTGCTCGGTTAATTCGAGAATATTGCTATATTCATTGTTTG
1 TTTGTTCGATGAGCTGAAATTTGGTTGCTCGGTAAATTCGAGAATATCACTATATTCATTGTTTG
* *
63071495 TTGAAGATTATCATAGAATGTGTAGGAGCATGT
66 TTGAAGATGATCATACAATGTGTAGGAGCATGT
* *
63071528 TTTGTTCGATGAGCTGAAATTTGTTTGCTTGGTAAATTCGAGAATATCACTATATGT-ATTGTTT
1 TTTGTTCGATGAGCTGAAATTTGGTTGCTCGGTAAATTCGAGAATATCACTATAT-TCATTGTTT
* * *
63071592 GTTTAAGATGATGATACATTGTGTAGGAGCATG
65 GTTGAAGATGATCATACAATGTGTAGGAGCATG
63071625 CTTTCTTCAG
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
98 83 0.99
99 1 0.01
ACGTcount: A:0.26, C:0.09, G:0.24, T:0.42
Consensus pattern (98 bp):
TTTGTTCGATGAGCTGAAATTTGGTTGCTCGGTAAATTCGAGAATATCACTATATTCATTGTTTG
TTGAAGATGATCATACAATGTGTAGGAGCATGT
Found at i:63071964 original size:186 final size:186
Alignment explanation
Indices: 63071529--63072192 Score: 963
Period size: 186 Copynumber: 3.6 Consensus size: 186
63071519 GGAGCATGTT
* * * * *
63071529 TTGTTCGATGAGCTGAAATTTGTTTGCTTGGTAAATTCGAGAATATCACTATATGTATTGTTTGT
1 TTGTTCGATTAGCTGAAATTTGATTGCTCGGTTAATTCAAGAATATCACTATATGTATTGTTTGT
63071594 TTAAGATGATGATACATTGTGTAGGAGCATGCTTTCTTCAGTATGAATCTCGTTGGTTTGTATAT
66 TTAAGATGATGATACATTGTGTAGGAGCATGCTTTCTTCAGTATGAATCTCGTTGGTTTGTATAT
* *
63071659 GAACTGTTTATATGCTCTGCTTCTGAGTCTGCTGAGGCTGCTCATCAACCCCAAAGGC
131 GAACTGTTTATATG--CTGCTTCTGAGTCTGTTGAGGCTGCTAATCAACCCCAAAGGC
* * * ** *
63071717 TTGTTCGGTTAGCTGAAATTCGATTGCTCGTTTAATTTGAGAATATCACTATATTTATTGTTTGT
1 TTGTTCGATTAGCTGAAATTTGATTGCTCGGTTAATTCAAGAATATCACTATATGTATTGTTTGT
**
63071782 TTAAGACAATGATACATTGTGTAGGAGCATGCTTTCTTCAGTATGAATCTCGTTGGTTTGTATAT
66 TTAAGATGATGATACATTGTGTAGGAGCATGCTTTCTTCAGTATGAATCTCGTTGGTTTGTATAT
*
63071847 GAACTGTTTATATGCTGCTTCAGAGTCTGTTGAGGCTGCTAATCAACCCCAAAGGC
131 GAACTGTTTATATGCTGCTTCTGAGTCTGTTGAGGCTGCTAATCAACCCCAAAGGC
* *
63071903 TTGTTCCATTAGCTGAAATTTGATTGCTCGGTTAATTCAAGAATATCACTATATTTATTGTTTGT
1 TTGTTCGATTAGCTGAAATTTGATTGCTCGGTTAATTCAAGAATATCACTATATGTATTGTTTGT
* * * *
63071968 TTACGATGATGATACATAGTGTAGGAGCATGCTTTCTTCAGTATGAAGCTCATTGGTTTGTATAT
66 TTAAGATGATGATACATTGTGTAGGAGCATGCTTTCTTCAGTATGAATCTCGTTGGTTTGTATAT
* * *
63072033 GAACT-TTCTATATGCTGCTGCTGAGTCTGTTGAGGCTGCTAATCAACCCTAAAGGT
131 GAACTGTT-TATATGCTGCTTCTGAGTCTGTTGAGGCTGCTAATCAACCCCAAAGGC
* * ** * **
63072089 TTGTTCAATTAGTTGAAATTTGATTGCTCAATTAATTCAAGAACATTGCTATATGTATTGTTTGT
1 TTGTTCGATTAGCTGAAATTTGATTGCTCGGTTAATTCAAGAATATCACTATATGTATTGTTTGT
* * * *
63072154 TTAAGATGATAATACATT-TTTAGTAGCATGTTTTCTTCA
66 TTAAGATGATGATACATTGTGTAGGAGCATGCTTTCTTCA
63072193 TTTAGCTGAA
Statistics
Matches: 431, Mismatches: 44, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
185 20 0.05
186 278 0.65
188 133 0.31
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.40
Consensus pattern (186 bp):
TTGTTCGATTAGCTGAAATTTGATTGCTCGGTTAATTCAAGAATATCACTATATGTATTGTTTGT
TTAAGATGATGATACATTGTGTAGGAGCATGCTTTCTTCAGTATGAATCTCGTTGGTTTGTATAT
GAACTGTTTATATGCTGCTTCTGAGTCTGTTGAGGCTGCTAATCAACCCCAAAGGC
Found at i:63076535 original size:31 final size:31
Alignment explanation
Indices: 63076497--63076557 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
63076487 AAAAAAGTTG
*
63076497 ACTTAAATAAAAACTTTCAAATAGTTCAGTA
1 ACTTAAATAAAAACTTTCAAATAGGTCAGTA
* * *
63076528 ACTTAAATGACAACTTTCGAATAGGTCAGT
1 ACTTAAATAAAAACTTTCAAATAGGTCAGT
63076558 GACCATATTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31
Consensus pattern (31 bp):
ACTTAAATAAAAACTTTCAAATAGGTCAGTA
Found at i:63078739 original size:2 final size:2
Alignment explanation
Indices: 63078732--63078774 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
63078722 TACCCATCAA
63078732 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
63078774 A
1 A
63078775 ACATTTAGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:63085916 original size:31 final size:31
Alignment explanation
Indices: 63085876--63085951 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
63085866 AAAAGCTCAG
*
63085876 TATTTAATTTGGTAT-TCGAGTTTTGCTTCAA
1 TATTTAATTTGGTATCT-GAGTTTGGCTTCAA
*
63085907 TGTTTAATTTGGTATCTGAGTTTGGCTTCAA
1 TATTTAATTTGGTATCTGAGTTTGGCTTCAA
63085938 TATTTAATTTGGTA
1 TATTTAATTTGGTA
63085952 GTCAAACCAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
31 40 0.98
32 1 0.02
ACGTcount: A:0.22, C:0.08, G:0.18, T:0.51
Consensus pattern (31 bp):
TATTTAATTTGGTATCTGAGTTTGGCTTCAA
Found at i:63086096 original size:31 final size:30
Alignment explanation
Indices: 63086057--63086135 Score: 95
Period size: 31 Copynumber: 2.6 Consensus size: 30
63086047 AAAAGCGCAA
* *
63086057 TATATTCAATTTGGTATTTGAGCTTGGCTT
1 TATATTCAATTTGGTACTTGAACTTGGCTT
* *
63086087 TGATATTCAATTTGTTACTTGAATTTGGCTT
1 T-ATATTCAATTTGGTACTTGAACTTGGCTT
*
63086118 TAGTATTCAATTTAGTAC
1 TA-TATTCAATTTGGTAC
63086136 CTAACGTTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
30 2 0.05
31 39 0.95
ACGTcount: A:0.24, C:0.10, G:0.16, T:0.49
Consensus pattern (30 bp):
TATATTCAATTTGGTACTTGAACTTGGCTT
Found at i:63089829 original size:27 final size:27
Alignment explanation
Indices: 63089791--63089844 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
63089781 TGATATATAC
63089791 CCATTAGAATAAATTTGGATCAGAAAA
1 CCATTAGAATAAATTTGGATCAGAAAA
63089818 CCATTAGAATAAATTTGGATCAGAAAA
1 CCATTAGAATAAATTTGGATCAGAAAA
63089845 GATAAAAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.11, G:0.15, T:0.26
Consensus pattern (27 bp):
CCATTAGAATAAATTTGGATCAGAAAA
Found at i:63093124 original size:299 final size:299
Alignment explanation
Indices: 63092586--63093183 Score: 1187
Period size: 299 Copynumber: 2.0 Consensus size: 299
63092576 CCCAAAGTTT
63092586 TAACTTGTAATTTATGACAATGACGAATAAATGATAGCCATGTACGGGGGCAGGCAAAAAAATTT
1 TAACTTGTAATTTATGACAATGACGAATAAATGATAGCCATGTACGGGGGCAGGCAAAAAAATTT
63092651 TTAGGGGTCAAAATTAAATTTTAAGTTTTACGGTAGTAAAATGTAATATTATTATTTGAATAGTT
66 TTAGGGGTCAAAATTAAATTTTAAGTTTTACGGTAGTAAAATGTAATATTATTATTTGAATAGTT
63092716 TATATCTTTATAAATTTTAAAGGATTAAATCATTTTTTTATCATCTTTAGTATCTTTAGGGGGCA
131 TATATCTTTATAAATTTTAAAGGATTAAATCATTTTTTTATCATCTTTAGTATCTTTAGGGGGCA
*
63092781 AAGTGTGGTTTTACATTTATTAATTTAAAATTTAAAAAAAGTTAAAAGGCCTAAATGAAAAATTT
196 AAGTGTGGTTTTACATTTATTAACTTAAAATTTAAAAAAAGTTAAAAGGCCTAAATGAAAAATTT
63092846 TCCATTTTAGGATGGGCCAAGGCCCCTACCAACCCCTGG
261 TCCATTTTAGGATGGGCCAAGGCCCCTACCAACCCCTGG
63092885 TAACTTGTAATTTATGACAATGACGAATAAATGATAGCCATGTACGGGGGCAGGCAAAAAAATTT
1 TAACTTGTAATTTATGACAATGACGAATAAATGATAGCCATGTACGGGGGCAGGCAAAAAAATTT
63092950 TTAGGGGTCAAAATTAAATTTTAAGTTTTACGGTAGTAAAATGTAATATTATTATTTGAATAGTT
66 TTAGGGGTCAAAATTAAATTTTAAGTTTTACGGTAGTAAAATGTAATATTATTATTTGAATAGTT
63093015 TATATCTTTATAAATTTTAAAGGATTAAATCATTTTTTTATCATCTTTAGTATCTTTAGGGGGCA
131 TATATCTTTATAAATTTTAAAGGATTAAATCATTTTTTTATCATCTTTAGTATCTTTAGGGGGCA
63093080 AAGTGTGGTTTTACATTTATTAACTTAAAATTTAAAAAAAGTTAAAAGGCCTAAATGAAAAATTT
196 AAGTGTGGTTTTACATTTATTAACTTAAAATTTAAAAAAAGTTAAAAGGCCTAAATGAAAAATTT
63093145 TCCATTTTAGGATGGGCCAAGGCCCCTACCAACCCCTGG
261 TCCATTTTAGGATGGGCCAAGGCCCCTACCAACCCCTGG
63093184 CCACGCCCTT
Statistics
Matches: 298, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
299 298 1.00
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (299 bp):
TAACTTGTAATTTATGACAATGACGAATAAATGATAGCCATGTACGGGGGCAGGCAAAAAAATTT
TTAGGGGTCAAAATTAAATTTTAAGTTTTACGGTAGTAAAATGTAATATTATTATTTGAATAGTT
TATATCTTTATAAATTTTAAAGGATTAAATCATTTTTTTATCATCTTTAGTATCTTTAGGGGGCA
AAGTGTGGTTTTACATTTATTAACTTAAAATTTAAAAAAAGTTAAAAGGCCTAAATGAAAAATTT
TCCATTTTAGGATGGGCCAAGGCCCCTACCAACCCCTGG
Found at i:63099380 original size:22 final size:22
Alignment explanation
Indices: 63099352--63099393 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
63099342 TTTATTGTTC
63099352 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
63099374 AAACATGAGAGCTTAGTACG
1 AAACATGAGAGCTTAGTACG
63099394 ATTAGAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.38, C:0.14, G:0.26, T:0.21
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:63099825 original size:67 final size:67
Alignment explanation
Indices: 63099703--63099828 Score: 180
Period size: 67 Copynumber: 1.9 Consensus size: 67
63099693 TGAATAAATT
* * * *
63099703 ACTCAAAATGATATAAACCTATGATGATCTAAATTAAAAGACTTAAGCTTAAAACTCGAATGACA
1 ACTCAAAATGATATAAACCCATAATGATCAAAATTAAAAGACTTAAACTTAAAACTCGAATGACA
63099768 TG
66 TG
* * * *
63099770 ACTCAAAATGATCTAAACCCGTAATGATCAAAATTAAAAGACTTAAATTTCAAACTCGA
1 ACTCAAAATGATATAAACCCATAATGATCAAAATTAAAAGACTTAAACTTAAAACTCGA
63099829 CTGGCATAAC
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
67 51 1.00
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.26
Consensus pattern (67 bp):
ACTCAAAATGATATAAACCCATAATGATCAAAATTAAAAGACTTAAACTTAAAACTCGAATGACA
TG
Found at i:63111446 original size:20 final size:20
Alignment explanation
Indices: 63111404--63111446 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
63111394 GTAATCTGAA
*
63111404 TATTTTCTAATAAATTAATT
1 TATTTTCTAATAAATTAAAT
*
63111424 TATTTT-TATTAAATTATAAT
1 TATTTTCTAATAAATTA-AAT
63111444 TAT
1 TAT
63111447 AAAAATATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
TATTTTCTAATAAATTAAAT
Found at i:63116802 original size:17 final size:18
Alignment explanation
Indices: 63116771--63116805 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
63116761 TTGGGAAACG
*
63116771 ATTCAACTCATTTCACTC
1 ATTCAACTCACTTCACTC
63116789 ATTC-ACTCACTTCACTC
1 ATTCAACTCACTTCACTC
63116806 CACCATTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.26, C:0.37, G:0.00, T:0.37
Consensus pattern (18 bp):
ATTCAACTCACTTCACTC
Found at i:63117893 original size:42 final size:42
Alignment explanation
Indices: 63117847--63117928 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
63117837 ATTAGATCGG
* * *
63117847 ACTAATAGGTTGAATCGAGAATTAGTGGTTCAATTAGTGGAA
1 ACTAATAGATTGAATCGAGAATTAGTAGTTCAATCAGTGGAA
*
63117889 ACTAATAGATTGAATCGAGAATTAGTAGTTGAATCAGTGG
1 ACTAATAGATTGAATCGAGAATTAGTAGTTCAATCAGTGG
63117929 TATAAAATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.37, C:0.07, G:0.26, T:0.30
Consensus pattern (42 bp):
ACTAATAGATTGAATCGAGAATTAGTAGTTCAATCAGTGGAA
Found at i:63118436 original size:57 final size:57
Alignment explanation
Indices: 63118348--63118460 Score: 208
Period size: 57 Copynumber: 2.0 Consensus size: 57
63118338 GAAACTACCC
* *
63118348 CGACGACAGGTTCAACACCACAAGGATCAGGGTCGGAATCGGGGTTAACTTATTCGT
1 CGACGACAAGTTCAACACCACAAGGATCAGGGTCGGAATCAGGGTTAACTTATTCGT
63118405 CGACGACAAGTTCAACACCACAAGGATCAGGGTCGGAATCAGGGTTAACTTATTCG
1 CGACGACAAGTTCAACACCACAAGGATCAGGGTCGGAATCAGGGTTAACTTATTCG
63118461 GGTAATGGTT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.20
Consensus pattern (57 bp):
CGACGACAAGTTCAACACCACAAGGATCAGGGTCGGAATCAGGGTTAACTTATTCGT
Found at i:63122095 original size:17 final size:17
Alignment explanation
Indices: 63122073--63122108 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
63122063 TTAAAGAAGC
63122073 ATTAAAA-ATTCAAAAAA
1 ATTAAAATATT-AAAAAA
63122090 ATTAAAATATTAAAAAA
1 ATTAAAATATTAAAAAA
63122107 AT
1 AT
63122109 AATTCAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 15 0.83
18 3 0.17
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (17 bp):
ATTAAAATATTAAAAAA
Found at i:63125809 original size:17 final size:19
Alignment explanation
Indices: 63125772--63125814 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
63125762 TAATCCCAAA
63125772 TTTGGTA-ATTATATCTAT
1 TTTGGTATATTATATCTAT
63125790 TTTGGTATA-TATAT-TAT
1 TTTGGTATATTATATCTAT
*
63125807 TTTAGTAT
1 TTTGGTAT
63125815 CTGAACCTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 10 0.43
18 12 0.52
19 1 0.04
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.58
Consensus pattern (19 bp):
TTTGGTATATTATATCTAT
Found at i:63125901 original size:2 final size:2
Alignment explanation
Indices: 63125894--63125945 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
63125884 ACATTTTTGC
63125894 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
63125936 TA TA TA TA TA
1 TA TA TA TA TA
63125946 GTAAATTGGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:63127561 original size:300 final size:298
Alignment explanation
Indices: 63126862--63127822 Score: 992
Period size: 300 Copynumber: 3.2 Consensus size: 298
63126852 TAAACCTTTA
* * * * * * ** *
63126862 ATCATAATTTAAGGAATACAAGTGAACTATACATGATCTATACCCGATCTTTACATGCTACACAC
1 ATCATAATTTGAGGGAGACAAATGAACTATACACGATCTACACGTGACCTTTACATGCTACACAC
63126927 TTGTCTCATGAGATTTGAGGGGCATATAAGCCTCCCATCATAATTGGGGGGAGACAAGTGAACTA
66 TTGTCTCATGAGATTTGA-GGGCATATAAGCCTCCCATCATAATT-GGGGGAGACAAGTGAACTA
* * * * * * * * * *
63126992 TACATGATTTATATGTGA-CTTTTCAATCCCACTCACTTGTCCTATGAAATTTGATGAC-TATAA
129 TACACGATCTACATGTGACCTTTAC-ATACTACACACTTGTCC-ATGAGATTTGAGGGCATATAA
* * * * * * *
63127055 GCCTTCCATCATAACTT-GAGGGAGACAAATGAATTCTACACGA-CTTACACGTGACATTTACAT
192 GCCTCCCATCATAA-TTAGAGGGAGACAAGTGGACTATACACGATC-TGCACGTGACTTTTACAT
*
63127118 GCACCACAC-TTGTCCTACAAGACTTGATGGCTATATAAGCCTCCC
255 -CACCACACATTGTCCTACGAGACTTGATGGC-ATATAAGCCTCCC
* * * *
63127163 ATCATAACTTAAGGGAGA-AAAGTGAACTATACAGGATCTACACGTGACCTTTACATACTACACA
1 ATCATAATTTGAGGGAGACAAA-TGAACTATACACGATCTACACGTGACCTTTACATGCTACACA
* * *
63127227 CTTGTATCATGAGATTTGAGGGCATATAAGCCTCCCATCATAATTAGGGGGAGACATGTGGACTA
65 CTTGTCTCATGAGATTTGAGGGCATATAAGCCTCCCATCATAATT-GGGGGAGACAAGTGAACTA
* * *
63127292 TACACGATCTGCACGTGACCTTTACATACTACACACTTGTACCATGCGATTTGAGGGGCATATAA
129 TACACGATCTACATGTGACCTTTACATACTACACACTTGT-CCATGAGATTTGA-GGGCATATAA
*
63127357 GCCTCCCATCATAATTAG-GAGGAGACAAGTGGACTATACACGATCTGCACGTGACTTTTAAATC
192 GCCTCCCATCATAATTAGAG-GGAGACAAGTGGACTATACACGATCTGCACGTGACTTTTACATC
*
63127421 -CCACACATTTGTCCTATGAGA-TTGATGGC-TATAAGCCTCCC
256 ACCACACA-TTGTCCTACGAGACTTGATGGCATATAAGCCTCCC
* * * * *
63127462 ATCATAGTTTGAGGGAGACAAATGAACTATACACGA-CTTACATGTGGCTTTTACATGCTCCACA
1 ATCATAATTTGAGGGAGACAAATGAACTATACACGATC-TACACGTGACCTTTACATGCTACACA
** * * * * *
63127526 CTTGTCGGATAAGACTTGATGGCTATATCAGCCTCCCATCATAACTTGAGGGAGACAAGTGAACT
65 CTTGTCTCATGAGATTTGAGGGC-ATATAAGCCTCCCATCATAA-TTGGGGGAGACAAGTGAACT
* * * * *
63127591 ATACACAATCTACATGTGACCTTTACATGCTCCACACTTGTCCCACGGGATTTGAAGGGCATATA
128 ATACACGATCTACATGTGACCTTTACATACTACACACTTGT-CCATGAGATTTG-AGGGCATATA
* ** * * * * *
63127656 AGGCTCTTATTATAATCAGAGGGAGACAAGTGGACAATACATGATCTGCATGTGACTTTTACA-C
191 AGCCTCCCATCATAATTAGAGGGAGACAAGTGGACTATACACGATCTGCACGTGACTTTTACATC
* * *
63127720 GCCACACACTTGTCCTACGAGATTTGATGGCTATATAAACCTCCC
256 ACCACACA-TTGTCCTACGAGACTTGATGGC-ATATAAGCCTCCC
* ** * * *
63127765 ATCATAATTTGAGGGAGACAAGTGAACTATACATAATCTGCACGTGGCCTTTTCATGC
1 ATCATAATTTGAGGGAGACAAATGAACTATACACGATCTACACGTGACCTTTACATGC
63127823 CCCATACTTA
Statistics
Matches: 555, Mismatches: 84, Indels: 40
0.82 0.12 0.06
Matches are distributed among these distances:
298 1 0.00
299 79 0.14
300 248 0.45
301 102 0.18
302 64 0.12
303 60 0.11
304 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (298 bp):
ATCATAATTTGAGGGAGACAAATGAACTATACACGATCTACACGTGACCTTTACATGCTACACAC
TTGTCTCATGAGATTTGAGGGCATATAAGCCTCCCATCATAATTGGGGGAGACAAGTGAACTATA
CACGATCTACATGTGACCTTTACATACTACACACTTGTCCATGAGATTTGAGGGCATATAAGCCT
CCCATCATAATTAGAGGGAGACAAGTGGACTATACACGATCTGCACGTGACTTTTACATCACCAC
ACATTGTCCTACGAGACTTGATGGCATATAAGCCTCCC
Found at i:63127769 original size:401 final size:400
Alignment explanation
Indices: 63126910--63127810 Score: 1207
Period size: 401 Copynumber: 2.2 Consensus size: 400
63126900 TATACCCGAT
63126910 CTTTACATGCTACACACTTGT-CTCATGAGATTTGAGGGGCATATAAGCCTCCCATCATAATTGG
1 CTTTACATGCTACACACTTGTCCT-ATGAGATTTGAGGGGCATATAAGCCTCCCATCATAATT-G
* * ** * * *
63126974 GGGGAGACAAGTGAACTATACATGATTTATATGTGACTTTTCAATCCCACTCACTTGTCCTATGA
64 GAGGAGACAAGTGAACTATACATGATCTGCACGTGACTTTTAAATCCCACACACTTGTCCTATGA
* * *
63127039 AATTTGATGACTATAAGCCTTCCATCATAACTTGAGGGAGACAAATGAATTCTACACGACTTACA
129 AATTTGATGACTATAAGCCTCCCATCATAACTTGAGGGAGACAAATGAACTATACACGACTTACA
*
63127104 CGTGACATTTACATGCACCACACTTGTCCTACAAGACTTGATGGCTATATAAGCCTCCCATCATA
194 CGTGACATTTACATGCACCACACTTGTCCGACAAGACTTGATGGCTATATAAGCCTCCCATCATA
** *
63127169 ACTTAAGGGAGAAAAGTGAACTATACAGGATCTACACGTGACCTTTACATACTACACACTTGTAT
259 ACTTAAGGGAGAAAAGTGAACTATACACAATCTACACGTGACCTTTACATACTACACACTTGTAC
* * * * *
63127234 CATGAGATTTGAGGGCATATAAGCCTCCCATCATAATTAGGGGGAGACATGTGGACTATACACGA
324 CACGAGATTTGAGGGCATATAAGCCTCCCATCATAATCAGAGGGAGACAAGTGGACAATACACGA
63127299 TCTGCACGTGAC
389 TCTGCACGTGAC
* *
63127311 CTTTACATACTACACACTTGTACC-ATGCGATTTGAGGGGCATATAAGCCTCCCATCATAATTAG
1 CTTTACATGCTACACACTTGT-CCTATGAGATTTGAGGGGCATATAAGCCTCCCATCATAATT-G
* * *
63127375 GAGGAGACAAGTGGACTATACACGATCTGCACGTGACTTTTAAATCCCACACATTTGTCCTATGA
64 GAGGAGACAAGTGAACTATACATGATCTGCACGTGACTTTTAAATCCCACACACTTGTCCTATGA
* * **
63127440 GA-TTGATGGCTATAAGCCTCCCATCATAGTTTGAGGGAGACAAATGAACTATACACGACTTACA
129 AATTTGATGACTATAAGCCTCCCATCATAACTTGAGGGAGACAAATGAACTATACACGACTTACA
* * * * * * *
63127504 TGTGGCTTTTACATGCTCCACACTTGTCGGATAAGACTTGATGGCTATATCAGCCTCCCATCATA
194 CGTGACATTTACATGCACCACACTTGTCCGACAAGACTTGATGGCTATATAAGCCTCCCATCATA
* * * * * *
63127569 ACTTGAGGGAGACAAGTGAACTATACACAATCTACATGTGACCTTTACATGCTCCACACTTGTCC
259 ACTTAAGGGAGAAAAGTGAACTATACACAATCTACACGTGACCTTTACATACTACACACTTGTAC
* * ** * *
63127634 CACGGGATTTGAAGGGCATATAAGGCTCTTATTATAATCAGAGGGAGACAAGTGGACAATACATG
324 CACGAGATTTG-AGGGCATATAAGCCTCCCATCATAATCAGAGGGAGACAAGTGGACAATACACG
*
63127699 ATCTGCATGTGAC
388 ATCTGCACGTGAC
* * * * * * *
63127712 TTTTACACGCCACACACTTGTCCTACGAGATTTGA-TGGCTATATAAACCTCCCATCATAATTTG
1 CTTTACATGCTACACACTTGTCCTATGAGATTTGAGGGGC-ATATAAGCCTCCCATCATAATTGG
*
63127776 AGGGAGACAAGTGAACTATACATAATCTGCACGTG
65 A-GGAGACAAGTGAACTATACATGATCTGCACGTG
63127811 GCCTTTTCAT
Statistics
Matches: 433, Mismatches: 61, Indels: 12
0.86 0.12 0.02
Matches are distributed among these distances:
400 185 0.43
401 247 0.57
403 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (400 bp):
CTTTACATGCTACACACTTGTCCTATGAGATTTGAGGGGCATATAAGCCTCCCATCATAATTGGA
GGAGACAAGTGAACTATACATGATCTGCACGTGACTTTTAAATCCCACACACTTGTCCTATGAAA
TTTGATGACTATAAGCCTCCCATCATAACTTGAGGGAGACAAATGAACTATACACGACTTACACG
TGACATTTACATGCACCACACTTGTCCGACAAGACTTGATGGCTATATAAGCCTCCCATCATAAC
TTAAGGGAGAAAAGTGAACTATACACAATCTACACGTGACCTTTACATACTACACACTTGTACCA
CGAGATTTGAGGGCATATAAGCCTCCCATCATAATCAGAGGGAGACAAGTGGACAATACACGATC
TGCACGTGAC
Found at i:63127798 original size:101 final size:100
Alignment explanation
Indices: 63126862--63127823 Score: 865
Period size: 101 Copynumber: 9.6 Consensus size: 100
63126852 TAAACCTTTA
* * * * * ** *
63126862 ATCATAATTTAAGGAATACAAGTGAACTATACATGATCTATACCCGA-TCTTTACATGCTACACA
1 ATCATAATTTGAGGGAGACAAGTGAACTATACACGATCTACACGTGACT-TTTACATGCCACACA
*
63126926 CTTGT-CTCATGAGATTTGAGGGGCATATAAGCCTCCC
65 CTTGTCCT-ATGAGATTTGA-TGGCATATAAGCCTCCC
* * * * * * * *
63126963 ATCATAATTGGGGGGAGACAAGTGAACTATACATGATTTATATGTGACTTTT-CAATCCCACTCA
1 ATCATAATTTGAGGGAGACAAGTGAACTATACACGATCTACACGTGACTTTTAC-ATGCCACACA
* * *
63127027 CTTGTCCTATGAAATTTGATGAC-TATAAGCCTTCC
65 CTTGTCCTATGAGATTTGATGGCATATAAGCCTCCC
* * * * *
63127062 ATCATAACTTGAGGGAGACAAATGAATTCTACACGA-CTTACACGTGACATTTACATG-CACCAC
1 ATCATAATTTGAGGGAGACAAGTGAACTATACACGATC-TACACGTGACTTTTACATGCCA-CAC
** *
63127125 ACTTGTCCTACAAGACTTGATGGCTATATAAGCCTCCC
64 ACTTGTCCTATGAGATTTGATGGC-ATATAAGCCTCCC
* * * * * * *
63127163 ATCATAACTTAAGGGAGAAAAGTGAACTATACAGGATCTACACGTGACCTTTACATACTACACAC
1 ATCATAATTTGAGGGAGACAAGTGAACTATACACGATCTACACGTGACTTTTACATGCCACACAC
* *
63127228 TTGT-ATCATGAGATTTGAGGGCATATAAGCCTCCC
66 TTGTCCT-ATGAGATTTGATGGCATATAAGCCTCCC
* * * * * * * *
63127263 ATCATAATTAGGGGGAGACATGTGGACTATACACGATCTGCACGTGACCTTTACATACTACACAC
1 ATCATAATTTGAGGGAGACAAGTGAACTATACACGATCTACACGTGACTTTTACATGCCACACAC
* *
63127328 TTGTACC-ATGCGATTTGAGGGGCATATAAGCCTCCC
66 TTGT-CCTATGAGATTTGA-TGGCATATAAGCCTCCC
* * * * *
63127364 ATCATAATTAG-GAGGAGACAAGTGGACTATACACGATCTGCACGTGACTTTTAAATCCCACACA
1 ATCATAATTTGAG-GGAGACAAGTGAACTATACACGATCTACACGTGACTTTTACATGCCACACA
*
63127428 TTTGTCCTATGAGA-TTGATGGC-TATAAGCCTCCC
65 CTTGTCCTATGAGATTTGATGGCATATAAGCCTCCC
* * * *
63127462 ATCATAGTTTGAGGGAGACAAATGAACTATACACGA-CTTACATGTGGCTTTTACATGCTC-CAC
1 ATCATAATTTGAGGGAGACAAGTGAACTATACACGATC-TACACGTGACTTTTACATGC-CACAC
** * * *
63127525 ACTTGTCGGATAAGACTTGATGGCTATATCAGCCTCCC
64 ACTTGTCCTATGAGATTTGATGGC-ATATAAGCCTCCC
* * * *
63127563 ATCATAACTTGAGGGAGACAAGTGAACTATACACAATCTACATGTGACCTTTACATGCTC-CACA
1 ATCATAATTTGAGGGAGACAAGTGAACTATACACGATCTACACGTGACTTTTACATGC-CACACA
* * * * * **
63127627 CTTGTCCCACGGGATTTGAAGGGCATATAAGGCTCTT
65 CTTGTCCTATGAGATTTG-ATGGCATATAAGCCTCCC
* ** * * * * * *
63127664 ATTATAATCAGAGGGAGACAAGTGGACAATACATGATCTGCATGTGACTTTTACACGCCACACAC
1 ATCATAATTTGAGGGAGACAAGTGAACTATACACGATCTACACGTGACTTTTACATGCCACACAC
* *
63127729 TTGTCCTACGAGATTTGATGGCTATATAAACCTCCC
66 TTGTCCTATGAGATTTGATGGC-ATATAAGCCTCCC
** * *
63127765 ATCATAATTTGAGGGAGACAAGTGAACTATACATAATCTGCACGTGGCCTTTT-CATGCC
1 ATCATAATTTGAGGGAGACAAGTGAACTATACACGATCTACACGT-GACTTTTACATGCC
63127824 CCATACTTAT
Statistics
Matches: 708, Mismatches: 126, Indels: 54
0.80 0.14 0.06
Matches are distributed among these distances:
97 1 0.00
98 73 0.10
99 87 0.12
100 100 0.14
101 431 0.61
102 16 0.02
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (100 bp):
ATCATAATTTGAGGGAGACAAGTGAACTATACACGATCTACACGTGACTTTTACATGCCACACAC
TTGTCCTATGAGATTTGATGGCATATAAGCCTCCC
Found at i:63132310 original size:31 final size:31
Alignment explanation
Indices: 63132257--63132335 Score: 74
Period size: 31 Copynumber: 2.6 Consensus size: 31
63132247 CCAAGGCTGA
* * * *
63132257 AAGGGGTCCAAAATATTATTTTTCAG-TTGTT
1 AAGGGGGCCAAATTTTTTTTTTTCAGCTT-TT
*
63132288 AAGGGGGCCAAATTTTTTTTTTTTAGCTTTT
1 AAGGGGGCCAAATTTTTTTTTTTCAGCTTTT
*
63132319 AA--GGGCCTAATTTTTTT
1 AAGGGGGCCAAATTTTTTT
63132336 ACCAACTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 14 0.34
31 25 0.61
32 2 0.05
ACGTcount: A:0.24, C:0.10, G:0.19, T:0.47
Consensus pattern (31 bp):
AAGGGGGCCAAATTTTTTTTTTTCAGCTTTT
Found at i:63144938 original size:16 final size:16
Alignment explanation
Indices: 63144919--63144962 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
63144909 TTTTATCGAG
* *
63144919 TCATTTTAGGTTTGAA
1 TCATTTTGGGTTTCAA
*
63144935 TCATTTCGGGTTTCAA
1 TCATTTTGGGTTTCAA
63144951 TCATTTTGGGTT
1 TCATTTTGGGTT
63144963 ATTTGTTTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.18, C:0.11, G:0.20, T:0.50
Consensus pattern (16 bp):
TCATTTTGGGTTTCAA
Found at i:63146844 original size:2 final size:2
Alignment explanation
Indices: 63146837--63146866 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
63146827 TATCAATCTT
63146837 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
63146867 AAGGATGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:63149959 original size:19 final size:18
Alignment explanation
Indices: 63149929--63149976 Score: 69
Period size: 19 Copynumber: 2.6 Consensus size: 18
63149919 TAAAATTTAT
63149929 ATTTTAAAAAAATATAAAA
1 ATTTTAAAAAAAT-TAAAA
*
63149948 ATTCTTAAAAAAATTTAAA
1 ATT-TTAAAAAAATTAAAA
63149967 ATTTTAAAAA
1 ATTTTAAAAA
63149977 TTTTCTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 7 0.26
19 10 0.37
20 10 0.37
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
ATTTTAAAAAAATTAAAA
Found at i:63150860 original size:16 final size:16
Alignment explanation
Indices: 63150841--63150871 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
63150831 TTGAAATTTT
63150841 TTTCAAATATATATGG
1 TTTCAAATATATATGG
*
63150857 TTTCAAATTTATATG
1 TTTCAAATATATATG
63150872 TTTTAACATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGG
Found at i:63155054 original size:27 final size:27
Alignment explanation
Indices: 63155003--63155055 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
63154993 ACTCTCTCTT
*
63155003 TTTCTCTTTATTTTCCATTATCTTCTG
1 TTTCTCTTTATTTTCCATTACCTTCTG
63155030 TTTCTCCTTCTATTTT-C-TTACCTTCT
1 TTTCT-CTT-TATTTTCCATTACCTTCT
63155056 CCATATCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 13 0.57
28 4 0.17
29 6 0.26
ACGTcount: A:0.09, C:0.26, G:0.02, T:0.62
Consensus pattern (27 bp):
TTTCTCTTTATTTTCCATTACCTTCTG
Found at i:63156861 original size:2 final size:2
Alignment explanation
Indices: 63156854--63156880 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
63156844 TTTCAAAAAC
63156854 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
63156881 TTTCAGCATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:63158402 original size:2 final size:2
Alignment explanation
Indices: 63158395--63158432 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
63158385 GGTGTCATTC
63158395 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
63158433 TAGTGGTCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:63161373 original size:31 final size:30
Alignment explanation
Indices: 63161315--63161373 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
63161305 TTAATTTATT
* *
63161315 ATTTGGTACCTGATTTGAATTCGATGTTCA
1 ATTTGGTACCAGATTTGAATTCAATGTTCA
**
63161345 ATTTGGTATCCAGATTTGGTTTCAATGTT
1 ATTTGGTA-CCAGATTTGAATTCAATGTT
63161374 GGTACCAAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 8 0.33
31 16 0.67
ACGTcount: A:0.22, C:0.12, G:0.20, T:0.46
Consensus pattern (30 bp):
ATTTGGTACCAGATTTGAATTCAATGTTCA
Found at i:63162275 original size:2 final size:2
Alignment explanation
Indices: 63162270--63162299 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
63162260 TATATATATT
63162270 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
63162300 ATTTATAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:63162411 original size:6 final size:6
Alignment explanation
Indices: 63162400--63162430 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
63162390 TTTCATTTGA
63162400 TTAATT TTAATT TTAATT TTAATT TTAATT T
1 TTAATT TTAATT TTAATT TTAATT TTAATT T
63162431 ATTCAATTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTAATT
Found at i:63163272 original size:24 final size:23
Alignment explanation
Indices: 63163224--63163279 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
63163214 AAATATCCCT
*
63163224 AGAATAAACAGAGTTAGACTGGG
1 AGAATAAACAGAGTTAGACTAGG
63163247 AGAATATAACAGAGTTTA-ACTAGG
1 AGAATA-AACAGAG-TTAGACTAGG
*
63163271 AGAAGAAAC
1 AGAATAAAC
63163280 TCAGTTGGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 9 0.31
24 17 0.59
25 3 0.10
ACGTcount: A:0.48, C:0.09, G:0.25, T:0.18
Consensus pattern (23 bp):
AGAATAAACAGAGTTAGACTAGG
Found at i:63165928 original size:26 final size:25
Alignment explanation
Indices: 63165899--63165948 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
63165889 CAATTTTCAC
* *
63165899 TTTGATACTTGAGATTTTTTTTTTAA
1 TTTGAGACTTGA-ATTTTTGTTTTAA
*
63165925 TTTGAGATTTGAATTTTTGTTTTA
1 TTTGAGACTTGAATTTTTGTTTTA
63165949 TCTCGTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.22, C:0.02, G:0.14, T:0.62
Consensus pattern (25 bp):
TTTGAGACTTGAATTTTTGTTTTAA
Found at i:63172692 original size:37 final size:38
Alignment explanation
Indices: 63172636--63172707 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
63172626 CCGAATATAA
*
63172636 TAAATATATTTTTTAA-TTTTTTAATTTTAAAATACTT
1 TAAAAATATTTTTTAATTTTTTTAATTTTAAAATACTT
* *
63172673 TAAAAATATTTTTTTATTTTTTTATTTTTAAAATA
1 TAAAAATATTTTTTAATTTTTTTAATTTTAAAATA
63172708 TTTTTTTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
37 14 0.45
38 17 0.55
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (38 bp):
TAAAAATATTTTTTAATTTTTTTAATTTTAAAATACTT
Found at i:63173109 original size:19 final size:22
Alignment explanation
Indices: 63173069--63173116 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
63173059 AAACAATGGA
63173069 AAAATAGTAGGAAAACAACAAC
1 AAAATAGTAGGAAAACAACAAC
*
63173091 AAAATAGT-GGAAAAACAACAAT
1 AAAATAGTAGG-AAAACAACAAC
63173113 AAAA
1 AAAA
63173117 CAACACCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 2 0.08
22 22 0.92
ACGTcount: A:0.67, C:0.10, G:0.12, T:0.10
Consensus pattern (22 bp):
AAAATAGTAGGAAAACAACAAC
Found at i:63176185 original size:197 final size:195
Alignment explanation
Indices: 63175659--63176320 Score: 941
Period size: 194 Copynumber: 3.4 Consensus size: 195
63175649 ATTCTTTATA
* * * *
63175659 TAATTCTGGTCACTAACATCATCAATTATTAGTTTTTTAGAATGATCAATAGAGGCATGAAGTTT
1 TAATTCTGGTCAATAACAACATCAATTATTAG-TGTTTAGAATGATCAATAGAGGAATGAAGTTT
* * *
63175724 TTTGCTTGGTTTGTGCTTTGTTTTACCTTCTCAGGGCTGCTATAAGTAGTTTTGTTCTTGTGTGT
65 TTTGCTCGGTTTGTGCTTTGTTTTACCTTGTCAGGGCTGCTATAAGGAGTTTTGTTCTTGTGTGT
*
63175789 TTATGTTGAAGTTATTTGTTGTAACTATATAGTTCATTTATTGTTTTAAGCATATCAACCATGTG
130 TTATGTTGAAGTTATTTGCTGTAACTATATAGTTCATTTATTGTTTTAAGCATATCAACCATGTG
63175854 G
195 G
* * * **
63175855 TAGTTCTGGTCCATAGCAACATCAATTATTAGTGACTA-AATGATCAATAGAGGAATGAAGTTTT
1 TAATTCTGGTCAATAACAACATCAATTATTAGTGTTTAGAATGATCAATAGAGGAATGAAGTTTT
* *
63175919 TTGCTCGGTTTGTGCTTTGTTTTACCTTGTCAGGGCTGCCATAAGGAGTTCTGTTCTTGTGTGTT
66 TTGCTCGGTTTGTGCTTTGTTTTACCTTGTCAGGGCTGCTATAAGGAGTTTTGTTCTTGTGTGTT
* *
63175984 TATGTTGAAGTTATATGCTGTAATTATATAGTTCATTTATTGTTTTAAGCATATCAACCATGTGG
131 TATGTTGAAGTTATTTGCTGTAACTATATAGTTCATTTATTGTTTTAAGCATATCAACCATGTGG
* ** *
63176049 TAATCCCAGTCAATAACAACATCAATTATTAGAGTTTAGAATATGATCAATAGAGGAATGAAGTT
1 TAATTCTGGTCAATAACAACATCAATTATTAGTGTTTAG-A-ATGATCAATAGAGGAATGAAGTT
* *
63176114 TTTTGCTCGGTTTGTGCTTCGTTTCACCTTGTCAGGGCTGCTATAAGGAGTTTTGTTCTTGTGTG
64 TTTTGCTCGGTTTGTGCTTTGTTTTACCTTGTCAGGGCTGCTATAAGGAGTTTTGTTCTTGTGTG
* * * * * * *
63176179 TTTATGTTGAAGTTATTTGCTGTAACTATACAGTTCGTTTGTCGGTCTAAGCATATCAACCATAT
129 TTTATGTTGAAGTTATTTGCTGTAACTATATAGTTCATTTATTGTTTTAAGCATATCAACCATGT
63176244 GG
194 GG
* ** * * *
63176246 CAATTCTGGTCAATAATGACATCAATTATTACTGTTTCGAATGA-CCATAGAGGAATGAAGTTTT
1 TAATTCTGGTCAATAACAACATCAATTATTAGTGTTTAGAATGATCAATAGAGGAATGAAGTTTT
* *
63176310 TTTCTTGGTTT
66 TTGCTCGGTTT
63176321 ATGCATGTTT
Statistics
Matches: 412, Mismatches: 51, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
194 204 0.50
195 7 0.02
196 29 0.07
197 172 0.42
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.42
Consensus pattern (195 bp):
TAATTCTGGTCAATAACAACATCAATTATTAGTGTTTAGAATGATCAATAGAGGAATGAAGTTTT
TTGCTCGGTTTGTGCTTTGTTTTACCTTGTCAGGGCTGCTATAAGGAGTTTTGTTCTTGTGTGTT
TATGTTGAAGTTATTTGCTGTAACTATATAGTTCATTTATTGTTTTAAGCATATCAACCATGTGG
Found at i:63176733 original size:5 final size:6
Alignment explanation
Indices: 63176718--63176742 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
63176708 TCGCATTGTG
63176718 TTTTTA TTTTTA TTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA T
63176743 CATTCTTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:63190950 original size:30 final size:31
Alignment explanation
Indices: 63190886--63190957 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 31
63190876 TTAATATAAA
*
63190886 AATTTA-TACTTAAGTTTGATTTTAATGTTC
1 AATTTAGTACTTAAGTTTGATTTTAATGTCC
**
63190916 AATTTAGTACTTAAG-TTG-TTTTTTTGTCC
1 AATTTAGTACTTAAGTTTGATTTTAATGTCC
*
63190945 TAATTTGGTACTT
1 -AATTTAGTACTT
63190958 GATTTTGACT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 8 0.22
30 20 0.56
31 8 0.22
ACGTcount: A:0.25, C:0.08, G:0.12, T:0.54
Consensus pattern (31 bp):
AATTTAGTACTTAAGTTTGATTTTAATGTCC
Found at i:63194808 original size:2 final size:2
Alignment explanation
Indices: 63194801--63194831 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
63194791 AAAGAAGAGA
63194801 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
63194832 CATAGCTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:63195496 original size:16 final size:16
Alignment explanation
Indices: 63195460--63195490 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
63195450 AAACTCTGAT
63195460 AATTTGAATCCAAAAC
1 AATTTGAATCCAAAAC
*
63195476 AATTTGAATCTAAAA
1 AATTTGAATCCAAAA
63195491 TGATTTAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.13, G:0.06, T:0.29
Consensus pattern (16 bp):
AATTTGAATCCAAAAC
Found at i:63195538 original size:16 final size:16
Alignment explanation
Indices: 63195517--63195552 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
63195507 TCAAAATTCA
63195517 AAATTAACCTCAATCT
1 AAATTAACCTCAATCT
* *
63195533 AAATTAACTTTAATCT
1 AAATTAACCTCAATCT
63195549 AAAT
1 AAAT
63195553 AAATCAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.36
Consensus pattern (16 bp):
AAATTAACCTCAATCT
Found at i:63197568 original size:168 final size:168
Alignment explanation
Indices: 63197196--63197535 Score: 479
Period size: 168 Copynumber: 2.0 Consensus size: 168
63197186 ATAGCCACCT
* * * * *
63197196 AATTATTAATAATTATTTTATTTAAATTTATTTATAAAAAATTATAAAAAAAATTATTTAACTAT
1 AATTATTAGTAATAATTTTATTCAAA-TTATTTATAAAAAATTATAAAAAAAATCATCTAACTAT
* * * *
63197261 TAATAAATTTTTTTTTTATATCACCAAACTATGAAAAGTTACAAGATGATCACCTAATATCCAAT
65 TAATAAATTTTCTTTTTATATCACCAAACTATGAAAAATTACAAAATGATCACCAAATATCCAAT
*
63197326 TCTATCTTTTTTTATCAACAACTTGCTAACGTGCTTTTAA
130 TC-ATCTTTTTTTATCAACAACTTACTAACGTGCTTTTAA
* * **
63197366 AATTATTAGTAATTATTTTATTCAAATTTATTTATGAAAAATTAT-AAAATGATCATCTAACTAT
1 AATTATTAGTAATAATTTTATTCAAA-TTATTTATAAAAAATTATAAAAAAAATCATCTAACTAT
* *
63197430 TAATAAA-TTTCTTTTTATATCACCAAACTATGAAAAATTACAAAATGGTCACCAAATATTCAAT
65 TAATAAATTTTCTTTTTATATCACCAAACTATGAAAAATTACAAAATGATCACCAAATATCCAAT
*
63197494 TC-TCTTTTTTTATCAACAACTTACTAATGTGCTTTTAA
130 TCATCTTTTTTTATCAACAACTTACTAACGTGCTTTTAA
63197532 AATT
1 AATT
63197536 GGCATTGTAG
Statistics
Matches: 155, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
166 38 0.25
168 53 0.34
169 22 0.14
170 42 0.27
ACGTcount: A:0.41, C:0.12, G:0.04, T:0.43
Consensus pattern (168 bp):
AATTATTAGTAATAATTTTATTCAAATTATTTATAAAAAATTATAAAAAAAATCATCTAACTATT
AATAAATTTTCTTTTTATATCACCAAACTATGAAAAATTACAAAATGATCACCAAATATCCAATT
CATCTTTTTTTATCAACAACTTACTAACGTGCTTTTAA
Found at i:63202854 original size:18 final size:19
Alignment explanation
Indices: 63202815--63202860 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
63202805 AACTATATAA
63202815 TATTATTTTTAAATAATGT
1 TATTATTTTTAAATAATGT
* *
63202834 TATTGTTTTTAAA-AATTT
1 TATTATTTTTAAATAATGT
63202852 TATTTATTT
1 TA-TTATTT
63202861 ATATATTATG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (19 bp):
TATTATTTTTAAATAATGT
Found at i:63209014 original size:66 final size:66
Alignment explanation
Indices: 63208901--63209100 Score: 319
Period size: 66 Copynumber: 3.0 Consensus size: 66
63208891 ACGTGGAATG
** * *
63208901 TAACAGGTAACTCATGGTGATGTATTAATTTTGATCTAATGTGTAAGAACTAATTTATCAGTTTT
1 TAACAGGTAACTCATGGTGATGTATTAATTTTGATCTAACATATAAGAACTAATTTGTCAGTTTT
63208966 T
66 T
63208967 TAACAGGTAACTCATGGTGATGTATTAATTTTGATCTAACATATAAGAACTAATTTGTCAGTTTT
1 TAACAGGTAACTCATGGTGATGTATTAATTTTGATCTAACATATAAGAACTAATTTGTCAGTTTT
63209032 T
66 T
* * * * *
63209033 TAACAGGTAACTCATGGTGATGTATTATTTTTTATCTAACTTATAAGAATTAATTTGTCAATTTT
1 TAACAGGTAACTCATGGTGATGTATTAATTTTGATCTAACATATAAGAACTAATTTGTCAGTTTT
63209098 T
66 T
63209099 TA
1 TA
63209101 GATAGAGAAA
Statistics
Matches: 125, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 125 1.00
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (66 bp):
TAACAGGTAACTCATGGTGATGTATTAATTTTGATCTAACATATAAGAACTAATTTGTCAGTTTT
T
Found at i:63211873 original size:350 final size:352
Alignment explanation
Indices: 63211237--63211911 Score: 1076
Period size: 350 Copynumber: 1.9 Consensus size: 352
63211227 AAGACAGATT
* * *
63211237 ACTAAGCTTTAGCCCTTACCTCGGAAGTAATTTAAGGTTATACTCTATAGTTTTTGGATGATGAC
1 ACTAAGCTTTAGCCCTTACCTCGGAAGTAATTTAAGGCTATACTATATAGTTCTTGGATGATGAC
*
63211302 AATCTATGGAAGTAATTGCGAGTAAATTCTCATGATATATTTCTATATATAATGTTTGCTGGTTG
66 AATCTATGGAAGTAATTGCGAGTAAATTCTCATGATATATTTCTATATATAATGTTTGCTGGTAG
* * * * *
63211367 ATCATGAGACTTCGATAGGGACTTAAGGGGTTAGTTTTGCTTATATAGAAACTCTGGGAAATTTT
131 ATCATGAGACTTCAATAGGGACTTAAGGAGTTAGCTTTGCTTATAAAGAAACTCTGGGAAAATTT
* *
63211432 GATGGTTGTTTCTGCTGAAATCATACCTATTTCAGCCATTTTATTTGTTGATTTCCGAGCTTGTG
196 GATGGTTGTTTCTGCTGAAATCAAACATATTTCAGCCATTTTATTTGTTGATTTCCGAGCTTGTG
* * * *
63211497 ATTTTTTTGCTCCGTTGTAGATTTTCCTATGCAGAATTCTGCTAGGTGGTTGAGTTTCCTTGTAG
261 ATTTTTTTGCTCCGTTGTAGATTTTCCTACGCAGAATTATGCTAGGTGGTTGAGATTCATTGTAG
63211562 CTCTTTAGCCACTACCAATTATGGATC
326 CTCTTTAGCCACTACCAATTATGGATC
63211589 ACTAAGCTTTAGCCCTTACCTC-GAAGTAATTTAAGGCTATACTATATAG-TCTTGGATGATGAC
1 ACTAAGCTTTAGCCCTTACCTCGGAAGTAATTTAAGGCTATACTATATAGTTCTTGGATGATGAC
* *
63211652 AATCTATGGAAGTAATTGTGAGTAAATTCTCATGATGTATTTCTATATATAATGTTTGCTGGTAG
66 AATCTATGGAAGTAATTGCGAGTAAATTCTCATGATATATTTCTATATATAATGTTTGCTGGTAG
63211717 ATCATGAGACTTCAATA-GGACTT-AGGAGTTAGACTTT-CTTATAAAGAAACTCTGGGAAAATT
131 ATCATGAGACTTCAATAGGGACTTAAGGAGTTAG-CTTTGCTTATAAAGAAACTCTGGGAAAATT
63211779 TGATGGTTGTTTCTGCTGAAATCAAACATATTTCAGCCATTTTATTTGTTGATTT-CGTAGCTTG
195 TGATGGTTGTTTCTGCTGAAATCAAACATATTTCAGCCATTTTATTTGTTGATTTCCG-AGCTTG
* * *
63211843 TGA-TTTTTTGCTCTGTTGTCGATTATTTTCCTACGCAGAATTATGTTAGGTGGTTGAGATTCAT
259 TGATTTTTTTGCTCCGTTGT--A-GATTTTCCTACGCAGAATTATGCTAGGTGGTTGAGATTCAT
63211907 TGTAG
321 TGTAG
63211912 AACTATAGGT
Statistics
Matches: 298, Mismatches: 20, Indels: 12
0.90 0.06 0.04
Matches are distributed among these distances:
347 17 0.06
348 93 0.31
349 10 0.03
350 131 0.44
351 25 0.08
352 22 0.07
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.40
Consensus pattern (352 bp):
ACTAAGCTTTAGCCCTTACCTCGGAAGTAATTTAAGGCTATACTATATAGTTCTTGGATGATGAC
AATCTATGGAAGTAATTGCGAGTAAATTCTCATGATATATTTCTATATATAATGTTTGCTGGTAG
ATCATGAGACTTCAATAGGGACTTAAGGAGTTAGCTTTGCTTATAAAGAAACTCTGGGAAAATTT
GATGGTTGTTTCTGCTGAAATCAAACATATTTCAGCCATTTTATTTGTTGATTTCCGAGCTTGTG
ATTTTTTTGCTCCGTTGTAGATTTTCCTACGCAGAATTATGCTAGGTGGTTGAGATTCATTGTAG
CTCTTTAGCCACTACCAATTATGGATC
Found at i:63217181 original size:18 final size:19
Alignment explanation
Indices: 63217158--63217203 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
63217148 GGTTTTGGGA
*
63217158 TTTTTTAA-TGTAACTTTT
1 TTTTTTAAGTGTAAATTTT
63217176 TTTTTTAAGTTGTAAATTTT
1 TTTTTTAAG-TGTAAATTTT
63217196 TATTTTTA
1 T-TTTTTA
63217204 TATGGATGGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 8 0.33
20 10 0.42
21 6 0.25
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.67
Consensus pattern (19 bp):
TTTTTTAAGTGTAAATTTT
Found at i:63224045 original size:18 final size:18
Alignment explanation
Indices: 63224022--63224078 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
63224012 CTTCAGATTC
63224022 AAGGTTTATATCGAATTT
1 AAGGTTTATATCGAATTT
* **
63224040 AAGGTTTGAGTTTAAAATTT
1 AAGGTTT-A-TATCGAATTT
**
63224060 AAGACTTATATCGAATTT
1 AAGGTTTATATCGAATTT
63224078 A
1 A
63224079 TATCAAATTT
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
18 15 0.52
19 2 0.07
20 12 0.41
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (18 bp):
AAGGTTTATATCGAATTT
Found at i:63225455 original size:75 final size:75
Alignment explanation
Indices: 63225323--63225624 Score: 453
Period size: 75 Copynumber: 4.0 Consensus size: 75
63225313 AGCATTCATG
* * * * ** * * * **
63225323 TTTTGGGGTGGTTGCCGTCGTTGATATGGGAACTGGGGTGCTGACCTAACTGTCTCTCTCATATT
1 TTTTGAGGTGGTTGCCGTGGTGGATATTGGAACCAGGGTTCTGACCTGACTGACTCTCTTGTATT
63225388 CTGGCCCATA
66 CTGGCCCATA
*
63225398 TTTTGTGGTGGTTGCCGTGGTGGATATTGGAACCAGGGTTCTGACCTGACTGACTCTCTTGTATT
1 TTTTGAGGTGGTTGCCGTGGTGGATATTGGAACCAGGGTTCTGACCTGACTGACTCTCTTGTATT
63225463 CTGGCCCATA
66 CTGGCCCATA
63225473 TTTTGAGGTGGTTGCCGTGGTGGAT-TATGGAACCAGGGTTCTGACCTGACTGACTCTCTTGTAT
1 TTTTGAGGTGGTTGCCGTGGTGGATAT-TGGAACCAGGGTTCTGACCTGACTGACTCTCTTGTAT
*
63225537 CCTGGCCCATA
65 TCTGGCCCATA
* *
63225548 TTTTGAGGTGGTTGCCGTGGTGGATTTTGGAACCAGGGTTCTGACCTGACTGACTCTCTTGTACT
1 TTTTGAGGTGGTTGCCGTGGTGGATATTGGAACCAGGGTTCTGACCTGACTGACTCTCTTGTATT
63225613 CTGGCCCATA
66 CTGGCCCATA
63225623 TT
1 TT
63225625 AGGTTGTTCC
Statistics
Matches: 210, Mismatches: 15, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
74 1 0.00
75 208 0.99
76 1 0.00
ACGTcount: A:0.15, C:0.21, G:0.29, T:0.35
Consensus pattern (75 bp):
TTTTGAGGTGGTTGCCGTGGTGGATATTGGAACCAGGGTTCTGACCTGACTGACTCTCTTGTATT
CTGGCCCATA
Found at i:63231992 original size:18 final size:19
Alignment explanation
Indices: 63231971--63232019 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
63231961 TCATTTTATT
63231971 TTTTAATTTTATTTAA-AA
1 TTTTAATTTTATTTAATAA
*
63231989 TTTTACATTAT-TTTAATAA
1 TTTTA-ATTTTATTTAATAA
63232008 TTTTAATATTTA
1 TTTTAAT-TTTA
63232020 ATGAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTAATTTTATTTAATAA
Found at i:63244931 original size:16 final size:17
Alignment explanation
Indices: 63244910--63244942 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
63244900 AGAGCTAAGG
63244910 TTTAC-TTCATTTTTTT
1 TTTACTTTCATTTTTTT
*
63244926 TTTACTTTCCTTTTTTT
1 TTTACTTTCATTTTTTT
63244943 GCTTACTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTACTTTCATTTTTTT
Found at i:63247063 original size:6 final size:6
Alignment explanation
Indices: 63247052--63247076 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
63247042 CTTGATTTCT
63247052 TATATG TATATG TATATG TATATG T
1 TATATG TATATG TATATG TATATG T
63247077 GCCTTCAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (6 bp):
TATATG
Found at i:63253353 original size:67 final size:67
Alignment explanation
Indices: 63253245--63253380 Score: 254
Period size: 67 Copynumber: 2.0 Consensus size: 67
63253235 TGTTCAAGTG
*
63253245 CTTTAGATGTTGATGACTGAAAGCTTTTAGGTGTCACTTATGTAATCATTAAGGTTCTCAAAACA
1 CTTTAGATGTGGATGACTGAAAGCTTTTAGGTGTCACTTATGTAATCATTAAGGTTCTCAAAACA
63253310 TA
66 TA
*
63253312 CTTTAGATGTGGATGACTGAAAGCTTTTAGGTGTCACTTATGTAATGATTAAGGTTCTCAAAACA
1 CTTTAGATGTGGATGACTGAAAGCTTTTAGGTGTCACTTATGTAATCATTAAGGTTCTCAAAACA
63253377 TA
66 TA
63253379 CT
1 CT
63253381 ATAGGAGATT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (67 bp):
CTTTAGATGTGGATGACTGAAAGCTTTTAGGTGTCACTTATGTAATCATTAAGGTTCTCAAAACA
TA
Found at i:63260433 original size:13 final size:13
Alignment explanation
Indices: 63260415--63260440 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
63260405 ATCACTTGTC
63260415 CTTGATCAGATAA
1 CTTGATCAGATAA
63260428 CTTGATCAGATAA
1 CTTGATCAGATAA
63260441 GTGTAGCTAG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
CTTGATCAGATAA
Found at i:63260505 original size:37 final size:37
Alignment explanation
Indices: 63260455--63260566 Score: 179
Period size: 37 Copynumber: 3.0 Consensus size: 37
63260445 AGCTAGGCTA
****
63260455 CCACTTATCACTTTACCACTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
*
63260492 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAA
1 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
63260529 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
1 CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
63260566 C
1 C
63260567 TAAAACTACC
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (37 bp):
CCACTTATCACTTTGTTTCTTGATCAGATAAGTGTAG
Found at i:63270408 original size:56 final size:57
Alignment explanation
Indices: 63270276--63270418 Score: 184
Period size: 55 Copynumber: 2.5 Consensus size: 57
63270266 CTATTTTCAT
* * * *
63270276 ATTGGAGCTTGAACTTTTTTTAGTCCAAGTTAGGCCTTGAACTTGGCGATTATTCCCGC
1 ATTGGGGCTTGAA-TTTTTTT-GTCCAAGTTAGGCCTTAAACTTGACAATTATTCCCGC
* * *
63270335 ATTGGGCCTTGAA-TTTTTTCTCCAAGTTAGGCC-TAAACTTGACAATTCTTCCC-C
1 ATTGGGGCTTGAATTTTTTTGTCCAAGTTAGGCCTTAAACTTGACAATTATTCCCGC
63270389 ATTGGGGCTTGAATTTTTTTGTCCAAGTTA
1 ATTGGGGCTTGAATTTTTTTGTCCAAGTTA
63270419 ATCCTTGATA
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
54 13 0.18
55 31 0.42
56 13 0.18
57 6 0.08
59 11 0.15
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (57 bp):
ATTGGGGCTTGAATTTTTTTGTCCAAGTTAGGCCTTAAACTTGACAATTATTCCCGC
Found at i:63275334 original size:22 final size:23
Alignment explanation
Indices: 63275304--63275346 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
63275294 CTCAACTTAA
* *
63275304 AAATGGGTAACTT-ATTCTTTTT
1 AAATAGGTAAATTAATTCTTTTT
63275326 AAATAGGTAAATTAATTCTTT
1 AAATAGGTAAATTAATTCTTT
63275347 CTATTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.47
Consensus pattern (23 bp):
AAATAGGTAAATTAATTCTTTTT
Found at i:63283149 original size:18 final size:18
Alignment explanation
Indices: 63283128--63283170 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
63283118 CGTCATTGCT
*
63283128 ATCATCGCCATCATTGTC
1 ATCATCGCCATCATTATC
* *
63283146 ATCATCACCGTCATTATC
1 ATCATCGCCATCATTATC
63283164 ATCATCG
1 ATCATCG
63283171 GACCAGGTCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.26, C:0.33, G:0.09, T:0.33
Consensus pattern (18 bp):
ATCATCGCCATCATTATC
Found at i:63283496 original size:240 final size:243
Alignment explanation
Indices: 63283164--63283647 Score: 769
Period size: 249 Copynumber: 2.0 Consensus size: 243
63283154 CGTCATTATC
* *
63283164 ATCATCGGACCAGGTCAGGTTCGAGTTGAGTTTTCGATTCGGGGCAGAATTGACAACTCTGCCAC
1 ATCATCGGACCAAGTCAGGTTCGAGTTGAGTTTTCGATTCGGGGCAGAATTGACAACTCTGCAAC
63283229 TGGCGCATCATTGTCCTCATCGTCGTCATCACCATCACCATCAATAGCTTTAAAAAG-ATCATCA
66 TGGCGCATCATTGTCCTCATCGTCGTCATCACCATCACCATCAATAGCTTTAAAAAGCATCATCA
* *
63283293 TCGTCG-TCAT-T-ATCATCATCATCTTCTTCTTCACCGTTCTACCAATCTAAAGAGAACAAATG
131 TCGTCGATCATATCATCATCATCATCTTCTTCTTCACCGTTCGACCAATCTAAAGAGAACAAACG
*
63283355 ACAGGAAGCTCGTTTTCAAACTTTTTGCAAAGAAGTAATAGCAGAAAG
196 ACAGGAAGCTCGTTTTCAAACCTTTTGCAAAGAAGTAATAGCAGAAAG
*
63283403 ATCATCGGACCAAGTCAGGTTTGAGTTGAGTTTTCGATTTCGGGGCAGAATTGACAACTCTGCAA
1 ATCATCGGACCAAGTCAGGTTCGAGTTGAGTTTTCGA-TTCGGGGCAGAATTGACAACTCTGCAA
* * *
63283468 CTGGCGCATCATTGTCCTCATTGTCGTCATCACCATCATCATCAATAGCTTTAAAAAGACCATCG
65 CTGGCGCATCATTGTCCTCATCGTCGTCATCACCATCACCATCAATAGCTTTAAAAAG--CATCA
* *
63283533 TCGTCGTCGTCATCATCATCATCATCATCATCTTCTTCTTCACCGTTCGACCAATCTAAGGAGAA
128 TCATCGTCG--ATCAT-ATCATCATCATCATCTTCTTCTTCACCGTTCGACCAATCTAAAGAGAA
* *
63283598 CAAACGACGGGAAGCTCGTTTTCGAACCTTTTGCAAAGAAGTAATAGCAG
190 CAAACGACAGGAAGCTCGTTTTCAAACCTTTTGCAAAGAAGTAATAGCAG
63283648 GGAGATCAGC
Statistics
Matches: 222, Mismatches: 13, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
239 35 0.16
240 82 0.37
243 11 0.05
246 4 0.02
248 1 0.00
249 89 0.40
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.29
Consensus pattern (243 bp):
ATCATCGGACCAAGTCAGGTTCGAGTTGAGTTTTCGATTCGGGGCAGAATTGACAACTCTGCAAC
TGGCGCATCATTGTCCTCATCGTCGTCATCACCATCACCATCAATAGCTTTAAAAAGCATCATCA
TCGTCGATCATATCATCATCATCATCTTCTTCTTCACCGTTCGACCAATCTAAAGAGAACAAACG
ACAGGAAGCTCGTTTTCAAACCTTTTGCAAAGAAGTAATAGCAGAAAG
Found at i:63292535 original size:20 final size:21
Alignment explanation
Indices: 63292510--63292550 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
63292500 GACGAAGCGG
*
63292510 TTTATAA-TTATTTAGTAATT
1 TTTATAATTTATTTACTAATT
63292530 TTTATAATTTATTTACTAATT
1 TTTATAATTTATTTACTAATT
63292551 ATTGAGCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (21 bp):
TTTATAATTTATTTACTAATT
Found at i:63298923 original size:14 final size:14
Alignment explanation
Indices: 63298887--63298920 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
63298877 TCATCATTTG
63298887 CCTATAACCAAAAC
1 CCTATAACCAAAAC
63298901 CCTATAACCAAAAC
1 CCTATAACCAAAAC
63298915 CC-ATAA
1 CCTATAA
63298921 ACCCATACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (14 bp):
CCTATAACCAAAAC
Found at i:63299889 original size:10 final size:10
Alignment explanation
Indices: 63299876--63299907 Score: 50
Period size: 9 Copynumber: 3.4 Consensus size: 10
63299866 CCAATTTTTT
63299876 ATTTTTAATA
1 ATTTTTAATA
63299886 A-TTTT-ATA
1 ATTTTTAATA
63299894 ATTTTTAATA
1 ATTTTTAATA
63299904 ATTT
1 ATTT
63299908 ATTTAATCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
8 4 0.20
9 8 0.40
10 8 0.40
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:63299890 original size:17 final size:17
Alignment explanation
Indices: 63299868--63299912 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 17
63299858 AATTAAATCC
63299868 AATTTTTTATTTTTAAT
1 AATTTTTTATTTTTAAT
*
63299885 AATTTTATAATTTTTAAT
1 AATTTT-TTATTTTTAAT
63299903 AATTTATTTA
1 AATTT-TTTA
63299913 ATCTAAGCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.25
18 17 0.71
19 1 0.04
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
AATTTTTTATTTTTAAT
Found at i:63302679 original size:2 final size:2
Alignment explanation
Indices: 63302672--63302697 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
63302662 ATACTTTCTC
63302672 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
63302698 TATTTTACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:63303301 original size:26 final size:25
Alignment explanation
Indices: 63303250--63303301 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
63303240 AATATTCAAA
* * * *
63303250 ATTTTCAAAAGCACTTTTCCACAGC
1 ATTTTCAAAAACACTTCTCAAAAGC
63303275 ATTTCTCAAAAACACTTCTCAAAAGC
1 ATTT-TCAAAAACACTTCTCAAAAGC
63303301 A
1 A
63303302 ATGAAGAACT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.38, C:0.27, G:0.06, T:0.29
Consensus pattern (25 bp):
ATTTTCAAAAACACTTCTCAAAAGC
Found at i:63309645 original size:21 final size:20
Alignment explanation
Indices: 63309621--63309663 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
63309611 TATATACGAG
63309621 TTTTGTTCAAATTAATTTTGA
1 TTTTG-TCAAATTAATTTTGA
* *
63309642 TTTTGTCCAATTATTTTTGA
1 TTTTGTCAAATTAATTTTGA
63309662 TT
1 TT
63309664 CTTTATGTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.23, C:0.07, G:0.09, T:0.60
Consensus pattern (20 bp):
TTTTGTCAAATTAATTTTGA
Found at i:63338818 original size:22 final size:22
Alignment explanation
Indices: 63338790--63338942 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
63338780 TGTTGATAGT
*
63338790 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
63338812 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
63338834 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
* * * **
63338856 ACGAACTAAACCCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
**
63338878 ACGTACTAAGCTCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
*
63338900 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
63338922 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
63338943 GAACAATAAA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTA
Found at i:63339620 original size:3 final size:3
Alignment explanation
Indices: 63339612--63339666 Score: 69
Period size: 3 Copynumber: 18.3 Consensus size: 3
63339602 TTTATTGTAA
*
63339612 TAT TAT TA- TAT TA- TAT TAT TAGT TTT GTAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT -TAT TAT TAT TAT TAT TAT
63339657 TAT TAT TAT T
1 TAT TAT TAT T
63339667 TATTCATTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
2 4 0.09
3 38 0.83
4 4 0.09
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:63339677 original size:8 final size:7
Alignment explanation
Indices: 63339612--63339677 Score: 52
Period size: 6 Copynumber: 9.4 Consensus size: 7
63339602 TTTATTGTAA
63339612 TATTATT
1 TATTATT
63339619 ATATTATAT
1 -TATTAT-T
63339628 TATTAGTT
1 TATTA-TT
63339636 T-TGTA-T
1 TAT-TATT
63339642 TATTA-T
1 TATTATT
63339648 TATTA-T
1 TATTATT
63339654 TATTA-T
1 TATTATT
63339660 TATTATT
1 TATTATT
63339667 TATTCATT
1 TATT-ATT
63339675 TAT
1 TAT
63339678 ACCATCTAGT
Statistics
Matches: 52, Mismatches: 0, Indels: 12
0.81 0.00 0.19
Matches are distributed among these distances:
6 22 0.42
7 7 0.13
8 21 0.40
9 2 0.04
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (7 bp):
TATTATT
Found at i:63342063 original size:2 final size:2
Alignment explanation
Indices: 63342056--63342090 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
63342046 ACAATTCATG
*
63342056 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
63342091 TTCACAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:63344950 original size:35 final size:35
Alignment explanation
Indices: 63344904--63344970 Score: 134
Period size: 35 Copynumber: 1.9 Consensus size: 35
63344894 CAATGGAACT
63344904 TTCTACTAGAGATAACCTAACTTAGATGCCATGAA
1 TTCTACTAGAGATAACCTAACTTAGATGCCATGAA
63344939 TTCTACTAGAGATAACCTAACTTAGATGCCAT
1 TTCTACTAGAGATAACCTAACTTAGATGCCAT
63344971 AAAAGTTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (35 bp):
TTCTACTAGAGATAACCTAACTTAGATGCCATGAA
Found at i:63345122 original size:41 final size:42
Alignment explanation
Indices: 63345066--63345154 Score: 144
Period size: 41 Copynumber: 2.1 Consensus size: 42
63345056 CCTAATTGTG
* * *
63345066 AAAATAATTCTCTTATTCTAATAAACTACTAAAAGATAAGA-
1 AAAATAATTCCCTTATTCTAATAAACTACTAAAACATAAAAT
63345107 AAAATAATTCCCTTATTCTAATAAACTACTAAAACATAAAAT
1 AAAATAATTCCCTTATTCTAATAAACTACTAAAACATAAAAT
63345149 AAAATA
1 AAAATA
63345155 TTTCTAGAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
41 38 0.86
42 6 0.14
ACGTcount: A:0.54, C:0.13, G:0.02, T:0.30
Consensus pattern (42 bp):
AAAATAATTCCCTTATTCTAATAAACTACTAAAACATAAAAT
Found at i:63345207 original size:19 final size:19
Alignment explanation
Indices: 63345183--63345223 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
63345173 TGATTTATTC
63345183 TAAGATTTATCTACCTAAA
1 TAAGATTTATCTACCTAAA
63345202 TAAGATTTATCTACCTAAA
1 TAAGATTTATCTACCTAAA
63345221 TAA
1 TAA
63345224 CTTTAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.37
Consensus pattern (19 bp):
TAAGATTTATCTACCTAAA
Found at i:63346102 original size:22 final size:22
Alignment explanation
Indices: 63346070--63346207 Score: 195
Period size: 22 Copynumber: 6.3 Consensus size: 22
63346060 AATGGGATGA
*
63346070 ATGTTTCACGTACTAAGCTCTC
1 ATGTTTAACGTACTAAGCTCTC
63346092 ATGTTTAACGTACTAAGCTCTC
1 ATGTTTAACGTACTAAGCTCTC
* * *
63346114 ATGTTTAACGAACTAAACCCTC
1 ATGTTTAACGTACTAAGCTCTC
**
63346136 ATGGCTAACGTACTAAGCTCTC
1 ATGTTTAACGTACTAAGCTCTC
**
63346158 ATGGCTAACGTACTAAGCTCTC
1 ATGTTTAACGTACTAAGCTCTC
*
63346180 ATGTTTCACGTACTAAGCTCTC
1 ATGTTTAACGTACTAAGCTCTC
63346202 ATGTTT
1 ATGTTT
63346208 GAACAATAAA
Statistics
Matches: 104, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 104 1.00
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.33
Consensus pattern (22 bp):
ATGTTTAACGTACTAAGCTCTC
Found at i:63359738 original size:2 final size:2
Alignment explanation
Indices: 63359713--63359777 Score: 91
Period size: 2 Copynumber: 34.0 Consensus size: 2
63359703 GTTGTTGATG
* *
63359713 TA TA -A TA TA AA T- TA TA TG TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
63359753 TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
63359778 AAATGGGGTC
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
1 3 0.05
2 53 0.95
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:63362469 original size:34 final size:34
Alignment explanation
Indices: 63362426--63362493 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
63362416 AGGAAGGAGA
*
63362426 AAACTTTTTTAAAGAATGAAACTTTTCTTCCCTT
1 AAACTTTTTTAAAGAATGAAACTTTCCTTCCCTT
* *
63362460 AAACTTTTTTAAGGGATGAAACTTTCCTTCCCTT
1 AAACTTTTTTAAAGAATGAAACTTTCCTTCCCTT
63362494 CCCTTTCTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.29, C:0.19, G:0.09, T:0.43
Consensus pattern (34 bp):
AAACTTTTTTAAAGAATGAAACTTTCCTTCCCTT
Found at i:63366939 original size:27 final size:26
Alignment explanation
Indices: 63366882--63366949 Score: 95
Period size: 27 Copynumber: 2.7 Consensus size: 26
63366872 CGAAACTATT
* *
63366882 ATGAGCGTCCCGA-TAAGGGCTTTTC
1 ATGAGCTTCCCGATTAAAGGCTTTTC
63366907 A-GAGCTTCCCGATTAAAGGCTCTTTC
1 ATGAGCTTCCCGATTAAAGGCT-TTTC
63366933 ATGAGCTTCCCGATTAA
1 ATGAGCTTCCCGATTAA
63366950 TTAGCTCTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
24 10 0.26
25 8 0.21
26 5 0.13
27 15 0.39
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (26 bp):
ATGAGCTTCCCGATTAAAGGCTTTTC
Found at i:63370307 original size:19 final size:19
Alignment explanation
Indices: 63370285--63370324 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
63370275 ATGCGCATTT
63370285 TGGCACACAAAGTGCATCC
1 TGGCACACAAAGTGCATCC
* *
63370304 TGGCACACGAGGTGCATCC
1 TGGCACACAAAGTGCATCC
63370323 TG
1 TG
63370325 ACGCATAAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.25, C:0.30, G:0.28, T:0.17
Consensus pattern (19 bp):
TGGCACACAAAGTGCATCC
Found at i:63371406 original size:14 final size:15
Alignment explanation
Indices: 63371387--63371416 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
63371377 GTTTAATTAT
63371387 AATTAAA-CTTAATC
1 AATTAAATCTTAATC
63371401 AATTAAATCTTAATC
1 AATTAAATCTTAATC
63371416 A
1 A
63371417 TCAATTAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (15 bp):
AATTAAATCTTAATC
Found at i:63388136 original size:15 final size:16
Alignment explanation
Indices: 63388116--63388145 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
63388106 TAACAAGAAG
63388116 TATATA-ATTTTTTTA
1 TATATACATTTTTTTA
63388131 TATATACATTTTTTT
1 TATATACATTTTTTT
63388146 GTTGATCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (16 bp):
TATATACATTTTTTTA
Found at i:63409638 original size:28 final size:26
Alignment explanation
Indices: 63409573--63409647 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 26
63409563 TAATTATTAT
*
63409573 TAATTTTTTTCTAATTTTCTAAAAAATA
1 TAATTTTTTT-TAATTTT-TGAAAAATA
63409601 TAATTTTTTTTGAATTTTTGAAAAATA
1 TAATTTTTTTT-AATTTTTGAAAAATA
** *
63409628 TTTTTTATTTTTTATTTTTG
1 TAATTT-TTTTTAATTTTTG
63409648 TATTTTTTGA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
27 20 0.49
28 21 0.51
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.63
Consensus pattern (26 bp):
TAATTTTTTTTAATTTTTGAAAAATA
Found at i:63409645 original size:6 final size:7
Alignment explanation
Indices: 63409626--63409655 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
63409616 TTTTGAAAAA
63409626 TATTTTT
1 TATTTTT
63409633 TATTTTT
1 TATTTTT
63409640 TATTTTT
1 TATTTTT
63409647 GTATTTTT
1 -TATTTTT
63409655 T
1 T
63409656 GATGAGATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.83
Consensus pattern (7 bp):
TATTTTT
Found at i:63413956 original size:30 final size:27
Alignment explanation
Indices: 63413900--63413957 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 27
63413890 TAGAACTACA
*
63413900 TAATTTAAAATAAAACAAATACTTTTT
1 TAATTTAAAATAAAAAAAATACTTTTT
*
63413927 TAATTTAAAAATTAAAAAAAAATATTTTTT
1 TAATTT-AAAA-T-AAAAAAAATACTTTTT
63413957 T
1 T
63413958 TAAAATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 6 0.23
28 4 0.15
29 1 0.04
30 15 0.58
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (27 bp):
TAATTTAAAATAAAAAAAATACTTTTT
Found at i:63424067 original size:12 final size:12
Alignment explanation
Indices: 63424050--63424080 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
63424040 CTTCGAATAC
63424050 CCGCCACCGCTG
1 CCGCCACCGCTG
63424062 CCGCCACCGCTG
1 CCGCCACCGCTG
63424074 CCGCCAC
1 CCGCCAC
63424081 TGCCACCGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.10, C:0.61, G:0.23, T:0.06
Consensus pattern (12 bp):
CCGCCACCGCTG
Found at i:63426838 original size:21 final size:22
Alignment explanation
Indices: 63426797--63426843 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
63426787 AGCAGAGGCG
63426797 TTTTATTCATTTTACTCAAAAA
1 TTTTATTCATTTTACTCAAAAA
*
63426819 TTTTATT-ATTTT-CATTAAAAA
1 TTTTATTCATTTTAC-TCAAAAA
63426840 TTTT
1 TTTT
63426844 GTCCTTTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 1 0.04
21 15 0.65
22 7 0.30
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTATTCATTTTACTCAAAAA
Found at i:63427259 original size:19 final size:19
Alignment explanation
Indices: 63427227--63427263 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
63427217 TGTCATGTCA
* *
63427227 ATAAATATTTAAAAAAATC
1 ATAAAAATTAAAAAAAATC
63427246 ATAAAAATTAAAAAAAAT
1 ATAAAAATTAAAAAAAAT
63427264 AAGTATACTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (19 bp):
ATAAAAATTAAAAAAAATC
Done.