Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008359.1 Hibiscus syriacus cultivar Beakdansim tig00111098_pilon, whole genome shotgun sequence
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: 1252926
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1089930 original size:31 final size:31
Alignment explanation
Indices: 1089889--1089968 Score: 108
Period size: 31 Copynumber: 2.6 Consensus size: 31
1089879 ACCATATGGT
* *
1089889 TTCGGAACATATGGACTGTTTACCTATGTCC
1 TTCGGAACATATGGACTGATTACCTAGGTCC
* *
1089920 TTCGGGACATATGGACTGATTACCTAGGTTC
1 TTCGGAACATATGGACTGATTACCTAGGTCC
1089951 TTCGGAATC-TATGGACTG
1 TTCGGAA-CATATGGACTG
1089969 GTCCTTCGGG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
31 42 0.98
32 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.34
Consensus pattern (31 bp):
TTCGGAACATATGGACTGATTACCTAGGTCC
Found at i:1092743 original size:21 final size:21
Alignment explanation
Indices: 1092717--1092761 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1092707 GATTTCTGGG
* *
1092717 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1092738 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1092759 CAA
1 CAA
1092762 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1093677 original size:29 final size:30
Alignment explanation
Indices: 1093626--1093745 Score: 172
Period size: 31 Copynumber: 4.0 Consensus size: 30
1093616 GGGTCGAGGG
1093626 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATG-TCTTCGGAACATATGGACTGT
1093657 TTACCTATGT-TTCGGAACATATGGACTGT
1 TTACCTATGTCTTCGGAACATATGGACTGT
* *
1093686 TTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGT-CTTCGGAACATATGGACTGT
*
1093717 TTACCTAGGTCTTCGGAATC-TATGGACTG
1 TTACCTATGTCTTCGGAA-CATATGGACTG
1093746 GTCATTCGGG
Statistics
Matches: 82, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
29 29 0.35
30 17 0.21
31 36 0.44
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.36
Consensus pattern (30 bp):
TTACCTATGTCTTCGGAACATATGGACTGT
Found at i:1093694 original size:60 final size:61
Alignment explanation
Indices: 1093626--1093745 Score: 181
Period size: 60 Copynumber: 2.0 Consensus size: 61
1093616 GGGTCGAGGG
* * *
1093626 TTACCTATGTTCTTCGGAACATATGGACTGTTTACCTATGT-TTCGGAA-CATATGGACTGT
1 TTACCTATGTCCTTCGGAACATATGGACTGATTACCTAGGTCTTCGGAATC-TATGGACTGT
*
1093686 TTACCTATGTCCTTCGGGACATATGGACTGATTACCTAGGTCTTCGGAATCTATGGACTG
1 TTACCTATGTCCTTCGGAACATATGGACTGATTACCTAGGTCTTCGGAATCTATGGACTG
1093746 GTCATTCGGG
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
60 37 0.69
61 16 0.30
62 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.36
Consensus pattern (61 bp):
TTACCTATGTCCTTCGGAACATATGGACTGATTACCTAGGTCTTCGGAATCTATGGACTGT
Found at i:1096656 original size:23 final size:23
Alignment explanation
Indices: 1096630--1096676 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1096620 GAGTCGAGGG
*
1096630 ATTTCATAGTGGTCATTCGGGAC
1 ATTTCATAGTAGTCATTCGGGAC
1096653 ATTTCATAGTAGTCATTCGGGAC
1 ATTTCATAGTAGTCATTCGGGAC
1096676 A
1 A
1096677 AATTCATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (23 bp):
ATTTCATAGTAGTCATTCGGGAC
Found at i:1099371 original size:2 final size:2
Alignment explanation
Indices: 1099364--1099445 Score: 79
Period size: 2 Copynumber: 43.0 Consensus size: 2
1099354 TGTAACATGT
*
1099364 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA CCA -A TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
1099404 TA TA TA TCA CTA -A T- TA -A TA -A TA TA TA TA TA TA TA TA TA TA
1 TA TA TA T-A -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1099444 TA
1 TA
1099446 AACGCAAATG
Statistics
Matches: 69, Mismatches: 1, Indels: 20
0.77 0.01 0.22
Matches are distributed among these distances:
1 7 0.10
2 58 0.84
3 3 0.04
4 1 0.01
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1101520 original size:25 final size:25
Alignment explanation
Indices: 1101492--1101542 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
1101482 GGTGGAAATG
*
1101492 GGCGGTAG-ACTTGGTTGGCTCTAGT
1 GGCGGTAGAACTT-GCTGGCTCTAGT
1101517 GGCGGTAGAACTTGCTGGCTCTAGT
1 GGCGGTAGAACTTGCTGGCTCTAGT
1101542 G
1 G
1101543 ACAGTGGCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.14, C:0.18, G:0.39, T:0.29
Consensus pattern (25 bp):
GGCGGTAGAACTTGCTGGCTCTAGT
Found at i:1102037 original size:59 final size:60
Alignment explanation
Indices: 1101941--1102074 Score: 162
Period size: 59 Copynumber: 2.2 Consensus size: 60
1101931 GAAATGTTGG
* * ** * * *
1101941 TCCCTCGAGTAAGGCGTCACTGATTTGAAATGACGTAAATCAAGCCA-AGGTAATATTAA
1 TCCCTCGAGTGAGGCATCACTGATTCAAAATGACGTAAATCAAGCAATAAGAAATATTAA
* * *
1102000 TCCCTCGAGTGAGGCATCACTGATTCAAAATGTCGTAAATCTAGCAATAAGAAATGTTAA
1 TCCCTCGAGTGAGGCATCACTGATTCAAAATGACGTAAATCAAGCAATAAGAAATATTAA
*
1102060 TCCCTCAAGTGAGGC
1 TCCCTCGAGTGAGGC
1102075 GTAGTTTGTT
Statistics
Matches: 63, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
59 40 0.63
60 23 0.37
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.25
Consensus pattern (60 bp):
TCCCTCGAGTGAGGCATCACTGATTCAAAATGACGTAAATCAAGCAATAAGAAATATTAA
Found at i:1102322 original size:75 final size:74
Alignment explanation
Indices: 1102164--1102623 Score: 487
Period size: 75 Copynumber: 6.2 Consensus size: 74
1102154 AAGGGAAACC
* * ****
1102164 TTCTCAAGCGAGATGAAATTTGTTTTTACAAAAACAATCT----TGAG-TAAAATGAAATGTTTC
1 TTCTCAAGCGAGAT-AAATTTGTTTTAAGAAAAACAATCTCAAGTGAGAT-AAATCTTCTGTTTC
*
1102224 GAGT-AAAAAC
64 GAGTGAAAAAA
* *
1102234 TGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAAACACTCTCAAGTGAGATAAAAT-TTCTGTTT
1 T-TCTCAAGCGAGATAAA-TTTGTTTTAAGAAAAACAATCTCAAGTGAGAT-AAATCTTCTGTTT
1102298 CGAGTGAAAAAA
63 CGAGTGAAAAAA
* * *
1102310 TTCTCAACCGAGATGAATCTTGTTTTAAGAAAAACAATCTCAAGTAAGATAAAAT-TTCTGTTTC
1 TTCTCAAGCGAGATAAAT-TTGTTTTAAGAAAAACAATCTCAAGTGAGAT-AAATCTTCTGTTTC
**
1102374 GAGTGAAACTA
64 GAGTGAAAAAA
* * *
1102385 -TCTCAAGCGAGATGAATCTTGTTTTAAGAAAAATAATCTCAAGTGAGATAAATCTTCTGTTTTG
1 TTCTCAAGCGAGATAAAT-TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCG
**
1102449 AGTGAAACTA
65 AGTGAAAAAA
* * *
1102459 -TCTCAAGCAAGATAAAATTTGTTTTAAGAAAAATAATATCAAGTGAGATAAATCTTCTGTTTCG
1 TTCTCAAGCGAGAT-AAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCG
*
1102523 AGTG-AAAAT
65 AGTGAAAAAA
1102532 TATCTCAAGCGAGATAAAATTTGTTTTAAGAAAAA-AGATCTCAAGTGAGATAAATCTTCTGTTT
1 T-TCTCAAGCGAGAT-AAATTTGTTTTAAGAAAAACA-ATCTCAAGTGAGATAAATCTTCTGTTT
**
1102596 CGAGTGAAACTA
63 CGAGTGAAAAAA
*
1102608 -TCTCAAACGAGATAAA
1 TTCTCAAGCGAGATAAA
1102624 ATTTTTGCTT
Statistics
Matches: 343, Mismatches: 32, Indels: 27
0.85 0.08 0.07
Matches are distributed among these distances:
70 4 0.01
71 31 0.09
73 9 0.03
74 139 0.41
75 146 0.43
76 14 0.04
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.31
Consensus pattern (74 bp):
TTCTCAAGCGAGATAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGA
GTGAAAAAA
Found at i:1102423 original size:74 final size:73
Alignment explanation
Indices: 1102218--1102623 Score: 539
Period size: 74 Copynumber: 5.5 Consensus size: 73
1102208 TAAAATGAAA
* * * *
1102218 TGTTTCGAGTAAAAACTGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAAACACTCTCAAGTGAG
1 TGTTTCGAGT-GAAACTATCTCAAGCGAGATAAA-TTTGTTTTAAGAAAAACAATCTCAAGTGAG
1102283 ATAAAAT-TTC
64 AT-AAATCTTC
** * * *
1102293 TGTTTCGAGTGAAAAAATTCTCAACCGAGATGAATCTTGTTTTAAGAAAAACAATCTCAAGTAAG
1 TGTTTCGAGTGAAACTA-TCTCAAGCGAGATAAAT-TTGTTTTAAGAAAAACAATCTCAAGTGAG
1102358 ATAAAAT-TTC
64 AT-AAATCTTC
* *
1102368 TGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAATAATCTCAAGTGAGA
1 TGTTTCGAGTGAAACTATCTCAAGCGAGATAAAT-TTGTTTTAAGAAAAACAATCTCAAGTGAGA
1102433 TAAATCTTC
65 TAAATCTTC
* * * *
1102442 TGTTTTGAGTGAAACTATCTCAAGCAAGATAAAATTTGTTTTAAGAAAAATAATATCAAGTGAGA
1 TGTTTCGAGTGAAACTATCTCAAGCGAGAT-AAATTTGTTTTAAGAAAAACAATCTCAAGTGAGA
1102507 TAAATCTTC
65 TAAATCTTC
*
1102516 TGTTTCGAGTGAAAATTATCTCAAGCGAGATAAAATTTGTTTTAAGAAAAA-AGATCTCAAGTGA
1 TGTTTCGAGTG-AAACTATCTCAAGCGAGAT-AAATTTGTTTTAAGAAAAACA-ATCTCAAGTGA
1102580 GATAAATCTTC
63 GATAAATCTTC
*
1102591 TGTTTCGAGTGAAACTATCTCAAACGAGATAAA
1 TGTTTCGAGTGAAACTATCTCAAGCGAGATAAA
1102624 ATTTTTGCTT
Statistics
Matches: 301, Mismatches: 24, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
73 7 0.02
74 147 0.49
75 147 0.49
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.31
Consensus pattern (73 bp):
TGTTTCGAGTGAAACTATCTCAAGCGAGATAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGAT
AAATCTTC
Found at i:1102433 original size:149 final size:145
Alignment explanation
Indices: 1102164--1102604 Score: 525
Period size: 149 Copynumber: 3.0 Consensus size: 145
1102154 AAGGGAAACC
* * ** *
1102164 TTCTCAAGCGAGATGAAATTTGTTTTTACAAAAACAATCTTGAGTAAAATGAAA----TGTTTCG
1 TTCTCAAGCGAGATG-AATTTGTTTTAAGAAAAACAATCTCAAGTAAGAT-AAATTTCTGTTTCG
* * * *
1102225 AGTAAAAACTGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAAACACTCTCAAGTGAGATAAAAT
64 AGT-GAAACTATCTCAAGCGAGATAAA-TTTGTTTTAAGAAAAA-AATCTCAAGTGAGAT-AAAT
1102290 -TTCTGTTTCGAGTGAAAAAA
125 CTTCTGTTTCGAGTGAAAAAA
*
1102310 TTCTCAACCGAGATGAATCTTGTTTTAAGAAAAACAATCTCAAGTAAGATAAAATTTCTGTTTCG
1 TTCTCAAGCGAGATGAAT-TTGTTTTAAGAAAAACAATCTCAAGTAAGAT-AAATTTCTGTTTCG
*
1102375 AGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAATAATCTCAAGTGAGATAAATCT
64 AGTGAAACTATCTCAAGCGAGATAAAT-TTGTTTTAAGAAAAA-AATCTCAAGTGAGATAAATCT
* **
1102440 TCTGTTTTGAGTGAAACTA
127 TCTGTTTCGAGTGAAAAAA
* * * * *
1102459 -TCTCAAGCAAGATAAAATTTGTTTTAAGAAAAATAATATCAAGTGAGATAAATCTTCTGTTTCG
1 TTCTCAAGCGAGAT-GAATTTGTTTTAAGAAAAACAATCTCAAGTAAGATAAAT-TTCTGTTTCG
*
1102523 AGTGAAAATTATCTCAAGCGAGATAAAATTTGTTTTAAGAAAAAAGATCTCAAGTGAGATAAATC
64 AGTG-AAACTATCTCAAGCGAGAT-AAATTTGTTTTAAGAAAAAA-ATCTCAAGTGAGATAAATC
1102588 TTCTGTTTCGAGTGAAA
126 TTCTGTTTCGAGTGAAA
1102605 CTATCTCAAA
Statistics
Matches: 258, Mismatches: 25, Indels: 21
0.85 0.08 0.07
Matches are distributed among these distances:
145 3 0.01
146 43 0.17
147 4 0.02
148 59 0.23
149 136 0.53
150 13 0.05
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.32
Consensus pattern (145 bp):
TTCTCAAGCGAGATGAATTTGTTTTAAGAAAAACAATCTCAAGTAAGATAAATTTCTGTTTCGAG
TGAAACTATCTCAAGCGAGATAAATTTGTTTTAAGAAAAAAATCTCAAGTGAGATAAATCTTCTG
TTTCGAGTGAAAAAA
Found at i:1102605 original size:149 final size:149
Alignment explanation
Indices: 1102218--1102627 Score: 562
Period size: 149 Copynumber: 2.8 Consensus size: 149
1102208 TAAAATGAAA
* * * * *
1102218 TGTTTCGAGTAAAAACTGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAAACACTCTCAAGTGAG
1 TGTTTCGAGTGAAAACTATCTCAAGCGAGATAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAG
** * *
1102283 ATAAAAT-TTCTGTTTCGAGTGAAAAAATTCTCAACCGAGAT-GAATCTTGTTTTAAGAAAAACA
66 AT-AAATCTTCTGTTTCGAGTGAAACTA-TCTCAAACGAGATAAAAT-TTGTTTTAAGAAAAACA
*
1102346 ATCTCAAGTAAGATAAAATTTC
128 ATATCAAGTAAGATAAAATTTC
* *
1102368 TGTTTCGAGTG-AAACTATCTCAAGCGAGAT-GAATCTTGTTTTAAGAAAAATAATCTCAAGTGA
1 TGTTTCGAGTGAAAACTATCTCAAGCGAGATAAAAT-TTGTTTTAAGAAAAACAATCTCAAGTGA
* * * *
1102431 GATAAATCTTCTGTTTTGAGTGAAACTATCTCAAGCAAGATAAAATTTGTTTTAAGAAAAATAAT
65 GATAAATCTTCTGTTTCGAGTGAAACTATCTCAAACGAGATAAAATTTGTTTTAAGAAAAACAAT
*
1102496 ATCAAGTGAGAT-AAATCTTC
130 ATCAAGTAAGATAAAAT-TTC
*
1102516 TGTTTCGAGTGAAAATTATCTCAAGCGAGATAAAATTTGTTTTAAGAAAAA-AGATCTCAAGTGA
1 TGTTTCGAGTGAAAACTATCTCAAGCGAGATAAAATTTGTTTTAAGAAAAACA-ATCTCAAGTGA
1102580 GATAAATCTTCTGTTTCGAGTGAAACTATCTCAAACGAGATAAAATTT
65 GATAAATCTTCTGTTTCGAGTGAAACTATCTCAAACGAGATAAAATTT
1102628 TTGCTTTGGG
Statistics
Matches: 232, Mismatches: 21, Indels: 15
0.87 0.08 0.06
Matches are distributed among these distances:
147 4 0.02
148 60 0.26
149 155 0.67
150 13 0.06
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (149 bp):
TGTTTCGAGTGAAAACTATCTCAAGCGAGATAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAG
ATAAATCTTCTGTTTCGAGTGAAACTATCTCAAACGAGATAAAATTTGTTTTAAGAAAAACAATA
TCAAGTAAGATAAAATTTC
Found at i:1102669 original size:74 final size:74
Alignment explanation
Indices: 1102533--1103027 Score: 373
Period size: 74 Copynumber: 6.7 Consensus size: 74
1102523 AGTGAAAATT
** ** ** ** *
1102533 ATCTCAAGCGAGATAAAA--TTTGTTTTAAGAAAAAAGATCTCAAGTGAGATAAATCTTCTGTTT
1 ATCTCAAGCGAGATAAAATTTTTGTTTCGAGTGAAACTATCTCAAGCAAGATGAATC-T-TGTTT
* * *
1102596 CGAGTGAAACT
64 CAAGAGAAACA
* * *
1102607 ATCTCAAACGAGATAAAATTTTTGCTTT-GGGTGAAACTATCTCAAGCAAGATGAATCTTGTTTT
1 ATCTCAAGCGAGATAAAATTTTTG-TTTCGAGTGAAACTATCTCAAGCAAGATGAATCTTGTTTC
*
1102671 AAGAAAAACA
65 AAGAGAAACA
* * * *
1102681 ATCTCAAGGGAGATAAAATTTATGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTA
1 ATCTCAAGCGAGATAAAATTTTTGTTTCGAGTGAAACTATCTCAAGCAAGATGAATCTTGTTTCA
1102746 AGAGAAACA
66 AGAGAAACA
* * * * *
1102755 ATCTCAAGTGAGAT-AAATCTTCTATTTCGTGTGAAACTATCTCAAGCAAGATAAAAT-TTGTTT
1 ATCTCAAGCGAGATAAAAT-TTTTGTTTCGAGTGAAACTATCTCAAGCAAGAT-GAATCTTGTTT
* *
1102818 AAAGAAAAACA
64 CAAGAGAAACA
* * * * * *
1102829 ATATCAAGTGAGAT-AAATCTTCTGTTTCGAGTGAAACAATCTCAAGCGAGATAAAATCTTGTTT
1 ATCTCAAGCGAGATAAAAT-TTTTGTTTCGAGTGAAACTATCTCAAGCAAGAT-GAATCTTGTTT
* *
1102893 TAAGAAAAACA
64 CAAGAGAAACA
* * * * * * *
1102904 ATCTCAAGTGAGAT-AAATCTTCG-TACTAAGTGAAACTATCTCAACCAAGATAAAAT-TTGTTT
1 ATCTCAAGCGAGATAAAATTTTTGTTTC-GAGTGAAACTATCTCAAGCAAGAT-GAATCTTGTTT
* *
1102966 TAAGAAAAACA
64 CAAGAGAAACA
* * * * * *
1102977 ATCTCAAGTGAGAT-AAATCTTCG-TACTAAGTGAAACTATCTCAACCAAGAT
1 ATCTCAAGCGAGATAAAATTTTTGTTTC-GAGTGAAACTATCTCAAGCAAGAT
1103028 AAAATTTTTG
Statistics
Matches: 369, Mismatches: 44, Indels: 17
0.86 0.10 0.04
Matches are distributed among these distances:
73 77 0.21
74 228 0.62
75 37 0.10
76 24 0.07
77 3 0.01
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (74 bp):
ATCTCAAGCGAGATAAAATTTTTGTTTCGAGTGAAACTATCTCAAGCAAGATGAATCTTGTTTCA
AGAGAAACA
Found at i:1102669 original size:149 final size:148
Alignment explanation
Indices: 1102218--1102701 Score: 534
Period size: 149 Copynumber: 3.3 Consensus size: 148
1102208 TAAAATGAAA
* * * *
1102218 TGTTTCGAGTAAAAACTGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAAACACTCTCAAGTGAG
1 TGTTTCGAGTAAAAACTATCTCAAGCGAGATAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAG
** * * * *
1102283 ATAAAAT-TTCTGTTTCGAGTGAAAAAATTCTCAACCGAGAT-GAATCTTGTTTTAAGAAAAACA
66 AT-AAATCTTCTGTTTCGAGTGAAACTA-TCTCAAACGAGATAAAATTTTGTTTTAAG-AAAACT
*
1102346 ATCTCAAGTAAGATAAAATTTC
128 ATCTCAAGTAAGAT-AAATCTC
* * *
1102368 TGTTTCGAGT-GAAACTATCTCAAGCGAGAT-GAATCTTGTTTTAAGAAAAATAATCTCAAGTGA
1 TGTTTCGAGTAAAAACTATCTCAAGCGAGATAAAAT-TTGTTTTAAGAAAAACAATCTCAAGTGA
* * * *
1102431 GATAAATCTTCTGTTTTGAGTGAAACTATCTCAAGCAAGATAAAA-TTTGTTTTAAGAAAAATAA
65 GATAAATCTTCTGTTTCGAGTGAAACTATCTCAAACGAGATAAAATTTTGTTTTAAGAAAACT-A
* *
1102495 TATCAAGTGAGATAAATCTTC
129 TCTCAAGTAAGATAAATC-TC
* *
1102516 TGTTTCGAGTGAAAATTATCTCAAGCGAGATAAAATTTGTTTTAAGAAAAA-AGATCTCAAGTGA
1 TGTTTCGAGTAAAAACTATCTCAAGCGAGATAAAATTTGTTTTAAGAAAAACA-ATCTCAAGTGA
* ** *
1102580 GATAAATCTTCTGTTTCGAGTGAAACTATCTCAAACGAGATAAAATTTTTGCTTTGGGTGAAACT
65 GATAAATCTTCTGTTTCGAGTGAAACTATCTCAAACGAGATAAAA-TTTTGTTTTAAG-AAAACT
* *
1102645 ATCTCAAGCAAGATGAATCT-
128 ATCTCAAGTAAGATAAATCTC
** * *
1102665 TGTTTTAAG-AAAAACAATCTCAAGGGAGATAAAATTT
1 TGTTTCGAGTAAAAACTATCTCAAGCGAGATAAAATTT
1102702 ATGTTTCGAG
Statistics
Matches: 283, Mismatches: 40, Indels: 24
0.82 0.12 0.07
Matches are distributed among these distances:
147 8 0.03
148 76 0.27
149 158 0.56
150 14 0.05
151 23 0.08
152 4 0.01
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (148 bp):
TGTTTCGAGTAAAAACTATCTCAAGCGAGATAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAG
ATAAATCTTCTGTTTCGAGTGAAACTATCTCAAACGAGATAAAATTTTGTTTTAAGAAAACTATC
TCAAGTAAGATAAATCTC
Found at i:1102687 original size:223 final size:223
Alignment explanation
Indices: 1102236--1103117 Score: 575
Period size: 223 Copynumber: 4.0 Consensus size: 223
1102226 GTAAAAACTG
* * * *
1102236 TCTCAAGCGAGACAAAGTTTGTTTTAAGAAAAACACTCTCAAGTGAGATAAAATTTCTGTTTCGA
1 TCTCAAGCGAGATAAAATTTGTTTTAAGAAAAACAATATCAAGTGAGATAAAATTTCTGTTTCGA
*
1102301 GTGAAAAAATTCTCAACCGAGATGAATCTTGTTTTAAGAAAAACAATCTCAAGTAAGATAAAATT
66 GTGAAAAAATTCTCAACCGAGATAAATCTTGTTTTAAGAAAAACAATCTCAAGTAAGATAAAATT
* * * **
1102366 TCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAATAATCTCAAGTGA
131 TCTGTTTCGAGTGAAACTATCTCAAACGAGATAAATCTTGCTTTAAGAAAAATAATCTCAAGCAA
* ** *
1102431 GATAAATCTTCTGTTTTGAGTGAAACTA
196 GATAAATCTTCTGTTTTAAGAAAAACAA
* *
1102459 TCTCAAGCAAGATAAAATTTGTTTTAAGAAAAATAATATCAAGTGAGAT-AAATCTTCTGTTTCG
1 TCTCAAGCGAGATAAAATTTGTTTTAAGAAAAACAATATCAAGTGAGATAAAAT-TTCTGTTTCG
* * *
1102523 AGTG-AAAATTATCTCAAGCGAGATAAAAT-TTGTTTTAAGAAAAA-AGATCTCAAGTGAGAT-A
65 AGTGAAAAAAT-TCTCAACCGAGAT-AAATCTTGTTTTAAGAAAAACA-ATCTCAAGTAAGATAA
* ** * *
1102584 AATCTTCTGTTTCGAGTGAAACTATCTCAAACGAGATAAAATTTTTGCTTTGGGTGAAACT-ATC
127 AAT-TTCTGTTTCGAGTGAAACTATCTCAAACGAGAT-AAA-TCTTGCTTTAAG-AAAAATAATC
*
1102648 TCAAGCAAGATGAATC-T-TGTTTTAAGAAAAACAA
188 TCAAGCAAGATAAATCTTCTGTTTTAAGAAAAACAA
* ** ** * * * * * *
1102682 TCTCAAGGGAGATAAAATTTATGTTTCGAGTGAAACTATCTCAAGCGAGAT-GAATCT-TGTTTT
1 TCTCAAGCGAGATAAAA-TT-TGTTTTAAGAAAAACAATATCAAGTGAGATAAAATTTCTGTTTC
* * * ** * ** ** * *
1102745 AAGAGAAACAA-TCTCAAGTGAGATAAATCTTCTATTTCGTGTGAAACTATCTCAAGCAAGATAA
64 GAGTGAAAAAATTCTCAACCGAGATAAATCTTGT-TTT-AAGAAAAACAATCTCAAGTAAGATAA
** ** * * ** * ** *
1102809 AA-TT-TGTTTAAAGAAAAACAATATCAAGTGAGATAAATCTT-CTGTTTCGAGTGAAACAATCT
127 AATTTCTGTTTCGAGTGAAACTATCTCAAACGAGATAAATCTTGC--TTT-AAGAAAAATAATCT
*
1102871 CAAGCGAGATAAAATC-T-TGTTTTAAGAAAAACAA
189 CAAGCAAGAT-AAATCTTCTGTTTTAAGAAAAACAA
* ** ** * * ***
1102905 TCTCAAGTGAGAT-AAATCTTCGTACTAAGTGAAACTATCTCAACCAAGATAAAA-TT-TGTTT-
1 TCTCAAGCGAGATAAAAT-TT-GTTTTAAGAAAAACAATATCAAGTGAGATAAAATTTCTGTTTC
* * * ** ** ** * **
1102966 TA-AGAAAAACAATCTCAAGTGAGATAAATCTTCGTACTAAGTGAAACTATCTCAACCAAGATAA
64 GAGTGAAAAA-ATTCTCAACCGAGATAAATCTT-GTTTTAAGAAAAACAATCTCAAGTAAGATAA
* * * ** * * *
1103030 AATTTTTGCTTCGAGTGAAACTATGTCAAGGGAGATGAATCTTGTTTTAAGAAAAACAATCTCAA
127 AATTTCTGTTTCGAGTGAAACTATCTCAAACGAGATAAATCTTGCTTTAAGAAAAATAATCTCAA
** *
1103095 GTGAGATAAAAT-TTCTGTATTAA
192 GCAAGAT-AAATCTTCTGTTTTAA
1103118 ATGAGACTGT
Statistics
Matches: 528, Mismatches: 99, Indels: 65
0.76 0.14 0.09
Matches are distributed among these distances:
219 1 0.00
220 9 0.02
221 67 0.13
222 132 0.25
223 235 0.45
224 28 0.05
225 52 0.10
226 4 0.01
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (223 bp):
TCTCAAGCGAGATAAAATTTGTTTTAAGAAAAACAATATCAAGTGAGATAAAATTTCTGTTTCGA
GTGAAAAAATTCTCAACCGAGATAAATCTTGTTTTAAGAAAAACAATCTCAAGTAAGATAAAATT
TCTGTTTCGAGTGAAACTATCTCAAACGAGATAAATCTTGCTTTAAGAAAAATAATCTCAAGCAA
GATAAATCTTCTGTTTTAAGAAAAACAA
Found at i:1102713 original size:335 final size:333
Alignment explanation
Indices: 1102280--1103112 Score: 1201
Period size: 335 Copynumber: 2.5 Consensus size: 333
1102270 ACTCTCAAGT
* * *
1102280 GAGATAAAATTTCTGTTTCGAGTGAAAAAATTCTCAACCGAGATGAATCTTGTTTTAAGAAAAAC
1 GAGATAAAATTTTTGTTT-GAGTGAAACAA-TCTCAAGCGAGATGAATCTTGTTTTAAGAAAAAC
* *
1102345 AATCTCAAGTAAGATAAAATTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTT
64 AATCTCAAGCAAGATAAAATTTATGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTT
* *
1102410 AAGAAAAATAATCTCAAGTGAGATAAATCTTCTGTTTTGAGTGAAACTATCTCAAGCAAGATAAA
129 AAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCAAGATAAA
* *
1102475 ATTTGTTTTAAGAAAAATAATATCAAGTGAGATAAATCTTCTGTTTCGAGTGAAA-ATTATCTCA
194 ATTTGTTTAAAGAAAAACAATATCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACA--ATCTCA
* *
1102539 AGCGAGATAAAAT-TTGTTTTAAGAAAAA-AGATCTCAAGTGAGATAAATCTTCTGT-TTCGAGT
257 AGCGAGATAAAATCTTGTTTTAAGAAAAACA-ATCTCAAGTGAGATAAATCTTC-GTACT-AAGT
1102601 GAAACTATCTCAAAC
319 GAAACTATCTCAAAC
* * *
1102616 GAGATAAAATTTTTGCTTTGGGTGAAACTATCTCAAGCAAGATGAATCTTGTTTTAAGAAAAACA
1 GAGATAAAATTTTTG-TTTGAGTGAAACAATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACA
**
1102681 ATCTCAAGGGAGATAAAATTTATGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTA
65 ATCTCAAGCAAGATAAAATTTATGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTA
* * *
1102746 AGAGAAACAATCTCAAGTGAGATAAATCTTCTATTTCGTGTGAAACTATCTCAAGCAAGATAAAA
130 AGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCAAGATAAAA
1102811 TTTGTTTAAAGAAAAACAATATCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACAATCTCAAGC
195 TTTGTTTAAAGAAAAACAATATCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACAATCTCAAGC
1102876 GAGATAAAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCGTACTAAGTGAAACT
260 GAGATAAAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCGTACTAAGTGAAACT
*
1102941 ATCTCAACC
325 ATCTCAAAC
* * * ** * * ** ** *
1102950 AAGATAAAATTTGT-TTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCGTACTAAGTGAAACT
1 GAGATAAAATTTTTGTTTGAGTGAAACAATCTCAAGCGAGATGAATCTT-GTTTTAAGAAAAACA
* * * * *
1103014 ATCTCAACCAAGATAAAATTTTTGCTTCGAGTGAAACTATGTCAAGGGAGATGAATCTTGTTTTA
65 ATCTCAAGCAAGATAAAATTTATGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTA
1103079 AGAAAAACAATCTCAAGTGAGATAAAAT-TTCTGT
130 AGAAAAACAATCTCAAGTGAGAT-AAATCTTCTGT
1103113 ATTAAATGAG
Statistics
Matches: 447, Mismatches: 43, Indels: 17
0.88 0.08 0.03
Matches are distributed among these distances:
332 26 0.06
333 95 0.21
334 54 0.12
335 245 0.55
336 24 0.05
337 3 0.01
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (333 bp):
GAGATAAAATTTTTGTTTGAGTGAAACAATCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAA
TCTCAAGCAAGATAAAATTTATGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAA
GAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCAAGATAAAAT
TTGTTTAAAGAAAAACAATATCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACAATCTCAAGCG
AGATAAAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCGTACTAAGTGAAACTA
TCTCAAAC
Found at i:1102759 original size:148 final size:147
Alignment explanation
Indices: 1102569--1102997 Score: 533
Period size: 148 Copynumber: 2.9 Consensus size: 147
1102559 AAGAAAAAAG
* ** * * **
1102569 ATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAACGAGATAAAATTTTTGCTT
1 ATCTCAAGCGAGATAAATC-T-TGTTTTAAGAGAAACAATCTCAAGTGAGAT-AAATTTTTG-TT
* * *
1102634 TGGGTGAAACTATCTCAAGCAAGAT-GAATCTTGTTTTAAGAAAAACAATCTCAAGGGAGATAAA
62 TGAGTGAAACTATCTCAAGCAAGATAAAAT-TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAA
*
1102698 AT-TTATGTTTCGAGTGAAACT
126 ATCTTATGTTTCGAGTGAAACA
* * *
1102719 ATCTCAAGCGAGATGAATCTTGTTTTAAGAGAAACAATCTCAAGTGAGATAAATCTTCTATTTCG
1 ATCTCAAGCGAGATAAATCTTGTTTTAAGAGAAACAATCTCAAGTGAGATAAAT-TTTTGTTT-G
* * *
1102784 TGTGAAACTATCTCAAGCAAGATAAAATTTGTTTAAAGAAAAACAATATCAAGTGAGAT-AAATC
64 AGTGAAACTATCTCAAGCAAGATAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATC
*
1102848 TTCTGTTTCGAGTGAAACA
129 TTATGTTTCGAGTGAAACA
* * * * *
1102867 ATCTCAAGCGAGATAAAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCGTACTA
1 ATCTCAAGCGAGAT-AAATCTTGTTTTAAGAGAAACAATCTCAAGTGAGATAAATTTTTGT-TTG
*
1102932 AGTGAAACTATCTCAACCAAGATAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGAT-AAATC
64 AGTGAAACTATCTCAAGCAAGATAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATC
1102996 TT
129 TT
1102998 CGTACTAAGT
Statistics
Matches: 244, Mismatches: 29, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
147 11 0.05
148 173 0.71
149 43 0.18
150 17 0.07
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.31
Consensus pattern (147 bp):
ATCTCAAGCGAGATAAATCTTGTTTTAAGAGAAACAATCTCAAGTGAGATAAATTTTTGTTTGAG
TGAAACTATCTCAAGCAAGATAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATCTT
ATGTTTCGAGTGAAACA
Found at i:1102998 original size:148 final size:149
Alignment explanation
Indices: 1102637--1103032 Score: 563
Period size: 148 Copynumber: 2.7 Consensus size: 149
1102627 TTTGCTTTGG
* *
1102637 GTGAAACTATCTCAAGCAAGAT-GAATCTTGTTTTAAGAAAAACAATCTCAAGGGAGATAAAAT-
1 GTGAAACTATCTCAAGCAAGATAAAAT-TTGTTTTAAGAAAAACAATCTCAAGTGAGAT-AAATC
* * *
1102700 TTATGTTTCGAGTGAAACTATCTCAAGCGAGAT-GAATCTTGTTTTAAGAGAAACAATCTCAAGT
64 TTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTGTTTTAAGAAAAACAATCTCAAGT
* **
1102764 GAGATAAATCTTCTATTTCGT
129 GAGATAAATCTTCTATCTCAA
* *
1102785 GTGAAACTATCTCAAGCAAGATAAAATTTGTTTAAAGAAAAACAATATCAAGTGAGATAAATCTT
1 GTGAAACTATCTCAAGCAAGATAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTT
*
1102850 CTGTTTCGAGTGAAACAATCTCAAGCGAGATAAAATCTTGTTTTAAGAAAAACAATCTCAAGTGA
66 CTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTGTTTTAAGAAAAACAATCTCAAGTGA
1102915 GATAAATCTTCGTA-CT-AA
131 GATAAATCTTC-TATCTCAA
*
1102933 GTGAAACTATCTCAACCAAGATAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTT
1 GTGAAACTATCTCAAGCAAGATAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTT
* * * *
1102998 C-G-TACTAAGTGAAACTATCTCAACCAAGATAAAAT
66 CTGTTTC-GAGTGAAACTATCTCAAGCGAGATAAAAT
1103033 TTTTGCTTCG
Statistics
Matches: 224, Mismatches: 19, Indels: 11
0.88 0.07 0.04
Matches are distributed among these distances:
146 2 0.01
147 30 0.13
148 144 0.64
149 46 0.21
150 2 0.01
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (149 bp):
GTGAAACTATCTCAAGCAAGATAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTT
CTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTGTTTTAAGAAAAACAATCTCAAGTGA
GATAAATCTTCTATCTCAA
Found at i:1105366 original size:14 final size:14
Alignment explanation
Indices: 1105347--1105380 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
1105337 GTTGAGATGC
1105347 AATGTAT-ATCATGT
1 AATGTATAAT-ATGT
1105361 AATGTATAATATGT
1 AATGTATAATATGT
1105375 AATGTA
1 AATGTA
1105381 CAATGTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 17 0.89
15 2 0.11
ACGTcount: A:0.41, C:0.03, G:0.15, T:0.41
Consensus pattern (14 bp):
AATGTATAATATGT
Found at i:1112601 original size:20 final size:20
Alignment explanation
Indices: 1112557--1112612 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
1112547 TAAGTTATCC
1112557 CAGTATCAATA-CCATCCTA
1 CAGTATCAATACCCATCCTA
1112576 CGAGTATCAATACCTCA-CCTA
1 C-AGTATCAATACC-CATCCTA
*
1112597 CAGTATCGATACCCAT
1 CAGTATCAATACCCAT
1112613 TGTTTAAGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
19 3 0.09
20 21 0.66
21 6 0.19
22 2 0.06
ACGTcount: A:0.34, C:0.32, G:0.09, T:0.25
Consensus pattern (20 bp):
CAGTATCAATACCCATCCTA
Found at i:1114004 original size:73 final size:75
Alignment explanation
Indices: 1113925--1114071 Score: 253
Period size: 75 Copynumber: 2.0 Consensus size: 75
1113915 TATAATTAAA
*
1113925 TAATTATACATATACT-AAAACATAAAAAAAAAC-TGACATAAAAGCACTCTCCAAACACACACC
1 TAATTATACATATACTAAAAACATAAAAAAAAACATGAAATAAAAGCACTCTCCAAACACACACC
1113988 TCAATCCCAT
66 TCAATCCCAT
* *
1113998 TAATTATACATATACTAAAAACATTACAAAAAACATGAAATAAAAGCACTCTCCAAACACACACC
1 TAATTATACATATACTAAAAACATAAAAAAAAACATGAAATAAAAGCACTCTCCAAACACACACC
1114063 TCAATCCCA
66 TCAATCCCA
1114072 CCCTATTAGG
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
73 16 0.23
74 15 0.22
75 38 0.55
ACGTcount: A:0.51, C:0.26, G:0.03, T:0.20
Consensus pattern (75 bp):
TAATTATACATATACTAAAAACATAAAAAAAAACATGAAATAAAAGCACTCTCCAAACACACACC
TCAATCCCAT
Found at i:1117483 original size:138 final size:138
Alignment explanation
Indices: 1117280--1117535 Score: 485
Period size: 138 Copynumber: 1.9 Consensus size: 138
1117270 GGATTCCAGT
* *
1117280 AACTATGGAGGTAACATAAGGTAATAGTTCAAGTTTCAGTCAGATCCTATCAGGTTAAGTAAAAT
1 AACTATGGAGGTAAAATAAGGTAATAGTTCAAGTTTCAGTCAGATCCTATCAGGTCAAGTAAAAT
1117345 CAGATACAGGTCATGTCAAGTCAATTTGATGGTCCGACTCGGATCCAGGTCAACCAGTTACTAAC
66 CAGATACAGGTCATGTCAAGTCAATTTGATGGTCCGACTCGGATCCAGGTCAACCAGTTACTAAC
1117410 TTCCTTGA
131 TTCCTTGA
*
1117418 AACTATGGAGGTAAAATAAGGTAATAGTTCAAGTTTTAGTCAGATCCTATCAGGTCAAGTAAAAT
1 AACTATGGAGGTAAAATAAGGTAATAGTTCAAGTTTCAGTCAGATCCTATCAGGTCAAGTAAAAT
1117483 CAGATACAGGTCATGTCAAGTCAATTTGATGGTCCGACTCGGATCCAGGTCAA
66 CAGATACAGGTCATGTCAAGTCAATTTGATGGTCCGACTCGGATCCAGGTCAA
1117536 ATCAGTTCGG
Statistics
Matches: 115, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
138 115 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.28
Consensus pattern (138 bp):
AACTATGGAGGTAAAATAAGGTAATAGTTCAAGTTTCAGTCAGATCCTATCAGGTCAAGTAAAAT
CAGATACAGGTCATGTCAAGTCAATTTGATGGTCCGACTCGGATCCAGGTCAACCAGTTACTAAC
TTCCTTGA
Found at i:1131684 original size:2 final size:2
Alignment explanation
Indices: 1131672--1131706 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1131662 TTAATTTCCT
1131672 TC TC T- TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1131707 GTGTAAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1132364 original size:15 final size:17
Alignment explanation
Indices: 1132329--1132362 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1132319 CCTTTTAAAA
1132329 ATTTAAAATTATTATAT
1 ATTTAAAATTATTATAT
* *
1132346 ATTTAAATTTTTTATAT
1 ATTTAAAATTATTATAT
1132363 TTTTTATTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTAAAATTATTATAT
Found at i:1132417 original size:17 final size:17
Alignment explanation
Indices: 1132395--1132428 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1132385 ATCCTTTAAA
1132395 TTTTATAAATTCAATAC
1 TTTTATAAATTCAATAC
1132412 TTTTATAAATTCAATAC
1 TTTTATAAATTCAATAC
1132429 GAGAGAGGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTTATAAATTCAATAC
Found at i:1134064 original size:23 final size:23
Alignment explanation
Indices: 1134032--1134076 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1134022 TTTTAAATTT
* *
1134032 TATATTTTTTCTTTTTAAAAATA
1 TATATATTTTATTTTTAAAAATA
*
1134055 TATATATTTTATTTTTTAAAAT
1 TATATATTTTATTTTTAAAAAT
1134077 TTTATATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
TATATATTTTATTTTTAAAAATA
Found at i:1134064 original size:24 final size:24
Alignment explanation
Indices: 1134032--1134084 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1134022 TTTTAAATTT
*
1134032 TATATTTTTTCTTTTTAAAAATATA
1 TATATTTTAT-TTTTTAAAAATATA
* *
1134057 TATATTTTATTTTTTAAAATTTTA
1 TATATTTTATTTTTTAAAAATATA
1134081 TATA
1 TATA
1134085 AAACTTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 16 0.64
25 9 0.36
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (24 bp):
TATATTTTATTTTTTAAAAATATA
Found at i:1138060 original size:34 final size:34
Alignment explanation
Indices: 1138011--1138078 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
1138001 GTAAAAAGTA
*
1138011 TAATTATCATATAATTTCATGTTAATATTCAGCC
1 TAATAATCATATAATTTCATGTTAATATTCAGCC
* *
1138045 TAATAATCATTTAATTTCATGTTAATCTTCAGCC
1 TAATAATCATATAATTTCATGTTAATATTCAGCC
1138079 AAGGGTTGAA
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:0.34, C:0.16, G:0.06, T:0.44
Consensus pattern (34 bp):
TAATAATCATATAATTTCATGTTAATATTCAGCC
Found at i:1148910 original size:22 final size:22
Alignment explanation
Indices: 1148885--1148954 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 22
1148875 CTTTATTTTA
1148885 TAATTAAAAATTATACTTAAAT
1 TAATTAAAAATTATACTTAAAT
** *
1148907 TAATT--GTATTCTA--T-AAT
1 TAATTAAAAATTATACTTAAAT
*
1148924 TAA--AAAAATTATACTTAAAA
1 TAATTAAAAATTATACTTAAAT
1148944 TAATTAAAAAT
1 TAATTAAAAAT
1148955 ATATTATCCA
Statistics
Matches: 34, Mismatches: 7, Indels: 14
0.62 0.13 0.25
Matches are distributed among these distances:
17 11 0.32
18 1 0.03
19 1 0.03
20 10 0.29
22 11 0.32
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (22 bp):
TAATTAAAAATTATACTTAAAT
Found at i:1148929 original size:35 final size:36
Alignment explanation
Indices: 1148878--1148948 Score: 108
Period size: 37 Copynumber: 2.0 Consensus size: 36
1148868 AACTCGACTT
* *
1148878 TATTTTATAATT-AAAAATTATACTTAAATTAATTG
1 TATTCTATAATTAAAAAATTATACTTAAAATAATTG
1148913 TATTCTATAATTAAAAAAATTATACTTAAAATAATT
1 TATTCTATAATT-AAAAAATTATACTTAAAATAATT
1148949 AAAAATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 11 0.34
37 21 0.66
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (36 bp):
TATTCTATAATTAAAAAATTATACTTAAAATAATTG
Found at i:1153986 original size:20 final size:20
Alignment explanation
Indices: 1153963--1154012 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
1153953 AAAGTAAAAA
1153963 AGGCAAAAGAATTTCATTAC
1 AGGCAAAAGAATTTCATTAC
1153983 AGGCAAAAGAATTTCATTAC
1 AGGCAAAAGAATTTCATTAC
*
1154003 AGTCAAAAGA
1 AGGCAAAAGA
1154013 TCTCCCCTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.48, C:0.14, G:0.16, T:0.22
Consensus pattern (20 bp):
AGGCAAAAGAATTTCATTAC
Found at i:1154431 original size:2 final size:2
Alignment explanation
Indices: 1154424--1154455 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1154414 GAGAAAGGAT
1154424 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1154456 TAAATGTGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1156002 original size:16 final size:16
Alignment explanation
Indices: 1155981--1156015 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1155971 AAATTCCTGG
*
1155981 TTATTTTTTTAAATTA
1 TTATTTCTTTAAATTA
*
1155997 TTATTTCTTTGAATTA
1 TTATTTCTTTAAATTA
1156013 TTA
1 TTA
1156016 GTTGTTCTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (16 bp):
TTATTTCTTTAAATTA
Found at i:1166734 original size:87 final size:86
Alignment explanation
Indices: 1166555--1167127 Score: 249
Period size: 87 Copynumber: 6.7 Consensus size: 86
1166545 TTACAGAACG
** * *
1166555 AAAGTGAGATTGAAAAAATTAAGGGCCTCAATTATAAAGGTGAAAATTGAGATTAAAAAAATTAG
1 AAAGTGAGATCAAAAAAATTAAGGGCCTCAATTATAAAGGTAAAAAGTGAGATTAAAAAAATTAG
* * *
1166620 GGGATTCAGCTACAAAGATAG
66 GGGACTCAACTACAAAGATAA
* * * * * *
1166641 ATAGTGAGATCAAAAAATATTAGGGGCCTCGATTTTAAAGGTAAAAAAGTGGGATTGAAAAAATT
1 AAAGTGAGATCAAAAAA-ATTAAGGGCCTCAATTATAAAGGT-AAAAAGTGAGATTAAAAAAATT
* * *
1166706 AGGGGCCTCAAC-ATAAATATAA
64 AGGGGACTCAACTACAAAGATAA
**** * * *
1166728 AAAGTGAGAT--AATTTTTTTAGGAGCTTCAATTATAAAGGTAAAAACTAAAAAGTGAGATTGAA
1 AAAGTGAGATCAAAAAAATTAAGG-GCCTCAATTATAAAGG-------TAAAAAGTGAGATTAAA
** * * * ** *
1166791 AATTTTAGGAGCCTCAATTTTAATTG-TAA
58 AAAATTAGGGGACTCAACTACAA-AGATAA
* * * * * * * * *
1166820 AAAGTGAGATTAAAAAAATCAA-GGCTTTAATTGTAAAGGTAGAAACTGAGATTAGAAAAAGTA-
1 AAAGTGAGATCAAAAAAATTAAGGGCCTCAATTATAAAGGTAAAAAGTGAGATTAAAAAAATTAG
* *
1166883 GGGATCTCAATTATAAA-AGTAA
66 GGGA-CTCAACTACAAAGA-TAA
* * * *
1166905 AAAGTGGGATTGAAAAAAAATT-AGGGCCTCAATTATAAATGTAAAAAGTGATATT-AAAAAATT
1 AAAGTGAGA-T-CAAAAAAATTAAGGGCCTCAATTATAAAGGTAAAAAGTGAGATTAAAAAAATT
* * * *
1166968 -GAGG-CTTCAATTATAAAAGA-AG
64 AGGGGAC-TCAACTA-CAAAGATAA
* * * * * *
1166990 AAAGTGAGGT-AGAAAAATTATGGGCCTAAATTATAAATGT-AAAAGTAAGATTAAAAAAATTA-
1 AAAGTGAGATCAAAAAAATTAAGGGCCTCAATTATAAAGGTAAAAAGTGAGATTAAAAAAATTAG
* *
1167052 GGG-C-C--TTA-AATG-TAA
66 GGGACTCAACTACAAAGATAA
* * *
1167067 AAA-TAGATATTAAAAAAATT-AGGAACCTCAATTATAAAGGTAAAAAGTG-GAATTAAAAAAA
1 AAAGT-GAGATCAAAAAAATTAAGG-GCCTCAATTATAAAGGTAAAAAGTGAG-ATTAAAAAAA
1167128 CAATAGGCCT
Statistics
Matches: 368, Mismatches: 86, Indels: 73
0.70 0.16 0.14
Matches are distributed among these distances:
76 1 0.00
77 12 0.03
78 23 0.06
79 19 0.05
81 1 0.00
82 18 0.05
83 29 0.08
84 8 0.02
85 68 0.18
86 27 0.07
87 70 0.19
88 27 0.07
91 29 0.08
92 31 0.08
93 1 0.00
94 4 0.01
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.26
Consensus pattern (86 bp):
AAAGTGAGATCAAAAAAATTAAGGGCCTCAATTATAAAGGTAAAAAGTGAGATTAAAAAAATTAG
GGGACTCAACTACAAAGATAA
Found at i:1166978 original size:41 final size:42
Alignment explanation
Indices: 1166774--1167127 Score: 275
Period size: 43 Copynumber: 8.5 Consensus size: 42
1166764 AGGTAAAAAC
* ** * *
1166774 TAAAAAGTGAGATTGAAAATTTTAGGAGCCTCAATTTTAATTG
1 TAAAAAGTGAGATTAAAAAAATTAGG-GCCTCAATTATAAATG
* * * * * *
1166817 TAAAAAGTGAGATTAAAAAAATCAAGGCTTTAATTGTAAAGG
1 TAAAAAGTGAGATTAAAAAAATTAGGGCCTCAATTATAAATG
* * * * * *
1166859 TAGAAACTGAGATTAGAAAAAGTAGGGATCTCAATTATAAAAG
1 TAAAAAGTGAGATTAAAAAAATTAGGG-CCTCAATTATAAATG
*
1166902 TAAAAAGTGGGATTGAAAAAAAATTAGGGCCTCAATTATAAATG
1 TAAAAAGTGAGATT--AAAAAAATTAGGGCCTCAATTATAAATG
* * *
1166946 TAAAAAGTGATATT-AAAAAATT-GAGGCTTCAATTATAAAAG
1 TAAAAAGTGAGATTAAAAAAATTAG-GGCCTCAATTATAAATG
* * *
1166987 -AAGAAAGTGAG-GTAGAAAAATTATGGGCCTAAATTATAAATG
1 TAA-AAAGTGAGATTAAAAAAATTA-GGGCCTCAATTATAAATG
*
1167029 T-AAAAGTAAGATTAAAAAAATTAGGG-C-C---T-TAAATG
1 TAAAAAGTGAGATTAAAAAAATTAGGGCCTCAATTATAAATG
* * *
1167064 TAAAAA-TAGATATTAAAAAAATTAGGAACCTCAATTATAAAGG
1 TAAAAAGT-GAGATTAAAAAAATTAGG-GCCTCAATTATAAATG
1167107 TAAAAAGTG-GAATTAAAAAAA
1 TAAAAAGTGAG-ATTAAAAAAA
1167128 CAATAGGCCT
Statistics
Matches: 243, Mismatches: 47, Indels: 42
0.73 0.14 0.13
Matches are distributed among these distances:
35 8 0.03
36 21 0.09
38 1 0.00
39 1 0.00
40 5 0.02
41 47 0.19
42 58 0.24
43 65 0.27
44 26 0.11
45 11 0.05
ACGTcount: A:0.50, C:0.06, G:0.18, T:0.26
Consensus pattern (42 bp):
TAAAAAGTGAGATTAAAAAAATTAGGGCCTCAATTATAAATG
Found at i:1168791 original size:42 final size:43
Alignment explanation
Indices: 1168715--1168810 Score: 149
Period size: 42 Copynumber: 2.3 Consensus size: 43
1168705 AATCTGTACA
*
1168715 AATAACGTCAAAATTTTAAATTTTAAATACTATTTTAAATCAG
1 AATAAAGTCAAAATTTTAAATTTTAAATACTATTTTAAATCAG
* * *
1168758 AATAAGGTCAAAA-TTTAGATTTTGAATACTATTTTAAATCAG
1 AATAAAGTCAAAATTTTAAATTTTAAATACTATTTTAAATCAG
1168800 AATAAAGTCAA
1 AATAAAGTCAA
1168811 TAAGTTGGTG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 37 0.76
43 12 0.24
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.36
Consensus pattern (43 bp):
AATAAAGTCAAAATTTTAAATTTTAAATACTATTTTAAATCAG
Found at i:1171411 original size:3 final size:3
Alignment explanation
Indices: 1171405--1171457 Score: 56
Period size: 3 Copynumber: 18.0 Consensus size: 3
1171395 TTTTTTTCCG
** *
1171405 TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TT- TTA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
1171452 TTA TTA
1 TTA TTA
1171458 CAATTTTTGC
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
2 3 0.07
3 35 0.85
4 3 0.07
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1171452 original size:20 final size:22
Alignment explanation
Indices: 1171411--1171452 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
1171401 TCCGTTATTA
1171411 TTATTATTATTATTATCGTTATC
1 TTATTATTATTATTATC-TTATC
1171434 TTATTATT-TTATTAT-TTAT
1 TTATTATTATTATTATCTTAT
1171453 TATTACAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
22 7 0.37
23 8 0.42
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (22 bp):
TTATTATTATTATTATCTTATC
Found at i:1171582 original size:25 final size:25
Alignment explanation
Indices: 1171553--1171652 Score: 175
Period size: 25 Copynumber: 4.0 Consensus size: 25
1171543 CCAACAACCC
1171553 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
1171578 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
1171603 ATCAGATTAGGGTTTCAAACCCTAAA
1 ATCAGATTAGGGTTTCAAACCCT-AA
*
1171629 ACCA-ATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
1171653 TCCCCTTCCA
Statistics
Matches: 73, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
24 2 0.03
25 66 0.90
26 5 0.07
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:1173195 original size:16 final size:17
Alignment explanation
Indices: 1173174--1173212 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
1173164 CTTATAGAAA
*
1173174 TTATTTTATTG-TTATT
1 TTATTTTATTGATTAAT
*
1173190 TTATTTTTTTGATTAAT
1 TTATTTTATTGATTAAT
1173207 TTATTT
1 TTATTT
1173213 GATGTTCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (17 bp):
TTATTTTATTGATTAAT
Found at i:1185872 original size:43 final size:43
Alignment explanation
Indices: 1185824--1186192 Score: 252
Period size: 43 Copynumber: 8.5 Consensus size: 43
1185814 TGACCGGACT
*
1185824 TCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCG
1 TCCTCATCACGTAGGAACCGTGTCAACCATAGATAACCAGCCG
* * ** *
1185867 TCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGATC-
1 TCCTCATCACGTAGGAACCGTGTCA--ACC-ATAGATAACCAG-CCG
* *
1185913 TCTTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCG
1 TCCTCATCACGTAGGAACCGTGTCAACCATAGATAACCAGCCG
* * ** *
1185956 TCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGATC-
1 TCCTCATCACGTAGGAACCGTGTCA--ACC-ATAGATAACCAG-CCG
* * * *
1186002 TCTTCATCACGTATGAGCCGTGTCAACCATAGATAACCAACCG
1 TCCTCATCACGTAGGAACCGTGTCAACCATAGATAACCAGCCG
* * * ** *
1186045 TCCTCATCACGTAGGAACCGTGTTATCACCTTTAGGTGGCCAG-AG
1 TCCTCATCACGTAGGAACCGTGTCA--ACC-ATAGATAACCAGCCG
* * * * ** *
1186090 T-TTCATCAGGTATGAACCGTGTCATCCCCAG---ACCAGATC-
1 TCCTCATCACGTAGGAACCGTGTCAACCATAGATAACCAG-CCG
* * *
1186129 TCTTCATCACGTAAGAGCCGTGTCAA-CATTAGGATAACCAGCCG
1 TCCTCATCACGTAGGAACCGTGTCAACCA-TA-GATAACCAGCCG
1186173 TCCTCATCACGTAGGAACCG
1 TCCTCATCACGTAGGAACCG
1186193 AGTTATCACC
Statistics
Matches: 246, Mismatches: 58, Indels: 43
0.71 0.17 0.12
Matches are distributed among these distances:
38 4 0.02
39 2 0.01
40 21 0.09
41 3 0.01
42 4 0.02
43 84 0.34
44 47 0.19
45 11 0.04
46 68 0.28
47 2 0.01
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (43 bp):
TCCTCATCACGTAGGAACCGTGTCAACCATAGATAACCAGCCG
Found at i:1185978 original size:89 final size:89
Alignment explanation
Indices: 1185827--1186113 Score: 497
Period size: 89 Copynumber: 3.2 Consensus size: 89
1185817 CCGGACTTCC
1185827 TCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
1 TCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
1185892 TCACCTTTAGATGGCCAGATCTCT
66 TCACCTTTAGATGGCCAGATCTCT
1185916 TCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
1 TCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
1185981 TCACCTTTAGATGGCCAGATCTCT
66 TCACCTTTAGATGGCCAGATCTCT
* *
1186005 TCATCACGTATGAGCCGTGTCAACCATAGATAACCAACCGTCCTCATCACGTAGGAACCGTGTTA
1 TCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
* *
1186070 TCACCTTTAGGTGGCCAGA-GT-T
66 TCACCTTTAGATGGCCAGATCTCT
* * *
1186092 TCATCAGGTATGAACCGTGTCA
1 TCATCACGTAGGAGCCGTGTCA
1186114 TCCCCAGACC
Statistics
Matches: 192, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
87 21 0.11
88 1 0.01
89 170 0.89
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (89 bp):
TCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
TCACCTTTAGATGGCCAGATCTCT
Found at i:1186457 original size:3 final size:3
Alignment explanation
Indices: 1186451--1186503 Score: 56
Period size: 3 Copynumber: 18.0 Consensus size: 3
1186441 TTTTTTTCCG
** *
1186451 TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TT- TTA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
1186498 TTA TTA
1 TTA TTA
1186504 CAATTTTTGC
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
2 3 0.07
3 35 0.85
4 3 0.07
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1186498 original size:20 final size:22
Alignment explanation
Indices: 1186457--1186498 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
1186447 TCCGTTATTA
1186457 TTATTATTATTATTATCGTTATC
1 TTATTATTATTATTATC-TTATC
1186480 TTATTATT-TTATTAT-TTAT
1 TTATTATTATTATTATCTTAT
1186499 TATTACAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
22 7 0.37
23 8 0.42
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (22 bp):
TTATTATTATTATTATCTTATC
Found at i:1186640 original size:25 final size:25
Alignment explanation
Indices: 1186611--1186710 Score: 175
Period size: 25 Copynumber: 4.0 Consensus size: 25
1186601 CCAACAACCC
1186611 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
1186636 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
1186661 ATCAGATTAGGGTTTCAAACCCTAAA
1 ATCAGATTAGGGTTTCAAACCCT-AA
*
1186687 ACCA-ATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
1186711 TCCCCTTCCA
Statistics
Matches: 73, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
24 2 0.03
25 66 0.90
26 5 0.07
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:1189418 original size:2 final size:2
Alignment explanation
Indices: 1189411--1189492 Score: 164
Period size: 2 Copynumber: 41.0 Consensus size: 2
1189401 GATTAAAATC
1189411 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
1189453 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
1189493 TTAAGACCAT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 80 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1193458 original size:14 final size:14
Alignment explanation
Indices: 1193439--1193468 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1193429 CTCAATGTTA
1193439 TTATTTGATTTTAT
1 TTATTTGATTTTAT
1193453 TTATTTGATTTTAT
1 TTATTTGATTTTAT
1193467 TT
1 TT
1193469 CAATCACGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (14 bp):
TTATTTGATTTTAT
Found at i:1198438 original size:22 final size:23
Alignment explanation
Indices: 1198407--1198449 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1198397 ATCTAACAAG
* *
1198407 TAAATTATATTTTATATTATATA
1 TAAATTATATATTAAATTATATA
1198430 TAAA-TATATATTAAATTATA
1 TAAATTATATATTAAATTATA
1198450 GTTAATGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TAAATTATATATTAAATTATATA
Found at i:1200456 original size:23 final size:24
Alignment explanation
Indices: 1200430--1200482 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1200420 TGTTGTTGTA
1200430 GTTTATGTTCATT-TATTGTGTTC
1 GTTTATGTTCATTCTATTGTGTTC
*
1200453 GTTTATGTTCATTCTTTTGTGTTC
1 GTTTATGTTCATTCTATTGTGTTC
1200477 GTTTAT
1 GTTTAT
1200483 TATGTTCGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 13 0.46
24 15 0.54
ACGTcount: A:0.11, C:0.09, G:0.17, T:0.62
Consensus pattern (24 bp):
GTTTATGTTCATTCTATTGTGTTC
Found at i:1200457 original size:13 final size:13
Alignment explanation
Indices: 1200435--1200494 Score: 54
Period size: 13 Copynumber: 4.8 Consensus size: 13
1200425 TTGTAGTTTA
*
1200435 TGTTCATTTATTG
1 TGTTCGTTTATTG
1200448 TGTTCGTTTA---
1 TGTTCGTTTATTG
* *
1200458 TGTTCATTCTTTTG
1 TGTTCGTT-TATTG
*
1200472 TGTTCGTTTATTA
1 TGTTCGTTTATTG
1200485 TGTTCGTTTA
1 TGTTCGTTTA
1200495 CATCCGTTCG
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
10 7 0.19
11 1 0.03
13 22 0.59
14 7 0.19
ACGTcount: A:0.12, C:0.10, G:0.17, T:0.62
Consensus pattern (13 bp):
TGTTCGTTTATTG
Found at i:1200513 original size:37 final size:37
Alignment explanation
Indices: 1200430--1200516 Score: 102
Period size: 37 Copynumber: 2.4 Consensus size: 37
1200420 TGTTGTTGTA
* * ** *
1200430 GTTTATGTTCATTTATTGTGTTCGTTTATGTTCATTC
1 GTTTATGTTCGTTTATTATGTTCGTTTACATCCATTC
* * *
1200467 TTTTGTGTTCGTTTATTATGTTCGTTTACATCCGTTC
1 GTTTATGTTCGTTTATTATGTTCGTTTACATCCATTC
1200504 GTTTATGTTCGTT
1 GTTTATGTTCGTT
1200517 CGTTTATATT
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.11, C:0.13, G:0.17, T:0.59
Consensus pattern (37 bp):
GTTTATGTTCGTTTATTATGTTCGTTTACATCCATTC
Found at i:1200523 original size:14 final size:14
Alignment explanation
Indices: 1200449--1200523 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
1200439 CATTTATTGT
1200449 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
*
1200463 ATTC-TTT-TG-T-
1 GTTCGTTTATGTTC
1200473 GTTCGTTTAT-TAT-
1 GTTCGTTTATGT-TC
** *
1200486 GTTCGTTTACATCC
1 GTTCGTTTATGTTC
1200500 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
1200514 GTTCGTTTAT
1 GTTCGTTTAT
1200524 ATTCATTTAT
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
10 3 0.06
11 4 0.08
12 3 0.06
13 13 0.27
14 25 0.52
ACGTcount: A:0.11, C:0.15, G:0.17, T:0.57
Consensus pattern (14 bp):
GTTCGTTTATGTTC
Found at i:1207684 original size:19 final size:20
Alignment explanation
Indices: 1207660--1207713 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
1207650 AAATGACCAA
1207660 CAAATTCGCAACACGATCT-
1 CAAATTCGCAACACGATCTC
* *
1207679 CAAATTCGCAACGCGATTTC
1 CAAATTCGCAACACGATCTC
*
1207699 CAAATTCACAACACG
1 CAAATTCGCAACACG
1207714 GAATTTCAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.37, C:0.31, G:0.11, T:0.20
Consensus pattern (20 bp):
CAAATTCGCAACACGATCTC
Found at i:1207805 original size:40 final size:40
Alignment explanation
Indices: 1207744--1207851 Score: 110
Period size: 40 Copynumber: 2.7 Consensus size: 40
1207734 AATTTATTTT
* * * *
1207744 TCGCAACAC-AAGTTTCCTTTTCGCGACAATATTTTCTAAA
1 TCGCAACACGAA-TTTTCTTTTCGCAACAAGATTTTCGAAA
* ** *
1207784 TCGCAACACGAATTTTGTTTTCGCAACTCGATTTTCGAAT
1 TCGCAACACGAATTTTCTTTTCGCAACAAGATTTTCGAAA
**
1207824 TCGCAACACGAATTTTAATTTCGCAACA
1 TCGCAACACGAATTTTCTTTTCGCAACA
1207852 GCTTTTATTT
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
40 54 0.96
41 2 0.04
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (40 bp):
TCGCAACACGAATTTTCTTTTCGCAACAAGATTTTCGAAA
Found at i:1207809 original size:20 final size:20
Alignment explanation
Indices: 1207784--1207851 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
1207774 ATTTTCTAAA
*
1207784 TCGCAACACGAATTTTGTTT
1 TCGCAACACGAATTTTGATT
* *
1207804 TCGCAACTCG-ATTTTCGAAT
1 TCGCAACACGAATTTT-GATT
*
1207824 TCGCAACACGAATTTTAATT
1 TCGCAACACGAATTTTGATT
1207844 TCGCAACA
1 TCGCAACA
1207852 GCTTTTATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
19 5 0.12
20 30 0.75
21 5 0.12
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (20 bp):
TCGCAACACGAATTTTGATT
Found at i:1208027 original size:14 final size:15
Alignment explanation
Indices: 1208008--1208045 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1207998 TCCCCATCTC
1208008 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
1208022 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
1208038 TAATTTTT
1 TAATTTTT
1208046 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:1208658 original size:12 final size:12
Alignment explanation
Indices: 1208637--1208670 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1208627 ACCATATTTC
*
1208637 CAATACCAAACA
1 CAATATCAAACA
1208649 CAATATCAAACA
1 CAATATCAAACA
*
1208661 CAATCTCAAA
1 CAATATCAAA
1208671 ACCCACAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1208823 original size:24 final size:24
Alignment explanation
Indices: 1208796--1208849 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1208786 GTATTCGAAA
1208796 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1208820 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1208844 TTTGAT
1 TTTGAT
1208850 GATGTTTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1212993 original size:21 final size:21
Alignment explanation
Indices: 1212931--1213064 Score: 117
Period size: 21 Copynumber: 6.4 Consensus size: 21
1212921 GTGAATCGGA
* * * *
1212931 CTCTTGAACGGTGGGAGTGAC
1 CTCTTGAACGATGAGAGGGGC
* *
1212952 CACTTGAACGATGAGAAGGGC
1 CTCTTGAACGATGAGAGGGGC
* * *
1212973 CTCTTAAACGGTGGGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
*
1212994 CTCTTCAACGATGAGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
* * *
1213015 CTATTCAACGATGATAGGGGC
1 CTCTTGAACGATGAGAGGGGC
* *
1213036 CTATTGAACAAT-AGGAGGGGC
1 CTCTTGAACGATGA-GAGGGGC
1213057 CTCTTGAA
1 CTCTTGAA
1213065 TAATGACAGG
Statistics
Matches: 92, Mismatches: 20, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
20 1 0.01
21 91 0.99
ACGTcount: A:0.26, C:0.19, G:0.34, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGC
Found at i:1213502 original size:21 final size:21
Alignment explanation
Indices: 1213478--1213527 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
1213468 ACCATTGTCG
*
1213478 TCACGTAAAGTACCGACCTTA
1 TCACGTAAAGTACCGACCTCA
* *
1213499 TCACGCAAAGTACTGACCTCA
1 TCACGTAAAGTACCGACCTCA
1213520 TCACGTAA
1 TCACGTAA
1213528 CTCCCCTAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.30, G:0.14, T:0.22
Consensus pattern (21 bp):
TCACGTAAAGTACCGACCTCA
Found at i:1215093 original size:14 final size:14
Alignment explanation
Indices: 1215074--1215107 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1215064 TGCGATTTTC
1215074 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
*
1215088 ATTTTCGTGTTGCG
1 ATTTTCGCGTTGCG
*
1215102 AATTTC
1 ATTTTC
1215108 ATTTTCGTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.12, C:0.18, G:0.24, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:1215111 original size:20 final size:20
Alignment explanation
Indices: 1215088--1215126 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1215078 TCGCGTTGCG
1215088 ATTTTCGTGTTGCGAATTTC
1 ATTTTCGTGTTGCGAATTTC
1215108 ATTTTCGTGTTGCGAATTT
1 ATTTTCGTGTTGCGAATTT
1215127 AAGTTTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.13, G:0.21, T:0.51
Consensus pattern (20 bp):
ATTTTCGTGTTGCGAATTTC
Found at i:1215133 original size:20 final size:20
Alignment explanation
Indices: 1215090--1215133 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1215080 GCGTTGCGAT
* *
1215090 TTTCGTGTTGCGAATTTCAT
1 TTTCGTGTTGCGAATTTAAG
1215110 TTTCGTGTTGCGAATTTAAG
1 TTTCGTGTTGCGAATTTAAG
1215130 TTTC
1 TTTC
1215134 AAAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.14, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGTGTTGCGAATTTAAG
Found at i:1215379 original size:22 final size:23
Alignment explanation
Indices: 1215343--1215385 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1215333 TTTAAATATG
*
1215343 AAAAATATAATAATAATAATACA
1 AAAAATATAATAATAAAAATACA
*
1215366 AAAAATTTAA-AATAAAAATA
1 AAAAATATAATAATAAAAATA
1215386 ATTAAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (23 bp):
AAAAATATAATAATAAAAATACA
Found at i:1215720 original size:19 final size:20
Alignment explanation
Indices: 1215673--1215720 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1215663 TAAACGCGCT
1215673 TTGCGAATTTGACTTATGTG
1 TTGCGAATTTGACTTATGTG
* *
1215693 TTGTGAATTTGAC-TCTGTG
1 TTGCGAATTTGACTTATGTG
*
1215712 TTGCAAATT
1 TTGCGAATT
1215721 ACAAATTCCC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.21, C:0.10, G:0.23, T:0.46
Consensus pattern (20 bp):
TTGCGAATTTGACTTATGTG
Found at i:1222557 original size:31 final size:32
Alignment explanation
Indices: 1222500--1222559 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
1222490 AAATAAAAAT
*
1222500 TAATTTGAAAGTGAGAGTGATTAAATTAAGAG
1 TAATTTGAAAGTGAGAGTAATTAAATTAAGAG
*
1222532 TAATTTGAAAGTTA-AGTAATTAAATTAA
1 TAATTTGAAAGTGAGAGTAATTAAATTAA
1222560 AAAAATAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 13 0.50
32 13 0.50
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (32 bp):
TAATTTGAAAGTGAGAGTAATTAAATTAAGAG
Found at i:1243496 original size:95 final size:95
Alignment explanation
Indices: 1243392--1243566 Score: 296
Period size: 95 Copynumber: 1.8 Consensus size: 95
1243382 TGTCGCTCGA
*
1243392 GACTCTGATTTACGATTTATCGGTGATCTTTTAATAGTTTCATCATATTTTGTAGTTTGTTTGCC
1 GACTCTGATTTACGATTTATCGGTGATCTTTCAATAGTTTCATCATATTTTGTAGTTTGTTTGCC
1243457 GATGCAGTCAAATTTATTCTCATGCTGCTC
66 GATGCAGTCAAATTTATTCTCATGCTGCTC
* * * *
1243487 GACTCTGATTTACGATTTATCGGTGGTCTTTCAGTAGTTTCATCCTCTTTTGTAGTTTGTTTGCC
1 GACTCTGATTTACGATTTATCGGTGATCTTTCAATAGTTTCATCATATTTTGTAGTTTGTTTGCC
*
1243552 GATGCAGTCATATTT
66 GATGCAGTCAAATTT
1243567 GTTCGTATCT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
95 74 1.00
ACGTcount: A:0.19, C:0.17, G:0.18, T:0.46
Consensus pattern (95 bp):
GACTCTGATTTACGATTTATCGGTGATCTTTCAATAGTTTCATCATATTTTGTAGTTTGTTTGCC
GATGCAGTCAAATTTATTCTCATGCTGCTC
Found at i:1244279 original size:2 final size:2
Alignment explanation
Indices: 1244274--1244334 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
1244264 GGTTTTTTAA
1244274 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
1244316 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
1244335 CTTTGAGTGT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1250406 original size:16 final size:16
Alignment explanation
Indices: 1250385--1250418 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1250375 TTACTATTCA
*
1250385 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
1250401 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
1250417 CG
1 CG
1250419 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Done.