Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008228.1 Hibiscus syriacus cultivar Beakdansim tig00110864_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: 3739947
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 20
Found at i:2960125 original size:3 final size:3
Alignment explanation
Indices: 2960117--2960231 Score: 187
Period size: 3 Copynumber: 38.7 Consensus size: 3
2960107 TTTTTATCCA
* *
2960117 TAT TAT TAT TAT TAA TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2960165 TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
2960212 CAT TAT TAC TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
2960232 AATATATTAA
Statistics
Matches: 103, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
2 2 0.02
3 101 0.98
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:2960745 original size:19 final size:20
Alignment explanation
Indices: 2960723--2960764 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
2960713 CCAGAGACAG
2960723 AAACAGA-AAACGAAAAAAA
1 AAACAGAGAAACGAAAAAAA
*
2960742 AAACAGAGAAAGGAAAAAAA
1 AAACAGAGAAACGAAAAAAA
2960762 AAA
1 AAA
2960765 ACAACAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (20 bp):
AAACAGAGAAACGAAAAAAA
Found at i:2961686 original size:20 final size:21
Alignment explanation
Indices: 2961648--2961686 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
2961638 TGATATTTTT
**
2961648 ATTTTATTATATTGTTAAAAA
1 ATTTTATTATATTCATAAAAA
2961669 ATTTTA-TATATTCATAAA
1 ATTTTATTATATTCATAAA
2961687 TATACATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (21 bp):
ATTTTATTATATTCATAAAAA
Found at i:2961933 original size:17 final size:17
Alignment explanation
Indices: 2961873--2961935 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 17
2961863 TTCTTTTCGG
2961873 ATATTTTTAAA-TAAAT
1 ATATTTTTAAATTAAAT
* *
2961889 ATAATTTTGAAAAT-AAT
1 AT-ATTTTTAAATTAAAT
* *
2961906 AGGA-TTATAAATTAAAT
1 A-TATTTTTAAATTAAAT
2961923 ATATTTTTAAATT
1 ATATTTTTAAATT
2961936 TTTAAATTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 9
0.69 0.14 0.18
Matches are distributed among these distances:
16 9 0.26
17 25 0.71
18 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (17 bp):
ATATTTTTAAATTAAAT
Found at i:2973017 original size:10 final size:10
Alignment explanation
Indices: 2973002--2973070 Score: 56
Period size: 10 Copynumber: 7.0 Consensus size: 10
2972992 TGCTTGAAGA
2973002 AAAAAGAAAG
1 AAAAAGAAAG
2973012 AAAAAGAAAAG
1 AAAAAG-AAAG
*
2973023 AAAGAA-AAGG
1 AAA-AAGAAAG
*
2973033 AAAAAAAATAG
1 AAAAAGAA-AG
*
2973044 AAAATG-AA-
1 AAAAAGAAAG
2973052 AAAAA-AAAG
1 AAAAAGAAAG
2973061 AAAAAGAAAG
1 AAAAAGAAAG
2973071 GGGGTCAAGG
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
8 6 0.13
9 8 0.17
10 19 0.40
11 12 0.26
12 2 0.04
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:2973018 original size:17 final size:17
Alignment explanation
Indices: 2972998--2973069 Score: 87
Period size: 17 Copynumber: 4.4 Consensus size: 17
2972988 ATTATGCTTG
2972998 AAGAAAAAAGAAAGAAA
1 AAGAAAAAAGAAAGAAA
2973015 AAG--AAAAGAAAGAAA
1 AAGAAAAAAGAAAGAAA
*
2973030 AGGAAAAAA-AATAGAAA
1 AAGAAAAAAGAA-AGAAA
* *
2973047 ATGAAAAAAAAAAGAAA
1 AAGAAAAAAGAAAGAAA
2973064 AAGAAA
1 AAGAAA
2973070 GGGGGTCAAG
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
15 14 0.29
16 2 0.04
17 30 0.62
18 2 0.04
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.03
Consensus pattern (17 bp):
AAGAAAAAAGAAAGAAA
Found at i:2973023 original size:15 final size:15
Alignment explanation
Indices: 2973002--2973069 Score: 64
Period size: 15 Copynumber: 4.2 Consensus size: 15
2972992 TGCTTGAAGA
2973002 AAAAAGAAAGAAAAAG
1 AAAAA-AAAGAAAAAG
* *
2973018 AAAAGAAAGAAAAGG
1 AAAAAAAAGAAAAAG
*
2973033 AAAAAAAATAGAAAATGAA
1 -AAAAAAA-AGAAAA--AG
2973052 AAAAAAAAGAAAAAG
1 AAAAAAAAGAAAAAG
2973067 AAA
1 AAA
2973070 GGGGGTCAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
15 13 0.31
16 10 0.24
17 12 0.29
18 7 0.17
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (15 bp):
AAAAAAAAGAAAAAG
Found at i:2973047 original size:7 final size:6
Alignment explanation
Indices: 2972998--2973069 Score: 66
Period size: 6 Copynumber: 13.0 Consensus size: 6
2972988 ATTATGCTTG
* *
2972998 AAGAAA AA-AGA AAGAAA AAG-AA AAG--A AAGAAA AGGAAA AA-AAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
* *
2973041 TAGAAA ATGAAA AA-AAA AAGAAA AAGAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
2973070 GGGGGTCAAG
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
4 4 0.08
5 18 0.34
6 31 0.58
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.03
Consensus pattern (6 bp):
AAGAAA
Found at i:2973453 original size:19 final size:18
Alignment explanation
Indices: 2973402--2973453 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 18
2973392 TTCAAGTTCA
2973402 ATTTATTTGAGATTCAATTT
1 ATTT-TTTGA-ATTCAATTT
*
2973422 ATTTTTGGAAATTCAATTT
1 ATTTTTTG-AATTCAATTT
2973441 ATTCTTTTGAATT
1 ATT-TTTTGAATT
2973454 AACATAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 19 0.68
20 9 0.32
ACGTcount: A:0.29, C:0.06, G:0.10, T:0.56
Consensus pattern (18 bp):
ATTTTTTGAATTCAATTT
Found at i:2974778 original size:84 final size:84
Alignment explanation
Indices: 2974189--2974761 Score: 1121
Period size: 84 Copynumber: 6.8 Consensus size: 84
2974179 ATATCTTAGT
*
2974189 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
2974254 CTGATCTGGTTTGGCAGAA
66 CTGATCTGGTTTGGCAGAA
2974273 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
2974338 CTGATCTGGTTTGGCAGAA
66 CTGATCTGGTTTGGCAGAA
*
2974357 CCAATCATTGAATTTGGAAGATGAATTTTCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
2974422 CTGATCTGGTTTGGCAGAA
66 CTGATCTGGTTTGGCAGAA
2974441 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
2974506 CTGATCTGGTTTGGCAGAA
66 CTGATCTGGTTTGGCAGAA
2974525 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
2974590 CTGATCTGGTTTGGCAGAA
66 CTGATCTGGTTTGGCAGAA
2974609 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
2974674 CTGATCTGGTTTGGCAGAA
66 CTGATCTGGTTTGGCAGAA
2974693 CCAATCATTGAATTTGGAAGATGAATTTGCT-AATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
2974757 CTGAT
66 CTGAT
2974762 TTGATTCAGT
Statistics
Matches: 486, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
83 38 0.08
84 448 0.92
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (84 bp):
CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
CTGATCTGGTTTGGCAGAA
Found at i:2975601 original size:113 final size:113
Alignment explanation
Indices: 2975398--2976180 Score: 1327
Period size: 113 Copynumber: 6.9 Consensus size: 113
2975388 ATTCAAATCT
* *
2975398 ATCATTTGATGGATCATTTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCATTTGATGGATCATCTTTTCCAGGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
2975463 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
* *
2975511 ATCAATTGATGGATTATCTTTTCCAGGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCATTTGATGGATCATCTTTTCCAGGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
2975576 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
* * *
2975624 ATCACTTGATGGATCATTTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCATTTGATGGATCATCTTTTCCAGGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
2975689 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
* * *
2975737 ATCACTTGATGGATCATTTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCATTTGATGGATCATCTTTTCCAGGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
2975802 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
2975850 ATCATTTGATGGATCATCTTTTCCA-GAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATCATTTGATGGATCATCTTTTCCAGGA-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
2975914 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
65 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
* * * * *
2975963 ATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAATTCGTCATCTGAAGAAG
1 ATCATTTGATGGATCATCTTTTCCAGGAAAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAG
2976028 GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
63 GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
* * * *
2976079 ATCAATTGATGGATTATCTTTTCCA-GAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAA
1 ATCATTTGATGGATCATCTTTTCCAGGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* *
2976143 GAAGAAGTTCATAATAAGAAGAATTTATTCAACCTTTT
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
2976181 GAACGACTCT
Statistics
Matches: 638, Mismatches: 27, Indels: 11
0.94 0.04 0.02
Matches are distributed among these distances:
112 52 0.08
113 481 0.75
114 1 0.00
115 20 0.03
116 84 0.13
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (113 bp):
ATCATTTGATGGATCATCTTTTCCAGGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
Found at i:2976506 original size:3 final size:3
Alignment explanation
Indices: 2976498--2976610 Score: 190
Period size: 3 Copynumber: 37.7 Consensus size: 3
2976488 TTTTTATCCA
*
2976498 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
2976546 TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
2976594 TAT TAC TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
2976611 AATATATTAA
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 102 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:2977140 original size:22 final size:21
Alignment explanation
Indices: 2977103--2977146 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
2977093 AGAGACAGAA
2977103 ACAGAAAACGAAAAAAAAAAC
1 ACAGAAAACGAAAAAAAAAAC
*
2977124 ACAGAGAAAGGAAAAAAAAAAC
1 ACAGA-AAACGAAAAAAAAAAC
2977146 A
1 A
2977147 ACAACAACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.75, C:0.11, G:0.14, T:0.00
Consensus pattern (21 bp):
ACAGAAAACGAAAAAAAAAAC
Found at i:2978293 original size:17 final size:17
Alignment explanation
Indices: 2978233--2978295 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 17
2978223 TTCTTTTCGG
2978233 ATATTTTTAAA-TAAAT
1 ATATTTTTAAATTAAAT
* *
2978249 ATAATTTTGAAAAT-AAT
1 AT-ATTTTTAAATTAAAT
* *
2978266 AGGA-TTATAAATTAAAT
1 A-TATTTTTAAATTAAAT
2978283 ATATTTTTAAATT
1 ATATTTTTAAATT
2978296 TTTAAATTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 9
0.69 0.14 0.18
Matches are distributed among these distances:
16 9 0.26
17 25 0.71
18 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (17 bp):
ATATTTTTAAATTAAAT
Found at i:2988529 original size:78 final size:77
Alignment explanation
Indices: 2988441--2988598 Score: 280
Period size: 78 Copynumber: 2.0 Consensus size: 77
2988431 TGAATAAATT
2988441 CAATTCAAGTCCAAAAACATTTTACCATAAACTGTTATATCAAAACATAGTTCAACAATCTCTCC
1 CAATTCAAGTCCAAAAACATTTTACCATAAACTGTTATATCAAAACATAGTTCAACAATCTCT-C
*
2988506 CTTTTTGATATAA
65 ATTTTTGATATAA
* *
2988519 CAATTCAAGTCCAAAAACATTTTGCCATAAATTGTTATATCAAAACATAGTTCAACAATCTCTCA
1 CAATTCAAGTCCAAAAACATTTTACCATAAACTGTTATATCAAAACATAGTTCAACAATCTCTCA
2988584 TTTTTGATATAA
66 TTTTTGATATAA
2988596 CAA
1 CAA
2988599 AACATTTGAA
Statistics
Matches: 77, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
77 16 0.21
78 61 0.79
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.34
Consensus pattern (77 bp):
CAATTCAAGTCCAAAAACATTTTACCATAAACTGTTATATCAAAACATAGTTCAACAATCTCTCA
TTTTTGATATAA
Found at i:2988693 original size:19 final size:19
Alignment explanation
Indices: 2988650--2988693 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
2988640 AAATGTTTAA
*
2988650 TGAAAACGATATCAATTGT
1 TGAAAACGATACCAATTGT
*
2988669 T-AAAAAGATACCAATTGT
1 TGAAAACGATACCAATTGT
2988687 TGGAAAA
1 T-GAAAA
2988694 TATATGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 16 0.76
19 1 0.05
20 4 0.19
ACGTcount: A:0.48, C:0.09, G:0.16, T:0.27
Consensus pattern (19 bp):
TGAAAACGATACCAATTGT
Found at i:2989080 original size:141 final size:141
Alignment explanation
Indices: 2988895--2989175 Score: 517
Period size: 141 Copynumber: 2.0 Consensus size: 141
2988885 AAACAAAATT
* *
2988895 AAGCTTTTAGAGTTTGATACTTAAACAAAATTGAATTTCAACAAAGATTAACAAACATGTTAGTA
1 AAGCTTTTAGAGTTTGACACTTAAACAAAATTGAATTTCAACAAAAATTAACAAACATGTTAGTA
*
2988960 GAACATGAAATTCAATGTATCCAAGTCTAAAATACTTTATGCAATATCAATTATTGAAATTAAGT
66 GAACATGAAATTCAATGTATCCAAGTCTAAAATAATTTATGCAATATCAATTATTGAAATTAAGT
2989025 GCATATGCATA
131 GCATATGCATA
2989036 AAGCTTTTAGAGTTTGACACTTAAACAAAATTGAATTTCAACAAAAATTAACAAACATGTTAGTA
1 AAGCTTTTAGAGTTTGACACTTAAACAAAATTGAATTTCAACAAAAATTAACAAACATGTTAGTA
* *
2989101 GTACATGAAATTCAATGTATCCAAGTCTAAAATAATTTATGCAATATCAATTGTTGAAATTAAGT
66 GAACATGAAATTCAATGTATCCAAGTCTAAAATAATTTATGCAATATCAATTATTGAAATTAAGT
2989166 GCATATGCAT
131 GCATATGCAT
2989176 CATAAAGCTT
Statistics
Matches: 135, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
141 135 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (141 bp):
AAGCTTTTAGAGTTTGACACTTAAACAAAATTGAATTTCAACAAAAATTAACAAACATGTTAGTA
GAACATGAAATTCAATGTATCCAAGTCTAAAATAATTTATGCAATATCAATTATTGAAATTAAGT
GCATATGCATA
Found at i:2990001 original size:17 final size:19
Alignment explanation
Indices: 2989959--2990002 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2989949 TTTCATTTTG
2989959 ATTTTCAAAATCAACTCTT
1 ATTTTCAAAATCAACTCTT
* *
2989978 GTTTTCAAAATCGA-T-TT
1 ATTTTCAAAATCAACTCTT
2989995 ATTTTCAA
1 ATTTTCAA
2990003 TTTTGAGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 9 0.41
18 1 0.05
19 12 0.55
ACGTcount: A:0.34, C:0.16, G:0.05, T:0.45
Consensus pattern (19 bp):
ATTTTCAAAATCAACTCTT
Found at i:2990511 original size:14 final size:15
Alignment explanation
Indices: 2990494--2990524 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2990484 TTTTTCTTGT
2990494 TTTTC-TTCTCTTCA
1 TTTTCTTTCTCTTCA
2990508 TTTTCTTTCTCTTCA
1 TTTTCTTTCTCTTCA
2990523 TT
1 TT
2990525 CAACATCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.06, C:0.26, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTTCTTTCTCTTCA
Found at i:2992033 original size:20 final size:20
Alignment explanation
Indices: 2991985--2992040 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
2991975 TACTTTTCAT
2991985 TACTGTTCACACAATATCGA
1 TACTGTTCACACAATATCGA
* * *
2992005 TATTGTTCACACAGTATCGG
1 TACTGTTCACACAATATCGA
* *
2992025 TACTATTCATACAATA
1 TACTGTTCACACAATA
2992041 CAATACTATT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (20 bp):
TACTGTTCACACAATATCGA
Found at i:2995025 original size:4 final size:4
Alignment explanation
Indices: 2995016--2995052 Score: 58
Period size: 4 Copynumber: 9.2 Consensus size: 4
2995006 CTAAGGAATG
2995016 ATAA ATAA ATAA ATAA ATAA ATAA AT-A ATGAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT-AA ATAA A
2995053 ATAATGAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 3 0.10
4 25 0.81
5 3 0.10
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:2997903 original size:17 final size:17
Alignment explanation
Indices: 2997881--2997915 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2997871 ACCTTACTAA
2997881 CTCTTTTCATTTT-TTTT
1 CTCTTTT-ATTTTATTTT
2997898 CTCTTTTATTTTATTTT
1 CTCTTTTATTTTATTTT
2997915 C
1 C
2997916 ATCATCTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (17 bp):
CTCTTTTATTTTATTTT
Found at i:2999482 original size:95 final size:95
Alignment explanation
Indices: 2999308--2999568 Score: 337
Period size: 95 Copynumber: 2.7 Consensus size: 95
2999298 ATATTATATA
* * * * *
2999308 TATATATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTAGTTAAATG-CCCTGATTTTAT
1 TATA-ATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAG-CTTTAT
* * *
2999372 GGATAAGATTTAGCTAGCTTGATAAAGGTGAT
64 GGATAAGATTCAGCTAGCCTGATAAAAGTGAT
*
2999404 TATAATATACAATAAAGCTTGAGTTTTCCCTCTAGAGCAATTGGTTAAACGCCCCAGCTTTATGG
1 TATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAGCTTTATGG
*
2999469 ATAATATTCAGCTAGCCTGATAAAAGTGAT
66 ATAAGATTCAGCTAGCCTGATAAAAGTGAT
* * *
2999499 TATAATAT-CTATAAAATGATATTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAGCTTT
1 TATAATATACAAT-AAA-G--CTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAGCTTT
2999563 ATGGAT
62 ATGGAT
2999569 CCAGCTAGCC
Statistics
Matches: 146, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
94 3 0.02
95 87 0.60
96 9 0.06
98 47 0.32
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Consensus pattern (95 bp):
TATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAGCTTTATGG
ATAAGATTCAGCTAGCCTGATAAAAGTGAT
Found at i:3001027 original size:84 final size:84
Alignment explanation
Indices: 3000710--3001407 Score: 934
Period size: 84 Copynumber: 8.3 Consensus size: 84
3000700 AGCGTAACAA
* *
3000710 AAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTTAGCTCCAAGGCAC
1 AAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAC
**
3000775 ATCATTTGCAATATAGCTC
66 ATCATTTGCAGCATAGCTC
* * * *
3000794 AAGGCAAGAA-GGCTATTTTCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAATGCAC
1 AAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAC
* ** *
3000858 ATAATTTATAGCATAACTC
66 ATCATTTGCAGCATAGCTC
* * * * *
3000877 AAGGGTAGAAGGGTTATCTGCCAACAAAAGA-CTTTGAGTTTGACTACGCTTAGCTCCAAGGCAC
1 AAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAC
*
3000941 ATCATTTGCAACATAGCTC
66 ATCATTTGCAGCATAGCTC
* * *
3000960 AAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCATCTCCAAGGCAC
1 AAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAC
* * *
3001025 ATCGTTTGCAGTATAGATC
66 ATCATTTGCAGCATAGCTC
* *
3001044 AAGG-TGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTTGACTACGTTCAGCTCCAAGGCA
1 AAGGCT-AGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA
*
3001108 CATCATTTACAGCATAGCTC
65 CATCATTTGCAGCATAGCTC
* *
3001128 AAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCAC
1 AAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAC
*
3001193 ATCATTTGCAGCATAGCTT
66 ATCATTTGCAGCATAGCTC
* * * * * * ** *
3001212 AAGTCAAGAAGGGCTATCTGTCAACCAAAGACCTTCGAGTTTGATTACATTCAGCTCAAAGGCAC
1 AAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAC
*
3001277 ATCATTTGCAGCATAACTC
66 ATCATTTGCAGCATAGCTC
* *
3001296 AAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTAAGCTCCAAGGCAC
1 AAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAC
** *
3001361 ATCATTTATAGCATAACTC
66 ATCATTTGCAGCATAGCTC
* * *
3001380 AAGGCTAGAAGAGTTATCTGTCAACAAA
1 AAGGCTAGAAGGGCTATCTGCCAACAAA
3001408 GATTTCTTAG
Statistics
Matches: 531, Mismatches: 79, Indels: 8
0.86 0.13 0.01
Matches are distributed among these distances:
83 140 0.26
84 390 0.73
85 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (84 bp):
AAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAC
ATCATTTGCAGCATAGCTC
Found at i:3002954 original size:9 final size:9
Alignment explanation
Indices: 3002940--3003093 Score: 63
Period size: 9 Copynumber: 16.8 Consensus size: 9
3002930 CGTATCTCTA
3002940 TTTATTTAT
1 TTTATTTAT
3002949 TTTATTATTAT
1 TTTA-T-TTAT
*
3002960 ATTATTTAT
1 TTTATTTAT
*
3002969 ATTATTTA-
1 TTTATTTAT
3002977 TTTATTTATT
1 TTTATTTA-T
3002987 TTTATTT-T
1 TTTATTTAT
3002995 TATTATCCTTA-
1 T-TTAT--TTAT
*
3003006 -TTATTTTT
1 TTTATTTAT
3003014 TTTATTT-T
1 TTTATTTAT
*
3003022 TTTATTCA-
1 TTTATTTAT
* *
3003030 ATTATTTTT
1 TTTATTTAT
* *
3003039 TCTTTTTTCT
1 T-TTATTTAT
*
3003049 TTTGACTT-T
1 TTT-ATTTAT
3003058 TTTATTTA-
1 TTTATTTAT
3003066 TTTATTTTAT
1 TTTA-TTTAT
*
3003076 TTTGATGTAT
1 TTT-ATTTAT
3003086 TTTCATTT
1 TTT-ATTT
3003094 TTCCCTCTCC
Statistics
Matches: 111, Mismatches: 16, Indels: 35
0.69 0.10 0.22
Matches are distributed among these distances:
7 2 0.02
8 28 0.25
9 40 0.36
10 31 0.28
11 10 0.09
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (9 bp):
TTTATTTAT
Found at i:3002966 original size:20 final size:19
Alignment explanation
Indices: 3002941--3003000 Score: 72
Period size: 20 Copynumber: 3.2 Consensus size: 19
3002931 GTATCTCTAT
3002941 TTATTTATTTTATTATTATA
1 TTATTTATTTTATT-TTATA
*
3002961 TTATTTATATTA-TTTAT-
1 TTATTTATTTTATTTTATA
3002978 TTATTTATTTTTATTTT-TA
1 TTATTTA-TTTTATTTTATA
3002997 TTAT
1 TTAT
3003001 CCTTATTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
17 7 0.20
18 9 0.26
19 8 0.23
20 11 0.31
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (19 bp):
TTATTTATTTTATTTTATA
Found at i:3002971 original size:17 final size:17
Alignment explanation
Indices: 3002941--3002985 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
3002931 GTATCTCTAT
3002941 TTAT-TTATTT-TATTA
1 TTATATTATTTATATTA
3002956 TTATATTATTTATATTA
1 TTATATTATTTATATTA
3002973 TT-TATTTATTTAT
1 TTATA-TTATTTAT
3002986 TTTTATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.15
16 8 0.30
17 15 0.56
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATATTATTTATATTA
Found at i:3002975 original size:29 final size:27
Alignment explanation
Indices: 3002941--3003020 Score: 85
Period size: 27 Copynumber: 2.9 Consensus size: 27
3002931 GTATCTCTAT
3002941 TTATTTATTT-TATTATTATATTATTTATA
1 TTATTTATTTAT-TTATT-T-TTATTTATA
*
3002970 TTATTTATTTATTTATTTTTATTTTTA
1 TTATTTATTTATTTATTTTTATTTATA
3002997 TTATCCTTA-TTATTT-TTTTTATTT
1 TTAT--TTATTTATTTATTTTTATTT
3003021 TTTTATTCAA
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
27 21 0.45
28 7 0.15
29 18 0.38
30 1 0.02
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (27 bp):
TTATTTATTTATTTATTTTTATTTATA
Found at i:3002980 original size:33 final size:29
Alignment explanation
Indices: 3002938--3003078 Score: 102
Period size: 28 Copynumber: 4.8 Consensus size: 29
3002928 TACGTATCTC
3002938 TATTTATTTATTTTATTATTATATTATTTATAT
1 TATTTATTTA-TTTATT-TT-TATT-TTTATAT
3002971 TATTTATTTATTTATTTTTA-TTTT-TAT
1 TATTTATTTATTTATTTTTATTTTTATAT
*
3002998 TATCCTTA-TTATTT-TTTTTATTTTTTTAT
1 TAT--TTATTTATTTATTTTTATTTTTATAT
* *
3003027 TCAATTATTT-TTTCTTTTT-TCTTTTGACT-T
1 T-ATTTATTTATTTATTTTTAT-TTTT-A-TAT
3003057 T-TTTATTTATTTA-TTTTATTTT
1 TATTTATTTATTTATTTTTATTTT
3003079 GATGTATTTT
Statistics
Matches: 92, Mismatches: 4, Indels: 29
0.74 0.03 0.23
Matches are distributed among these distances:
27 12 0.13
28 33 0.36
29 23 0.25
30 5 0.05
31 3 0.03
32 6 0.07
33 10 0.11
ACGTcount: A:0.21, C:0.04, G:0.01, T:0.74
Consensus pattern (29 bp):
TATTTATTTATTTATTTTTATTTTTATAT
Found at i:3002983 original size:41 final size:41
Alignment explanation
Indices: 3002938--3003037 Score: 103
Period size: 45 Copynumber: 2.3 Consensus size: 41
3002928 TACGTATCTC
3002938 TATTTATTTATTTTATTAT-TATATTATTTATATTATTTATT
1 TATTTATTTATTTTATTATCT-TATTATTTATATTATTTATT
* * *
3002979 TATTTATTTTTATTTTTATTATCCTTATTATTTTTTTTATTTTTT
1 TATTTA--TTTA-TTTTATTAT-CTTATTATTTATATTATTTATT
* *
3003024 TATTCAATTATTTT
1 TATTTATTTATTTT
3003038 TTCTTTTTTC
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
41 6 0.12
42 4 0.08
43 7 0.14
44 9 0.18
45 22 0.45
46 1 0.02
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (41 bp):
TATTTATTTATTTTATTATCTTATTATTTATATTATTTATT
Found at i:3003006 original size:21 final size:19
Alignment explanation
Indices: 3002938--3003019 Score: 69
Period size: 21 Copynumber: 4.1 Consensus size: 19
3002928 TACGTATCTC
*
3002938 TATTTATTTATT-TTATTAT
1 TATTTATTT-TTATTTTTAT
*
3002957 TATATTATTTATATTATTTATT
1 TAT-TTATTTTTATT-TTTA-T
3002979 TATTTATTTTTATTTTTAT
1 TATTTATTTTTATTTTTAT
3002998 TATCCTTATTATTT-TTTTTAT
1 TAT--TTATT-TTTATTTTTAT
3003019 T
1 T
3003020 TTTTTATTCA
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
19 8 0.15
20 12 0.23
21 26 0.49
22 7 0.13
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (19 bp):
TATTTATTTTTATTTTTAT
Found at i:3003034 original size:28 final size:28
Alignment explanation
Indices: 3002961--3003045 Score: 79
Period size: 27 Copynumber: 3.1 Consensus size: 28
3002951 TATTATTATA
*
3002961 TTATTTATATTAT--TTATTTATTTATTT
1 TTATTTTTATTATCATTA-TTATTTATTT
*
3002988 TTATTTTTATTATCCTTATTATTT-TTT
1 TTATTTTTATTATCATTATTATTTATTT
* *
3003015 TTATTTTT-TTATTCAATTATTTTTTCTTT
1 TTATTTTTATTA-TC-ATTATTATTTATTT
3003044 TT
1 TT
3003046 TCTTTTGACT
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
26 3 0.06
27 25 0.50
28 14 0.28
29 8 0.16
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (28 bp):
TTATTTTTATTATCATTATTATTTATTT
Found at i:3003132 original size:12 final size:11
Alignment explanation
Indices: 3003107--3003142 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
3003097 CCTCTCCGAT
*
3003107 TTATTATTTTA
1 TTATTTTTTTA
3003118 TTATTTTTATTA
1 TTATTTTT-TTA
3003130 TTATTTTTTTA
1 TTATTTTTTTA
3003141 TT
1 TT
3003143 TTGTTCTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.52
12 11 0.48
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (11 bp):
TTATTTTTTTA
Found at i:3003132 original size:20 final size:20
Alignment explanation
Indices: 3003107--3003144 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3003097 CCTCTCCGAT
3003107 TTATTATTTTATTATTTTTA
1 TTATTATTTTATTATTTTTA
*
3003127 TTATTATTTTTTTATTTT
1 TTATTATTTTATTATTTT
3003145 GTTCTTGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (20 bp):
TTATTATTTTATTATTTTTA
Found at i:3003138 original size:14 final size:14
Alignment explanation
Indices: 3003105--3003144 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
3003095 TCCCTCTCCG
3003105 ATTTATTATTTTATT
1 ATTT-TTATTTTATT
3003120 ATTTTTATTATTATT
1 ATTTTTATT-TTATT
3003135 -TTTTTATTTT
1 ATTTTTATTTT
3003145 GTTCTTGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.08
14 13 0.54
15 9 0.38
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
ATTTTTATTTTATT
Found at i:3014301 original size:24 final size:25
Alignment explanation
Indices: 3014267--3014360 Score: 95
Period size: 25 Copynumber: 3.7 Consensus size: 25
3014257 TTTCAAAAGA
*
3014267 AGAAAAAGTTTGAT-AAAGAAGTTTC
1 AGAAAATGTTTGATGAAAGAA-TTTC
*
3014292 -GAAAATGTTTTATGAAAGAATTTC
1 AGAAAATGTTTGATGAAAGAATTTC
*
3014316 AAAAAAATTGTTTGATGAAAGAA-TTC
1 -AGAAAA-TGTTTGATGAAAGAATTTC
*
3014342 TGAAAAATGTTTGATGAAA
1 AG-AAAATGTTTGATGAAA
3014361 TTTTTTAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
24 15 0.26
25 18 0.31
26 11 0.19
27 14 0.24
ACGTcount: A:0.47, C:0.03, G:0.18, T:0.32
Consensus pattern (25 bp):
AGAAAATGTTTGATGAAAGAATTTC
Found at i:3014334 original size:27 final size:25
Alignment explanation
Indices: 3014293--3014360 Score: 91
Period size: 27 Copynumber: 2.6 Consensus size: 25
3014283 AGAAGTTTCG
*
3014293 AAAATGTTTTATGAAAGAATTTCAAA
1 AAAATGTTTGATGAAAGAA-TTCAAA
**
3014319 AAAATTGTTTGATGAAAGAATTCTGA
1 AAAA-TGTTTGATGAAAGAATTCAAA
3014345 AAAATGTTTGATGAAA
1 AAAATGTTTGATGAAA
3014361 TTTTTTAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
25 12 0.32
26 12 0.32
27 14 0.37
ACGTcount: A:0.47, C:0.03, G:0.16, T:0.34
Consensus pattern (25 bp):
AAAATGTTTGATGAAAGAATTCAAA
Found at i:3015985 original size:55 final size:55
Alignment explanation
Indices: 3015901--3016104 Score: 275
Period size: 55 Copynumber: 3.7 Consensus size: 55
3015891 CATTTCATAC
* * * * * *
3015901 TTGGGGGTATCGATACACTCCTCAGTGTACCAATACATAATTAGCACTTGATGTT
1 TTGGGTGTATCGAAACACTCCTCAGTGTACCGATACACAAATAACACTTGATGTT
*
3015956 TTGGGTGTATTGAAACACTCCTCAGTGTACCGATACACAAATAACACTTGATGTT
1 TTGGGTGTATCGAAACACTCCTCAGTGTACCGATACACAAATAACACTTGATGTT
* * *
3016011 TTGGGTGAATC-AATGCACTCCTCAGTGTACCGATACACAAATAACACTCGATGTT
1 TTGGGTGTATCGAA-ACACTCCTCAGTGTACCGATACACAAATAACACTTGATGTT
* * *
3016066 TTGGGTGTATCGATACACTACTCAGTATACCGATACACA
1 TTGGGTGTATCGAAACACTCCTCAGTGTACCGATACACA
3016105 CTCATACAAT
Statistics
Matches: 131, Mismatches: 16, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
54 2 0.02
55 128 0.98
56 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (55 bp):
TTGGGTGTATCGAAACACTCCTCAGTGTACCGATACACAAATAACACTTGATGTT
Found at i:3022193 original size:21 final size:21
Alignment explanation
Indices: 3022167--3022221 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
3022157 CATAAAGTAT
3022167 ATTCACATTCACTGATTCGAA
1 ATTCACATTCACTGATTCGAA
3022188 ATTCACATTCACTGATTCGAA
1 ATTCACATTCACTGATTCGAA
*
3022209 ATTCATATTCACT
1 ATTCACATTCACT
3022222 TATCAAGGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.36
Consensus pattern (21 bp):
ATTCACATTCACTGATTCGAA
Found at i:3022670 original size:55 final size:55
Alignment explanation
Indices: 3022576--3022773 Score: 299
Period size: 55 Copynumber: 3.6 Consensus size: 55
3022566 ATACTTGAGG
* * *
3022576 GTATCGATACACTCCTCAGTGTACCGATAAACAATTAGCACTCGATGTTTTGGGT
1 GTATCGATACACTACTCAGTGTACCGATACACAAATAGCACTCGATGTTTTGGGT
3022631 GTATCGATACACT-CTTCAGTGTACCGATACACAAATAGCACTCGATGTTTTGGGT
1 GTATCGATACACTAC-TCAGTGTACCGATACACAAATAGCACTCGATGTTTTGGGT
* * * *
3022686 GTATCGATACACTACTCAGTATACTGATACACAAATAACACTAGATGTTTTGGGT
1 GTATCGATACACTACTCAGTGTACCGATACACAAATAGCACTCGATGTTTTGGGT
* *
3022741 GTATCGATATACTGCTCAGTGTACCGATACACA
1 GTATCGATACACTACTCAGTGTACCGATACACA
3022774 CTCATACAAT
Statistics
Matches: 131, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
54 1 0.01
55 129 0.98
56 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (55 bp):
GTATCGATACACTACTCAGTGTACCGATACACAAATAGCACTCGATGTTTTGGGT
Found at i:3024309 original size:26 final size:26
Alignment explanation
Indices: 3024259--3024318 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
3024249 ATTTATTTTT
*
3024259 TAAAA-TAATTTGATAAATATTGTAA
1 TAAAATTAATTTGATAAACATTGTAA
*
3024284 TAAAATTAATTT-ATATACATTAGTAA
1 TAAAATTAATTTGATAAACATT-GTAA
*
3024310 GAAAATTAA
1 TAAAATTAA
3024319 AATTATTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
25 12 0.40
26 18 0.60
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (26 bp):
TAAAATTAATTTGATAAACATTGTAA
Found at i:3029076 original size:24 final size:24
Alignment explanation
Indices: 3029048--3029101 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
3029038 TTTTTGGATC
*
3029048 ATTGTTTTGTTGTCTCCAATAATG
1 ATTGTCTTGTTGTCTCCAATAATG
3029072 ATTGTCTTGTTGTCTCCAATAATG
1 ATTGTCTTGTTGTCTCCAATAATG
3029096 ATTGTC
1 ATTGTC
3029102 ATCACTGCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.48
Consensus pattern (24 bp):
ATTGTCTTGTTGTCTCCAATAATG
Found at i:3031980 original size:43 final size:42
Alignment explanation
Indices: 3031911--3032215 Score: 328
Period size: 43 Copynumber: 7.2 Consensus size: 42
3031901 AAGGTAATTA
* * * *
3031911 GCGGCGTTTGTACCACAAACGCCGCTATTGATCTGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATATGACCTTTT
* * * **
3031953 ACGGCGTTTGTATCCAAAAACGCCGCTATAAATTTGA-AATTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATATGACCTTTT
* * *
3031995 GCGGCGTTTGTTTC-AAAACGCCGCTATAGATCTGACATTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATATGACCTTTT
* *
3032036 GCGGCGTTTGTATCCAAAAATGCCGCTATATATATGACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATATGACCTTTT
* * * *
3032079 ACGGCGTTTGTTACAAAAACGCCGCAATAAATATCGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATAT-GACCTTTT
* *
3032122 -CGGCGTTTATTCCAAAAACGCCGCTATTGATATCGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATAT-GACCTTTT
* * * *
3032164 GCGGTGTTTGTTCCAAAAACGCCGCAATAGATCTTGACCTATT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGAT-ATGACCTTTT
3032207 GCGGCGTTT
1 GCGGCGTTT
3032216 TTTGTTCTCA
Statistics
Matches: 221, Mismatches: 35, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
40 19 0.09
41 17 0.08
42 81 0.37
43 103 0.47
44 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (42 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAGATATGACCTTTT
Found at i:3032173 original size:85 final size:84
Alignment explanation
Indices: 3031911--3032215 Score: 332
Period size: 85 Copynumber: 3.6 Consensus size: 84
3031901 AAGGTAATTA
* * *
3031911 GCGGCGTTTG-TACCACAAACGCCGCTATTGATCTGACCTTTTACGGCGTTTGTATCCAAAAACG
1 GCGGCGTTTGTTA-CAAAAACGCCGCAATAGATCTGACCTTTTACGGCGTTTGTATCCAAAAACG
* * **
3031975 CCGCTATAAATTTGA-AATTT
65 CCGCTAT-TATATGACCTTTT
* * * * *
3031995 GCGGCGTTTGTTTC-AAAACGCCGCTATAGATCTGACATTTTGCGGCGTTTGTATCCAAAAATGC
1 GCGGCGTTTGTTACAAAAACGCCGCAATAGATCTGACCTTTTACGGCGTTTGTATCCAAAAACGC
3032059 CGCTATATATATGACCTTTT
66 CGCTAT-TATATGACCTTTT
* * * *
3032079 ACGGCGTTTGTTACAAAAACGCCGCAATAAATATCGACCTTTT-CGGCGTTTAT-TCCAAAAACG
1 GCGGCGTTTGTTACAAAAACGCCGCAATAGATCT-GACCTTTTACGGCGTTTGTATCCAAAAACG
3032142 CCGCTATTGATATCGACCTTTT
65 CCGCTATT-ATAT-GACCTTTT
* * * *
3032164 GCGGTGTTTGTTCCAAAAACGCCGCAATAGATCTTGACCTATTGCGGCGTTT
1 GCGGCGTTTGTTACAAAAACGCCGCAATAGATC-TGACCTTTTACGGCGTTT
3032216 TTTGTTCTCA
Statistics
Matches: 189, Mismatches: 24, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
83 58 0.31
84 46 0.24
85 69 0.37
86 16 0.08
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (84 bp):
GCGGCGTTTGTTACAAAAACGCCGCAATAGATCTGACCTTTTACGGCGTTTGTATCCAAAAACGC
CGCTATTATATGACCTTTT
Found at i:3034628 original size:3 final size:3
Alignment explanation
Indices: 3034620--3034665 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
3034610 AATAGAAAGA
*
3034620 AAT AAT AAT AAT AAT AAT AAT AAT -AT AAA AAT AA- AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3034666 TCATCTACCT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 4 0.10
3 35 0.90
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:3040706 original size:3 final size:3
Alignment explanation
Indices: 3040694--3040732 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
3040684 TAAATATTAT
3040694 TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3040733 TTACTAGATA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3041210 original size:139 final size:139
Alignment explanation
Indices: 3040992--3041352 Score: 519
Period size: 139 Copynumber: 2.6 Consensus size: 139
3040982 ATGACATTGA
* * * *
3040992 TCCTACGCGTTGAGGAGATCTGGTCGGTGGACGACATTGTTCTTACGTGATGAGGACGTCTAGCC
1 TCCTACGTGATGAGGAGGTCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGACGTCTAGCC
* *** * * *
3041057 GTCTTTAGGGATAATTTGGAGATAACATGGTTTCA-ACTTGATGAGGAAGTATGGTTATTTGAGG
66 GTCTTTAGGGATAATTTGGACATAACA-CAATTCATACGTGATAAGGAAGTATGGTTATCTGAGG
3041121 ATGA-CACTGC
130 ATGATCA-TGC
*
3041131 TTCTACGTGATGAGGAGGTCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGACGTCTAGCC
1 TCCTACGTGATGAGGAGGTCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGACGTCTAGCC
* *
3041196 GTCTTTAGGAATAATTTGGACATAACACAATTCATACGTGATAAGGAAGTCTGGTTATCTGAGGA
66 GTCTTTAGGGATAATTTGGACATAACACAATTCATACGTGATAAGGAAGTATGGTTATCTGAGGA
*
3041261 TGATGATGC
131 TGATCATGC
* * * *
3041270 TCCTACGTGATGAGGAGGTTTGGTCGGTGGACGACATTGTTCCTATGTGATGAGGATGTCTAGCT
1 TCCTACGTGATGAGGAGGTCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGACGTCTAGCC
3041335 GTCTTTAGGGATAATTTG
66 GTCTTTAGGGATAATTTG
3041353 TTTCAAGAGA
Statistics
Matches: 199, Mismatches: 21, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
138 4 0.02
139 194 0.97
140 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.31
Consensus pattern (139 bp):
TCCTACGTGATGAGGAGGTCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGACGTCTAGCC
GTCTTTAGGGATAATTTGGACATAACACAATTCATACGTGATAAGGAAGTATGGTTATCTGAGGA
TGATCATGC
Found at i:3041545 original size:74 final size:73
Alignment explanation
Indices: 3041419--3041615 Score: 297
Period size: 74 Copynumber: 2.7 Consensus size: 73
3041409 AAGGTTTATA
*
3041419 TTTCAAGAGAAATTGTCTCAAGAGAGA-AAAATTTTTGTTTCAAGAGAAACTGTCTCAAGCGAGA
1 TTTCGAGAGAAATTGTCTCAAGAGAGACAAAA--TTTGTTTCAAGAGAAACTGTCTCAAGCGAGA
*
3041483 CTAAACTTTG
64 CCAAACTTTG
* * *
3041493 TTTTGAGAGAAACTATCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGCGAGAC
1 TTTCGAGAGAAATTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGAGAAACTGTCTCAAGCGAGAC
3041558 CAAACTTTG
65 CAAACTTTG
* *
3041567 TTTCGAGAGAAATTGTCTCAAGTGAGACAAAATTTGTTTCAAGGGAAAC
1 TTTCGAGAGAAATTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAAC
3041616 AATCTCAATT
Statistics
Matches: 111, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
73 16 0.14
74 91 0.82
75 4 0.04
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.28
Consensus pattern (73 bp):
TTTCGAGAGAAATTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGCGAGACC
AAACTTTG
Found at i:3041576 original size:111 final size:110
Alignment explanation
Indices: 3041349--3041623 Score: 289
Period size: 111 Copynumber: 2.6 Consensus size: 110
3041339 TTAGGGATAA
* * * * *
3041349 TTTGTTTCAAGAGAAACTGCCTCAAGTGAGATAAAATTTGTTTCAAGGGAAATAATCTCAA-AG-
1 TTTGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAGAGA
* * * *
3041412 G------TTTATATTTCAAGAGAAATTGTCTCAAGAGAGAAAAATT
66 GACAAAACTT-TGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAATC
* ** *
3041452 TTTGTTTCAAGAGAAACTGTCTCAAGCGAGACTAAACTTTGTTTTGAGAGAAACTATCTCAAGAG
1 TTTGTTTCAAGAGAAACTGTCTCAAGCGAGAC-AAAATTTGTTTCAAGAGAAACAATCTCAAGAG
* *
3041517 AGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGCGAGACCAAA-C
65 AGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAGA-AAAATC
* * * *
3041563 TTTGTTTCGAGAGAAATTGTCTCAAGTGAGACAAAATTTGTTTCAAGGGAAACAATCTCAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAA
3041624 TTATTTATGT
Statistics
Matches: 139, Mismatches: 23, Indels: 13
0.79 0.13 0.07
Matches are distributed among these distances:
103 29 0.21
104 23 0.17
105 2 0.01
106 1 0.01
110 24 0.17
111 55 0.40
112 5 0.04
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (110 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAGAGA
GACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAATC
Found at i:3041671 original size:66 final size:66
Alignment explanation
Indices: 3041565--3041689 Score: 196
Period size: 66 Copynumber: 1.9 Consensus size: 66
3041555 GACCAAACTT
* * * *
3041565 TGTTTCGAGAGAAATTGTCTCAAGTGAGACAAAATTTGTTTCAAGGGAAACAATCTCAATTATTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAATTATTT
3041630 A
66 A
* *
3041631 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAGAAACATTCTCAA
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAA
3041690 AGGTTTATCA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 53 1.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.31
Consensus pattern (66 bp):
TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAATTATTT
A
Found at i:3041688 original size:36 final size:36
Alignment explanation
Indices: 3041419--3041689 Score: 254
Period size: 37 Copynumber: 7.6 Consensus size: 36
3041409 AAGGTTTATA
* *
3041419 TTTCAAGAGAAATTGTCTCAAGAGAGA-AAAATTTTTG
1 TTTCAAGAGAAACTGTCTCAAGCGAGACAAAA--TTTG
*
3041456 TTTCAAGAGAAACTGTCTCAAGCGAGACTAAACTTTG
1 TTTCAAGAGAAACTGTCTCAAGCGAGAC-AAAATTTG
** * *
3041493 TTTTGAGAGAAACTATCTCAAGAGAGACAAAACTTTG
1 TTTCAAGAGAAACTGTCTCAAGCGAGACAAAA-TTTG
*
3041530 TTTCAAGAGAAACTGTCTCAAGCGAGACCAAACTTTG
1 TTTCAAGAGAAACTGTCTCAAGCGAGA-CAAAATTTG
* * *
3041567 TTTCGAGAGAAATTGTCTCAAGTGAGACAAAATTTG
1 TTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTG
* ** ** *
3041603 TTTCAAGGGAAACAATCT----C-A-A-TTATTTATG
1 TTTCAAGAGAAACTGTCTCAAGCGAGACAAAATT-TG
3041633 TTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTG
1 TTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTG
*
3041669 TTTTAAGAGAAACAT-TCTCAA
1 TTTCAAGAGAAAC-TGTCTCAA
3041690 AGGTTTATCA
Statistics
Matches: 188, Mismatches: 33, Indels: 27
0.76 0.13 0.11
Matches are distributed among these distances:
29 3 0.02
30 18 0.10
31 1 0.01
34 1 0.01
35 1 0.01
36 45 0.24
37 112 0.60
38 4 0.02
39 3 0.02
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (36 bp):
TTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTG
Found at i:3042068 original size:105 final size:102
Alignment explanation
Indices: 3041539--3042142 Score: 505
Period size: 104 Copynumber: 5.9 Consensus size: 102
3041529 GTTTCAAGAG
* * ** *** * * *
3041539 AAACTGTCTCAAGCGAGACCAAACTTTGTTTCGAGAGAAATTGTCTCAAGTGAGA-CAAAATTTG
1 AAACTGTCTCAAGTGAGA-CAAAATTTGTTTTAAGAGAAACAATCTCAAATGTGATC-AATTTTG
* * * * *
3041603 TTTCAAGGGAAACAATCTCAATTATTTATGTTTC-AA-GAG
64 TTTCAAGTGAAACAATTTCAA--ATTTGTATTTCGAAGGAA
* * * *
3041642 AAACTGTCTCAAGCGAGACAAAATTTGTTTTAAGAGAAACATTCTCAAAGGTTTATCAATTTTGT
1 AAACTGTCTCAAGTGAGACAAAATTTGTTTTAAGAGAAACAATCTCAAATG-TGATCAATTTTGT
* * *
3041707 TTCAAGTGAAACAATTTCCAAATTTTGTGTTTTG-AGGGA
65 TTCAAGTGAAACAATTT-CAAA-TTTGTATTTCGAAGGAA
* * * * * *
3041746 AAACTGTCTCAAGCGAAATAAAATTTTCTTTTTAAGAAAAACAATCTCAAATGTAATCAATTTTG
1 AAACTGTCTCAAGTGAGACAAAA-TTT-GTTTTAAGAGAAACAATCTCAAATGTGATCAATTTTG
* *
3041811 TTTCAAGTGAAATAATTTCAGAATTTGTTTTTCGAA-GAA
64 TTTCAAGTGAAACAATTTCA-AATTTGTATTTCGAAGGAA
* * * * * * *
3041850 AATCTGTCTCAAGTGAGACGAAATTTGTTTT--GAG-AACAATTTCAAGTGAGATAAACTTTGTT
1 AAACTGTCTCAAGTGAGACAAAATTTGTTTTAAGAGAAACAATCTCAAATGTGATCAATTTTGTT
* **
3041912 TCAAGTGAAACAAATTTCCAAATTTGTATTTC-TAGGGG
66 TCAAGTGAAAC-AATTT-CAAATTTGTATTTCGAAGGAA
* *
3041950 AAACTGTCTCAAGTGAGACAAAATTTGTTTTTAAGAGAAACAATCTCAATTGTTTATCAATTTTG
1 AAACTGTCTCAAGTGAGACAAAATTTG-TTTTAAGAGAAACAATCTCAAATG-TGATCAATTTTG
* *
3042015 TTTCCAGTGAAACAATTTCAGAATTTGTATTTCGAAGAAAA
64 TTTCAAGTGAAACAATTTCA-AATTTGTATTTCGAAG-GAA
* * * * *
3042056 AAAAT-TCTCAAGTGAGACGAAATTTGTTTT--GAG-AACAATCTCAAGTGAGATAAATTTTGTT
1 AAACTGTCTCAAGTGAGACAAAATTTGTTTTAAGAGAAACAATCTCAAATGTGATCAATTTTGTT
* *
3042117 TTAAGTGAAACATTTTCAAAATTTGT
66 TCAAGTGAAACAATTTC-AAATTTGT
3042143 GGAAATCCGT
Statistics
Matches: 411, Mismatches: 68, Indels: 47
0.78 0.13 0.09
Matches are distributed among these distances:
99 33 0.08
100 76 0.18
101 20 0.05
102 33 0.08
103 58 0.14
104 90 0.22
105 76 0.18
106 25 0.06
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (102 bp):
AAACTGTCTCAAGTGAGACAAAATTTGTTTTAAGAGAAACAATCTCAAATGTGATCAATTTTGTT
TCAAGTGAAACAATTTCAAATTTGTATTTCGAAGGAA
Found at i:3042107 original size:205 final size:203
Alignment explanation
Indices: 3041599--3042142 Score: 641
Period size: 204 Copynumber: 2.6 Consensus size: 203
3041589 TGAGACAAAA
* * * * * * * *
3041599 TTTGTTTCAAGGGAAACAATCTCA-ATTATTTATGTTTC-AAGAGAAACTGTCTCAAGCGAGACA
1 TTTGTTTCAAGTGAAACAATTTCAGA--ATTTGTATTTCGAAGAAAAAATGTCTCAAGTGAGACG
* ** * *
3041662 AAATTTGTTTTAAGAGAAACATTCTCAAAG-GTTTATCAATTTTGTTTCAAGTGAAACAATTTCC
64 AAATTTGTTTT--GAG-AACAATCTC-AAGTG-AGATAAACTTTGTTTCAAGTGAAACAATTTCC
* *
3041726 AAATTTTGTGTTTTGAGGGAAAACTGTCTCAAGCGAAATAAAATTTTCTTTTTAAGAAAAACAAT
124 AAA-TTTGTATTTTGAGGGAAAACTGTCTCAAGCGAAACAAAATTTTCTTTTTAAGAAAAACAAT
3041791 CTCAAATGTAATCAAT
188 CTCAAATGTAATCAAT
* * **
3041807 TTTGTTTCAAGTGAAATAATTTCAGAATTTGTTTTTCGAAGAAAATCTGTCTCAAGTGAGACGAA
1 TTTGTTTCAAGTGAAACAATTTCAGAATTTGTATTTCGAAGAAAAAATGTCTCAAGTGAGACGAA
*
3041872 ATTTGTTTTGAGAACAATTTCAAGTGAGATAAACTTTGTTTCAAGTGAAACAAATTTCCAAATTT
66 ATTTGTTTTGAGAACAATCTCAAGTGAGATAAACTTTGTTTCAAGTGAAAC-AATTTCCAAATTT
* * * * * *
3041937 GTATTTCT-AGGGGAAACTGTCTCAAGTGAGACAAAA-TTTGTTTTTAAGAGAAACAATCTCAAT
130 GTATTT-TGAGGGAAAACTGTCTCAAGCGAAACAAAATTTTCTTTTTAAGAAAAACAATCTCAAA
*
3042000 TGTTTATCAAT
194 TG-TAATCAAT
*
3042011 TTTGTTTCCAGTGAAACAATTTCAGAATTTGTATTTCGAAGAAAAAAAAT-TCTCAAGTGAGACG
1 TTTGTTTCAAGTGAAACAATTTCAGAATTTGTATTTCGAAG--AAAAAATGTCTCAAGTGAGACG
* * * *
3042075 AAATTTGTTTTGAGAACAATCTCAAGTGAGATAAATTTTGTTTTAAGTGAAACATTTTCAAAATT
64 AAATTTGTTTTGAGAACAATCTCAAGTGAGATAAACTTTGTTTCAAGTGAAACAATTTCCAAATT
3042140 TGT
129 TGT
3042143 GGAAATCCGT
Statistics
Matches: 294, Mismatches: 34, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
203 26 0.09
204 114 0.39
205 83 0.28
206 8 0.03
207 9 0.03
208 53 0.18
209 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.36
Consensus pattern (203 bp):
TTTGTTTCAAGTGAAACAATTTCAGAATTTGTATTTCGAAGAAAAAATGTCTCAAGTGAGACGAA
ATTTGTTTTGAGAACAATCTCAAGTGAGATAAACTTTGTTTCAAGTGAAACAATTTCCAAATTTG
TATTTTGAGGGAAAACTGTCTCAAGCGAAACAAAATTTTCTTTTTAAGAAAAACAATCTCAAATG
TAATCAAT
Found at i:3044803 original size:12 final size:12
Alignment explanation
Indices: 3044786--3044815 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3044776 TCTTGTTCTC
3044786 TTTTCTTTATTT
1 TTTTCTTTATTT
*
3044798 TTTTCTTTGTTT
1 TTTTCTTTATTT
3044810 TTTTCT
1 TTTTCT
3044816 CTTTGTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.03, C:0.10, G:0.03, T:0.83
Consensus pattern (12 bp):
TTTTCTTTATTT
Found at i:3044808 original size:26 final size:26
Alignment explanation
Indices: 3044778--3044827 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
3044768 CATGTGCTTC
3044778 TTGTTCTCTTT-TCTTTATTTTTTTCT
1 TTGTT-TCTTTCTCTTTATTTTTTTCT
* *
3044804 TTGTTTTTTTCTCTTTGTTTTTTT
1 TTGTTTCTTTCTCTTTATTTTTTT
3044828 TTCTCTTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.02, C:0.12, G:0.06, T:0.80
Consensus pattern (26 bp):
TTGTTTCTTTCTCTTTATTTTTTTCT
Found at i:3044828 original size:16 final size:16
Alignment explanation
Indices: 3044781--3044837 Score: 66
Period size: 16 Copynumber: 3.6 Consensus size: 16
3044771 GTGCTTCTTG
3044781 TTCTCTTT-TCTTTATTT
1 TTCTCTTTGT-TTT-TTT
*
3044798 TTTTCTTTG--TTTTT
1 TTCTCTTTGTTTTTTT
3044812 TTCTCTTTGTTTTTTT
1 TTCTCTTTGTTTTTTT
3044828 TTCTCTTTGT
1 TTCTCTTTGT
3044838 AGTTTGCATT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
14 11 0.31
15 2 0.06
16 15 0.43
17 7 0.20
ACGTcount: A:0.02, C:0.14, G:0.05, T:0.79
Consensus pattern (16 bp):
TTCTCTTTGTTTTTTT
Found at i:3060987 original size:5 final size:5
Alignment explanation
Indices: 3060977--3061038 Score: 124
Period size: 5 Copynumber: 12.4 Consensus size: 5
3060967 TCACAGGAAA
3060977 AGAAG AGAAG AGAAG AGAAG AGAAG AGAAG AGAAG AGAAG AGAAG AGAAG
1 AGAAG AGAAG AGAAG AGAAG AGAAG AGAAG AGAAG AGAAG AGAAG AGAAG
3061027 AGAAG AGAAG AG
1 AGAAG AGAAG AG
3061039 TTTAAGTTAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 57 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (5 bp):
AGAAG
Found at i:3075977 original size:13 final size:13
Alignment explanation
Indices: 3075959--3075983 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3075949 AAGAAAAAAA
3075959 TAAAATAAATAAG
1 TAAAATAAATAAG
3075972 TAAAATAAATAA
1 TAAAATAAATAA
3075984 ACATAAAATA
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:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (13 bp):
TAAAATAAATAAG
Found at i:3076027 original size:16 final size:16
Alignment explanation
Indices: 3075914--3076041 Score: 50
Period size: 17 Copynumber: 7.8 Consensus size: 16
3075904 AAGAGGAGGA
3075914 AAAAATAATAATAATAA-
1 AAAAATAA-AATAA-AAG
* **
3075931 AATAAATAATATAAGGG
1 AA-AAATAAAATAAAAG
* *
3075948 AAAGAAAAAAATAAAAT
1 AAA-AATAAAATAAAAG
*
3075965 AAATAAGTAAAAT-AAAT
1 AAA-AA-TAAAATAAAAG
*
3075982 AAACATAAAAT-AAAG
1 AAAAATAAAATAAAAG
** *
3075997 CGAAAT-GAATAAAAAG
1 AAAAATAAAAT-AAAAG
*
3076013 AAATAA-AAAATAAAAT
1 AAA-AATAAAATAAAAG
3076029 AAAAATAAAATAA
1 AAAAATAAAATAA
3076042 GAGTAAGAGT
Statistics
Matches: 82, Mismatches: 20, Indels: 19
0.68 0.17 0.16
Matches are distributed among these distances:
14 3 0.04
15 14 0.17
16 21 0.26
17 33 0.40
18 11 0.13
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (16 bp):
AAAAATAAAATAAAAG
Found at i:3076032 original size:11 final size:11
Alignment explanation
Indices: 3075954--3076041 Score: 53
Period size: 11 Copynumber: 8.2 Consensus size: 11
3075944 AGGGAAAGAA
3075954 AAAAATAAAAT
1 AAAAATAAAAT
3075965 AAATAAGTAAAAT
1 AAA-AA-TAAAAT
3075978 --AAATAAACAT
1 AAAAATAAA-AT
*
3075988 -AAAAT-AAAG
1 AAAAATAAAAT
** *
3075997 CGAAAT-GAAT
1 AAAAATAAAAT
*
3076007 AAAAA-GAAAT
1 AAAAATAAAAT
3076017 AAAAAATAAAAT
1 -AAAAATAAAAT
3076029 AAAAATAAAAT
1 AAAAATAAAAT
3076040 AA
1 AA
3076042 GAGTAAGAGT
Statistics
Matches: 61, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
9 5 0.08
10 18 0.30
11 26 0.43
12 6 0.10
13 6 0.10
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.17
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:3076133 original size:8 final size:8
Alignment explanation
Indices: 3076092--3076141 Score: 50
Period size: 8 Copynumber: 6.0 Consensus size: 8
3076082 GCATTAACAA
3076092 AAAAATAAT
1 AAAAA-AAT
3076101 AAAAAAACT
1 AAAAAAA-T
3076110 AGAAAGAAAT
1 A-AAA-AAAT
3076120 --AAAAAT
1 AAAAAAAT
3076126 AAAAAAAT
1 AAAAAAAT
3076134 AAAAAAAT
1 AAAAAAAT
3076142 TAATATAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
6 4 0.11
7 2 0.06
8 16 0.44
9 7 0.19
10 4 0.11
11 3 0.08
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.14
Consensus pattern (8 bp):
AAAAAAAT
Found at i:3076149 original size:22 final size:22
Alignment explanation
Indices: 3076090--3076158 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 22
3076080 AAGCATTAAC
*
3076090 AAAAAAA-TAATA-AAAAAACT
1 AAAAAAATTAATATAAAAAAAT
* *
3076110 AGAAAGAAATAAAAATAAAAAAAT
1 A-AAA-AAATTAATATAAAAAAAT
*
3076134 AAAAAAATTAATATAATAATAAT
1 AAAAAAATTAATATAA-AAAAAT
3076157 AA
1 AA
3076159 TGGGTCAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
20 1 0.03
21 3 0.08
22 13 0.34
23 13 0.34
24 8 0.21
ACGTcount: A:0.77, C:0.01, G:0.03, T:0.19
Consensus pattern (22 bp):
AAAAAAATTAATATAAAAAAAT
Found at i:3076151 original size:25 final size:26
Alignment explanation
Indices: 3076094--3076152 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 26
3076084 ATTAACAAAA
3076094 AAATAATAAAAAAACTAGAAAGAAAT
1 AAATAATAAAAAAACTAGAAAGAAAT
3076120 AAA-AATAAAAAAA-TA-AAA-AAATT
1 AAATAATAAAAAAACTAGAAAGAAA-T
3076143 AATATAATAA
1 AA-ATAATAA
3076153 TAATAATGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
22 3 0.10
23 6 0.20
24 3 0.10
25 15 0.50
26 3 0.10
ACGTcount: A:0.76, C:0.02, G:0.03, T:0.19
Consensus pattern (26 bp):
AAATAATAAAAAAACTAGAAAGAAAT
Found at i:3077400 original size:36 final size:35
Alignment explanation
Indices: 3077242--3077697 Score: 310
Period size: 36 Copynumber: 12.4 Consensus size: 35
3077232 TTTTTGAAAT
*** *
3077242 TATATATTTTCAAAACCCTTGTTTTCAAAACCATACTA
1 TATATATTTTCAAAAATGTT-TTTT-AAAACTATA-TA
*
3077280 CATATATTTTCCAAAAAAT-TATTTTTAAAACTATATA
1 TATATATTTT-C-AAAAATGT-TTTTTAAAACTATATA
* **
3077317 -ACATATTTTC-AAAA-GCATTTT-AAACTATATA
1 TATATATTTTCAAAAATGTTTTTTAAAACTATATA
*
3077348 TTATATATATTT-AAAAATGTTTTTATAAAATTATATA
1 -TATATAT-TTTCAAAAATGTTTTT-TAAAACTATATA
*
3077385 TATATATTTTCAAAAATATTTTTTAAAAACTATATTGTA
1 TATATATTTTCAAAAATGTTTTTT-AAAACTATA---TA
3077424 TATATATGTTTTC-AAAATG-TTTTTAAAACTATATAA
1 TATATA--TTTTCAAAAATGTTTTTTAAAACTATAT-A
3077460 TATATATGGTTTCAAAAATG-TTTTTAAAACTATATAA
1 TATATAT--TTTCAAAAATGTTTTTTAAAACTATAT-A
3077497 TATATATGTTTTCAAAAATGTTTTTTTAAAAAACTATATA
1 TATATA--TTTTCAAAAATG-TTTTTT--AAAACTATATA
* *
3077537 TTATATATATTTTAAAAATG-TTTTCAAAACTATATA
1 -TATATAT-TTTCAAAAATGTTTTTTAAAACTATATA
* ** *
3077573 TTATATATTTTC-GAAATGTTTTAAAAAACCATATA
1 -TATATATTTTCAAAAATGTTTTTTAAAACTATATA
* *
3077608 TTATATAATTTTC-AAAATG--ATTTCAAACTATATAA
1 -TATAT-ATTTTCAAAAATGTTTTTTAAAACTATAT-A
** *
3077643 TATATACATTTAAAAAAATCGTTTTTCAAAACTATATA
1 TATAT--ATTTTCAAAAAT-GTTTTTTAAAACTATATA
3077681 TATTATATATTTCAAAA
1 TA-TATAT-TTTCAAAA
3077698 TCATTTGCAA
Statistics
Matches: 343, Mismatches: 35, Indels: 80
0.75 0.08 0.17
Matches are distributed among these distances:
31 10 0.03
32 4 0.01
33 9 0.03
34 27 0.08
35 37 0.11
36 81 0.24
37 54 0.16
38 39 0.11
39 40 0.12
40 21 0.06
41 21 0.06
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.45
Consensus pattern (35 bp):
TATATATTTTCAAAAATGTTTTTTAAAACTATATA
Found at i:3079310 original size:20 final size:21
Alignment explanation
Indices: 3079284--3079329 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
3079274 AATAATTGTA
3079284 ATAATTTA-AATCAT-ATGTTT
1 ATAATTTATAAT-ATAATGTTT
*
3079304 TTAATTTATAATATAATGTTT
1 ATAATTTATAATATAATGTTT
3079325 ATAAT
1 ATAAT
3079330 GAACATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.52
Consensus pattern (21 bp):
ATAATTTATAATATAATGTTT
Found at i:3080585 original size:22 final size:22
Alignment explanation
Indices: 3080556--3080614 Score: 100
Period size: 22 Copynumber: 2.7 Consensus size: 22
3080546 GCAATCCCTA
3080556 ATTTTTAAAACATGTTCATTTT
1 ATTTTTAAAACATGTTCATTTT
*
3080578 CTTTTTAAAACATGTTCATTTT
1 ATTTTTAAAACATGTTCATTTT
*
3080600 ATTTTCAAAACATGT
1 ATTTTTAAAACATGT
3080615 GATATGTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.32, C:0.12, G:0.05, T:0.51
Consensus pattern (22 bp):
ATTTTTAAAACATGTTCATTTT
Found at i:3082579 original size:58 final size:59
Alignment explanation
Indices: 3082517--3082714 Score: 143
Period size: 59 Copynumber: 3.4 Consensus size: 59
3082507 ATATTAAAGG
* * * * * *
3082517 ATTTTTTTTTACAAATTATAAT-AGAGGAGAAATCTTTTTGTAAATTATAAT-ATAAGAA
1 ATTTTTTTTTACAAATTACAATCA-AGGAAAAATATTTTTATAAATTACAATCAAAAGAA
* * * *
3082575 ATTTTATTTTATAAATTACAATCAAGGAAAAATATTTTTATAATTTACAATCAAAAGAC
1 ATTTTTTTTTACAAATTACAATCAAGGAAAAATATTTTTATAAATTACAATCAAAAGAA
* * * * * *** * *
3082634 AGTTCTTTTTACAAATTAAAATGAAAGTAAAAA-ATTCACATAAATTACAAT-AATGACAA
1 ATTTTTTTTTACAAATTACAAT-CAAGGAAAAATATTTTTATAAATTACAATCAA-AAGAA
* *
3082693 ATATTTTTTTACAAATTGCAAT
1 ATTTTTTTTTACAAATTACAAT
3082715 AACATCTCAT
Statistics
Matches: 107, Mismatches: 29, Indels: 7
0.75 0.20 0.05
Matches are distributed among these distances:
58 43 0.40
59 56 0.52
60 8 0.07
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (59 bp):
ATTTTTTTTTACAAATTACAATCAAGGAAAAATATTTTTATAAATTACAATCAAAAGAA
Found at i:3087395 original size:31 final size:31
Alignment explanation
Indices: 3087360--3087420 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
3087350 AGTCCATACT
3087360 ATGAGTTTGGCATCAGCTTTCCAAGGCAATG
1 ATGAGTTTGGCATCAGCTTTCCAAGGCAATG
3087391 ATGAGTTTGGCATCAGCTTTCCAAGGCAAT
1 ATGAGTTTGGCATCAGCTTTCCAAGGCAAT
3087421 TACCGTATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.30
Consensus pattern (31 bp):
ATGAGTTTGGCATCAGCTTTCCAAGGCAATG
Found at i:3088203 original size:14 final size:14
Alignment explanation
Indices: 3088181--3088231 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
3088171 TTAGGGGGCC
*
3088181 AGGGTTTATGGTTT
1 AGGGTTTATAGTTT
**
3088195 ATAGTTTATAGTTT
1 AGGGTTTATAGTTT
*
3088209 AGGGTTTAGAGTTT
1 AGGGTTTATAGTTT
3088223 AGGGTTTAT
1 AGGGTTTAT
3088232 TGCAAGGACA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.22, C:0.00, G:0.29, T:0.49
Consensus pattern (14 bp):
AGGGTTTATAGTTT
Found at i:3088229 original size:21 final size:21
Alignment explanation
Indices: 3088181--3088230 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
3088171 TTAGGGGGCC
* *
3088181 AGGGTTTATGGTTTATAGTTT
1 AGGGTTTAGGGTTTAGAGTTT
**
3088202 ATAGTTTAGGGTTTAGAGTTT
1 AGGGTTTAGGGTTTAGAGTTT
3088223 AGGGTTTA
1 AGGGTTTA
3088231 TTGCAAGGAC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.48
Consensus pattern (21 bp):
AGGGTTTAGGGTTTAGAGTTT
Found at i:3089102 original size:20 final size:20
Alignment explanation
Indices: 3089055--3089282 Score: 203
Period size: 20 Copynumber: 11.2 Consensus size: 20
3089045 AATGACCAAC
**
3089055 AAAATCGCAACGCGA-TATC
1 AAAATCGCAACGCGATTAAG
* *
3089074 AAAACCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* * *
3089094 AAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
* * ***
3089114 AAGATCGCAACACGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
* *
3089135 AAGAATCGCAATGCGATTCAG
1 AA-AATCGCAACGCGATTAAG
*
3089156 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTAAG
***
3089176 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
3089197 AAGAATCGCAACGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
3089218 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
3089238 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
3089260 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
3089278 AAAAT
1 AAAAT
3089283 GAGTAAATTC
Statistics
Matches: 169, Mismatches: 29, Indels: 21
0.77 0.13 0.10
Matches are distributed among these distances:
18 3 0.02
19 16 0.09
20 109 0.64
21 13 0.08
22 28 0.17
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:3089158 original size:62 final size:62
Alignment explanation
Indices: 3089055--3089282 Score: 306
Period size: 62 Copynumber: 3.8 Consensus size: 62
3089045 AATGACCAAC
* * * * * *
3089055 AAAATCGCAACGCGAT-AT-CAA-AACCGCAACGCGATTTAGAAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACG-CGATTAAG
* * * * *
3089114 AAGATCGCAACACGATCTTCCAAGAATCGCAATGCGATTCAGAAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTAAG
3089176 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTAAG
3089238 AAAATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTAAGAAAAT
1 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAAT
3089283 GAGTAAATTC
Statistics
Matches: 150, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
59 14 0.09
60 31 0.21
61 5 0.03
62 100 0.67
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.16
Consensus pattern (62 bp):
AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTAAG
Found at i:3089360 original size:6 final size:6
Alignment explanation
Indices: 3089349--3089528 Score: 339
Period size: 6 Copynumber: 30.5 Consensus size: 6
3089339 GACACGTATT
3089349 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
3089397 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
3089445 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
3089493 ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
3089529 CGAGACGAGA
Statistics
Matches: 174, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 15 0.09
6 159 0.91
ACGTcount: A:0.32, C:0.51, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:3090046 original size:6 final size:6
Alignment explanation
Indices: 3090025--3090139 Score: 216
Period size: 6 Copynumber: 19.5 Consensus size: 6
3090015 TCTCGTCTCG
3090025 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
3090071 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
3090119 GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGT
3090140 AATACGTGTC
Statistics
Matches: 109, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 10 0.09
6 99 0.91
ACGTcount: A:0.00, C:0.17, G:0.51, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:3090319 original size:20 final size:19
Alignment explanation
Indices: 3090237--3090611 Score: 228
Period size: 20 Copynumber: 18.2 Consensus size: 19
3090227 ATTTACTCAT
3090237 TTTCTGAATCGCGTTGCGA
1 TTTCTGAATCGCGTTGCGA
*
3090256 -TTCTTGGAATATCACGTTGCGA
1 TTTC-T-G-A-ATCGCGTTGCGA
*
3090278 TTTTCTTGGAAGATCGCATTGCGA
1 -TTTC-T-G-A-ATCGCGTTGCGA
3090302 TTTACTGAATCGCGTTGCGA
1 TTT-CTGAATCGCGTTGCGA
3090322 -TTCTTGGAAGATCGCGTTGCGA
1 TTTC-T-G-A-ATCGCGTTGCGA
*
3090344 TTTTCTTAATCGCGTTGCGA
1 -TTTCTGAATCGCGTTGCGA
3090364 -TTCTTGGAATCGCGTTGCGA
1 TTTC-T-GAATCGCGTTGCGA
*
3090384 TTTTCTGAATCGGGTTGCGA
1 -TTTCTGAATCGCGTTGCGA
3090404 -TTCTTGGAATCGCGTTGCGA
1 TTTC-T-GAATCGCGTTGCGA
3090424 -TTCTTGGAAGATCGCGTTGCGA
1 TTTC-T-G-A-ATCGCGTTGCGA
3090446 TTTTCTGAATCGCGTTGCGA
1 -TTTCTGAATCGCGTTGCGA
3090466 TTTTCTGAATCGCGTTGCGA
1 -TTTCTGAATCGCGTTGCGA
3090486 -TTCTTGGAAGATCGCGTTGCGA
1 TTTC-T-G-A-ATCGCGTTGCGA
* *
3090508 TTTTATGAATCGCATTGCGA
1 -TTTCTGAATCGCGTTGCGA
3090528 -TTCTTGGAAGATCGCGTTGCGA
1 TTTC-T-G-A-ATCGCGTTGCGA
** * *
3090550 TCTTCT-TTTCAACGTTGCGCT
1 T-TTCTGAATC-GCGTTGCG-A
* *
3090571 TTTCTAAATCGCGTTGCGG
1 TTTCTGAATCGCGTTGCGA
3090590 TTT-TGATATCGCGTTGCGA
1 TTTCTGA-ATCGCGTTGCGA
3090609 TTT
1 TTT
3090612 TGTTGGTCAT
Statistics
Matches: 294, Mismatches: 23, Indels: 78
0.74 0.06 0.20
Matches are distributed among these distances:
18 17 0.06
19 27 0.09
20 134 0.46
21 13 0.04
22 64 0.22
23 8 0.03
24 31 0.11
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (19 bp):
TTTCTGAATCGCGTTGCGA
Found at i:3090321 original size:66 final size:61
Alignment explanation
Indices: 3090237--3090385 Score: 201
Period size: 66 Copynumber: 2.3 Consensus size: 61
3090227 ATTTACTCAT
*
3090237 TTTCTGAATCGCGTTGCGATTCTTGGAATATCACGTTGCGATTTTCTTGGAAGATCGCATTGCGA
1 TTTCTGAATCGCGTTGCGATTCTTGGAAGATCACGTTGCGATTTTCTT---A-ATCGCATTGCGA
* *
3090302 TTTACTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTTAATCGCGTTGCGA
1 TTT-CTGAATCGCGTTGCGATTCTTGGAAGATCACGTTGCGATTTTCTTAATCGCATTGCGA
3090364 -TTCTTGGAATCGCGTTGCGATT
1 TTTC-T-GAATCGCGTTGCGATT
3090386 TTCTGAATCG
Statistics
Matches: 78, Mismatches: 3, Indels: 9
0.87 0.03 0.10
Matches are distributed among these distances:
60 1 0.01
61 3 0.04
62 27 0.35
63 1 0.01
65 3 0.04
66 43 0.55
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.38
Consensus pattern (61 bp):
TTTCTGAATCGCGTTGCGATTCTTGGAAGATCACGTTGCGATTTTCTTAATCGCATTGCGA
Found at i:3090334 original size:42 final size:42
Alignment explanation
Indices: 3090244--3090555 Score: 381
Period size: 42 Copynumber: 7.4 Consensus size: 42
3090234 CATTTTCTGA
* *
3090244 ATCGCGTTGCGATTCTT-GGAATATCACGTTGCGATTTTCTTGGAAG
1 ATCGCGTTGCGATT-TTCTG-A-ATCGCGTTGCGA--TTCTTGGAAG
* *
3090290 ATCGCATTGCGATTTACTGAATCGCGTTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAG
*
3090332 ATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGG-A-
1 ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAG
*
3090372 ATCGCGTTGCGATTTTCTGAATCGGGTTGCGATTCTTGG-A-
1 ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAG
* *
3090412 ATCGCGTTGCGATTCTT-GGAAGATCGCGTTGCGATT-TTCTG-A-
1 ATCGCGTTGCGATT-TTCTG-A-ATCGCGTTGCGATTCTT-GGAAG
3090454 ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAG
* *
3090496 ATCGCGTTGCGATTTTATGAATCGCATTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAG
*
3090538 ATCGCGTTGCGATCTTCT
1 ATCGCGTTGCGATTTTCT
3090556 TTTCAACGTT
Statistics
Matches: 239, Mismatches: 18, Indels: 22
0.86 0.06 0.08
Matches are distributed among these distances:
40 68 0.28
41 12 0.05
42 132 0.55
44 11 0.05
45 2 0.01
46 14 0.06
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.37
Consensus pattern (42 bp):
ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAAG
Found at i:3090438 original size:62 final size:62
Alignment explanation
Indices: 3090310--3090550 Score: 323
Period size: 62 Copynumber: 3.9 Consensus size: 62
3090300 GATTTACTGA
*
3090310 ATCGCGTTGCGATTCTT-GGAAGATCGCGTTGCGATTTTCTT--AATCGCGTTGCGATTCTTGG-
1 ATCGCGTTGCGATT-TTCTG-A-ATCGCGTTGCGA--TTCTTGGAATCGCGTTGCGATTCTTGGA
3090371 A-
61 AG
*
3090372 ATCGCGTTGCGATTTTCTGAATCGGGTTGCGATTCTTGGAATCGCGTTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTCTTGGAAG
*
3090434 ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATT-TTCTGAATCGCGTTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTT-GGAATCGCGTTGCGATTCTTGGAAG
* *
3090496 ATCGCGTTGCGATTTTATGAATCGCATTGCGATTCTTGGAAGATCGCGTTGCGAT
1 ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCGAT
3090551 CTTCTTTTCA
Statistics
Matches: 163, Mismatches: 7, Indels: 16
0.88 0.04 0.09
Matches are distributed among these distances:
58 5 0.03
60 31 0.19
61 6 0.04
62 105 0.64
63 3 0.02
64 13 0.08
ACGTcount: A:0.17, C:0.19, G:0.28, T:0.36
Consensus pattern (62 bp):
ATCGCGTTGCGATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTCTTGGAAG
Found at i:3090568 original size:42 final size:40
Alignment explanation
Indices: 3090265--3090610 Score: 230
Period size: 42 Copynumber: 8.4 Consensus size: 40
3090255 ATTCTTGGAA
*
3090265 TATCACGTTGCGATTTTCTTGGAAGATCGCATTGCGATTTACT
1 TATCACGTTGCGA--TTCTTGGAAGATCGCGTTGCGATTT-CT
* *
3090308 GAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCT
1 -TATCACGTTGCGATTCTTGGAAGATCGCGTTGCGA-TTTCT
*
3090350 TAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCGATTTTCT
1 T-ATCACGTTGCGATTCTTGGAAGATCGCGTTGCGA-TTTCT
* **
3090390 GAATCGGGTTGCGATTCTTGG-A-ATCGCGTTGCGA-TTCT
1 -TATCACGTTGCGATTCTTGGAAGATCGCGTTGCGATTTCT
* *
3090428 TGGAAGATCGCGTTGCGATT-TTCTG-A-ATCGCGTTGCGATTTTCT
1 T-----ATCACGTTGCGATTCTT-GGAAGATCGCGTTGCGA-TTTCT
* *
3090472 GAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTT-T
1 -TATCACGTTGCGATTCTTGGAAGATCGCGTTGCGATTTCT
* *
3090512 ATGAATCGCATTGCGATTCTTGGAAGATCGCGTTGCGATCTTCT
1 -T--ATCACGTTGCGATTCTTGGAAGATCGCGTTGCGAT-TTCT
* * ** *
3090556 TTTCAACGTTGCGCTT-TTCTAA-ATCGCGTTGCGGTTT-T
1 TATC-ACGTTGCGATTCTTGGAAGATCGCGTTGCGATTTCT
*
3090594 GATATCGCGTTGCGATT
1 --TATCACGTTGCGATT
3090611 TTGTTGGTCA
Statistics
Matches: 256, Mismatches: 24, Indels: 49
0.78 0.07 0.15
Matches are distributed among these distances:
38 5 0.02
39 11 0.04
40 80 0.31
41 15 0.06
42 123 0.48
43 6 0.02
44 16 0.06
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (40 bp):
TATCACGTTGCGATTCTTGGAAGATCGCGTTGCGATTTCT
Found at i:3092452 original size:17 final size:17
Alignment explanation
Indices: 3092399--3092464 Score: 59
Period size: 16 Copynumber: 4.1 Consensus size: 17
3092389 GAAATATAAG
*
3092399 TTCAAAC-ATCCATAAA
1 TTCAAACAATCCACAAA
*
3092415 TTCAAACAAAT--TCAAA
1 TTCAAAC-AATCCACAAA
*
3092431 GTCAAACAATCCACAAA
1 TTCAAACAATCCACAAA
*
3092448 TTCAAACATTCCA-AAA
1 TTCAAACAATCCACAAA
3092464 T
1 T
3092465 ATCCAAAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
15 3 0.08
16 20 0.50
17 15 0.38
18 2 0.05
ACGTcount: A:0.52, C:0.24, G:0.02, T:0.23
Consensus pattern (17 bp):
TTCAAACAATCCACAAA
Found at i:3094406 original size:22 final size:23
Alignment explanation
Indices: 3094359--3094420 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
3094349 ATTCCCCTAT
3094359 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
3094382 AGGGGGAATCGGTTCCCCTTC-A
1 AGGGGGAATCGGTTCCCCTTCAA
* *
3094404 AGGGGGTATCGATTCCC
1 AGGGGGAATCGGTTCCC
3094421 TCTGCACCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
22 16 0.43
23 21 0.57
ACGTcount: A:0.19, C:0.26, G:0.32, T:0.23
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCCTTCAA
Found at i:3094421 original size:21 final size:22
Alignment explanation
Indices: 3094339--3094420 Score: 96
Period size: 23 Copynumber: 3.7 Consensus size: 22
3094329 TAAAACCCAG
*
3094339 GGGGGTATCGATTCCCC-T-ATA
1 GGGGGAATCGATTCCCCTTCA-A
*
3094360 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATTCCCCTTC-AA
*
3094383 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGAATCGATTCCCCTTCAA
*
3094405 GGGGGTATCGATTCCC
1 GGGGGAATCGATTCCC
3094421 TCTGCACCAA
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
21 15 0.28
22 17 0.31
23 21 0.39
24 1 0.02
ACGTcount: A:0.18, C:0.26, G:0.32, T:0.24
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCTTCAA
Found at i:3100113 original size:20 final size:21
Alignment explanation
Indices: 3100077--3100127 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
3100067 TGGAGCGTGG
* *
3100077 GGGGGATCGGTATCCCCTCAT
1 GGGGAATCGGTACCCCCTCAT
3100098 GGGGAATCGGTACCCCCTCAT
1 GGGGAATCGGTACCCCCTCAT
3100119 GGGGAATCG
1 GGGGAATCG
3100128 ATTCCGTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.18, C:0.27, G:0.35, T:0.20
Consensus pattern (21 bp):
GGGGAATCGGTACCCCCTCAT
Found at i:3102081 original size:100 final size:101
Alignment explanation
Indices: 3101896--3102103 Score: 391
Period size: 100 Copynumber: 2.1 Consensus size: 101
3101886 AATTAAGCCA
*
3101896 TCAAACTATAAAATTACATTAATTATGGTCTTTGATCAACCTTTAAGTCTTAACCTTTTTTAGGT
1 TCAAACTATAAAATTACATTAATTATGGTCTTTGATCAACCTTTAAGTCTTAACCTTTTTTAAGT
*
3101961 TATTTCTCATGTTGCAGCGTCAAATGGAATTACATG
66 TATTTCTCATGTTGCAGCGTCAAAGGGAATTACATG
3101997 TCAAACTATAAAATTACATTAATTATGGTCTTTGATCAA-CTTTAAGTCTTAACCTTTTTTAAGT
1 TCAAACTATAAAATTACATTAATTATGGTCTTTGATCAACCTTTAAGTCTTAACCTTTTTTAAGT
3102061 TATTTCTCATGTTGCAGCGTCAAAGGGAATTACATG
66 TATTTCTCATGTTGCAGCGTCAAAGGGAATTACATG
3102097 TCAAACT
1 TCAAACT
3102104 TTAGGGATGT
Statistics
Matches: 105, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
100 66 0.63
101 39 0.37
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (101 bp):
TCAAACTATAAAATTACATTAATTATGGTCTTTGATCAACCTTTAAGTCTTAACCTTTTTTAAGT
TATTTCTCATGTTGCAGCGTCAAAGGGAATTACATG
Found at i:3102411 original size:22 final size:24
Alignment explanation
Indices: 3102386--3102435 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 24
3102376 AATTTATTCA
3102386 AAAATAAAAATA-CTTTTAAA-AT
1 AAAATAAAAATATCTTTTAAATAT
*
3102408 -AAA-AAAAATATTTTTTAAATAT
1 AAAATAAAAATATCTTTTAAATAT
3102430 AAAATA
1 AAAATA
3102436 TTACATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
20 7 0.30
21 10 0.43
22 2 0.09
23 3 0.13
24 1 0.04
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (24 bp):
AAAATAAAAATATCTTTTAAATAT
Found at i:3102416 original size:20 final size:22
Alignment explanation
Indices: 3102391--3102433 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
3102381 ATTCAAAAAT
3102391 AAAAATA-CTTTTAAA-ATAAA
1 AAAAATATCTTTTAAATATAAA
*
3102411 AAAAATATTTTTTAAATATAAA
1 AAAAATATCTTTTAAATATAAA
3102433 A
1 A
3102434 TATTACATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 7 0.35
22 6 0.30
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
AAAAATATCTTTTAAATATAAA
Found at i:3102462 original size:30 final size:31
Alignment explanation
Indices: 3102427--3102494 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 31
3102417 ATTTTTTAAA
3102427 TATAAAATATTAC-ATAATTACTTTAAAA-AT
1 TATAAAATATTACAAT-ATTACTTTAAAATAT
* *
3102457 TATAAAATCTTACAATATTATTTTAAAATAT
1 TATAAAATATTACAATATTACTTTAAAATAT
*
3102488 TAAAAAA
1 TATAAAA
3102495 ATCTAAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 23 0.70
31 10 0.30
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (31 bp):
TATAAAATATTACAATATTACTTTAAAATAT
Found at i:3102511 original size:24 final size:24
Alignment explanation
Indices: 3102478--3102553 Score: 82
Period size: 24 Copynumber: 3.0 Consensus size: 24
3102468 ACAATATTAT
3102478 TTTAAAATATTAAAAAAATCTAAAA
1 TTTAAAATATT-AAAAAATCTAAAA
* *
3102503 -TTAAAATATGTAGAAAATATAAAA
1 TTTAAAATAT-TAAAAAATCTAAAA
3102527 TTTTAAGAATTATTAAAAAATCTAAAA
1 -TTTAA-AA-TATTAAAAAATCTAAAA
3102554 AAAATCTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
24 20 0.48
25 1 0.02
26 4 0.10
27 14 0.33
28 3 0.07
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.33
Consensus pattern (24 bp):
TTTAAAATATTAAAAAATCTAAAA
Found at i:3102713 original size:16 final size:16
Alignment explanation
Indices: 3102692--3102725 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3102682 AATATTTTTT
*
3102692 AAATATAAATTATTAA
1 AAATATAAAATATTAA
3102708 AAATATAAAATATTAA
1 AAATATAAAATATTAA
3102724 AA
1 AA
3102726 CTTTATTAAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATATAAAATATTAA
Found at i:3103116 original size:3 final size:3
Alignment explanation
Indices: 3103110--3103159 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
3103100 GAGGCTTGAG
3103110 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
3103158 AT
1 AT
3103160 TCCATCAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3104908 original size:29 final size:29
Alignment explanation
Indices: 3104842--3104977 Score: 123
Period size: 29 Copynumber: 4.7 Consensus size: 29
3104832 TTTTCCTTTG
* *
3104842 ATTGTAATCTATAAAAAGTTTTGGTGTTT
1 ATTGTAATTTATAAAAAGTTTTGGTATTT
*
3104871 ATTGTAATTTTTAGAAAA-TTTTGGTATTT
1 ATTGTAATTTATA-AAAAGTTTTGGTATTT
* * * *
3104900 ATTGTAATTTACATAAAGTTCTGATATTT
1 ATTGTAATTTATAAAAAGTTTTGGTATTT
* * ** **
3104929 ATTATAATTTACAAAAA-AATTGGTAACT
1 ATTGTAATTTATAAAAAGTTTTGGTATTT
*
3104957 ATTATAATTTATAAAAAGTTT
1 ATTGTAATTTATAAAAAGTTT
3104978 AGTCTTGATT
Statistics
Matches: 85, Mismatches: 19, Indels: 6
0.77 0.17 0.05
Matches are distributed among these distances:
28 24 0.28
29 57 0.67
30 4 0.05
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (29 bp):
ATTGTAATTTATAAAAAGTTTTGGTATTT
Found at i:3105028 original size:29 final size:29
Alignment explanation
Indices: 3104996--3105056 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 29
3104986 TTGTGATATT
*
3104996 TAAA-AAATAGACTTTTATTGTAATTTATA
1 TAAATAAATAGACTTTTATGGTAATTT-TA
** *
3105025 TAAATATTTATACTTTTATGGTAATTTTA
1 TAAATAAATAGACTTTTATGGTAATTTTA
3105054 TAA
1 TAA
3105057 TTTTAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 9 0.33
30 18 0.67
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (29 bp):
TAAATAAATAGACTTTTATGGTAATTTTA
Found at i:3113136 original size:433 final size:432
Alignment explanation
Indices: 3112491--3113605 Score: 1370
Period size: 433 Copynumber: 2.6 Consensus size: 432
3112481 TACTGTAGTG
* * * * **
3112491 GTATAGATACTTAAGGTCTTGATTAGAAACGTCGAAACTAATTTTGGTATCGGTACTCGAAGGAG
1 GTATAGATACTCAGGGTCTTGATCAGAAACATCGAAACTAATTTTGGTATCGAAACTCGAAGGAG
*
3112556 TATTGATAACAAGGGTAGAGTATCGATACTCCCTAAAGGGGTATCGATACCGGGTATTTTTCAAA
66 TATTGATAACAAGGGTAGAGTATCGATACTCCCCAAAGGGGTATCGATACCGGGTATTTTTCAAA
* * * *
3112621 ACATCGAAAGTAATTTTGGTAACGGTACTTATGAGAGTATCGATAT-TGAGGACGGTGGGTATCG
131 ACATCGAAAGCAATTTTGGTATCGGTACTTATGGGAGTATCGAT-TCTGAGGAGGGTGGGTATCG
** * * *
3112685 ATAC-TCACAGTTGAGTATCAATATTGAGTCTAATTCTCAAACATTGAAGGTAAATTCAG-TATC
195 ATACTTC-CAGAAGAGTATCGATATTGAGTCTAATTTTCAAACATCGAAGGTAAATT-AGATATC
*
3112748 AATACTATTAAGAATGAATTGAAGGATTTTAAAAGAAAGAAAATAGAGTTT-TGGGTCAAGGGTA
258 AATACTATTAAGAATGAATTAAAGGATTTTAAAAGAAAGAAAATAGAGTTTCTGGGTCAAGGGTA
* * * *
3112812 TTGATAATATCCATCGAGTGAGGGTAAACTTCAAAGGAATTGTGAGAGTAGTAT-TGATACCCCA
323 TCGATAATACCCATCGAGTG-GGGTAAAATGCAAAGGAATTGTGAGAGTAGTATCT-ATACCCCA
*
3112876 TCAAGGAGTATCGATATTGCTCAAGTGGTATCGATACTCAGGGCCTA
386 TCAAGGAGTATCGATATTGCTCAAGTGGTATCGATACACAGGGCCTA
* *
3112923 GTATAGATACTCAGGGTCTTGATCAGAAACATCGAAGCTAATTTTAGT-TACGAAACTCGAAGGA
1 GTATAGATACTCAGGGTCTTGATCAGAAACATCGAAACTAATTTTGGTAT-CGAAACTCGAAGGA
* * * ** * ** *
3112987 GTATCGATATCTAGGGTAGAGTATCGATACTCCCCAATTGGGTATCAATATTGGTATATTTTTCA
65 GTATTGATAACAAGGGTAGAGTATCGATACTCCCCAAAGGGGTATCGATACCGG-GTATTTTTCA
* *
3113052 AAACATCGAAAG-AAGTTATGGTATCGGTACTTATGGGAGTATCGATTCTGAGGAGGGTAGGTAT
129 AAACATCGAAAGCAA-TTTTGGTATCGGTACTTATGGGAGTATCGATTCTGAGGAGGGTGGGTAT
* * * * * *
3113116 CGATACTTCCAGAAGAGTATCGATATCGAGTATAATTTTCAAATATCAAAGGTAAATTTGATATT
193 CGATACTTCCAGAAGAGTATCGATATTGAGTCTAATTTTCAAACATCGAAGGTAAATTAGATATC
* * * * * *
3113181 TATACTTTTATGAATGAATTAAAGGATTTTAAATGAAAGGAAATAGAGTTTCTGGGTCGAGGGTA
258 AATACTATTAAGAATGAATTAAAGGATTTTAAAAGAAAGAAAATAGAGTTTCTGGGTCAAGGGTA
* * *
3113246 TCGATACTACCCATCGAGTGGGGTAAAATGCAAAGGAATTGTGAGAGTTGTATCTATACCCCATT
323 TCGATAATACCCATCGAGTGGGGTAAAATGCAAAGGAATTGTGAGAGTAGTATCTATACCCCATC
* * *
3113311 AAGGGGTATCGGTATTGCTCAAGTGGTATCGATACACGGGGCCTA
388 AAGGAGTATCGATATTGCTCAAGTGGTATCGATACACAGGGCCTA
* ** * * * * * * *
3113356 GTATCGATACTCAGGACCTTGACCAAAAAAATTGAATA-TAATATTGGCATC-AATACTCAAAGG
1 GTATAGATACTCAGGGTCTTGATCAGAAACATCGAA-ACTAATTTTGGTATCGAA-ACTCGAAGG
*
3113419 AGTATTGATACCAAGGGTAGAGTATCGATACTCCCCAAAGGGGTATCGATACCGGGTATTTTTCA
64 AGTATTGATAACAAGGGTAGAGTATCGATACTCCCCAAAGGGGTATCGATACCGGGTATTTTTCA
* * * * * * * *
3113484 AAACATTGAAAGCAATTTTGGTATCAGCACTCATGGGAGTATCAATACTGAGGAGGATGGGTATT
129 AAACATCGAAAGCAATTTTGGTATCGGTACTTATGGGAGTATCGATTCTGAGGAGGGTGGGTATC
* * *
3113549 GATACTCCCA-AACGAGTATTGATATCT-AGTCTATTTTTCAAACATCGAAGGTAAATT
194 GATACTTCCAGAA-GAGTATCGATAT-TGAGTCTAATTTTCAAACATCGAAGGTAAATT
3113606 TGGTATCGAT
Statistics
Matches: 579, Mismatches: 90, Indels: 28
0.83 0.13 0.04
Matches are distributed among these distances:
431 3 0.01
432 212 0.37
433 331 0.57
434 33 0.06
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.30
Consensus pattern (432 bp):
GTATAGATACTCAGGGTCTTGATCAGAAACATCGAAACTAATTTTGGTATCGAAACTCGAAGGAG
TATTGATAACAAGGGTAGAGTATCGATACTCCCCAAAGGGGTATCGATACCGGGTATTTTTCAAA
ACATCGAAAGCAATTTTGGTATCGGTACTTATGGGAGTATCGATTCTGAGGAGGGTGGGTATCGA
TACTTCCAGAAGAGTATCGATATTGAGTCTAATTTTCAAACATCGAAGGTAAATTAGATATCAAT
ACTATTAAGAATGAATTAAAGGATTTTAAAAGAAAGAAAATAGAGTTTCTGGGTCAAGGGTATCG
ATAATACCCATCGAGTGGGGTAAAATGCAAAGGAATTGTGAGAGTAGTATCTATACCCCATCAAG
GAGTATCGATATTGCTCAAGTGGTATCGATACACAGGGCCTA
Found at i:3133746 original size:25 final size:26
Alignment explanation
Indices: 3133697--3133750 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
3133687 TAAAAATGAT
*
3133697 TTTATTTTAAAAAATATGTATTATAA
1 TTTATTTTAAAAAATATATATTATAA
* *
3133723 TTTATTTTTAAAATTATATA-TATAA
1 TTTATTTTAAAAAATATATATTATAA
3133748 TTT
1 TTT
3133751 TTAATAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (26 bp):
TTTATTTTAAAAAATATATATTATAA
Found at i:3135609 original size:20 final size:18
Alignment explanation
Indices: 3135564--3135609 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
3135554 ATTTTCTATT
3135564 ATTTTA-TTATAAATATA
1 ATTTTATTTATAAATATA
*
3135581 ATATT-TTTATAAATTATCA
1 ATTTTATTTATAAA-TAT-A
3135600 ATTTTATTTA
1 ATTTTATTTA
3135610 AATTAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 11 0.48
18 3 0.13
19 5 0.22
20 4 0.17
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTTATTTATAAATATA
Found at i:3135613 original size:18 final size:18
Alignment explanation
Indices: 3135564--3135614 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
3135554 ATTTTCTATT
3135564 ATTTTATTATAAA-TATA
1 ATTTTATTATAAATTATA
3135581 ATATTT-TTATAAATTATCA
1 AT-TTTATTATAAATTAT-A
3135600 ATTTTATT-TAAATTA
1 ATTTTATTATAAATTA
3135615 ATTTATTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 9 0.30
18 16 0.53
19 5 0.17
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTTATTATAAATTATA
Found at i:3135753 original size:22 final size:22
Alignment explanation
Indices: 3135728--3135773 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
3135718 TTTGAGTTTC
3135728 TTTCGGTTTGGGTAAATTTCGG
1 TTTCGGTTTGGGTAAATTTCGG
* *
3135750 TTTCGGTTTGGGTTAATTTTGG
1 TTTCGGTTTGGGTAAATTTCGG
3135772 TT
1 TT
3135774 CTAGTTGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.11, C:0.07, G:0.30, T:0.52
Consensus pattern (22 bp):
TTTCGGTTTGGGTAAATTTCGG
Found at i:3136765 original size:23 final size:23
Alignment explanation
Indices: 3136735--3136781 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
3136725 TTCGATTATC
3136735 ACTGGAAAACTAACAGAAAAGTG
1 ACTGGAAAACTAACAGAAAAGTG
*
3136758 ACTGGAAAACTAACGGAAAAGTG
1 ACTGGAAAACTAACAGAAAAGTG
3136781 A
1 A
3136782 TATTTTCTGA
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:0.51, C:0.13, G:0.23, T:0.13
Consensus pattern (23 bp):
ACTGGAAAACTAACAGAAAAGTG
Found at i:3137035 original size:83 final size:83
Alignment explanation
Indices: 3136896--3137049 Score: 249
Period size: 83 Copynumber: 1.9 Consensus size: 83
3136886 CAAAGTTTTT
* *
3136896 CTCCAACTGAATCTCTTTTAATATTTAAATTTAAACATATAATAATATCTTTTAAATTTAAAATA
1 CTCCAACTGAATATCTTTTAATATATAAATTTAAACATATAATAATATCTTTTAAATTTAAAATA
3136961 TTAAACCTGAGAGATTTA
66 TTAAACCTGAGAGATTTA
*
3136979 CTCCAACT-ATATATCTTTTAATATATAAATTTAAA-TTGATAATAATATCTTTTAAATTTAAAA
1 CTCCAACTGA-ATATCTTTTAATATATAAATTTAAACAT-ATAATAATATCTTTTAAATTTAAAA
3137042 TATTAAAC
64 TATTAAAC
3137050 ATATATACAC
Statistics
Matches: 66, Mismatches: 3, Indels: 4
0.90 0.04 0.05
Matches are distributed among these distances:
82 2 0.03
83 64 0.97
ACGTcount: A:0.44, C:0.11, G:0.03, T:0.42
Consensus pattern (83 bp):
CTCCAACTGAATATCTTTTAATATATAAATTTAAACATATAATAATATCTTTTAAATTTAAAATA
TTAAACCTGAGAGATTTA
Found at i:3138888 original size:31 final size:31
Alignment explanation
Indices: 3138830--3138890 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
3138820 TCACATTTTA
* * *
3138830 ATTAAACAAAATTGAAAGTGACCAAATATTG
1 ATTAAACAAAAATGAAAGTAACAAAATATTG
* *
3138861 ATTAAATAAAAATGAAAGTAATAAAATATT
1 ATTAAACAAAAATGAAAGTAACAAAATATT
3138891 AAGTTTTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.57, C:0.05, G:0.10, T:0.28
Consensus pattern (31 bp):
ATTAAACAAAAATGAAAGTAACAAAATATTG
Found at i:3139404 original size:24 final size:25
Alignment explanation
Indices: 3139372--3139419 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 25
3139362 CCCACCAAAC
3139372 ACAAAAAAAGATGAAAAGA-AAAAT
1 ACAAAAAAAGATGAAAAGACAAAAT
3139396 ACAAAAAAAGATGAAAAGACAAAA
1 ACAAAAAAAGATGAAAAGACAAAA
3139420 AAACAAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.75, C:0.06, G:0.12, T:0.06
Consensus pattern (25 bp):
ACAAAAAAAGATGAAAAGACAAAAT
Found at i:3140208 original size:28 final size:28
Alignment explanation
Indices: 3140163--3140223 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
3140153 GCAAGAAGCC
*
3140163 AACCAGAAACACATTACCTCCCCAA-ATT
1 AACCTGAAACACATTACCTCCCCAAGA-T
*
3140191 AACCTGAAACAC-TCTACCTTCCCAAGAT
1 AACCTGAAACACAT-TACCTCCCCAAGAT
3140219 AACCT
1 AACCT
3140224 AAGCCTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 1 0.03
28 27 0.93
29 1 0.03
ACGTcount: A:0.39, C:0.36, G:0.05, T:0.20
Consensus pattern (28 bp):
AACCTGAAACACATTACCTCCCCAAGAT
Found at i:3141653 original size:54 final size:55
Alignment explanation
Indices: 3141567--3141715 Score: 187
Period size: 54 Copynumber: 2.7 Consensus size: 55
3141557 ATTTTAGGGG
* * * **
3141567 GTTTCTTGAT-ATTTTTAAATAAATTTTGAAAGAAGTTAAATC-CGATTTTCAGAA
1 GTTTCTTGATGATTTTTAAATGAGTTTTCAAAGAAACTAAATCTC-ATTTTCAGAA
* *
3141621 GTTTCTTGATGATTATT-AATGAGTTTTCAAAGAAACTAAGTCTCATTTTCAGAA
1 GTTTCTTGATGATTTTTAAATGAGTTTTCAAAGAAACTAAATCTCATTTTCAGAA
*
3141675 GATTCTTTGATGATTTTTAAATGAGTTTTCAAAGAAACTAA
1 GTTTC-TTGATGATTTTTAAATGAGTTTTCAAAGAAACTAA
3141716 GGGATTGTTT
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
54 43 0.52
55 17 0.21
56 22 0.27
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.42
Consensus pattern (55 bp):
GTTTCTTGATGATTTTTAAATGAGTTTTCAAAGAAACTAAATCTCATTTTCAGAA
Found at i:3142085 original size:22 final size:20
Alignment explanation
Indices: 3142060--3142099 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
3142050 CGCTGAATGA
3142060 TGAACGGTTCAACATTCAGCGC
1 TGAACGGTTC--CATTCAGCGC
*
3142082 TGAATGGTTCCATTCAGC
1 TGAACGGTTCCATTCAGC
3142100 AGTAAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
22 9 0.53
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (20 bp):
TGAACGGTTCCATTCAGCGC
Found at i:3142296 original size:54 final size:55
Alignment explanation
Indices: 3142115--3142428 Score: 278
Period size: 54 Copynumber: 5.6 Consensus size: 55
3142105 ATAAACAACC
* * * * * *
3142115 CTAAGTCTCATTTTCAAAAGTTTCTTGATAACTTTTTAAATGATTTTTCAAAGAAG
1 CTAAGTCTGATTTTCAGAAGTTTCTTGATGA-TTTTCAAATGAATTTTCAAAGAAA
* * * * * *
3142171 TTAAGTTTGATTTTTAGAAGTTTCTTGATGATTTTTTTTAAAATGAGTTTTCAAAGAAG
1 CTAAGTCTGATTTTCAGAAGTTTCTTGATGA----TTTTCAAATGAATTTTCAAAGAAA
* * * * *
3142230 CTAAGCCTTATTTTCAGAGGTTTCTTGATG-TTTTCAAAAGAATTTTCAAATAAA
1 CTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGAATTTTCAAAGAAA
*
3142284 CTAAGTCAT-ATTTTCAGAAGTTTCTTAATGATTTAT-AAATGAATTTTCAAAG-AA
1 CTAAGTC-TGATTTTCAGAAGTTTCTTGATGATTT-TCAAATGAATTTTCAAAGAAA
* * *
3142338 GTCAAGTCTGATTTTCGGAAGTTTCTTGATGATTTCTTCAAATG-ATCTTTCAAAGACA
1 CT-AAGTCTGATTTTCAGAAGTTTCTTGATGA-TT-TTCAAATGAAT-TTTCAAAGAAA
* * *
3142396 CTAAGGCTGATTTTCAGAGGTTTCTTGAAGATT
1 CTAAGTCTGATTTTCAGAAGTTTCTTGATGATT
3142429 AAAATGGTGT
Statistics
Matches: 211, Mismatches: 34, Indels: 26
0.78 0.13 0.10
Matches are distributed among these distances:
54 48 0.23
55 43 0.20
56 33 0.16
57 39 0.18
58 2 0.01
59 46 0.22
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (55 bp):
CTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTCAAATGAATTTTCAAAGAAA
Found at i:3142421 original size:112 final size:111
Alignment explanation
Indices: 3142115--3142421 Score: 304
Period size: 109 Copynumber: 2.7 Consensus size: 111
3142105 ATAAACAACC
* * * *
3142115 CTAAGTCTCATTTTCAAAAGTTTCTTGATAACTTTTT-AAATGATTTTTCAAAGAAGTTAAGTTT
1 CTAAGTCTCATTTTCAGAAGTTTCTTGATGA-TTTTTCAAATGA-TTTTCAAAGAA-CTAAGTCT
* * * *
3142179 GATTTTTAGAAGTTTCTTGATGATTTTTTTTAAAATGAGTTTTCAAAGAAG
63 GATTTTCAGAAGTTTCTTAATGA--TTTTATAAAATGAATTTTCAAAGAAG
* * * * *
3142230 CTAAGCCTTATTTTCAGAGGTTTCTTGATG--TTTTCAAAAGAATTTTCAAATAAACTAAGTCAT
1 CTAAGTCTCATTTTCAGAAGTTTCTTGATGATTTTTCAAATG-ATTTTCAAA-GAACTAAGTC-T
3142293 -ATTTTCAGAAGTTTCTTAATGA-TTTAT-AAATGAATTTTCAAAGAAG
63 GATTTTCAGAAGTTTCTTAATGATTTTATAAAATGAATTTTCAAAGAAG
* * *
3142339 -TCAAGTCTGATTTTCGGAAGTTTCTTGATGATTTCTTCAAATGATCTTTCAAAGACACTAAGGC
1 CT-AAGTCTCATTTTCAGAAGTTTCTTGATGATTT-TTCAAATGAT-TTTCAAAGA-ACTAAGTC
*
3142403 TGATTTTCAGAGGTTTCTT
62 TGATTTTCAGAAGTTTCTT
3142422 GAAGATTAAA
Statistics
Matches: 160, Mismatches: 21, Indels: 25
0.78 0.10 0.12
Matches are distributed among these distances:
108 1 0.01
109 42 0.26
110 4 0.03
111 6 0.04
112 41 0.26
113 37 0.23
114 4 0.03
115 25 0.16
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.43
Consensus pattern (111 bp):
CTAAGTCTCATTTTCAGAAGTTTCTTGATGATTTTTCAAATGATTTTCAAAGAACTAAGTCTGAT
TTTCAGAAGTTTCTTAATGATTTTATAAAATGAATTTTCAAAGAAG
Found at i:3142543 original size:54 final size:53
Alignment explanation
Indices: 3142450--3142597 Score: 165
Period size: 54 Copynumber: 2.8 Consensus size: 53
3142440 TCAAAAGAAT
* * * *
3142450 TTTTAAAAGAAGCTAATCTTAATTTTTAGGGTTTATTGATGT-TTTTAATTG-G
1 TTTTAAAAGAAGCTAAGCCTAATTTTTAGGGTTTCTTGATGTCTTCTAA-TGAG
*
3142502 ATTTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTCTTCTAATGAG
1 -TTTTAAAAGAAGCTAAGCCTAATTTTTA-GGGTTTCTTGATGTCTTCTAATGAG
* ** * *
3142557 TTTTTAAAGAATTTAAGCCTAATTTGTATGGTTTCTTGATG
1 TTTTAAAAGAAGCTAAGCCTAATTTTTAGGGTTTCTTGATG
3142598 ATAACTGTAA
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
53 37 0.45
54 39 0.48
55 6 0.07
ACGTcount: A:0.28, C:0.07, G:0.19, T:0.46
Consensus pattern (53 bp):
TTTTAAAAGAAGCTAAGCCTAATTTTTAGGGTTTCTTGATGTCTTCTAATGAG
Found at i:3144342 original size:160 final size:160
Alignment explanation
Indices: 3144146--3144588 Score: 636
Period size: 160 Copynumber: 2.8 Consensus size: 160
3144136 ATTATTCAAC
* * *
3144146 CTTAACATGATTCCATCTTTGAAGGAGGTGGATCAACATTTCCAATGGGAGAGTTCATAATAAGA
1 CTTAACATGATTCCATCATAGAAGGAGGTGGATCAACATTTCCAATGGGAGAGTTCATAATGAGA
*
3144211 AGAACTCATCCAATGAGGGAGAAGAAGTTCATAATGAGAAGAAATTGTTCAACCTTGGCTCATCC
66 AGAACTCATCTAATGAGGGAGAAGAAGTTCATAATGAGAAGAAATTGTTCAACCTTGGCTCATCC
* * * *
3144276 ATCGCATATGGAGTTGGATCAACATTATCA
131 ATCGCATATAGAGTTAGATCAAAATCATCA
* * * *
3144306 CTTAACACGATTCCATCACAGAAGGAGGTTGATCAACATTTCCAATGGGAGAGTTCAGAATGAGA
1 CTTAACATGATTCCATCATAGAAGGAGGTGGATCAACATTTCCAATGGGAGAGTTCATAATGAGA
* * * * * *
3144371 AGAACTCATCTAATAAGGGAGAATATGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTTATCC
66 AGAACTCATCTAATGAGGGAGAAGAAGTTCATAATGAGAAGAAATTGTTCAACCTTGGCTCATCC
3144436 ATCGCATATAGAGTTAGATCAAAATCATCA
131 ATCGCATATAGAGTTAGATCAAAATCATCA
** * * * * *
3144466 CATT-ATTTGATTCCATCATAGAATGAGGTGGATCGATATTTCGAATGGCAGAGTTCATAATGAG
1 C-TTAACATGATTCCATCATAGAAGGAGGTGGATCAACATTTCCAATGGGAGAGTTCATAATGAG
*
3144530 AAGAACTCATCTAATGAGGGAGAAGAAGTTCATAATGAGAAGAAGTTGTTCAACCTTGG
65 AAGAACTCATCTAATGAGGGAGAAGAAGTTCATAATGAGAAGAAATTGTTCAACCTTGG
3144589 TTCGATTCCA
Statistics
Matches: 248, Mismatches: 34, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
160 246 0.99
161 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (160 bp):
CTTAACATGATTCCATCATAGAAGGAGGTGGATCAACATTTCCAATGGGAGAGTTCATAATGAGA
AGAACTCATCTAATGAGGGAGAAGAAGTTCATAATGAGAAGAAATTGTTCAACCTTGGCTCATCC
ATCGCATATAGAGTTAGATCAAAATCATCA
Found at i:3145035 original size:117 final size:117
Alignment explanation
Indices: 3144477--3145231 Score: 685
Period size: 118 Copynumber: 6.5 Consensus size: 117
3144467 ATTATTTGAT
* * * *
3144477 TCCATCATAGAATGAGGTGGATCGATATTTCGAATGGCAGAGTTCATAATGAGAAGAACTCATCT
1 TCCATCACAGAATGAGGTGGATCGACATTTCCAATGG-AGAGTTCATAATGAGAAGAACTCATCC
* * * ** * *
3144542 AATGAGGGAGAAGAAGTTCATAATGAGAAGAAGTTGTTCAACCTTGGTTCGAT
65 AATGAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTGCCCAAA
** * * * * *
3144595 TCCAGAACAGAATGATGTGGATCAATATTTCCAATGAGATAGTTCATAATGAGAAGAATTCATCC
1 TCCATCACAGAATGAGGTGGATCGACATTTCCAATG-GAGAGTTCATAATGAGAAGAACTCATCC
* * * * **** *
3144660 AATGATGGG-GAAGAAGTTCACAATAAGAAGAACTTGTTCAACCTTGGTTTGAT
65 AATGA-GGGAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTGCCCAAA
** * * **
3144713 TTTATCACAGAATGAGGTGGATCAACGTTTCCAATGGGAGAGTTCATAATGAGAAGAACTCGCCC
1 TCCATCACAGAATGAGGTGGATCGACATTTCCAAT-GGAGAGTTCATAATGAGAAGAACTCATCC
* * * * *
3144778 GATGAGGGAGAAAAAGTTTATAATGAGAAGCACTTGTTCAACCTTTGCTCGAA
65 AATGAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTGCCCAAA
* * * * * *
3144831 TCCATCACATAA-GAAGTTTGATCAACATTTCCAATGGA-AG---GT--T-AGAAGAACTCATTC
1 TCCATCACAGAATG-AGGTGGATCGACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCC
* * * ** * * *
3144888 GAGGAGGAAGAGGAAGTTCATAATGAGAAGAACTTGTTTAAACTTTACCCAAA
65 AATGAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTGCCCAAA
* * * *
3144941 TCCATCACAGAAGGAGGTGGATCGACATTTCCAATTGAGAGTTCGTAATGAGAATAACTCATCCA
1 TCCATCACAGAATGAGGTGGATCGACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCA
* ** * *
3145006 AAGAGGGAGAAAAAGTTTGTAATGAGAAGAACATGTTCGAA-CTTTTCCCAAA
66 ATGAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTC-AACCTTTGCCCAAA
* * * *
3145058 TCAATCACAG-ATGGAGGTGGATCGACATTTCCAATGGAGAGTTCATAATGTGAAGAAATCCTCC
1 TCCATCACAGAAT-GAGGTGGATCGACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCC
* *
3145122 AAAGAGGAAGAAGAAA-TTCATAAT---AAGAACTTGTTCAACCTTTGCCCAAA
65 AATGAGGGAGAA-AAAGTTCATAATGAGAAGAACTTGTTCAACCTTTGCCCAAA
* * * * *
3145172 TCCATCATAGAATGAGGTGGATTGATATTTCTAATGGAAAGTTCATAATGAGAAGAACTC
1 TCCATCACAGAATGAGGTGGATCGACATTTCCAATGGAGAGTTCATAATGAGAAGAACTC
3145232 GTTCGAAAAA
Statistics
Matches: 526, Mismatches: 93, Indels: 40
0.80 0.14 0.06
Matches are distributed among these distances:
110 84 0.16
111 4 0.01
113 3 0.01
114 72 0.14
115 2 0.00
116 4 0.01
117 130 0.25
118 222 0.42
119 5 0.01
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (117 bp):
TCCATCACAGAATGAGGTGGATCGACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCA
ATGAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTGCCCAAA
Found at i:3146505 original size:22 final size:22
Alignment explanation
Indices: 3146458--3146510 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
3146448 TTTCATTTAA
* *
3146458 TTATTTT-A-AATTTTGTCTTT
1 TTATTTTCATAATTTTCTATTT
3146478 TT-TTTTCATAATTTTCTATTT
1 TTATTTTCATAATTTTCTATTT
3146499 TTATTTTC-TAAT
1 TTATTTTCATAAT
3146511 ACTAATTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 4 0.14
20 3 0.11
21 16 0.57
22 5 0.18
ACGTcount: A:0.21, C:0.08, G:0.02, T:0.70
Consensus pattern (22 bp):
TTATTTTCATAATTTTCTATTT
Found at i:3146659 original size:17 final size:18
Alignment explanation
Indices: 3146620--3146660 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
3146610 TTATTTTTGT
3146620 TTTATTTTAATTTAGTCA
1 TTTATTTTAATTTAGTCA
* *
3146638 -CTATTTTATTTTA-TCA
1 TTTATTTTAATTTAGTCA
3146654 TTTATTT
1 TTTATTT
3146661 GAAATTGATC
Statistics
Matches: 19, Mismatches: 3, Indels: 3
0.76 0.12 0.12
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.66
Consensus pattern (18 bp):
TTTATTTTAATTTAGTCA
Found at i:3151281 original size:60 final size:60
Alignment explanation
Indices: 3151215--3151389 Score: 246
Period size: 60 Copynumber: 2.9 Consensus size: 60
3151205 TATTTGGATG
**
3151215 AGTTTAGGGATGAAATTAGAATATTCAAAAGTTTGTGGACTAATTTAGAAA-GAGGGTCAT
1 AGTTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTA-AAATGAGGGTCAT
* **
3151275 AGTTTAGGGAT-AACATTAGAATGTTCAAAAGTTTAAGGACTAATTTAAAATGAAAGTCAT
1 AGTTTAGGGATGAA-ATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAGGGTCAT
* * *
3151335 AGTTTGGGGATGTAATTAGAAGATTCAAAAGTTTAAGGACTAATTTAAAATGAGG
1 AGTTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAGG
3151390 ATTCTAATTT
Statistics
Matches: 101, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
59 5 0.05
60 95 0.94
61 1 0.01
ACGTcount: A:0.41, C:0.05, G:0.23, T:0.31
Consensus pattern (60 bp):
AGTTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAGGGTCAT
Found at i:3154498 original size:2 final size:2
Alignment explanation
Indices: 3154491--3154543 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
3154481 TATTTTCTTA
3154491 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
3154533 AT AT AT AT AT A
1 AT AT AT AT AT A
3154544 AAATTAAAGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3156983 original size:2 final size:2
Alignment explanation
Indices: 3156978--3157008 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3156968 GAGAGTTACA
3156978 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3157009 TTTTTAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3164682 original size:81 final size:81
Alignment explanation
Indices: 3164547--3164700 Score: 218
Period size: 81 Copynumber: 1.9 Consensus size: 81
3164537 TAAAATTTCG
* * * * * * *
3164547 TCTTTTACTCAACGATATTTAATCATTTATCTAATTGGCATAATTGGTACCTTTCTACCAATTGC
1 TCTTTTACTCAACGATATTTAACCATTCATCTAACTAGCATAATTGGCAACTTTCTACAAATTGC
*
3164612 ACGGTTAGACCATTAT
66 ACAGTTAGACCATTAT
* *
3164628 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATAATTGGCAACTTTCTACAAATTGC
1 TCTTTTACTCAACGATATTTAACCATTCATCTAACTAGCATAATTGGCAACTTTCTACAAATTGC
3164693 ACAGTTAG
66 ACAGTTAG
3164701 TCCTCAAAGG
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
81 63 1.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (81 bp):
TCTTTTACTCAACGATATTTAACCATTCATCTAACTAGCATAATTGGCAACTTTCTACAAATTGC
ACAGTTAGACCATTAT
Found at i:3164750 original size:68 final size:68
Alignment explanation
Indices: 3164653--3164976 Score: 438
Period size: 68 Copynumber: 4.8 Consensus size: 68
3164643 TATTTAACCG
* * * * * *
3164653 TTCATCTAACTAGCATAATTGGCAACTTTCT-ACAAATTGCACAGTTAGTCCTCAAAGGCACTTA
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAA-TGCACAGTTAGGCCTCAAAGGCACTTA
3164717 GCCT
65 GCCT
*
3164721 TTCATCTAACTGGCATAAATTACACCTTTCTGTCAAATGCACA-TATAGGCCTCAAAGGCACTTA
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGT-TAGGCCTCAAAGGCACTTA
3164785 GCCT
65 GCCT
* *
3164789 TTCATCTAACCGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
*
3164854 ACT
66 CCT
* * * * * *
3164857 TTCATATAACTAGCATAAATGGA-ACCTTTCTCTCAAATGCACAGCTACGCCTCAAAGACACTTA
1 TTCATCTAACTGGCATAAAT-GACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
3164921 GCCT
65 GCCT
* *
3164925 TTCATCTAACTGGCATAAATGATACCTTTCTGTCAAATTCACAGTTAGGCCT
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCT
3164977 ATTAATCTTT
Statistics
Matches: 225, Mismatches: 26, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
67 3 0.01
68 215 0.96
69 7 0.03
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:3165298 original size:58 final size:59
Alignment explanation
Indices: 3165226--3165341 Score: 189
Period size: 59 Copynumber: 2.0 Consensus size: 59
3165216 TTCTTATTTC
* * *
3165226 GCACACATAGTGCCC-ATATGGAAATTCATACACTTAGTATGAATTTCTTAATATTTTA
1 GCACACAAAGTGCCCAATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTA
*
3165284 GCACACAAAGTGCCCAATACGGAAATTCGTACACTTAGTATGAATTTCTTAACATTTT
1 GCACACAAAGTGCCCAATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTT
3165342 GCAGACTTAG
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
58 14 0.26
59 39 0.74
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (59 bp):
GCACACAAAGTGCCCAATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTA
Found at i:3166098 original size:22 final size:22
Alignment explanation
Indices: 3166073--3166122 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
3166063 GATAGATGTT
3166073 GGAGCGGAGTGAGCGAGGGAAC
1 GGAGCGGAGTGAGCGAGGGAAC
3166095 GGAGCGGAGTGAGCGAGGGAAC
1 GGAGCGGAGTGAGCGAGGGAAC
3166117 GGAGCG
1 GGAGCG
3166123 ATCAACATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.26, C:0.14, G:0.56, T:0.04
Consensus pattern (22 bp):
GGAGCGGAGTGAGCGAGGGAAC
Found at i:3173767 original size:5 final size:5
Alignment explanation
Indices: 3173759--3173787 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
3173749 TGAGTTGGGC
3173759 TTGGA TTGGA TTGGA TTGGA TTGGA TTGG
1 TTGGA TTGGA TTGGA TTGGA TTGGA TTGG
3173788 GCCCAAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.41, T:0.41
Consensus pattern (5 bp):
TTGGA
Found at i:3175835 original size:35 final size:36
Alignment explanation
Indices: 3175739--3175837 Score: 121
Period size: 36 Copynumber: 2.8 Consensus size: 36
3175729 TCTTGATCAA
* * *
3175739 TCTGAACCTATATAAGAAATTACCAATTTGATTGAG
1 TCTGAACCTATATAAGGAATTACCAGTTCGATTGAG
* **
3175775 T-AGAACCTACCGTAAGGAATTACCAGTTCGATTG-G
1 TCTGAACCTA-TATAAGGAATTACCAGTTCGATTGAG
3175810 TCTGAACCTATATAAGGAATTACCAGTT
1 TCTGAACCTATATAAGGAATTACCAGTT
3175838 TAATCGAACT
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
35 25 0.48
36 27 0.52
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (36 bp):
TCTGAACCTATATAAGGAATTACCAGTTCGATTGAG
Done.