Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006937.1 Hibiscus syriacus cultivar Beakdansim tig00017809_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: 157939
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:2488 original size:16 final size:15
Alignment explanation
Indices: 2462--2495 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
2452 GCTACAAGCT
2462 AACAAACTATTCTAG
1 AACAAACTATTCTAG
2477 AACAACACTATTCTAG
1 AACAA-ACTATTCTAG
2493 AAC
1 AAC
2496 TCACAACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.47, C:0.24, G:0.06, T:0.24
Consensus pattern (15 bp):
AACAAACTATTCTAG
Found at i:8089 original size:16 final size:15
Alignment explanation
Indices: 8063--8096 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
8053 GCTACAAGCT
8063 AACAAACTATTCTAG
1 AACAAACTATTCTAG
8078 AACAACACTATTCTAG
1 AACAA-ACTATTCTAG
8094 AAC
1 AAC
8097 TCACAACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.47, C:0.24, G:0.06, T:0.24
Consensus pattern (15 bp):
AACAAACTATTCTAG
Found at i:12891 original size:166 final size:166
Alignment explanation
Indices: 12693--12991 Score: 433
Period size: 166 Copynumber: 1.8 Consensus size: 166
12683 ATTTAATATT
* ** * *
12693 TTTTATATTTTAATATTAATTAGGTGATGATACATGTAAATCTTAAAA-TATAAAAATATTATTG
1 TTTTATATTTTAATATCAATTAGGCAATGATACATCTAAAT-TTAAAATTATAAAAATATTATTA
* *
12757 CAAATCTTAGATTTGATATTTATTTTA-TT-TTTTTATAATTTCATTTTTTGTAGTTTAAAATTA
65 CAAATCTTAGATTTAATATTT-TTATACTTATTTTTATAATTTCATTTTTT-TAGTTTAAAATTA
12820 AATATTTTTATAATATTTTTAATATTTTTAAACTTAAGA
128 AATATTTTTATAATATTTTTAATATTTTTAAACTTAAGA
* * *
12859 TTTTATATTTTAATATCAATTAGGCAATGATACTTCTAAATTTAAAATTTTAAAAATATTATTAT
1 TTTTATATTTTAATATCAATTAGGCAATGATACATCTAAATTTAAAATTATAAAAATATTATTAC
* * *
12924 AAATTTTAGATTTAATATTTTTATACTTATTTTTATAATTTCATTTTTTTATTTTAAAATTAAGT
66 AAATCTTAGATTTAATATTTTTATACTTATTTTTATAATTTCATTTTTTTAGTTTAAAATTAAAT
12989 ATT
131 ATT
12992 AAATTTAATA
Statistics
Matches: 117, Mismatches: 13, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
165 10 0.09
166 87 0.74
167 20 0.17
ACGTcount: A:0.37, C:0.04, G:0.05, T:0.53
Consensus pattern (166 bp):
TTTTATATTTTAATATCAATTAGGCAATGATACATCTAAATTTAAAATTATAAAAATATTATTAC
AAATCTTAGATTTAATATTTTTATACTTATTTTTATAATTTCATTTTTTTAGTTTAAAATTAAAT
ATTTTTATAATATTTTTAATATTTTTAAACTTAAGA
Found at i:13045 original size:26 final size:28
Alignment explanation
Indices: 13009--13076 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
12999 ATATAACTAG
* *
13009 AAATATTAAATTTA-ATTTAAAAT-TTA
1 AAATATTAAATTTAGACTTAAAATATAA
*
13035 AAATATTAAATTTAGCCTTAAAATATAA
1 AAATATTAAATTTAGACTTAAAATATAA
*
13063 AAATCTTAAATTTA
1 AAATATTAAATTTA
13077 TTTTTATTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
26 14 0.39
27 7 0.19
28 15 0.42
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.41
Consensus pattern (28 bp):
AAATATTAAATTTAGACTTAAAATATAA
Found at i:21431 original size:15 final size:15
Alignment explanation
Indices: 21388--21434 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
21378 CTGATCTTTT
21388 AATT-TTATCAATT-
1 AATTATTATCAATTA
* *
21401 AATTATCTAACTATTA
1 AATTAT-TATCAATTA
21417 AATTATTATCAATTA
1 AATTATTATCAATTA
21432 AAT
1 AAT
21435 CACTAACAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 4 0.15
14 1 0.04
15 16 0.59
16 6 0.22
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTATTATCAATTA
Found at i:29625 original size:31 final size:31
Alignment explanation
Indices: 29566--29630 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
29556 GATTCTTTTA
* *
29566 TTACAAATAGATAACGTTAGTGATCAATTTG
1 TTACAAATAGATAACATTAGTGACCAATTTG
*
29597 TTACAAATAGATAACATTAGTGGCCAATTTG
1 TTACAAATAGATAACATTAGTGACCAATTTG
29628 TTA
1 TTA
29631 TTTTTGAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.35
Consensus pattern (31 bp):
TTACAAATAGATAACATTAGTGACCAATTTG
Found at i:34548 original size:30 final size:29
Alignment explanation
Indices: 34512--34574 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
34502 CCAAAAAAAT
*
34512 CACCGGTGATCAGTATATTTACCGATCTAA
1 CACCGGTGA-CACTATATTTACCGATCTAA
* * *
34542 CACCGGTTAGACTATATTTCCCGATCTAA
1 CACCGGTGACACTATATTTACCGATCTAA
34571 CACC
1 CACC
34575 CTTTGCAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 21 0.72
30 8 0.28
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (29 bp):
CACCGGTGACACTATATTTACCGATCTAA
Found at i:37324 original size:35 final size:35
Alignment explanation
Indices: 37285--37364 Score: 85
Period size: 35 Copynumber: 2.3 Consensus size: 35
37275 GTATTTCAGT
37285 TAATTTTGTT-T-A-TAACCATTTAATATCAGTTATTG
1 TAATTTTGTTATCATTAACCATTTAATAT---TTATTG
* *
37320 TAATTTGGTTATCATTTACCATTTAATATTTATTG
1 TAATTTTGTTATCATTAACCATTTAATATTTATTG
*
37355 TAAGTTTGTT
1 TAATTTTGTT
37365 GTATTTAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
35 23 0.61
36 1 0.03
37 1 0.03
38 13 0.34
ACGTcount: A:0.29, C:0.07, G:0.10, T:0.54
Consensus pattern (35 bp):
TAATTTTGTTATCATTAACCATTTAATATTTATTG
Found at i:41627 original size:20 final size:21
Alignment explanation
Indices: 41602--41653 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
41592 TTTTCCCAAT
*
41602 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
41622 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
41643 TCGCAATGCGA
1 TCGCAATGCGA
41654 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:41667 original size:20 final size:20
Alignment explanation
Indices: 41642--41755 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
41632 AATTGGGAAA
*
41642 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
41662 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
41682 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
41703 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
41723 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
41743 TTCGCAACGCGAT
1 ATCGCAACGCGAT
41756 TTACATAGCG
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:41686 original size:61 final size:61
Alignment explanation
Indices: 41639--41755 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
41629 GCGAATTGGG
* * * * *
41639 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
41700 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
41756 TTACATAGCG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:42312 original size:19 final size:19
Alignment explanation
Indices: 42274--42340 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
42264 TTCGAGAATG
42274 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
42294 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
42313 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
42332 AAAATCGCA
1 AAAATCGCA
42341 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 30 0.73
20 11 0.27
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:42358 original size:19 final size:19
Alignment explanation
Indices: 42336--42576 Score: 304
Period size: 19 Copynumber: 13.1 Consensus size: 19
42326 GAAACCAAAA
*
42336 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
42355 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
42374 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
42393 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
42412 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
42431 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
42450 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
42469 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
42483 TCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
42502 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
42516 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
42535 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
42555 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
42575 TC
1 TC
42577 AACCAAAAGA
Statistics
Matches: 196, Mismatches: 14, Indels: 24
0.84 0.06 0.10
Matches are distributed among these distances:
14 19 0.10
16 4 0.02
17 5 0.03
19 136 0.69
20 31 0.16
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:42501 original size:33 final size:33
Alignment explanation
Indices: 42464--42551 Score: 158
Period size: 33 Copynumber: 2.6 Consensus size: 33
42454 GTTGCGATTT
42464 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
42497 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
42530 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
42552 ATTATCTCGT
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 38 0.72
34 15 0.28
ACGTcount: A:0.11, C:0.27, G:0.23, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:44745 original size:21 final size:21
Alignment explanation
Indices: 44721--44829 Score: 53
Period size: 21 Copynumber: 5.2 Consensus size: 21
44711 TCATTCCTCG
44721 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** *
44742 AGAGGCCACTGTCATCC-CTCA
1 AGAGTCCCCTCCCA-CCGTTCA
* * * *
44763 AGAGTCCACTCCTATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
* ** *
44784 AGAGGCCCCTATCATTCC--TCG
1 AGAGTCCCCTCCCA--CCGTTCA
44805 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
44826 AGAG
1 AGAG
44830 GCCACTGTCA
Statistics
Matches: 58, Mismatches: 24, Indels: 12
0.62 0.26 0.13
Matches are distributed among these distances:
19 2 0.03
20 1 0.02
21 52 0.90
22 2 0.03
23 1 0.02
ACGTcount: A:0.22, C:0.39, G:0.18, T:0.21
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:44745 original size:42 final size:42
Alignment explanation
Indices: 44669--44841 Score: 202
Period size: 42 Copynumber: 4.1 Consensus size: 42
44659 GACTCGCCTG
* * *
44669 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * * * *
44711 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * *
44753 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * * * *
44795 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
44837 TCATC
1 TCATC
44842 GTTGAATAGG
Statistics
Matches: 106, Mismatches: 25, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 106 1.00
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.23
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
Found at i:44807 original size:84 final size:84
Alignment explanation
Indices: 44666--44841 Score: 352
Period size: 84 Copynumber: 2.1 Consensus size: 84
44656 CCCGACTCGC
44666 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
44731 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
44750 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
44815 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
44834 CTGTCATC
1 CTGTCATC
44842 GTTGAATAGG
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 92 1.00
ACGTcount: A:0.21, C:0.38, G:0.18, T:0.23
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:44844 original size:21 final size:21
Alignment explanation
Indices: 44736--44844 Score: 60
Period size: 21 Copynumber: 5.2 Consensus size: 21
44726 CCCCTCCCAC
44736 CGTTCAAGAGGCCACTGTCAT
1 CGTTCAAGAGGCCACTGTCAT
** * *
44757 CCCTCAAGAGTCCACT-CCTAT
1 CGTTCAAGAGGCCACTGTC-AT
* * *
44778 CGTTGAAGAGGCCCCTATCATT
1 CGTTCAAGAGGCCACTGTCA-T
* * * * ** *
44800 C-CTCGAGAGTCCCCTCCCAC
1 CGTTCAAGAGGCCACTGTCAT
44820 CGTTCAAGAGGCCACTGTCAT
1 CGTTCAAGAGGCCACTGTCAT
44841 CGTT
1 CGTT
44845 GAATAGGTCC
Statistics
Matches: 60, Mismatches: 24, Indels: 8
0.65 0.26 0.09
Matches are distributed among these distances:
20 2 0.03
21 55 0.92
22 3 0.05
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (21 bp):
CGTTCAAGAGGCCACTGTCAT
Found at i:44860 original size:42 final size:41
Alignment explanation
Indices: 44666--44871 Score: 146
Period size: 42 Copynumber: 4.9 Consensus size: 41
44656 CCCGACTCGC
* * * * * *
44666 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCC
1 CTGTCATCCTTGAAGAGTCCA-TCCCACCGTTCAAGAGGCCA
* * *
44708 CTATCATTCCTCG-AGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCA-TCCTTGAAGAGT-CCATCCCACCGTTCAAGAGGCCA
* * * * * *
44750 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCC
1 CTGTCATCCTTGAAGAGTCCA-TCCCACCGTTCAAGAGGCCA
* * *
44792 CTATCATTCCTCG-AGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCA-TCCTTGAAGAGT-CCATCCCACCGTTCAAGAGGCCA
* * *
44834 CTGTCATCGTTGAATAGGTCCATCCCACCATTCAAGAG
1 CTGTCATCCTTGAAGA-GTCCATCCCACCGTTCAAGAG
44872 CCCGATTCAC
Statistics
Matches: 123, Mismatches: 33, Indels: 16
0.72 0.19 0.09
Matches are distributed among these distances:
41 9 0.07
42 102 0.83
43 12 0.10
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.23
Consensus pattern (41 bp):
CTGTCATCCTTGAAGAGTCCATCCCACCGTTCAAGAGGCCA
Found at i:44871 original size:84 final size:84
Alignment explanation
Indices: 44666--44871 Score: 288
Period size: 84 Copynumber: 2.5 Consensus size: 84
44656 CCCGACTCGC
* * * *
44666 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
44731 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
* * * *
44750 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
44815 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
** * *
44834 CTGTCATCGTTGAATAGGTCCA-TCCCACCATTCAAGAG
1 CTGTCATCCCTCAAGA-GTCCACTCCCACCATTCAAGAG
44872 CCCGATTCAC
Statistics
Matches: 113, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
84 108 0.96
85 5 0.04
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.23
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:46247 original size:14 final size:14
Alignment explanation
Indices: 46228--46263 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
46218 ATTGTTTAAT
46228 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
46242 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
46256 TGATTTGT
1 TGATTTGT
46264 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:46445 original size:19 final size:19
Alignment explanation
Indices: 46370--46436 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 19
46360 AAAAAGTACT
*
46370 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
* *
46389 ATCTCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
46403 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
46422 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
46437 TAAATTCGCG
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
14 9 0.23
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 24 0.62
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:46463 original size:19 final size:19
Alignment explanation
Indices: 46441--46591 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
46431 CGAAATTAAA
46441 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
46460 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
46475 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
46493 TTCGCATTGCGA---T-A-
1 TTCGCGTTGCGATTTTCAT
*
46507 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
46526 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
46541 -TCTCGTTGAGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
46559 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
46578 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
46592 AGACATTAAG
Statistics
Matches: 95, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 26 0.27
15 1 0.01
16 7 0.07
17 7 0.07
18 1 0.01
19 43 0.45
20 10 0.11
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:46487 original size:33 final size:33
Alignment explanation
Indices: 46445--46571 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
46435 ATTAAATTCG
*
46445 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
**
46478 CGTTGCGATTTTCATTTCGCATTGCGATAT-TAG
1 CGTTGCGATTTTCATTTCGCATTGCGAT-TCTCT
46511 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
46544 CGTTGAGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
46572 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
32 1 0.01
33 84 0.98
34 1 0.01
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:46521 original size:66 final size:66
Alignment explanation
Indices: 46444--46572 Score: 240
Period size: 66 Copynumber: 2.0 Consensus size: 66
46434 AATTAAATTC
*
46444 GCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGATATT
1 GCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGAGATTTTCATTTCGCATTGCGATATT
46509 A
66 A
*
46510 GCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGAGATTTTCATTTCGCATTGCGATA
1 GCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGAGATTTTCATTTCGCATTGCGATA
46573 GTAATTTCCG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.43
Consensus pattern (66 bp):
GCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGAGATTTTCATTTCGCATTGCGATATT
A
Found at i:49092 original size:24 final size:24
Alignment explanation
Indices: 49058--49111 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
49048 CTGAAACATC
*
49058 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
49082 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
49106 ATCAAA
1 ATCAAA
49112 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:49881 original size:20 final size:20
Alignment explanation
Indices: 49856--49906 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
49846 TGTATTATCT
*
49856 CGTTGCAAAAGTCAAAATCG
1 CGTTGCGAAAGTCAAAATCG
*
49876 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAAAATCG
49896 CGTTGCGAAAG
1 CGTTGCGAAAG
49907 GCAATCATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.20, G:0.27, T:0.20
Consensus pattern (20 bp):
CGTTGCGAAAGTCAAAATCG
Found at i:49963 original size:33 final size:33
Alignment explanation
Indices: 49921--50048 Score: 175
Period size: 33 Copynumber: 3.8 Consensus size: 33
49911 TCATTTGACC
* *
49921 ATCGCAATGCGAAATGCAAATCGCAACGATAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
49954 ATCGCAATGCGAAATGAAAAAGGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
49987 ATCGCAATGCGAAATGAAAATCGTAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
50020 ATCGCAAAGCGAAAATTAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
50049 CAATTTTAGT
Statistics
Matches: 83, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
33 68 0.82
34 15 0.18
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:50073 original size:19 final size:19
Alignment explanation
Indices: 50051--50123 Score: 79
Period size: 18 Copynumber: 4.2 Consensus size: 19
50041 TCGCAACGCA
50051 ATTTTAGTTTCGCGTTGCG
1 ATTTTAGTTTCGCGTTGCG
50070 A-TTTAGTTTCGCGTTGCG
1 ATTTTAGTTTCGCGTTGCG
50088 ATTTT-G--T--CGTTGCG
1 ATTTTAGTTTCGCGTTGCG
*
50102 ATTTTCA-TTTCGCATTGCG
1 ATTTT-AGTTTCGCGTTGCG
50121 ATT
1 ATT
50124 CTATCGTTGC
Statistics
Matches: 46, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
14 12 0.26
16 1 0.02
17 1 0.02
18 19 0.41
19 13 0.28
ACGTcount: A:0.12, C:0.16, G:0.23, T:0.48
Consensus pattern (19 bp):
ATTTTAGTTTCGCGTTGCG
Found at i:50120 original size:33 final size:33
Alignment explanation
Indices: 50063--50169 Score: 146
Period size: 33 Copynumber: 3.3 Consensus size: 33
50053 TTTAGTTTCG
* * *
50063 CGTTGCGA-TTT-AGTTTCGCGTTGCGATTTTGT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTAT
50095 CGTTGCGATTTTCATTTCGCATTGCGATTCTAT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTAT
* *
50128 CGTTGCGATTTTCTTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTAT
50161 CGTTGCGAT
1 CGTTGCGAT
50170 AGTCAGTTTC
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
32 8 0.12
33 59 0.87
34 1 0.01
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTAT
Found at i:50154 original size:19 final size:18
Alignment explanation
Indices: 50058--50156 Score: 70
Period size: 19 Copynumber: 5.8 Consensus size: 18
50048 GCAATTTTAG
* **
50058 TTTCGCGTTGCGATTTAG
1 TTTCGCATTGCGATTTTC
*
50076 TTTCGCGTTGCGA-TTT-
1 TTTCGCATTGCGATTTTC
*
50092 TGTCG--TTGCGATTTTC
1 TTTCGCATTGCGATTTTC
50108 ATTTCGCATTGCGA--TTC
1 -TTTCGCATTGCGATTTTC
*
50125 TATCG--TTGCGATTTTC
1 TTTCGCATTGCGATTTTC
50141 TTTTCGCATTGCGATT
1 -TTTCGCATTGCGATT
50157 CTCTCGTTGC
Statistics
Matches: 66, Mismatches: 5, Indels: 19
0.73 0.06 0.21
Matches are distributed among these distances:
14 12 0.18
15 3 0.05
16 11 0.17
17 13 0.20
18 13 0.20
19 14 0.21
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.47
Consensus pattern (18 bp):
TTTCGCATTGCGATTTTC
Found at i:50689 original size:19 final size:20
Alignment explanation
Indices: 50631--50700 Score: 133
Period size: 20 Copynumber: 3.5 Consensus size: 20
50621 ATTCATTTGA
50631 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
50651 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
50671 CTATCGCAACGCG-AAATGG
1 CTATCGCAACGCGAAAATGG
50690 CTATCGCAACG
1 CTATCGCAACG
50701 ACAAAATCGC
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
19 17 0.34
20 33 0.66
ACGTcount: A:0.33, C:0.27, G:0.24, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:50803 original size:20 final size:20
Alignment explanation
Indices: 50778--50815 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
50768 GATTCTCTCA
50778 TTGCGATAGTCAGTTTTGTG
1 TTGCGATAGTCAGTTTTGTG
*
50798 TTGCGATAGTCTGTTTTG
1 TTGCGATAGTCAGTTTTG
50816 CCTTCAACAT
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:0.13, C:0.11, G:0.29, T:0.47
Consensus pattern (20 bp):
TTGCGATAGTCAGTTTTGTG
Found at i:50917 original size:14 final size:14
Alignment explanation
Indices: 50898--50934 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
50888 CATCAATTAA
50898 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
50912 ACAAATCATCTTTT
1 ACAAATCAACATTT
50926 ACAAATCAA
1 ACAAATCAA
50935 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:52822 original size:20 final size:19
Alignment explanation
Indices: 52799--52866 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
52789 GAAACTTAAA
52799 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
*
52819 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
52839 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
52858 ATCGCAACG
1 ATCGCAACG
52867 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 14 0.34
20 26 0.63
21 1 0.02
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:53408 original size:18 final size:18
Alignment explanation
Indices: 53382--53426 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
53372 GTCGATCAGA
*
53382 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
* *
53400 TGATAGCTCTGGGCGAGT
1 TGATGGCTCTGGGCGAGG
53418 TGATGGCTC
1 TGATGGCTC
53427 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.13, C:0.16, G:0.42, T:0.29
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:54791 original size:20 final size:20
Alignment explanation
Indices: 54743--54801 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
54733 AATAGTTTCT
** *
54743 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
54763 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
54783 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
54802 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:55091 original size:22 final size:22
Alignment explanation
Indices: 55064--55107 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
55054 GATGGAGATA
55064 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
55086 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
55108 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:55398 original size:20 final size:20
Alignment explanation
Indices: 55375--55425 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
55365 ATAGTCAGTA
*
55375 TCGCATTGCGATTTTCCAAT
1 TCGCATTGCGATTTACCAAT
* **
55395 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
55415 TCGCATTGCGA
1 TCGCATTGCGA
55426 ATTGGGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACCAAT
Found at i:56431 original size:134 final size:132
Alignment explanation
Indices: 56279--56529 Score: 317
Period size: 134 Copynumber: 1.9 Consensus size: 132
56269 AAGTAAAAAA
** * **
56279 ATATAAAATCATTAATAAAATTTTTAAAATTATTACTCAAA-TTAAAAAAATTAATTTAATGATT
1 ATATAAAATCATTAATAAAAAGTTTAAAATGATTACT-AAAGTTAAAAAAATTAAAGTAATGATT
* * *
56343 ATATATATAAATTGTTGTTAAATTTATCAGAA-AATTTAAGGTTTTTAAATAATTTTGAATTAAA
65 ATATATATAAATTATTATTAAATTTATCA-AATAATTTAA--ATTTTAAATAATTTTGAATTAAA
56407 ATATAT
127 ATATAT
* * * * * *
56413 ATATGAAATTATTAATAAAAAGTTTAAAATGATTACTAAAGTTAAACAATTTAAAGTGATGATTG
1 ATATAAAATCATTAATAAAAAGTTTAAAATGATTACTAAAGTTAAAAAAATTAAAGTAATGATTA
*
56478 TATATATAAATTATTATTAACTTTATCAAATAATTTAAATTTTAAATAATTT
66 TATATATAAATTATTATTAAATTTATCAAATAATTTAAATTTTAAATAATTT
56530 CATAATTTTT
Statistics
Matches: 100, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
132 13 0.13
133 5 0.05
134 82 0.82
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (132 bp):
ATATAAAATCATTAATAAAAAGTTTAAAATGATTACTAAAGTTAAAAAAATTAAAGTAATGATTA
TATATATAAATTATTATTAAATTTATCAAATAATTTAAATTTTAAATAATTTTGAATTAAAATAT
AT
Found at i:57451 original size:4 final size:4
Alignment explanation
Indices: 57442--57467 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
57432 TCTAATTCGT
57442 TAAA TAAA TAAA TAAA TAAA TAAA TA
1 TAAA TAAA TAAA TAAA TAAA TAAA TA
57468 TTTTTATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:59352 original size:22 final size:22
Alignment explanation
Indices: 59324--59375 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
59314 TAATCAATTA
59324 TCGAGTTGTAGTATTTACCTAG
1 TCGAGTTGTAGTATTTACCTAG
59346 TCGAGTTGTAGTATTTACCTAG
1 TCGAGTTGTAGTATTTACCTAG
*
59368 TCGTGTTG
1 TCGAGTTG
59376 AACTCTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.19, C:0.13, G:0.25, T:0.42
Consensus pattern (22 bp):
TCGAGTTGTAGTATTTACCTAG
Found at i:59996 original size:33 final size:33
Alignment explanation
Indices: 59959--60059 Score: 202
Period size: 33 Copynumber: 3.1 Consensus size: 33
59949 ATAAAAGATT
59959 TTAAGAAAAACCTAACGTGGGGATAAAGAAATC
1 TTAAGAAAAACCTAACGTGGGGATAAAGAAATC
59992 TTAAGAAAAACCTAACGTGGGGATAAAGAAATC
1 TTAAGAAAAACCTAACGTGGGGATAAAGAAATC
60025 TTAAGAAAAACCTAACGTGGGGATAAAGAAATC
1 TTAAGAAAAACCTAACGTGGGGATAAAGAAATC
60058 TT
1 TT
60060 TTATTGATTA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 68 1.00
ACGTcount: A:0.48, C:0.12, G:0.21, T:0.20
Consensus pattern (33 bp):
TTAAGAAAAACCTAACGTGGGGATAAAGAAATC
Found at i:61114 original size:16 final size:16
Alignment explanation
Indices: 61093--61123 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
61083 TAATATTGAA
61093 ACTTGAACTCAAAAAG
1 ACTTGAACTCAAAAAG
61109 ACTTGAACTCAAAAA
1 ACTTGAACTCAAAAA
61124 AATTTTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.19, G:0.10, T:0.19
Consensus pattern (16 bp):
ACTTGAACTCAAAAAG
Found at i:68783 original size:14 final size:14
Alignment explanation
Indices: 68766--68801 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
68756 ATGTTTAGAG
68766 TTTAGGATTTAAAA
1 TTTAGGATTTAAAA
*
68780 TTTAGGATTTTAAA
1 TTTAGGATTTAAAA
*
68794 TTAAGGAT
1 TTTAGGAT
68802 AGGGTTATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.17, T:0.44
Consensus pattern (14 bp):
TTTAGGATTTAAAA
Found at i:69280 original size:33 final size:33
Alignment explanation
Indices: 69240--69344 Score: 92
Period size: 33 Copynumber: 3.2 Consensus size: 33
69230 AATAAAATAA
*
69240 TATTAAATGAAACCCAAATCCAATTAGAAAATC
1 TATTAAATGAAATCCAAATCCAATTAGAAAATC
* ** * * *
69273 TATTAAAT-ATATGTATAA---AATAATAAAATAA
1 TATTAAATGAAATCCA-AATCCAATTAGAAAAT-C
*
69304 TATTAAATGAAATCCAAATCCAATTAGAAAAAC
1 TATTAAATGAAATCCAAATCCAATTAGAAAATC
69337 TATTAAAT
1 TATTAAAT
69345 ATATGTATAA
Statistics
Matches: 52, Mismatches: 14, Indels: 12
0.67 0.18 0.15
Matches are distributed among these distances:
30 9 0.17
31 10 0.19
32 7 0.13
33 18 0.35
34 8 0.15
ACGTcount: A:0.55, C:0.10, G:0.05, T:0.30
Consensus pattern (33 bp):
TATTAAATGAAATCCAAATCCAATTAGAAAATC
Found at i:69389 original size:63 final size:63
Alignment explanation
Indices: 69229--69486 Score: 408
Period size: 63 Copynumber: 4.1 Consensus size: 63
69219 GACTAGGATT
* * * *
69229 TAATAAAATAATATTAAATGAAACCCAAATCCAATTAGAAAATCTATTAAATATATGTATAAAA
1 TAATAAAATAATATTAAAAGAAATCCAAATCCAAATAGAAAAACTATTAAATATATGTAT-AAA
* *
69293 TAATAAAATAATATTAAATGAAATCCAAATCCAATTAGAAAAACTATTAAATATATGTATAAA
1 TAATAAAATAATATTAAAAGAAATCCAAATCCAAATAGAAAAACTATTAAATATATGTATAAA
* * *
69356 TAATAAAATCATATTAAAAGAAATCCGAATCCAAATAGAAAAACTATTAAATATATGTATGAA
1 TAATAAAATAATATTAAAAGAAATCCAAATCCAAATAGAAAAACTATTAAATATATGTATAAA
* *
69419 TAATAAAATAATATTAAAAGAAATCCGAATCCAAATAGAAAATCTATTAAATATATGTATAAA
1 TAATAAAATAATATTAAAAGAAATCCAAATCCAAATAGAAAAACTATTAAATATATGTATAAA
69482 TAATA
1 TAATA
69487 CAACATGCAT
Statistics
Matches: 184, Mismatches: 10, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
63 126 0.68
64 58 0.32
ACGTcount: A:0.57, C:0.09, G:0.06, T:0.29
Consensus pattern (63 bp):
TAATAAAATAATATTAAAAGAAATCCAAATCCAAATAGAAAAACTATTAAATATATGTATAAA
Found at i:69932 original size:29 final size:29
Alignment explanation
Indices: 69889--69971 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
69879 CTCACCTAAC
69889 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
69919 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
69948 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
69972 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:74702 original size:29 final size:29
Alignment explanation
Indices: 74659--74741 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
74649 CTCACCTAAC
74659 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
74689 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
74718 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
74742 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:77298 original size:15 final size:15
Alignment explanation
Indices: 77278--77308 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
77268 TATACAATTA
77278 ATAAAATAGTTTTAT
1 ATAAAATAGTTTTAT
*
77293 ATAAAATATTTTTAT
1 ATAAAATAGTTTTAT
77308 A
1 A
77309 GTATTTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
ATAAAATAGTTTTAT
Found at i:85512 original size:200 final size:200
Alignment explanation
Indices: 85120--85641 Score: 570
Period size: 200 Copynumber: 2.6 Consensus size: 200
85110 ACCTTTCACA
* * * *
85120 ACATAGATTAAGGTGAGAAAAGCTATCTGTCAACCAAAGTTTTTGAGTTCAATTCCACTCAGCTC
1 ACATAGATTAAGGCGAGAAGAGCTATTTGTCAGCCAAAGTTTTTGAGTTCAATTCCACTCAGCTC
* * * * ** * * *
85185 GAGAGCGCGTCGAACGCATGGTAGCAGTGAGGAACTACCTTCTAGTTAAATTTTAAATCAAAGTT
66 GATAGCGCATCGAATGCATGGTAGCAGCGAGGAACTACCTTCCGGTCAAATTTCAAATCAAAGTC
* * * * ** *
85250 CTTAAGCCAATAAGAAGACCTATATTGATTGTGATTTAGCAAAAAGGAAACACTTCCCAGTCAAA
131 CTTAAGCCAAAAAGAAAACCTAGATTGACTGCAATTTAGCAAAAAAGAAACACTTCCCAGTCAAA
85315 TTTCG
196 TTTCG
* *
85320 ACATAGCTTACGGCGAGAAGAGCTATTTGTCAGCCAAAGTTTTTGAGTTCAATTCCACTCAGCTC
1 ACATAGATTAAGGCGAGAAGAGCTATTTGTCAGCCAAAGTTTTTGAGTTCAATTCCACTCAGCTC
* * * **
85385 GATAGCGCATCGAATGCATGGAAGTAGCAAGGAACTACCTTCCGGTCAAATTTCAAA-CCGAGTC
66 GATAGCGCATCGAATGCATGGTAGCAGCGAGGAACTACCTTCCGGTCAAATTTCAAATCAAAGTC
* * *
85449 CTTTAAGCCAAAAAGAAAACCTAGGTTGACTGCAATTT-G-ATAATAAAGAACCTA-TTTCCAGT
131 C-TTAAGCCAAAAAGAAAACCTAGATTGACTGCAATTTAGCA-AA-AAAGAAAC-ACTTCCCAGT
*
85511 CAAATTTTG
192 CAAATTTCG
* * * * * *
85520 ACATAGTTTAAGGCAATAAGAGTTATTTGTC-GACCAAAGCTTTCGAGTTCAATTCCACTCAGCT
1 ACATAGATTAAGGCGAGAAGAGCTATTTGTCAG-CCAAAGTTTTTGAGTTCAATTCCACTCAGCT
* * * * *
85584 CGATAGCGCATCG-ATCGCATTGTACCAACGAGGAATTACCTTCCGGTCAAATTCCAAA
65 CGATAGCGCATCGAAT-GCATGGTAGCAGCGAGGAACTACCTTCCGGTCAAATTTCAAA
85642 GCTTTCAAGT
Statistics
Matches: 270, Mismatches: 46, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
198 1 0.00
199 11 0.04
200 257 0.95
201 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.27
Consensus pattern (200 bp):
ACATAGATTAAGGCGAGAAGAGCTATTTGTCAGCCAAAGTTTTTGAGTTCAATTCCACTCAGCTC
GATAGCGCATCGAATGCATGGTAGCAGCGAGGAACTACCTTCCGGTCAAATTTCAAATCAAAGTC
CTTAAGCCAAAAAGAAAACCTAGATTGACTGCAATTTAGCAAAAAAGAAACACTTCCCAGTCAAA
TTTCG
Found at i:86765 original size:13 final size:15
Alignment explanation
Indices: 86747--86784 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
86737 TTTATCATCA
86747 TTATTATTA-TTT-T
1 TTATTATTACTTTAT
86760 TTATTATTTACTTTAT
1 TTATTA-TTACTTTAT
86776 TTATTATTA
1 TTATTATTA
86785 GTACTAGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 6 0.27
14 3 0.14
15 6 0.27
16 7 0.32
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (15 bp):
TTATTATTACTTTAT
Found at i:86767 original size:16 final size:18
Alignment explanation
Indices: 86746--86789 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 18
86736 TTTTATCATC
86746 ATTATTATTA-TTT-TTT
1 ATTATTATTACTTTATTT
86762 ATTA-T-TTACTTTATTT
1 ATTATTATTACTTTATTT
*
86778 ATTATTAGTACT
1 ATTATTATTACT
86790 AGTATTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
14 3 0.13
15 4 0.17
16 11 0.48
17 1 0.04
18 4 0.17
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (18 bp):
ATTATTATTACTTTATTT
Found at i:87700 original size:296 final size:296
Alignment explanation
Indices: 87166--87762 Score: 1176
Period size: 296 Copynumber: 2.0 Consensus size: 296
87156 ATCCAAAATA
87166 ATCAGATTAAATGAAAAATATTTCAATATGAATACATAATGGTTGTATAAATCAGGGGACAATCG
1 ATCAGATTAAATGAAAAATATTTCAATATGAATACATAATGGTTGTATAAATCAGGGGACAATCG
87231 ATTGTAAGGGGTGGAACTGAATGAAAAAATAGTAGGGATAGTGGGGGTACGATTGTAACCTACAA
66 ATTGTAAGGGGTGGAACTGAATGAAAAAATAGTAGGGATAGTGGGGGTACGATTGTAACCTACAA
87296 ATCAAAAAATAAATAAAAGATCTTTTCTTATTTCAAATGAGACTACTTTTTCTTTCTTTCTTTTT
131 ATCAAAAAATAAATAAAAGATCTTTTCTTATTTCAAATGAGACTACTTTTTCTTTCTTTCTTTTT
* *
87361 TTGTATTCAAAACCAATTTCGGTGAGGCTTCCGTTGAGTCACCTGCAAATAGAGAGACAGAAGGG
196 TTGTATTCAAAACCAATTTCGGTGAGGCTTCAGTTGAGTCACCTGCAAATAGAGAGACAAAAGGG
87426 TAAGAGAGCGAAAACAAAATAAAAAAAGAGCATTTG
261 TAAGAGAGCGAAAACAAAATAAAAAAAGAGCATTTG
87462 ATCAGATTAAATGAAAAATATTTCAATATGAATACATAATGGTTGTATAAATCAGGGGACAATCG
1 ATCAGATTAAATGAAAAATATTTCAATATGAATACATAATGGTTGTATAAATCAGGGGACAATCG
87527 ATTGTAAGGGGTGGAACTGAATGAAAAAATAGTAGGGATAGTGGGGGTACGATTGTAACCTACAA
66 ATTGTAAGGGGTGGAACTGAATGAAAAAATAGTAGGGATAGTGGGGGTACGATTGTAACCTACAA
87592 ATCAAAAAATAAATAAAAGATCTTTTCTTATTTCAAATGAGACTACTTTTTCTTTCTTTCTTTTT
131 ATCAAAAAATAAATAAAAGATCTTTTCTTATTTCAAATGAGACTACTTTTTCTTTCTTTCTTTTT
87657 TTGTATTCAAAACCAATTTCGGTGAGGCTTCAGTTGAGTCACCTGCAAATAGAGAGACAAAAGGG
196 TTGTATTCAAAACCAATTTCGGTGAGGCTTCAGTTGAGTCACCTGCAAATAGAGAGACAAAAGGG
87722 TAAGAGAGCGAAAACAAAATAAAAAAAGAGCATTTG
261 TAAGAGAGCGAAAACAAAATAAAAAAAGAGCATTTG
87758 ATCAG
1 ATCAG
87763 TATCCTTCAC
Statistics
Matches: 299, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
296 299 1.00
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.29
Consensus pattern (296 bp):
ATCAGATTAAATGAAAAATATTTCAATATGAATACATAATGGTTGTATAAATCAGGGGACAATCG
ATTGTAAGGGGTGGAACTGAATGAAAAAATAGTAGGGATAGTGGGGGTACGATTGTAACCTACAA
ATCAAAAAATAAATAAAAGATCTTTTCTTATTTCAAATGAGACTACTTTTTCTTTCTTTCTTTTT
TTGTATTCAAAACCAATTTCGGTGAGGCTTCAGTTGAGTCACCTGCAAATAGAGAGACAAAAGGG
TAAGAGAGCGAAAACAAAATAAAAAAAGAGCATTTG
Found at i:88140 original size:27 final size:28
Alignment explanation
Indices: 88096--88151 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
88086 GAGAGAAGAG
* * *
88096 AGAGTTTCTCTCTGTAAA-AAAATGAAA
1 AGAGCTTCTCTATATAAAGAAAATGAAA
88123 AGAGCTTCTCTATATAAAGAAAATGAAA
1 AGAGCTTCTCTATATAAAGAAAATGAAA
88151 A
1 A
88152 TGAAAGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 15 0.60
28 10 0.40
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.27
Consensus pattern (28 bp):
AGAGCTTCTCTATATAAAGAAAATGAAA
Found at i:89789 original size:24 final size:24
Alignment explanation
Indices: 89757--89804 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
89747 TCTCAACGTG
89757 CTCAATTAAAGTAAATAAAACCTT
1 CTCAATTAAAGTAAATAAAACCTT
*
89781 CTCAGTTAAAGTAAATAAAACCTT
1 CTCAATTAAAGTAAATAAAACCTT
89805 GGAATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.48, C:0.17, G:0.06, T:0.29
Consensus pattern (24 bp):
CTCAATTAAAGTAAATAAAACCTT
Found at i:106545 original size:36 final size:36
Alignment explanation
Indices: 106505--106607 Score: 188
Period size: 36 Copynumber: 2.9 Consensus size: 36
106495 ACGGTGCTGG
106505 ACATTGATACACGAATGTACCAAAGCTGATAGGATA
1 ACATTGATACACGAATGTACCAAAGCTGATAGGATA
*
106541 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATAGGATA
*
106577 ACATTGATACAAGAATGTACCAAAGCTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
106608 ATACTCAACT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 65 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATAGGATA
Found at i:114442 original size:36 final size:36
Alignment explanation
Indices: 114402--114504 Score: 188
Period size: 36 Copynumber: 2.9 Consensus size: 36
114392 ACGGTGCTGG
114402 ACATTGATACACGAATGTACCAAAGCTGATAGGATA
1 ACATTGATACACGAATGTACCAAAGCTGATAGGATA
*
114438 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATAGGATA
*
114474 ACATTGATACAAGAATGTACCAAAGCTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
114505 ATACTCAACT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 65 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATAGGATA
Found at i:116870 original size:19 final size:19
Alignment explanation
Indices: 116846--116897 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
116836 ACACATTGGA
116846 CTATGAACTTGAAAATAAG
1 CTATGAACTTGAAAATAAG
116865 CTATGAA-TCTG-AAATAAG
1 CTATGAACT-TGAAAATAAG
*
116883 TTATGAGAC-TGAAAA
1 CTATGA-ACTTGAAAA
116898 CAAGTTCTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
18 15 0.54
19 13 0.46
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.27
Consensus pattern (19 bp):
CTATGAACTTGAAAATAAG
Found at i:120639 original size:20 final size:20
Alignment explanation
Indices: 120569--120642 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 20
120559 CTGTGCACTT
* * *
120569 AGTACCGATAATGTTCATCC
1 AGTACCGATACTATTCATCA
* * * *
120589 ATTACCAATACTATTCTTGA
1 AGTACCGATACTATTCATCA
*
120609 TTAGTATCGATACTATTCATCA
1 --AGTACCGATACTATTCATCA
120631 AGTACCGATACT
1 AGTACCGATACT
120643 TTTATTGCCA
Statistics
Matches: 39, Mismatches: 13, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
20 24 0.62
22 15 0.38
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (20 bp):
AGTACCGATACTATTCATCA
Found at i:129629 original size:64 final size:63
Alignment explanation
Indices: 129542--129702 Score: 182
Period size: 64 Copynumber: 2.5 Consensus size: 63
129532 TTGTTTAAGG
* * * * *
129542 TGCATCGATGCACATGCAATGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAGGATTTA
* * *
129606 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAGGATTTA
*
129670 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
129703 ACCTTCATTA
Statistics
Matches: 84, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
63 1 0.01
64 61 0.73
65 21 0.25
66 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAGGATTTA
Found at i:130962 original size:31 final size:31
Alignment explanation
Indices: 130868--130962 Score: 111
Period size: 31 Copynumber: 3.1 Consensus size: 31
130858 AGTCGAGGGT
*
130868 TTTACCTATG-TCTTTCGAGACATATGGACAG
1 TTTACCTATGTTCTTT-GGGACATATGGACAG
* ** *
130899 TATACCTATGTTCTAAGGAACATATGGACAG
1 TTTACCTATGTTCTTTGGGACATATGGACAG
* *
130930 TTTACCTAGGTTCTTTGGGACCTATGGACAG
1 TTTACCTATGTTCTTTGGGACATATGGACAG
130961 TT
1 TT
130963 GCCAAAGGTT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
31 49 0.94
32 3 0.06
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (31 bp):
TTTACCTATGTTCTTTGGGACATATGGACAG
Found at i:134107 original size:40 final size:40
Alignment explanation
Indices: 134062--134259 Score: 344
Period size: 40 Copynumber: 5.0 Consensus size: 40
134052 AGATAATTTG
*
134062 ATTTTTAAATATTTAATCTAATTATTTTAGACTTGAATAT
1 ATTTTTAAATATTTAACCTAATTATTTTAGACTTGAATAT
134102 ATTTTTAAATATTTAACCTAATTATTTTAGACTTGAATAT
1 ATTTTTAAATATTTAACCTAATTATTTTAGACTTGAATAT
*
134142 ATTTTTAAATATTTAACCTAATTATTTTAGATTTGAATAT
1 ATTTTTAAATATTTAACCTAATTATTTTAGACTTGAATAT
*
134182 ATTTTTAAATAGTTAACCTAATTATTTTAGACTTGAATAT
1 ATTTTTAAATATTTAACCTAATTATTTTAGACTTGAATAT
*
134222 -TTTTTAAATATTTAACCTAATTATTTTAGTCCTTGAAT
1 ATTTTTAAATATTTAACCTAATTATTTTAG-ACTTGAAT
134260 GTTAATATTA
Statistics
Matches: 151, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
39 28 0.19
40 123 0.81
ACGTcount: A:0.36, C:0.07, G:0.06, T:0.51
Consensus pattern (40 bp):
ATTTTTAAATATTTAACCTAATTATTTTAGACTTGAATAT
Found at i:134874 original size:12 final size:12
Alignment explanation
Indices: 134857--134896 Score: 71
Period size: 12 Copynumber: 3.2 Consensus size: 12
134847 TACAGCAGCC
134857 CCCCCTTAGCAG
1 CCCCCTTAGCAG
134869 CCCCCTTAGCAG
1 CCCCCTTAGCAG
134881 CCCCCCTTAGCAG
1 -CCCCCTTAGCAG
134894 CCC
1 CCC
134897 ATGTGTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 15 0.56
13 12 0.44
ACGTcount: A:0.15, C:0.55, G:0.15, T:0.15
Consensus pattern (12 bp):
CCCCCTTAGCAG
Found at i:134885 original size:13 final size:13
Alignment explanation
Indices: 134850--134896 Score: 78
Period size: 13 Copynumber: 3.6 Consensus size: 13
134840 AAAAAATTAC
134850 AGCAGCCCCCCCTT
1 AGCAG-CCCCCCTT
134864 AGCAG-CCCCCTT
1 AGCAGCCCCCCTT
134876 AGCAGCCCCCCTT
1 AGCAGCCCCCCTT
134889 AGCAGCCC
1 AGCAGCCC
134897 ATGTGTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.38
13 15 0.47
14 5 0.16
ACGTcount: A:0.17, C:0.53, G:0.17, T:0.13
Consensus pattern (13 bp):
AGCAGCCCCCCTT
Found at i:138185 original size:15 final size:16
Alignment explanation
Indices: 138157--138188 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
138147 AAAATCTTTC
138157 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
138173 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
138188 T
1 T
138189 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:138963 original size:16 final size:16
Alignment explanation
Indices: 138939--138972 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
138929 TATCGCCGAC
*
138939 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
138955 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
138971 CG
1 CG
138973 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:142557 original size:27 final size:27
Alignment explanation
Indices: 142525--142578 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
142515 AAAGAGTATG
142525 CTTGCAAATCGATCGCAAAGAGGAAGT
1 CTTGCAAATCGATCGCAAAGAGGAAGT
142552 CTTGCAAATCGATCGCAAAGAGGAAGT
1 CTTGCAAATCGATCGCAAAGAGGAAGT
142579 TATTAACTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.19, G:0.26, T:0.19
Consensus pattern (27 bp):
CTTGCAAATCGATCGCAAAGAGGAAGT
Found at i:144927 original size:15 final size:15
Alignment explanation
Indices: 144907--144937 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
144897 CGTATAGTTG
144907 GCTAGAAGAAAGAAA
1 GCTAGAAGAAAGAAA
144922 GCTAGAAGAAAGAAA
1 GCTAGAAGAAAGAAA
144937 G
1 G
144938 GGATCATATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.58, C:0.06, G:0.29, T:0.06
Consensus pattern (15 bp):
GCTAGAAGAAAGAAA
Found at i:150561 original size:40 final size:46
Alignment explanation
Indices: 150489--150589 Score: 108
Period size: 45 Copynumber: 2.3 Consensus size: 46
150479 ATAACTAATG
*
150489 AATAAAATAATAATAAACTAAACATGTCTTAA-C-TC-TAATTCCT
1 AATAAAATAATAATAAACTAAACATGTCTTAACCACCTTAATTCCT
*
150532 AATAAAATAATAACTAAA-T-AATAT-T-TTAACCCAACCTTAATTCCT
1 AATAAAATAATAA-TAAACTAAACATGTCTTAA-CC-ACCTTAATTCCT
150577 AATAAAATAATAA
1 AATAAAATAATAA
150590 ATCTAATCCT
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
40 4 0.08
41 1 0.02
42 5 0.10
43 14 0.28
44 5 0.10
45 21 0.42
ACGTcount: A:0.52, C:0.15, G:0.01, T:0.32
Consensus pattern (46 bp):
AATAAAATAATAATAAACTAAACATGTCTTAACCACCTTAATTCCT
Found at i:153597 original size:25 final size:22
Alignment explanation
Indices: 153568--153614 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
153558 ATTTTAACCC
153568 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
153593 AATCTAATCCTAAAAGATAATA
1 AATCTAATCCTAAAAAATAATA
153615 CATCATCCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 8 0.38
23 6 0.29
24 3 0.14
25 4 0.19
ACGTcount: A:0.53, C:0.13, G:0.02, T:0.32
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Done.