Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008955.1 Hibiscus syriacus cultivar Beakdansim tig00112285_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: 4658001
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 23
Found at i:1678353 original size:21 final size:21
Alignment explanation
Indices: 1678320--1678363 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1678310 TTACACTGAT
* *
1678320 AAATTAATTAATGATTTGTAA
1 AAATAAATAAATGATTTGTAA
1678341 AAATAAATAAATGATTTGTAA
1 AAATAAATAAATGATTTGTAA
1678362 AA
1 AA
1678364 GATATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (21 bp):
AAATAAATAAATGATTTGTAA
Found at i:1689723 original size:9 final size:9
Alignment explanation
Indices: 1689701--1689734 Score: 54
Period size: 8 Copynumber: 4.0 Consensus size: 9
1689691 ATATCGTTAT
1689701 ATTTTTAAA
1 ATTTTTAAA
1689710 A-TTTTAAA
1 ATTTTTAAA
1689718 ATTTTT-AA
1 ATTTTTAAA
1689726 ATTTTTAAA
1 ATTTTTAAA
1689735 TAATAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:1689723 original size:17 final size:17
Alignment explanation
Indices: 1689701--1689734 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1689691 ATATCGTTAT
1689701 ATTTTTAAAATTTTAAA
1 ATTTTTAAAATTTTAAA
*
1689718 ATTTTTAAATTTTTAAA
1 ATTTTTAAAATTTTAAA
1689735 TAATAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTTAAAATTTTAAA
Found at i:1692827 original size:13 final size:14
Alignment explanation
Indices: 1692776--1692830 Score: 55
Period size: 13 Copynumber: 4.1 Consensus size: 14
1692766 CAACAGTCAG
1692776 TCAAT-GAGTTGAC
1 TCAATCGAGTTGAC
1692789 T-ATATTCGAGTTGAC
1 TCA-A-TCGAGTTGAC
1692804 TCAATCG-GTTGAC
1 TCAATCGAGTTGAC
*
1692817 TCAGT-GAGTTGAC
1 TCAATCGAGTTGAC
1692830 T
1 T
1692831 TAGCTCGATC
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
12 2 0.06
13 19 0.53
14 4 0.11
15 10 0.28
16 1 0.03
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (14 bp):
TCAATCGAGTTGAC
Found at i:1695255 original size:2 final size:2
Alignment explanation
Indices: 1695248--1695280 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1695238 AATTCATAAA
1695248 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1695281 CAAAATTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1698017 original size:25 final size:25
Alignment explanation
Indices: 1697988--1698043 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
1697978 TTTATTAATA
1697988 ATATATTTCTGTC-ATTTAAAATTTT
1 ATATATTTCT-TCTATTTAAAATTTT
* *
1698013 ATATATTTGTTCTCTTTAAAATTTT
1 ATATATTTCTTCTATTTAAAATTTT
1698038 ATATAT
1 ATATAT
1698044 CCGTCCTCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 2 0.07
25 26 0.93
ACGTcount: A:0.32, C:0.07, G:0.04, T:0.57
Consensus pattern (25 bp):
ATATATTTCTTCTATTTAAAATTTT
Found at i:1698058 original size:25 final size:25
Alignment explanation
Indices: 1698005--1698066 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 25
1697995 TCTGTCATTT
** * * *
1698005 AAAATTTTATATATTTGTTCTCTTT
1 AAAATTTTATATATCCGTCCTCCTA
1698030 AAAATTTTATATATCCGTCCTCCTA
1 AAAATTTTATATATCCGTCCTCCTA
*
1698055 AAAATTTCATAT
1 AAAATTTTATAT
1698067 TCATCTGTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.34, C:0.15, G:0.03, T:0.48
Consensus pattern (25 bp):
AAAATTTTATATATCCGTCCTCCTA
Found at i:1699376 original size:41 final size:41
Alignment explanation
Indices: 1699307--1699394 Score: 97
Period size: 41 Copynumber: 2.1 Consensus size: 41
1699297 AGTGTTGCAA
* * **
1699307 AAAAAACAAATTTTAAGGGTAACTCCATAATAATATGTATT
1 AAAAAACAAATTTTAAGAGTAACTCCATAATAACAAATATT
* * *
1699348 AAAAAATAAATTTTAAGAGTATGC-CCATACTAACAAATATT
1 AAAAAACAAATTTTAAGAGTA-ACTCCATAATAACAAATATT
1699389 AAAAAA
1 AAAAAA
1699395 ATTGAACCTC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
41 38 0.97
42 1 0.03
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (41 bp):
AAAAAACAAATTTTAAGAGTAACTCCATAATAACAAATATT
Found at i:1699691 original size:31 final size:31
Alignment explanation
Indices: 1699624--1699705 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
1699614 AGTAGGCTCC
***
1699624 TAATAATAAATATTAGAAAAAAATTGAGTTCA
1 TAATAATAAATATTA-AAAAAAATTGAAAACA
*
1699656 TAATAATAAATATTAAGAAAAATT-AAAACA
1 TAATAATAAATATTAAAAAAAATTGAAAACA
*
1699686 TTAATAATAATTATTAAAAA
1 -TAATAATAAATATTAAAAA
1699706 TAAGTGACAC
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
30 3 0.07
31 25 0.58
32 15 0.35
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (31 bp):
TAATAATAAATATTAAAAAAAATTGAAAACA
Found at i:1703640 original size:35 final size:35
Alignment explanation
Indices: 1703601--1703681 Score: 126
Period size: 35 Copynumber: 2.3 Consensus size: 35
1703591 CAGAGTGCAA
* *
1703601 ACCAATTTTGAAGCAAGGGATAACTTGATTTTTCC
1 ACCAACTTTGAAGCAAGGGACAACTTGATTTTTCC
* *
1703636 ACCAACTTTGAAGCAAGGGGCAACTTGTTTTTTCC
1 ACCAACTTTGAAGCAAGGGACAACTTGATTTTTCC
1703671 ACCAACTTTGA
1 ACCAACTTTGA
1703682 GATTTGTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (35 bp):
ACCAACTTTGAAGCAAGGGACAACTTGATTTTTCC
Found at i:1704163 original size:15 final size:15
Alignment explanation
Indices: 1704145--1704177 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1704135 ATCAACAGAT
1704145 ATAATTTTTATATAA
1 ATAATTTTTATATAA
*
1704160 ATAATTTTTATTTAA
1 ATAATTTTTATATAA
1704175 ATA
1 ATA
1704178 TTTAGAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATAATTTTTATATAA
Found at i:1704350 original size:18 final size:19
Alignment explanation
Indices: 1704327--1704363 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1704317 CCAGTAATCC
1704327 TATTCCC-TGGTAATCTTT
1 TATTCCCATGGTAATCTTT
1704345 TATTCCCATTGGTAATCTT
1 TATTCCCA-TGGTAATCTT
1704364 ACATTCCGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.19, C:0.22, G:0.11, T:0.49
Consensus pattern (19 bp):
TATTCCCATGGTAATCTTT
Found at i:1707021 original size:16 final size:17
Alignment explanation
Indices: 1707000--1707035 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1706990 TCCACTTAAA
*
1707000 TTTTA-TTTTAAGTTTT
1 TTTTATTTTTAAATTTT
1707016 TTTTATTTTTAAATTTT
1 TTTTATTTTTAAATTTT
1707033 TTT
1 TTT
1707036 ACAAATATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (17 bp):
TTTTATTTTTAAATTTT
Found at i:1707333 original size:29 final size:29
Alignment explanation
Indices: 1707284--1707340 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
1707274 ACAACAATAT
* *
1707284 TAATTAAAAATAAAATTAATATAATTAAA
1 TAATTAAAAACAAAATCAATATAATTAAA
*
1707313 TAATTAATAAACAAAA-CAATATTATTAA
1 TAATTAA-AAACAAAATCAATATAATTAA
1707341 TTTGAATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (29 bp):
TAATTAAAAACAAAATCAATATAATTAAA
Found at i:1708512 original size:2 final size:2
Alignment explanation
Indices: 1708507--1708546 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1708497 TAATGCTTAA
1708507 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
1708547 CTTATAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1709931 original size:65 final size:65
Alignment explanation
Indices: 1709845--1709997 Score: 200
Period size: 65 Copynumber: 2.4 Consensus size: 65
1709835 CTTGGGGTGA
* * * *
1709845 ATCGGTACACTAATTACATTCGATGTTTCAA-AAGAGCCAGGAGTGCATCGATGCATGGCCTGTG
1 ATCGGTACACAAAATGCATTCGATGTTTCAATAA-AACCAGGAGTGCATCGATGCATGGCCTGTG
1709909 C
65 C
* * * * **
1709910 ATCGGTACATAAAATGCATTCGATGTTTCAATAAAATCATGAGTGCATCGATGCCTGGTTTGTGC
1 ATCGGTACACAAAATGCATTCGATGTTTCAATAAAACCAGGAGTGCATCGATGCATGGCCTGTGC
1709975 ATCGGTACACAAAATGCATTCGA
1 ATCGGTACACAAAATGCATTCGA
1709998 ATTAGGGTGT
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
65 74 0.97
66 2 0.03
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (65 bp):
ATCGGTACACAAAATGCATTCGATGTTTCAATAAAACCAGGAGTGCATCGATGCATGGCCTGTGC
Found at i:1715184 original size:20 final size:20
Alignment explanation
Indices: 1715147--1715185 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1715137 CGGAAATAAT
* *
1715147 AATAATAAGTTATGTGATTC
1 AATAATAAATGATGTGATTC
*
1715167 AATAATAAATGATTTGATT
1 AATAATAAATGATGTGATT
1715186 TTAAGATCCG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.03, G:0.13, T:0.41
Consensus pattern (20 bp):
AATAATAAATGATGTGATTC
Found at i:1715720 original size:27 final size:28
Alignment explanation
Indices: 1715679--1715732 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
1715669 TATAGAATTA
*
1715679 CCCCTGAAGTATAAAATGACC-AAAATG
1 CCCCTGAAGTATAAAATAACCTAAAATG
*
1715706 CCCCTGAAGTGTAAAATAACCTAAAAT
1 CCCCTGAAGTATAAAATAACCTAAAAT
1715733 ATCTCCAAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 19 0.79
28 5 0.21
ACGTcount: A:0.44, C:0.22, G:0.13, T:0.20
Consensus pattern (28 bp):
CCCCTGAAGTATAAAATAACCTAAAATG
Found at i:1718291 original size:2 final size:2
Alignment explanation
Indices: 1718284--1718315 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1718274 GTCCTTCCGA
1718284 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
1718316 TTTTCTGAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1726792 original size:17 final size:17
Alignment explanation
Indices: 1726770--1726807 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1726760 ATTTCTCAAT
1726770 GGTGATCTGGAAGAGGA
1 GGTGATCTGGAAGAGGA
1726787 GGTGATCTGGAAGAGGA
1 GGTGATCTGGAAGAGGA
1726804 GGTG
1 GGTG
1726808 TATATGAGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.26, C:0.05, G:0.50, T:0.18
Consensus pattern (17 bp):
GGTGATCTGGAAGAGGA
Found at i:1737246 original size:18 final size:19
Alignment explanation
Indices: 1737209--1737248 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1737199 TATAATTTTT
*
1737209 ATTTTAAATTGGTCCTTAA
1 ATTTTAAATTGATCCTTAA
*
1737228 ATTTTAAATTTAT-CTTAA
1 ATTTTAAATTGATCCTTAA
1737246 ATT
1 ATT
1737249 ATGACTGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (19 bp):
ATTTTAAATTGATCCTTAA
Found at i:1739112 original size:28 final size:24
Alignment explanation
Indices: 1739076--1739131 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 24
1739066 AAATTTTATC
1739076 TAAT-CTATAATATAAAGCATAAATAAA
1 TAATACTATAA-ATAAA--ATAAA-AAA
1739103 TAATACTATAAATAAAATAAAAAA
1 TAATACTATAAATAAAATAAAAAA
1739127 TAATA
1 TAATA
1739132 TATTCCTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
24 8 0.29
25 5 0.18
27 9 0.32
28 6 0.21
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (24 bp):
TAATACTATAAATAAAATAAAAAA
Found at i:1739265 original size:12 final size:12
Alignment explanation
Indices: 1739250--1739274 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1739240 AAATAAATAA
1739250 ATAAATAAAATT
1 ATAAATAAAATT
1739262 ATAAATAAAATT
1 ATAAATAAAATT
1739274 A
1 A
1739275 AAAAATAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAAATAAAATT
Found at i:1739374 original size:18 final size:18
Alignment explanation
Indices: 1739353--1739394 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
1739343 GATGATGATA
*
1739353 ATGATGACGACGACGATG
1 ATGATGACGACAACGATG
1739371 ATGATGACGACAACGATG
1 ATGATGACGACAACGATG
1739389 ATGATG
1 ATGATG
1739395 GTGGTTGTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.36, C:0.14, G:0.31, T:0.19
Consensus pattern (18 bp):
ATGATGACGACAACGATG
Found at i:1741351 original size:30 final size:30
Alignment explanation
Indices: 1741247--1741558 Score: 168
Period size: 30 Copynumber: 10.5 Consensus size: 30
1741237 TATACATTCA
* * *
1741247 TAAAGGATTAAAATAG-AACAATAAAAAAATT
1 TAAAGGACTAAAATAGTAA-AA-ACAAAAACT
* * * ** *
1741278 TAAAAGACCAAAATAGGATTAACAGAAACT
1 TAAAGGACTAAAATAGTAAAAACAAAAACT
* * *
1741308 TGAA-GACCAAAATAGTAAAAACAAAAAAT
1 TAAAGGACTAAAATAGTAAAAACAAAAACT
* * ***
1741337 TAAATGACTAAAATAGCAAAAATTGAAACT
1 TAAAGGACTAAAATAGTAAAAACAAAAACT
* *
1741367 TAAAGGACTAAAAT-GTCATAAACAAAAATT
1 TAAAGGACTAAAATAGT-AAAAACAAAAACT
* * * *
1741397 TAGAGGAATAAAAT-GGAAAAACATAAACT
1 TAAAGGACTAAAATAGTAAAAACAAAAACT
* * * *
1741426 TAAAGGGCTAAAATAATAAAAATAGAAACT
1 TAAAGGACTAAAATAGTAAAAACAAAAACT
* * * * *
1741456 TAAGGGTCT-AAATAG-AAAATACAGACATT
1 TAAAGGACTAAAATAGTAAAA-ACAAAAACT
** * * *
1741485 TAAAGGACTAAAATAACAAAAACAGACATT
1 TAAAGGACTAAAATAGTAAAAACAAAAACT
* ** *
1741515 TGAAGGACTAAAATAACAAGAACAAAAACT
1 TAAAGGACTAAAATAGTAAAAACAAAAACT
*
1741545 TAAGGGACTAAAAT
1 TAAAGGACTAAAAT
1741559 GGTATTAACA
Statistics
Matches: 217, Mismatches: 57, Indels: 15
0.75 0.20 0.05
Matches are distributed among these distances:
28 4 0.02
29 63 0.29
30 131 0.60
31 18 0.08
32 1 0.00
ACGTcount: A:0.58, C:0.10, G:0.13, T:0.19
Consensus pattern (30 bp):
TAAAGGACTAAAATAGTAAAAACAAAAACT
Found at i:1741395 original size:59 final size:60
Alignment explanation
Indices: 1741326--1741439 Score: 135
Period size: 59 Copynumber: 1.9 Consensus size: 60
1741316 AAAATAGTAA
* * *
1741326 AAACAAAAAA-TTAAATGACTAAAATAGCAAAAA-TTGAAACTTAAAGGACTAAAATGTCAT
1 AAACAAAAAATTTAAAGGAATAAAAT-GCAAAAACAT-AAACTTAAAGGACTAAAATGTCAT
* * *
1741386 AAAC-AAAAATTTAGAGGAATAAAATGGAAAAACATAAACTTAAAGGGCTAAAAT
1 AAACAAAAAATTTAAAGGAATAAAATGCAAAAACATAAACTTAAAGGACTAAAAT
1741440 AATAAAAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
59 29 0.63
60 17 0.37
ACGTcount: A:0.59, C:0.09, G:0.12, T:0.20
Consensus pattern (60 bp):
AAACAAAAAATTTAAAGGAATAAAATGCAAAAACATAAACTTAAAGGACTAAAATGTCAT
Found at i:1743032 original size:3 final size:3
Alignment explanation
Indices: 1743024--1743108 Score: 138
Period size: 3 Copynumber: 28.3 Consensus size: 3
1743014 TATAACTTGT
1743024 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
1743072 ATA ATA AT- ATA ATA ATA ATA ATTA A-A ATAA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A-TA ATA AT-A ATA ATA A
1743109 AAAAGACCCG
Statistics
Matches: 78, Mismatches: 0, Indels: 8
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.05
3 68 0.87
4 6 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1743692 original size:130 final size:130
Alignment explanation
Indices: 1743396--1743779 Score: 476
Period size: 130 Copynumber: 3.0 Consensus size: 130
1743386 TTTAGGAAGG
* * * * *
1743396 TGATAACACAATTCCTACGCGATGAGGACGACTGGTTATCTAAGGGTGACACGGCTCCTACATAA
1 TGATAACACAGTTCCTACGTGATGAGGACGACTGGTTATC-AGGGGTGACACGGCTCCTACGTGA
* * * ** *
1743461 TGAGGAGGTCTGGTCAGGGGATGACACGGTTAC-TATGTTAT---G-CGGTTGACCATCTTTAGG
65 TGAGGAGGTCTGGTCGGGGGATGACACGATT-CTTACGTTATGAGGACGACTGACCATCTTTAGA
1743521 GA
129 GA
* * *
1743523 TGATAACACGGTTCCTACGTGATGAGGACGACTAGTTATCAGGGGTGACACGGCTCCTACGTGGT
1 TGATAACACAGTTCCTACGTGATGAGGACGACTGGTTATCAGGGGTGACACGGCTCCTACGTGAT
* *
1743588 GAGGAGGTCTAGTCGGGGGATGACATGATTCTTACGTTATGAGGACGACTGACCATCTTTAGAGA
66 GAGGAGGTCTGGTCGGGGGATGACACGATTCTTACGTTATGAGGACGACTGACCATCTTTAGAGA
* * *
1743653 TTATAACACAGTTCCTACGTGATGAGGAC-AGTTGGTTATCAGGGGTGACAGGGCTCCTACGTGA
1 TGATAACACAGTTCCTACGTGATGAGGACGA-CTGGTTATCAGGGGTGACACGGCTCCTACGTGA
* ** *
1743717 TGAGGAGGTCTGGTTGGGGGATGACACGATT-TCTACGCGATGAGGACGACAGACCATCTTTAG
65 TGAGGAGGTCTGGTCGGGGGATGACACGATTCT-TACGTTATGAGGACGACTGACCATCTTTAG
1743780 GGATAATAGT
Statistics
Matches: 222, Mismatches: 28, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
125 1 0.00
126 54 0.24
127 36 0.16
129 3 0.01
130 128 0.58
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (130 bp):
TGATAACACAGTTCCTACGTGATGAGGACGACTGGTTATCAGGGGTGACACGGCTCCTACGTGAT
GAGGAGGTCTGGTCGGGGGATGACACGATTCTTACGTTATGAGGACGACTGACCATCTTTAGAGA
Found at i:1744214 original size:33 final size:33
Alignment explanation
Indices: 1744177--1744239 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
1744167 ATCCCTAAAT
*
1744177 ATGCCCCAACATTCGACGTTGATTGGTTCAAAG
1 ATGCCCCAACATTCGACGTTGATTGCTTCAAAG
* * *
1744210 ATGCCCCAATATTCTATGTTGATTGCTTCA
1 ATGCCCCAACATTCGACGTTGATTGCTTCA
1744240 GCACTGTTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.33
Consensus pattern (33 bp):
ATGCCCCAACATTCGACGTTGATTGCTTCAAAG
Found at i:1752584 original size:18 final size:18
Alignment explanation
Indices: 1752548--1752608 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 18
1752538 TCTTATCTTT
*
1752548 TTTTTCTTTCTTTTGTTC
1 TTTTTCTTTATTTTGTTC
1752566 TTTTTCTTTGATTTT-TTC
1 TTTTTCTTT-ATTTTGTTC
*
1752584 TTATTTGTTCTTTATTTTTTTC
1 ---TTT-TTCTTTATTTTGTTC
1752606 TTT
1 TTT
1752609 GCTTTGTTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
18 12 0.33
19 7 0.19
21 8 0.22
22 9 0.25
ACGTcount: A:0.05, C:0.11, G:0.05, T:0.79
Consensus pattern (18 bp):
TTTTTCTTTATTTTGTTC
Found at i:1752589 original size:10 final size:11
Alignment explanation
Indices: 1752566--1752608 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
1752556 TCTTTTGTTC
1752566 TTTTTCTTTGAT
1 TTTTTCTTT-AT
1752578 TTTTTC-TTAT
1 TTTTTCTTTAT
*
1752588 TTGTTCTTTATT
1 TTTTTCTTTA-T
1752600 TTTTTCTTT
1 TTTTTCTTT
1752609 GCTTTGTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 7 0.26
11 5 0.19
12 15 0.56
ACGTcount: A:0.07, C:0.09, G:0.05, T:0.79
Consensus pattern (11 bp):
TTTTTCTTTAT
Found at i:1752609 original size:34 final size:34
Alignment explanation
Indices: 1752566--1752653 Score: 115
Period size: 34 Copynumber: 2.6 Consensus size: 34
1752556 TCTTTTGTTC
* *
1752566 TTTTTCTTTGATTTTTTCTTATTTGTTCTTTATT
1 TTTTTCTTTGCTTTTTTCTTATTTGCTCTTTATT
*
1752600 TTTTTCTTTGCTTTGTTTC-TCTTTGCTCTTTATT
1 TTTTTCTTTGCTTT-TTTCTTATTTGCTCTTTATT
*
1752634 TTTTCCTTTGCTTATTTTCT
1 TTTTTCTTTGCTT-TTTTCT
1752654 CTTTGTTTTG
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
34 42 0.89
35 5 0.11
ACGTcount: A:0.06, C:0.15, G:0.07, T:0.73
Consensus pattern (34 bp):
TTTTTCTTTGCTTTTTTCTTATTTGCTCTTTATT
Found at i:1752657 original size:15 final size:15
Alignment explanation
Indices: 1752599--1752658 Score: 50
Period size: 15 Copynumber: 3.7 Consensus size: 15
1752589 TGTTCTTTAT
*
1752599 TTTTTTCTTTGCTT-
1 TTTTCTCTTTGCTTA
1752613 TGTTTCTCTTTGCTCTTTA
1 T-TTTCTCTTTG--C-TTA
*
1752632 TTTTTTCCTTTGCTTA
1 TTTTCT-CTTTGCTTA
1752648 TTTTCTCTTTG
1 TTTTCTCTTTG
1752659 TTTTGATTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
14 1 0.03
15 14 0.38
16 8 0.22
17 2 0.05
18 6 0.16
19 6 0.16
ACGTcount: A:0.03, C:0.18, G:0.08, T:0.70
Consensus pattern (15 bp):
TTTTCTCTTTGCTTA
Found at i:1754523 original size:30 final size:31
Alignment explanation
Indices: 1754487--1754549 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
1754477 TGATGAAAAA
* * *
1754487 TAACAC-AAACAAAAGAGAAAAATGAGTTAG
1 TAACACAAAAAAAAAGAGAAAAACGAATTAG
*
1754517 TAACACAAAAAAAAAGGGAAAAACGAATTAG
1 TAACACAAAAAAAAAGAGAAAAACGAATTAG
1754548 TA
1 TA
1754550 CAAGAAAGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 6 0.21
31 22 0.79
ACGTcount: A:0.62, C:0.10, G:0.16, T:0.13
Consensus pattern (31 bp):
TAACACAAAAAAAAAGAGAAAAACGAATTAG
Found at i:1756456 original size:30 final size:29
Alignment explanation
Indices: 1756384--1756665 Score: 151
Period size: 30 Copynumber: 9.5 Consensus size: 29
1756374 ATAAAAATAT
* * *
1756384 TTAAAGGACTAAAATAGATTAACA-GAAAC
1 TTAAAGGACTAAAATAG-TAAAAATAAAAC
* *
1756413 TT-GAGGACCAAAATAGTAAAAATGAAAAC
1 TTAAAGGACTAAAATAGTAAAAAT-AAAAC
* *
1756442 TTAAAGGACTAAAATAGAAAAAACCAAAAC
1 TTAAAGGACTAAAATAGTAAAAA-TAAAAC
* * *
1756472 TTAAAGGACTAAAATGGCACAAACAT-AAAT
1 TTAAAGGACTAAAATAGTA-AAA-ATAAAAC
* * * *
1756502 TTAGAGGAATAAAATGGCAAAAATAGAAAC
1 TTAAAGGACTAAAATAGTAAAAATA-AAAC
*
1756532 TTAAAGGGCTAAAATAGTAAAAATAGAAAC
1 TTAAAGGACTAAAATAGTAAAAATA-AAAC
* * * * * * *
1756562 TTAAGGGTCT-AAATAGCAAATACAGACAT
1 TTAAAGGACTAAAATAGTAAAAATA-AAAC
** ** * *
1756591 TTAAAGGACTAAAATAACAAAAGCAGACAT
1 TTAAAGGACTAAAATAGTAAAAATA-AAAC
**
1756621 TTAAAGGACTAAAATAACAAGAACA-AAAAC
1 TTAAAGGACTAAAATAGTAA-AA-ATAAAAC
*
1756651 TTAAGGGACTAAAAT
1 TTAAAGGACTAAAAT
1756666 GGTATTAACA
Statistics
Matches: 205, Mismatches: 37, Indels: 21
0.78 0.14 0.08
Matches are distributed among these distances:
27 4 0.02
28 14 0.07
29 33 0.16
30 147 0.72
31 6 0.03
32 1 0.00
ACGTcount: A:0.56, C:0.11, G:0.15, T:0.18
Consensus pattern (29 bp):
TTAAAGGACTAAAATAGTAAAAATAAAAC
Found at i:1756623 original size:119 final size:119
Alignment explanation
Indices: 1756382--1756695 Score: 271
Period size: 119 Copynumber: 2.6 Consensus size: 119
1756372 CAATAAAAAT
* * ** * * *
1756382 ATTTAAAGGACTAAAAT-AGATTAACAGAAACTTGA-GGACCAAAATAGTAAAAAT-GAAAACTT
1 ATTTAAAGGAATAAAATAACAAAAACAAAAACTTAAGGGACTAAAATAGTAAAAATAG-AAACTT
* ** *
1756444 AAAGGACTAAAATAGAAAAAACCAAAACTTAAAGGACTAAAATGGCACAAACATAA
65 AAGGGACT-AAATAGAAAAAACCAAAACTTAAAGGACTAAAATAACACAAACAGAA
* ** * *
1756500 ATTTAGAGGAATAAAATGGCAAAAATAGAAACTTAAAGGG-CTAAAATAGTAAAAATAGAAACTT
1 ATTTAAAGGAATAAAATAACAAAAACAAAAACTT-AAGGGACTAAAATAGTAAAAATAGAAACTT
* * * * * *
1756564 AAGGGTCTAAATAGCAAATA-CAGACATTTAAAGGACTAAAATAACA-AAAGCAGAC
65 AAGGGACTAAATAGAAAAAACCA-AAACTTAAAGGACTAAAATAACACAAA-CAGAA
* * * ** * *
1756619 ATTTAAAGGACTAAAATAACAAGAACAAAAACTTAAGGGACTAAAATGGTATTAACAGAAACTAA
1 ATTTAAAGGAATAAAATAACAAAAACAAAAACTTAAGGGACTAAAATAGTAAAAATAGAAACTTA
*
1756684 AGGGGCTAAATA
66 AGGGACTAAATA
1756696 TTAATTATAA
Statistics
Matches: 157, Mismatches: 32, Indels: 13
0.78 0.16 0.06
Matches are distributed among these distances:
118 25 0.16
119 101 0.64
120 28 0.18
121 3 0.02
ACGTcount: A:0.55, C:0.11, G:0.16, T:0.19
Consensus pattern (119 bp):
ATTTAAAGGAATAAAATAACAAAAACAAAAACTTAAGGGACTAAAATAGTAAAAATAGAAACTTA
AGGGACTAAATAGAAAAAACCAAAACTTAAAGGACTAAAATAACACAAACAGAA
Found at i:1756633 original size:89 final size:88
Alignment explanation
Indices: 1756438--1756663 Score: 231
Period size: 89 Copynumber: 2.5 Consensus size: 88
1756428 GTAAAAATGA
* * *
1756438 AAACTTAAAGGACTAAAATAGAAAAAACCAAAACTTAAAGGACTAAAATGGCACAAACATAAATT
1 AAACTTAAAGGACTAAAATAGAAAAAA-CAAAACTTAAGGGACT-AAATAGCACAAACAGAAATT
* ** *
1756503 TAGAGGAATAAAATGGCAAAAATAG
64 TAAAGGAATAAAATAACAAAAACAG
* * * * *
1756528 AAACTTAAAGGGCTAAAATAGTAAAAATAGAAACTTAAGGGTCTAAATAGCA-AATACAGACATT
1 AAACTTAAAGGACTAAAATAGAAAAAACA-AAACTTAAGGGACTAAATAGCACAA-ACAGAAATT
* *
1756592 TAAAGGACTAAAATAACAAAAGCAG
64 TAAAGGAATAAAATAACAAAAACAG
* * *
1756617 ACATTTAAAGGACTAAAATA-ACAAGAACAAAAACTTAAGGGACTAAA
1 AAACTTAAAGGACTAAAATAGA-AAAAAC-AAAACTTAAGGGACTAAA
1756664 ATGGTATTAA
Statistics
Matches: 111, Mismatches: 21, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
88 2 0.02
89 71 0.64
90 38 0.34
ACGTcount: A:0.56, C:0.12, G:0.15, T:0.18
Consensus pattern (88 bp):
AAACTTAAAGGACTAAAATAGAAAAAACAAAACTTAAGGGACTAAATAGCACAAACAGAAATTTA
AAGGAATAAAATAACAAAAACAG
Found at i:1758246 original size:35 final size:37
Alignment explanation
Indices: 1758168--1758239 Score: 94
Period size: 35 Copynumber: 2.0 Consensus size: 37
1758158 TAACAAGTTG
* *
1758168 AAAAATATTTATATATTTTCTTTAAAAAATTTAAATTC
1 AAAAA-ATTTATATATTTTCTTTAAAAAATTGAAAATC
*
1758206 AAAAAATTTATAT-TTTT-TTTACAAAATTGAAAAT
1 AAAAAATTTATATATTTTCTTTAAAAAATTGAAAAT
1758240 ATAAAAAGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 14 0.45
36 4 0.13
37 8 0.26
38 5 0.16
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (37 bp):
AAAAAATTTATATATTTTCTTTAAAAAATTGAAAATC
Found at i:1758252 original size:37 final size:37
Alignment explanation
Indices: 1758168--1758252 Score: 95
Period size: 37 Copynumber: 2.3 Consensus size: 37
1758158 TAACAAGTTG
*
1758168 AAAAATATTTATATATTTTCTTTAAAAAATTTAAATTC
1 AAAAA-ATTTATATATTTTCTTTAAAAAATTAAAATTC
*
1758206 AAAAAATTTATAT-TTTT-TTTACAAAATTGAAAATAT-
1 AAAAAATTTATATATTTTCTTTAAAAAATT-AAAAT-TC
1758242 AAAAAGATTTA
1 AAAAA-ATTTA
1758253 ATGAAAGGGT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
35 10 0.24
36 13 0.31
37 14 0.33
38 5 0.12
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (37 bp):
AAAAAATTTATATATTTTCTTTAAAAAATTAAAATTC
Found at i:1758779 original size:3 final size:3
Alignment explanation
Indices: 1758773--1758816 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
1758763 TGTATATTAT
* *
1758773 TAA TAA TAA TAAA TAA TAG TAA TAA TAA TTA TAA TAA TAA TAA T
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1758817 TAAAATAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1760477 original size:15 final size:15
Alignment explanation
Indices: 1760443--1760478 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1760433 CACCGATGAC
*
1760443 GATTTTAGAATTTAA
1 GATTTTAGAATTCAA
*
1760458 AATTTTAGAATTCAA
1 GATTTTAGAATTCAA
1760473 GATTTT
1 GATTTT
1760479 TAGAGTTTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.39, C:0.03, G:0.11, T:0.47
Consensus pattern (15 bp):
GATTTTAGAATTCAA
Found at i:1760536 original size:18 final size:17
Alignment explanation
Indices: 1760490--1760536 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
1760480 AGAGTTTTGG
1760490 ATTTATGATTTAAAATAT
1 ATTTAT-ATTTAAAATAT
* *
1760508 AATTAT-TTTAAATTAT
1 ATTTATATTTAAAATAT
1760524 ATTTATATATTAA
1 ATTTATAT-TTAA
1760537 TTAAATGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 14 0.58
17 1 0.04
18 9 0.38
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
ATTTATATTTAAAATAT
Found at i:1762223 original size:27 final size:24
Alignment explanation
Indices: 1762168--1762223 Score: 87
Period size: 24 Copynumber: 2.3 Consensus size: 24
1762158 CTATCTTCAT
*
1762168 AGTTGTTGTCTACCAGTAGTCCTC
1 AGTTGTTGTCTACCAGTAATCCTC
1762192 AGTTGTTGTCTACCA-TCAATCCTC
1 AGTTGTTGTCTACCAGT-AATCCTC
1762216 AGTTGTTG
1 AGTTGTTG
1762224 CCTCAATTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 1 0.03
24 29 0.97
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (24 bp):
AGTTGTTGTCTACCAGTAATCCTC
Found at i:1777242 original size:24 final size:24
Alignment explanation
Indices: 1777210--1777261 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
1777200 CTAGCAGTTC
1777210 TCCACCGTTGCATCTCATCAATGA
1 TCCACCGTTGCATCTCATCAATGA
*
1777234 TCCACCGTTGGATCTCATCAATGA
1 TCCACCGTTGCATCTCATCAATGA
1777258 TCCA
1 TCCA
1777262 ACGGTCTGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.25, C:0.33, G:0.13, T:0.29
Consensus pattern (24 bp):
TCCACCGTTGCATCTCATCAATGA
Found at i:1780327 original size:28 final size:28
Alignment explanation
Indices: 1780279--1780335 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
1780269 TTTTCGTTGC
**
1780279 TTTCAAGCACTAACTTGACGACATAATG
1 TTTCAAGCACTAACTCCACGACATAATG
*
1780307 TTTCAAGCACTGACTCCACGACATAATG
1 TTTCAAGCACTAACTCCACGACATAATG
1780335 T
1 T
1780336 AAATGGAGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (28 bp):
TTTCAAGCACTAACTCCACGACATAATG
Found at i:1792598 original size:9 final size:9
Alignment explanation
Indices: 1792586--1792646 Score: 50
Period size: 9 Copynumber: 5.9 Consensus size: 9
1792576 AAAAGAGGAA
1792586 AAAATAAAT
1 AAAATAAAT
1792595 AAAATAAAT
1 AAAATAAAT
1792604 AAAATTGAAAATT
1 AAAA-T--AAA-T
1792617 AAAATTAACAT
1 AAAA-TAA-AT
1792628 AGAAATGAAAT
1 A-AAAT-AAAT
1792639 AAAATAAA
1 AAAATAAA
1792647 ATATAAAACC
Statistics
Matches: 45, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
9 16 0.36
10 5 0.11
11 8 0.18
12 9 0.20
13 7 0.16
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (9 bp):
AAAATAAAT
Found at i:1792601 original size:5 final size:5
Alignment explanation
Indices: 1792586--1792649 Score: 51
Period size: 5 Copynumber: 12.2 Consensus size: 5
1792576 AAAAGAGGAA
*
1792586 AAAAT -AAAT AAAAT -AAAT AAAATT GAAAATT AAAATT AACAT AGAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAA-T -AAAA-T AAAA-T AAAAT A-AAAT
*
1792634 GAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT A
1792650 TAAAACCCTA
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
4 8 0.16
5 23 0.46
6 13 0.26
7 6 0.12
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:1792692 original size:15 final size:17
Alignment explanation
Indices: 1792658--1792695 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
1792648 TATAAAACCC
1792658 TAAAAAGAGAAATAAAA
1 TAAAAAGAGAAATAAAA
*
1792675 TAAAAA-AGAAGT-AAA
1 TAAAAAGAGAAATAAAA
1792690 TAAAAA
1 TAAAAA
1792696 TACATATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 9 0.45
16 5 0.25
17 6 0.30
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.13
Consensus pattern (17 bp):
TAAAAAGAGAAATAAAA
Found at i:1792931 original size:1 final size:1
Alignment explanation
Indices: 1792925--1792959 Score: 52
Period size: 1 Copynumber: 35.0 Consensus size: 1
1792915 CAAGTCAAAT
* *
1792925 AAAAAAAAAAAAAAAAAAAAAAAAACAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1792960 TAAATATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1792968 original size:2 final size:2
Alignment explanation
Indices: 1792963--1792992 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1792953 AACAAAATAA
1792963 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
1792993 TAGATTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1795116 original size:25 final size:26
Alignment explanation
Indices: 1795084--1795145 Score: 85
Period size: 25 Copynumber: 2.5 Consensus size: 26
1795074 TCTTAATTTA
*
1795084 TTATGAGAAAAAA-ATAATCTCTAAC
1 TTATGAGAAAAAATATAATATCTAAC
*
1795109 TTATGAGAAAAAATATAATATTTAAC
1 TTATGAGAAAAAATATAATATCTAAC
1795135 TTA-GA-AAAAAA
1 TTATGAGAAAAAA
1795146 CTTTCATTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
24 6 0.18
25 15 0.44
26 13 0.38
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.29
Consensus pattern (26 bp):
TTATGAGAAAAAATATAATATCTAAC
Found at i:1796095 original size:27 final size:27
Alignment explanation
Indices: 1796065--1796118 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
1796055 ATATGTTGAA
* *
1796065 AAAAATTGATGTTGACGCTATGCTTTT
1 AAAAATTGATGTTGACACTATGATTTT
1796092 AAAAATTGATGTTGACACTATGATTTT
1 AAAAATTGATGTTGACACTATGATTTT
1796119 GTATAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41
Consensus pattern (27 bp):
AAAAATTGATGTTGACACTATGATTTT
Found at i:1796486 original size:17 final size:18
Alignment explanation
Indices: 1796461--1796503 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
1796451 TAATGAATAT
1796461 TCTTTTTTTAAACAATGA
1 TCTTTTTTTAAACAATGA
1796479 TCTTTTTTTAAACAATGA
1 TCTTTTTTTAAACAATGA
1796497 TCTTTTT
1 TCTTTTT
1796504 AGGGTCAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.56
Consensus pattern (18 bp):
TCTTTTTTTAAACAATGA
Found at i:1796716 original size:17 final size:17
Alignment explanation
Indices: 1796691--1796724 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1796681 GTCATAGATC
1796691 TCAAAAATAAATTTTAA
1 TCAAAAATAAATTTTAA
* *
1796708 TCAATAATATATTTTAA
1 TCAAAAATAAATTTTAA
1796725 AATATTATTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
TCAAAAATAAATTTTAA
Found at i:1798191 original size:2 final size:2
Alignment explanation
Indices: 1798180--1798214 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1798170 TGAATGGTAA
1798180 AT AT -T 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
1798215 TTAAAAAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1800911 original size:20 final size:20
Alignment explanation
Indices: 1800888--1800953 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
1800878 TATGAATTTC
1800888 TTCTTCCTTCTTCAGATGAG
1 TTCTTCCTTCTTCAGATGAG
***
1800908 TTCTT--TTCATT-ATGAATTTC
1 TTCTTCCTTC-TTCA-G-ATGAG
1800928 TTCTTCCTTCTTCAGATGAG
1 TTCTTCCTTCTTCAGATGAG
1800948 TTCTTC
1 TTCTTC
1800954 TCATTATGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 12
0.65 0.12 0.23
Matches are distributed among these distances:
18 4 0.12
19 3 0.09
20 20 0.59
21 3 0.09
22 4 0.12
ACGTcount: A:0.15, C:0.23, G:0.11, T:0.52
Consensus pattern (20 bp):
TTCTTCCTTCTTCAGATGAG
Found at i:1800918 original size:40 final size:40
Alignment explanation
Indices: 1800868--1800969 Score: 186
Period size: 40 Copynumber: 2.5 Consensus size: 40
1800858 GTTGAACAAA
1800868 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAG
*
1800908 TTCTTTTCATTATGAATTTCTTCTTCCTTCTTCAGATGAG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAG
1800948 TTCTTCTCATTATGAACTTTCT
1 TTCTTCTCATTATGAA-TTTCT
1800970 ATGGAAGAGC
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
40 54 0.92
41 5 0.08
ACGTcount: A:0.18, C:0.22, G:0.09, T:0.52
Consensus pattern (40 bp):
TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAG
Found at i:1800938 original size:153 final size:152
Alignment explanation
Indices: 1800755--1801082 Score: 498
Period size: 153 Copynumber: 2.1 Consensus size: 152
1800745 ATTGAACAAA
*
1800755 TTCTTCTCATTATGATTTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTCTTCTA
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA-CT-TTCTA
* * * *
1800820 -GAAAAGTTGATCCATCGAGTAATGAATTC-AAGCAAAATGTTGAACAAATTCTTCTCATTATGA
64 GGAAAAGCTGATCCATCGAGTAATGAATTCGAA-CAAAAGGTTAAACAAATTCTTATCATTATGA
*
1800883 ATTTCTTCTTCCTTCTTCAGATGAG
128 ACTTCTTCTTCCTTCTTCAGATGAG
*
1800908 TTCTTTTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTATG
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTA-G
* * * *
1800973 GAAGAGCTGATCCATTGAGTAATGAATTCGAACCAAAGGTTAAACAAGTTCTTATCATTATGAAC
65 GAAAAGCTGATCCATCGAGTAATGAATTCGAACAAAAGGTTAAACAAATTCTTATCATTATGAAC
1801038 TTCTTCTTCCTTCTTCAGATGAG
130 TTCTTCTTCCTTCTTCAGATGAG
1801061 TTCTTCTCATTATGAACTTTCT
1 TTCTTCTCATTATGAA-TTTCT
1801083 CTGGAAAAGT
Statistics
Matches: 159, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
151 5 0.03
152 2 0.01
153 145 0.91
154 7 0.04
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.42
Consensus pattern (152 bp):
TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTAGG
AAAAGCTGATCCATCGAGTAATGAATTCGAACAAAAGGTTAAACAAATTCTTATCATTATGAACT
TCTTCTTCCTTCTTCAGATGAG
Found at i:1809202 original size:201 final size:202
Alignment explanation
Indices: 1808857--1809259 Score: 799
Period size: 201 Copynumber: 2.0 Consensus size: 202
1808847 TTCCCTACGA
1808857 GATCCTCTGGATTCCGCTCGATTAGTGTTTGTTTTCTCTTTCTTAACCCTTGGTTGGGTTATCGT
1 GATCCTCTGGATTCCGCTCGATTAGTGTTTGTTTTCTCTTTCTTAACCCTTGGTTGGGTTATCGT
1808922 AACACTTTTTGAGGTATCCTTGTTGTAAGAGTTCGCATTGTTAACTTCATTCTCTTTTTTCTGGT
66 AACACTTTTTGAGGTATCCTTGTTGTAAGAGTTCGCATTGTTAACTTCATTCTCTTTTTTCTGGT
1808987 ACATGGGTCTTTTGGAACTAGATCCCTCACTTGATT-CATTTTACCACTTTTCATGACATTTTCA
131 ACATGGGTCTTTTGGAACTAGATCCCTCACTTGATTCCATTTTACCACTTTTCATGACATTTTCA
1809051 ATGAGTT
196 ATGAGTT
1809058 GATCCTCTGGATTCCGCTCGATTAGTGTTTGTTTTCTCTTTCTTAACCCTTGGTTGGGTTATCGT
1 GATCCTCTGGATTCCGCTCGATTAGTGTTTGTTTTCTCTTTCTTAACCCTTGGTTGGGTTATCGT
1809123 AACACTTTTTGAGGTATCCTTGTTGTAAGAGTTCGCATTGTTAACTTCATTCTCTTTTTTCTGGT
66 AACACTTTTTGAGGTATCCTTGTTGTAAGAGTTCGCATTGTTAACTTCATTCTCTTTTTTCTGGT
1809188 ACATGGGTCTTTTGGAACTAGATCCCTCACTTGATTCCATTTTACCACTTTTCATGACATTTTCA
131 ACATGGGTCTTTTGGAACTAGATCCCTCACTTGATTCCATTTTACCACTTTTCATGACATTTTCA
1809253 ATGAGTT
196 ATGAGTT
1809260 CTCCAGATAT
Statistics
Matches: 201, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
201 166 0.83
202 35 0.17
ACGTcount: A:0.18, C:0.20, G:0.17, T:0.45
Consensus pattern (202 bp):
GATCCTCTGGATTCCGCTCGATTAGTGTTTGTTTTCTCTTTCTTAACCCTTGGTTGGGTTATCGT
AACACTTTTTGAGGTATCCTTGTTGTAAGAGTTCGCATTGTTAACTTCATTCTCTTTTTTCTGGT
ACATGGGTCTTTTGGAACTAGATCCCTCACTTGATTCCATTTTACCACTTTTCATGACATTTTCA
ATGAGTT
Found at i:1810354 original size:3 final size:3
Alignment explanation
Indices: 1810346--1810384 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1810336 AACCCTTTTG
1810346 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1810385 TAATGAATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1813792 original size:28 final size:27
Alignment explanation
Indices: 1813753--1813807 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 27
1813743 AATAAAGCAT
*
1813753 TAATAATATATATAAATATTATGAAAA
1 TAATAATATATATAAAAATTATGAAAA
*
1813780 TAATAAGTATATATAAAAATTTTGAAAA
1 TAATAA-TATATATAAAAATTATGAAAA
1813808 GAAAGAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 6 0.24
28 19 0.76
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.36
Consensus pattern (27 bp):
TAATAATATATATAAAAATTATGAAAA
Found at i:1814617 original size:3 final size:3
Alignment explanation
Indices: 1814609--1814634 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1814599 ATATATATGT
1814609 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
1814635 TAAATATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1815640 original size:22 final size:22
Alignment explanation
Indices: 1815612--1815653 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
1815602 AGGGCTCGAT
1815612 GGCTTTTATAGCCACCATCGGC
1 GGCTTTTATAGCCACCATCGGC
1815634 GGCTTTTATAGCCACCATCG
1 GGCTTTTATAGCCACCATCG
1815654 ACGATGTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.31, G:0.21, T:0.29
Consensus pattern (22 bp):
GGCTTTTATAGCCACCATCGGC
Found at i:1815997 original size:3 final size:3
Alignment explanation
Indices: 1815989--1816025 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
1815979 AATTTTTTAT
1815989 TAA TAA TAA TAA TAA TAA TAA -AA TAAA TAA -AA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TA
1816026 TTTAAAATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 4 0.13
3 24 0.77
4 3 0.10
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:1821135 original size:56 final size:56
Alignment explanation
Indices: 1821068--1821179 Score: 206
Period size: 56 Copynumber: 2.0 Consensus size: 56
1821058 TCTATGGATT
*
1821068 CTAACCTTATTAACCAAACTGTTAGCATTTAAATACTAAATAGTTTTATTTTCAAC
1 CTAACCTTATTAACCAAACTGTTAGCATTTAAATACTAAATAGTTTAATTTTCAAC
*
1821124 CTAACCTTATTAACCGAACTGTTAGCATTTAAATACTAAATAGTTTAATTTTCAAC
1 CTAACCTTATTAACCAAACTGTTAGCATTTAAATACTAAATAGTTTAATTTTCAAC
1821180 AACAATTACA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.38, C:0.18, G:0.06, T:0.38
Consensus pattern (56 bp):
CTAACCTTATTAACCAAACTGTTAGCATTTAAATACTAAATAGTTTAATTTTCAAC
Found at i:1821841 original size:30 final size:30
Alignment explanation
Indices: 1821807--1821873 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
1821797 GTTTACGGTA
1821807 TGTTAACTGTATCATTTAGTTTAAACAGTC
1 TGTTAACTGTATCATTTAGTTTAAACAGTC
1821837 TGTTAACTGTATCATTTAGTTTAAACAGTC
1 TGTTAACTGTATCATTTAGTTTAAACAGTC
1821867 TGGTTAA
1 T-GTTAA
1821874 TCATTATAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 31 0.86
31 5 0.14
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.43
Consensus pattern (30 bp):
TGTTAACTGTATCATTTAGTTTAAACAGTC
Found at i:1823542 original size:269 final size:256
Alignment explanation
Indices: 1823019--1823544 Score: 745
Period size: 274 Copynumber: 2.0 Consensus size: 256
1823009 TATATTCGGG
1823019 TCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTCGGATCGAGTTCGGGTTTAGGGTGAAAAATAC
1 TCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTCGGATCGAGTTCGGGTTTAGGGTGAAAAATAC
* *
1823084 CCGACCCGAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCACTA
66 CCGACCCGAAAAAATATATAATTTTACCTTATATATTTAAGAATAATTACAATAATACCCCACTA
1823149 TATATAATTTTTTTCAATTAAGTCACTGTTTTTATTGAATAAAAATAATTTTTTTATTATTTCGG
131 TATATAATTTTTTTCAATTAAGTCACTGTTTTTATTGAATAAAAATAATTTTTTTATTATTTCGG
*
1823214 GTCAAGTCGGGTCGGATTTCTAATTCATATATTCGGATCGGGTCGGGTGAAACTTTATTTTGGTT
196 GTCAA-----G--GGATTTCTAATTCATATATTCGGATCGAGTCGGGTGAAACTTTATTTTGGTT
1823279 GGA
254 GGA
* *
1823282 TCGGGTCGGTTTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAATA
1 TCGGGTCGG-TTTTTTTAAGTGTGATATTCGGGTCGGATCGAGTTCGGGTTTAGGGTG-AAAA-A
1823347 CCCTACCCGACCCGACCCAAAAAAATATATAATTTTACCTTATATATTTAAGAATAATTACAATA
63 ---TACCCGACCCG-----AAAAAATATATAATTTTACCTTATATATTTAAGAATAATTACAATA
* *
1823412 ATACCCCTCTATATATATATATATATTTTCCAATTAAGTCATTGTTTTTATTGAATAAAAATAAT
120 ATACCCCACTATATATA-AT-T-T-TTTT-CAATTAAGTCACTGTTTTTATTGAATAAAAATAAT
1823477 TTTTTTATTATTTCGGGTC-A-GG-TTTCTAATTCATATATTCAGG-TCGAGTCGGGTGAAACTT
180 TTTTTTATTATTTCGGGTCAAGGGATTTCTAATTCATATATTC-GGATCGAGTCGGGTGAAACTT
1823538 TATTTTG
244 TATTTTG
1823545 AACGGGTCGG
Statistics
Matches: 239, Mismatches: 7, Indels: 28
0.87 0.03 0.10
Matches are distributed among these distances:
263 9 0.04
264 46 0.19
265 4 0.02
266 1 0.00
269 53 0.22
270 4 0.02
274 60 0.25
275 2 0.01
276 1 0.00
277 1 0.00
278 5 0.02
279 53 0.22
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (256 bp):
TCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTCGGATCGAGTTCGGGTTTAGGGTGAAAAATAC
CCGACCCGAAAAAATATATAATTTTACCTTATATATTTAAGAATAATTACAATAATACCCCACTA
TATATAATTTTTTTCAATTAAGTCACTGTTTTTATTGAATAAAAATAATTTTTTTATTATTTCGG
GTCAAGGGATTTCTAATTCATATATTCGGATCGAGTCGGGTGAAACTTTATTTTGGTTGGA
Found at i:1823557 original size:269 final size:256
Alignment explanation
Indices: 1823015--1823557 Score: 743
Period size: 269 Copynumber: 2.0 Consensus size: 256
1823005 TTCATATATT
1823015 CGGGTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTCGGATCGAGTTCGGGTTTAGGGTGAAAA
1 CGGGTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTCGGATCGAGTTCGGGTTTAGGGTGAAAA
* *
1823080 ATACCCGACCCGAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCC
66 ATACCCGACCCGAAAAAATATATAATTTTACCTTATATATTTAAGAATAATTACAATAATACCCC
1823145 ACTATATATAATTTTTTTCAATTAAGTCACTGTTTTTATTGAATAAAAATAATTTTTTTATTATT
131 ACTATATATAATTTTTTTCAATTAAGTCACTGTTTTTATTGAATAAAAATAATTTTTTTATTATT
*
1823210 TCGGGTCAAGTCGGGTCGGATTTCTAATTCATATATTCGGATCGGGTCGGGTGAAACTTTATTTT
196 TCGGGTCAA-----G--GGATTTCTAATTCATATATTCGGATCGAGTCGGGTGAAACTTTATTTT
**
1823275 GGT
254 GAA
* * * *
1823278 TGGATCGGGTCGGTTTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAA
1 CGGGTCGGGTCGG-TTTTTTTAAGTGTGATATTCGGGTCGGATCGAGTTCGGGTTTAGGGTG-AA
1823343 AATACCCTACCCGACCCGACCCAAAAAAATATATAATTTTACCTTATATATTTAAGAATAATTAC
64 AA-A---TACCCGACCCG-----AAAAAATATATAATTTTACCTTATATATTTAAGAATAATTAC
* *
1823408 AATAATACCCCTCTATATATATATATATATTTTCCAATTAAGTCATTGTTTTTATTGAATAAAAA
120 AATAATACCCCACTATATATA-AT-T-T-TTTT-CAATTAAGTCACTGTTTTTATTGAATAAAAA
1823473 TAATTTTTTTATTATTTCGGGTC-A-GG-TTTCTAATTCATATATTCAGG-TCGAGTCGGGTGAA
180 TAATTTTTTTATTATTTCGGGTCAAGGGATTTCTAATTCATATATTC-GGATCGAGTCGGGTGAA
1823534 ACTTTATTTTGAA
244 ACTTTATTTTGAA
1823547 CGGGTCGGGTC
1 CGGGTCGGGTC
1823558 TCAGATGGAG
Statistics
Matches: 250, Mismatches: 13, Indels: 28
0.86 0.04 0.10
Matches are distributed among these distances:
263 11 0.04
264 46 0.18
265 4 0.02
266 1 0.00
269 62 0.25
270 4 0.02
274 60 0.24
275 2 0.01
276 1 0.00
277 1 0.00
278 5 0.02
279 53 0.21
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.39
Consensus pattern (256 bp):
CGGGTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTCGGATCGAGTTCGGGTTTAGGGTGAAAA
ATACCCGACCCGAAAAAATATATAATTTTACCTTATATATTTAAGAATAATTACAATAATACCCC
ACTATATATAATTTTTTTCAATTAAGTCACTGTTTTTATTGAATAAAAATAATTTTTTTATTATT
TCGGGTCAAGGGATTTCTAATTCATATATTCGGATCGAGTCGGGTGAAACTTTATTTTGAA
Found at i:1828528 original size:21 final size:22
Alignment explanation
Indices: 1828486--1828531 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
1828476 ATTTAAGATT
1828486 AAATATAAGGTAAATTAACATG
1 AAATATAAGGTAAATTAACATG
*
1828508 AAAT-TAAGGATAAATT-TCATG
1 AAATATAAGG-TAAATTAACATG
1828529 AAA
1 AAA
1828532 CCAAACTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.54, C:0.04, G:0.13, T:0.28
Consensus pattern (22 bp):
AAATATAAGGTAAATTAACATG
Found at i:1832343 original size:27 final size:27
Alignment explanation
Indices: 1832313--1832373 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 27
1832303 AATATTTGAT
*
1832313 AATGTTATGTGACA-ATATGCTACGTGA
1 AATGTTATGTGA-ATATATGCTAAGTGA
*
1832340 AATGTTATGTGAATATGTGCTAAGTGA
1 AATGTTATGTGAATATATGCTAAGTGA
1832367 ATATGTT
1 A-ATGTT
1832374 CTATGGAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 1 0.03
27 24 0.80
28 5 0.17
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.38
Consensus pattern (27 bp):
AATGTTATGTGAATATATGCTAAGTGA
Found at i:1832637 original size:23 final size:23
Alignment explanation
Indices: 1832604--1832706 Score: 93
Period size: 23 Copynumber: 4.4 Consensus size: 23
1832594 GAGTCGAGGG
*
1832604 TTCTACGTGGTCCTTCGAGACAAT
1 TTCTATGTGGTCCTTCGAGAC-AT
* * *
1832628 TT-TATGTGGTCCTTCAAGAAAAA
1 TTCTATGTGGTCCTTCGAG-ACAT
*
1832651 TTCTATGCT-GTCCTTCGGGACAT
1 TTCTATG-TGGTCCTTCGAGACAT
* * *
1832674 TTCTACGTGGTCTTTCGGGACAT
1 TTCTATGTGGTCCTTCGAGACAT
1832697 TTCTATGTGG
1 TTCTATGTGG
1832707 CACTTCGGTG
Statistics
Matches: 64, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
22 1 0.02
23 47 0.73
24 15 0.23
25 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.38
Consensus pattern (23 bp):
TTCTATGTGGTCCTTCGAGACAT
Found at i:1832713 original size:23 final size:23
Alignment explanation
Indices: 1832604--1832727 Score: 85
Period size: 23 Copynumber: 5.3 Consensus size: 23
1832594 GAGTCGAGGG
*
1832604 TTCTACGTGGTCCTTCGAGACAAT
1 TTCTACGTGGTCCTTCGGGAC-AT
* * * * *
1832628 TT-TATGTGGTCCTTCAAGAAAAA
1 TTCTACGTGGTCCTTC-GGGACAT
*
1832651 TTCTATGCT-GTCCTTCGGGACAT
1 TTCTACG-TGGTCCTTCGGGACAT
*
1832674 TTCTACGTGGTCTTTCGGGACAT
1 TTCTACGTGGTCCTTCGGGACAT
*
1832697 TTCTATGTGG-CACTTCGGTG-CAT
1 TTCTACGTGGTC-CTTCGG-GACAT
1832720 ATTCTACG
1 -TTCTACG
1832728 CGACACTTTG
Statistics
Matches: 78, Mismatches: 15, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
22 2 0.03
23 54 0.69
24 21 0.27
25 1 0.01
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.37
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAT
Found at i:1844949 original size:2 final size:2
Alignment explanation
Indices: 1844937--1844967 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
1844927 CAAAACAAAC
1844937 AT AT CAT 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
1844968 CATTGATGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1847368 original size:6 final size:6
Alignment explanation
Indices: 1847357--1847381 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1847347 GGTACCTCCA
1847357 TTGCAT TTGCAT TTGCAT TTGCAT T
1 TTGCAT TTGCAT TTGCAT TTGCAT T
1847382 CATATAGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (6 bp):
TTGCAT
Found at i:1852631 original size:3 final size:3
Alignment explanation
Indices: 1852625--1852716 Score: 175
Period size: 3 Copynumber: 30.7 Consensus size: 3
1852615 TTTTTACCCA
1852625 TAT TAT TAT TAT TAT 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
*
1852673 TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1852717 AATATATATT
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 87 1.00
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1853205 original size:25 final size:23
Alignment explanation
Indices: 1853157--1853213 Score: 60
Period size: 25 Copynumber: 2.4 Consensus size: 23
1853147 ACCCGAACCT
* * *
1853157 GAAAAAAAAGAGAGAAACGGAGA
1 GAAAAAACACAGAGAAACGAAGA
*
1853180 GACAAAGAACACAGAGAGACGAAGA
1 GA-AAA-AACACAGAGAAACGAAGA
1853205 GAAAAAACA
1 GAAAAAACA
1853214 GAGGAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 6 0.21
24 6 0.21
25 16 0.57
ACGTcount: A:0.63, C:0.11, G:0.26, T:0.00
Consensus pattern (23 bp):
GAAAAAACACAGAGAAACGAAGA
Found at i:1854160 original size:13 final size:13
Alignment explanation
Indices: 1854144--1854190 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
1854134 ATATAATAAA
1854144 TAAATATTTATTT
1 TAAATATTTATTT
*
1854157 TAAATAAATTATTT
1 TAAAT-ATTTATTT
1854171 T-AATATTTAGTTT
1 TAAATATTTA-TTT
*
1854184 TCAATAT
1 TAAATAT
1854191 CAAAGAACAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 4 0.14
13 12 0.41
14 13 0.45
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:1865497 original size:18 final size:17
Alignment explanation
Indices: 1865470--1865512 Score: 77
Period size: 18 Copynumber: 2.5 Consensus size: 17
1865460 ATTATGCTTG
1865470 AAGAAAAAGAAAAAAAA
1 AAGAAAAAGAAAAAAAA
1865487 AAGAGAAAAGAAAAAAAA
1 AAGA-AAAAGAAAAAAAA
1865505 AAGAAAAA
1 AAGAAAAA
1865513 AAGGGGGTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (17 bp):
AAGAAAAAGAAAAAAAA
Found at i:1865502 original size:16 final size:16
Alignment explanation
Indices: 1865474--1865511 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 16
1865464 TGCTTGAAGA
1865474 AAAAGAAAAAAAAAAGAG
1 AAAAG-AAAAAAAAA-AG
1865492 AAAAGAAAAAAAAAAG
1 AAAAGAAAAAAAAAAG
1865508 AAAA
1 AAAA
1865512 AAAGGGGGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 6 0.30
17 9 0.45
18 5 0.25
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAAAAAAG
Found at i:1865514 original size:11 final size:12
Alignment explanation
Indices: 1865470--1865512 Score: 63
Period size: 11 Copynumber: 3.7 Consensus size: 12
1865460 ATTATGCTTG
1865470 AAGAAAAAGAAA
1 AAGAAAAAGAAA
1865482 AA-AAAAAGAGAA
1 AAGAAAAAGA-AA
1865494 AAGAAAAA-AAA
1 AAGAAAAAGAAA
1865505 AAGAAAAA
1 AAGAAAAA
1865513 AAGGGGGTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 17 0.59
12 7 0.24
13 5 0.17
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAGAAAAAGAAA
Found at i:1866787 original size:83 final size:83
Alignment explanation
Indices: 1866647--1867355 Score: 1219
Period size: 83 Copynumber: 8.5 Consensus size: 83
1866637 GAAAGAGACT
1866647 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGAACCAATCATTGA
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAACCAATCATTGA
* *
1866711 ATTTGGAAGATGAATGTGC
65 ATTTAGAAGATGAATTTGC
* *
1866730 TAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGAACCAATCATTGA
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAACCAATCATTGA
* * *
1866794 ATTTGGAAGATGAATGTGTT
65 ATTTAGAAGATGAATTTG-C
* *
1866814 C-ATGGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGG-CAGAACCAATCATTGA
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAACCAATCATTGA
1866877 ATTTAGAAGATGAATTTGC
65 ATTTAGAAGATGAATTTGC
* *
1866896 CAAGAGAATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAA
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAA
1866961 TTTAGAAGATGAATTTGC
66 TTTAGAAGATGAATTTGC
*
1866979 CAAGAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAA
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAA
*
1867044 TTTAGAAGATAAATTTGC
66 TTTAGAAGATGAATTTGC
1867062 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAA
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAA
*
1867127 TTTAGAAGATAAATTTGC
66 TTTAGAAGATGAATTTGC
1867145 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAA
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAA
*
1867210 TTTAGAAGATAAATTTGC
66 TTTAGAAGATGAATTTGC
1867228 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAA
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAA
1867293 TTTAGAAGATGAATTTGC
66 TTTAGAAGATGAATTTGC
1867311 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
1867356 TGGTAGGAAC
Statistics
Matches: 605, Mismatches: 18, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
82 5 0.01
83 600 0.99
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (83 bp):
CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAA
TTTAGAAGATGAATTTGC
Found at i:1868293 original size:113 final size:113
Alignment explanation
Indices: 1868090--1868641 Score: 840
Period size: 113 Copynumber: 4.9 Consensus size: 113
1868080 ATTCAAATCT
* **
1868090 ATCATTTGATGGATTTACATTT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATCACTTGATGGA-TTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
1868154 AGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTAAC-TGAATTC
65 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-ACTTGAATTC
1868203 ATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* *
1868268 GAAGAAGTTCATAATGAGAAGAATTTATTCAACCTTTTACCTGAATTC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATTC
*
1868316 ATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAA
1 ATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1868381 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATTC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATTC
1868429 ATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* * *
1868494 GAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATTC
* * *** * *
1868542 ATCATTTGATGGATCAACATTACCA-AGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
1 ATCACTTGATGGATTATTTTTGCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAA
* * * *
1868606 GAAAGAAGAAGTTTATAATAAGAAGAACTTGTTCAA
62 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA
1868642 TAATTATATC
Statistics
Matches: 411, Mismatches: 22, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
112 10 0.02
113 355 0.86
115 1 0.00
116 45 0.11
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (113 bp):
ATCACTTGATGGATTATTTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATTC
Found at i:1868965 original size:3 final size:3
Alignment explanation
Indices: 1868959--1869002 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
1868949 TTTTTACCCA
*
1868959 TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1869003 AATATATATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1870448 original size:13 final size:13
Alignment explanation
Indices: 1870432--1870478 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
1870422 ATATAATAAA
1870432 TAAATATTTATTT
1 TAAATATTTATTT
*
1870445 TAAATAAATTATTT
1 TAAAT-ATTTATTT
1870459 T-AATATTTAGTTT
1 TAAATATTTA-TTT
*
1870472 TCAATAT
1 TAAATAT
1870479 CAAAGAACAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 4 0.14
13 12 0.41
14 13 0.45
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:1874246 original size:29 final size:29
Alignment explanation
Indices: 1874204--1874277 Score: 112
Period size: 29 Copynumber: 2.6 Consensus size: 29
1874194 AATTACTTTG
1874204 TACACGTGTAAGATGTGCTGTGCAATTCT
1 TACACGTGTAAGATGTGCTGTGCAATTCT
* * *
1874233 TACATGTGGAAGATGTGTTGTGCAATTCT
1 TACACGTGTAAGATGTGCTGTGCAATTCT
*
1874262 TACAGGTGTAAGATGT
1 TACACGTGTAAGATGT
1874278 AGGGTTATCA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.26, C:0.12, G:0.27, T:0.35
Consensus pattern (29 bp):
TACACGTGTAAGATGTGCTGTGCAATTCT
Found at i:1875372 original size:33 final size:33
Alignment explanation
Indices: 1875325--1875390 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1875315 GTCATGCGCT
*
1875325 TTACCGACTAAACTAAGA-TTACATCTGATCGTC
1 TTACCGACTAAACTAAGACCT-CATCTGATCGTC
* *
1875358 TTACCTACTGAACTAAGACCTCATCTGATCGTC
1 TTACCGACTAAACTAAGACCTCATCTGATCGTC
1875391 CTAAGCAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.30
Consensus pattern (33 bp):
TTACCGACTAAACTAAGACCTCATCTGATCGTC
Found at i:1879236 original size:20 final size:20
Alignment explanation
Indices: 1879195--1879237 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1879185 TTCTAACTTA
* *
1879195 TTTATTATTATTATTATTAT
1 TTTATTAATATTATTATCAT
1879215 TTTATTAATATTTATTA-CAT
1 TTTATTAATA-TTATTATCAT
1879235 TTT
1 TTT
1879238 GCAGGCCCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTATTAATATTATTATCAT
Found at i:1882691 original size:13 final size:13
Alignment explanation
Indices: 1882675--1882700 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1882665 AGGCTAAAAG
1882675 GGTAGGCGAGCTC
1 GGTAGGCGAGCTC
1882688 GGTAGGCGAGCTC
1 GGTAGGCGAGCTC
1882701 TAAGATACAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.46, T:0.15
Consensus pattern (13 bp):
GGTAGGCGAGCTC
Found at i:1884054 original size:13 final size:13
Alignment explanation
Indices: 1884038--1884063 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1884028 AGGCTAAAAG
1884038 GGTAGGCGAGCTC
1 GGTAGGCGAGCTC
1884051 GGTAGGCGAGCTC
1 GGTAGGCGAGCTC
1884064 TAAGATACAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.46, T:0.15
Consensus pattern (13 bp):
GGTAGGCGAGCTC
Found at i:1886342 original size:14 final size:14
Alignment explanation
Indices: 1886325--1886383 Score: 55
Period size: 14 Copynumber: 4.0 Consensus size: 14
1886315 AATCAAATGG
1886325 AAAAAATAAAATAA
1 AAAAAATAAAATAA
*
1886339 AAAAATTAAAATTTTAA
1 AAAAAATAAAA---TAA
**
1886356 AAGTAATAAAATAA
1 AAAAAATAAAATAA
*
1886370 ACAAAATAAAATAA
1 AAAAAATAAAATAA
1886384 GAAACATGCG
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
14 24 0.69
17 11 0.31
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (14 bp):
AAAAAATAAAATAA
Found at i:1886443 original size:22 final size:22
Alignment explanation
Indices: 1886418--1886464 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
1886408 ATTAGTGAAG
1886418 ATAGAATAATAATTAAATAAAA
1 ATAGAATAATAATTAAATAAAA
1886440 ATAGAATAATAATTAAATAAAA
1 ATAGAATAATAATTAAATAAAA
1886462 ATA
1 ATA
1886465 TTAAATCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (22 bp):
ATAGAATAATAATTAAATAAAA
Found at i:1888256 original size:85 final size:85
Alignment explanation
Indices: 1888088--1888408 Score: 410
Period size: 85 Copynumber: 3.7 Consensus size: 85
1888078 ATATGTCATC
* * * * * * *
1888088 GAGCTGAATGAAATCGAACTCGAAAAGTTTTTTGTTGACATATAGCCCTTCTCG-CTTCAAGCTA
1 GAGCTGAATGTAATCGAACTCG--AAGGTCTTTGTTGACAGATAACCCTTCTCGCCTT-GAGTTA
* * *
1888152 TGCTATAAATTTGACATGCCCTT
63 TACTATAAATTTGATATGCCTTT
* * * *
1888175 GAGCTGAATATAATTGAACTCGAAGGTCTTTGCTAACAGATAACCCTTCTCGCCTTGAGTTATAC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATAC
* *
1888240 TGTAAATTTAATATGCCTTT
66 TATAAATTTGATATGCCTTT
*
1888260 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCTTTCTCGCCTTGAGTTATAC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATAC
1888325 TATAAATTTGATATGCCTTT
66 TATAAATTTGATATGCCTTT
* * * *
1888345 GAGCTGAATGTAATCGAACTCGAAGGTCTTGGTTGACAAATAACTCTTCTCGTCTTTGAGTTAT
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCG-CCTTGAGTTAT
1888409 GTTGTACTTG
Statistics
Matches: 204, Mismatches: 28, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
85 172 0.84
86 13 0.06
87 19 0.09
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (85 bp):
GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATAC
TATAAATTTGATATGCCTTT
Found at i:1888678 original size:25 final size:25
Alignment explanation
Indices: 1888650--1888701 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
1888640 CCAATCTTGT
*
1888650 GTAAATTTCACCAAATTGGCTTTGA
1 GTAAATTTCACCAAATTGGATTTGA
***
1888675 GTAAATTTTGTCAAATTGGATTTGA
1 GTAAATTTCACCAAATTGGATTTGA
1888700 GT
1 GT
1888702 TGGATATCCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (25 bp):
GTAAATTTCACCAAATTGGATTTGA
Found at i:1890371 original size:29 final size:26
Alignment explanation
Indices: 1890316--1890375 Score: 84
Period size: 29 Copynumber: 2.2 Consensus size: 26
1890306 TTTTCATCAC
1890316 TTTTTCCTTTGTTTTTGTTTCCTTTT
1 TTTTTCCTTTGTTTTTGTTTCCTTTT
1890342 TATTTTCTCTTTGCTTTTTGTTTCTCTTTT
1 T-TTTTC-CTTTG-TTTTTGTTTC-CTTTT
1890372 TTTT
1 TTTT
1890376 ATTATGATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
26 1 0.03
27 5 0.17
28 5 0.17
29 13 0.43
30 6 0.20
ACGTcount: A:0.02, C:0.15, G:0.07, T:0.77
Consensus pattern (26 bp):
TTTTTCCTTTGTTTTTGTTTCCTTTT
Found at i:1892423 original size:135 final size:135
Alignment explanation
Indices: 1892181--1892450 Score: 531
Period size: 135 Copynumber: 2.0 Consensus size: 135
1892171 GCCGGACTTT
*
1892181 TGCATTTTTCACCTCTTGTATTACAACCCCTTTGTCCATTAATACAAATTATTTACGTTTAATGA
1 TGCATTTTTCACCTCTTGTATTACAACCCCTTTGTCCATTAATACAAATTATTTACGTTTAACGA
1892246 ACACGTTTTTGGTGGATCAACACCTCTTTTGAATGATGCAAATGATAAAAATGAAATAGAATAAA
66 ACACGTTTTTGGTGGATCAACACCTCTTTTGAATGATGCAAATGATAAAAATGAAATAGAATAAA
1892311 AATGA
131 AATGA
1892316 TGCATTTTTCACCTCTTGTATTACAACCCCTTTGTCCATTAATACAAATTATTTACGTTTAACGA
1 TGCATTTTTCACCTCTTGTATTACAACCCCTTTGTCCATTAATACAAATTATTTACGTTTAACGA
1892381 ACACGTTTTTGGTGGATCAACACCTCTTTTGAATGATGCAAATGATAAAAATGAAATAGAATAAA
66 ACACGTTTTTGGTGGATCAACACCTCTTTTGAATGATGCAAATGATAAAAATGAAATAGAATAAA
1892446 AATGA
131 AATGA
1892451 AAAGAGTTAG
Statistics
Matches: 134, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
135 134 1.00
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.35
Consensus pattern (135 bp):
TGCATTTTTCACCTCTTGTATTACAACCCCTTTGTCCATTAATACAAATTATTTACGTTTAACGA
ACACGTTTTTGGTGGATCAACACCTCTTTTGAATGATGCAAATGATAAAAATGAAATAGAATAAA
AATGA
Found at i:1894042 original size:24 final size:24
Alignment explanation
Indices: 1894015--1894077 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
1894005 CGTCCGTGAA
*
1894015 CGTTCGGTTATGTTTGTTTATATG
1 CGTTCAGTTATGTTTGTTTATATG
* * *
1894039 CGTTTAGTTATGTTCGTTTATGTG
1 CGTTCAGTTATGTTTGTTTATATG
*
1894063 CGTTCATTTATGTTT
1 CGTTCAGTTATGTTT
1894078 AACCTAATAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.13, C:0.10, G:0.22, T:0.56
Consensus pattern (24 bp):
CGTTCAGTTATGTTTGTTTATATG
Found at i:1895603 original size:10 final size:10
Alignment explanation
Indices: 1895588--1895662 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
1895578 GGGTCTCCAA
1895588 CGTTTATGTT
1 CGTTTATGTT
1895598 CGTTTATGTT
1 CGTTTATGTT
1895608 CG----TGTT
1 CGTTTATGTT
*
1895614 CATTTATGTT
1 CGTTTATGTT
*
1895624 CGTGTT-CGTTT
1 CGT-TTATG-TT
* *
1895635 ATGTTTGTGTT
1 -CGTTTATGTT
1895646 CGTTTATGTT
1 CGTTTATGTT
1895656 CGTTTAT
1 CGTTTAT
1895663 TTATTAAATG
Statistics
Matches: 50, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
6 5 0.10
10 34 0.68
11 8 0.16
12 3 0.06
ACGTcount: A:0.09, C:0.11, G:0.21, T:0.59
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:1895619 original size:16 final size:16
Alignment explanation
Indices: 1895594--1895658 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
1895584 CCAACGTTTA
1895594 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
1895610 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
*
1895626 TGTTCGTTTATGTTTG
1 TGTTCGTTTATGTTCG
1895642 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1895658 T
1 T
1895659 TTATTTATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.08, C:0.11, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1895749 original size:16 final size:16
Alignment explanation
Indices: 1895728--1895759 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1895718 AAAAAAATTT
1895728 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1895744 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1895760 CTTATTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.12, G:0.25, T:0.56
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1898863 original size:2 final size:2
Alignment explanation
Indices: 1898856--1898885 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1898846 AAACGTAAAC
1898856 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1898886 AAAGATGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1901012 original size:19 final size:18
Alignment explanation
Indices: 1900988--1901035 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 18
1900978 TTAATTTTAA
1900988 AAAATAATTTAATACATAC
1 AAAATAATTTAATA-ATAC
1901007 AAAATAATTT--TAATAC
1 AAAATAATTTAATAATAC
1901023 AAAATAATATTAA
1 AAAATAAT-TTAA
1901036 AAGTTCATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 12 0.46
17 4 0.15
19 10 0.38
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAATAATTTAATAATAC
Found at i:1902635 original size:27 final size:23
Alignment explanation
Indices: 1902577--1902709 Score: 84
Period size: 24 Copynumber: 5.8 Consensus size: 23
1902567 GAATATATTA
* * *
1902577 ATATTTTAAAATAATTAAAATAAG
1 ATATTTTATAATAA-TAAATTAAT
*
1902601 ATAATTTATAATAATAAATTTATAATT
1 ATATTTTATAATAATAAA--T-TAA-T
*
1902628 ATATTTTA-AACAATTAAATTAAT
1 ATATTTTATAATAA-TAAATTAAT
*
1902651 ATATTTTATAATAAT---TT-TT
1 ATATTTTATAATAATAAATTAAT
1902670 ATATTTT-TAATAATGAAA-TAAT
1 ATATTTTATAATAAT-AAATTAAT
1902692 ATATTTTAATAAT-ATAAA
1 ATATTTT-ATAATAATAAA
1902710 AATAAAATTA
Statistics
Matches: 87, Mismatches: 9, Indels: 28
0.70 0.07 0.23
Matches are distributed among these distances:
18 7 0.08
19 8 0.09
20 2 0.02
21 1 0.01
22 11 0.13
23 16 0.18
24 23 0.26
25 1 0.01
26 7 0.08
27 11 0.13
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.47
Consensus pattern (23 bp):
ATATTTTATAATAATAAATTAAT
Found at i:1902682 original size:21 final size:21
Alignment explanation
Indices: 1902622--1902705 Score: 66
Period size: 21 Copynumber: 4.0 Consensus size: 21
1902612 TAATAAATTT
* *
1902622 ATAATTATATTTTAAACAATTAA
1 ATAA-TATATTTTTAATAA-TAA
1902645 ATTAATATA-TTTT-ATAATAA
1 A-TAATATATTTTTAATAATAA
* **
1902665 TTTTTATATTTTTAATAATGAA
1 ATAATATATTTTTAATAAT-AA
1902687 ATAATATA-TTTTAATAATA
1 ATAATATATTTTTAATAATA
1902706 TAAAAATAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
19 5 0.10
20 8 0.16
21 18 0.37
22 10 0.20
23 5 0.10
24 3 0.06
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (21 bp):
ATAATATATTTTTAATAATAA
Found at i:1902696 original size:41 final size:43
Alignment explanation
Indices: 1902626--1902705 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 43
1902616 AAATTTATAA
*
1902626 TTATATTTTAAACAATTAAATTAATATATTTT-ATAATAATTT
1 TTATATTTTAAACAATGAAATTAATATATTTTAATAATAATTT
* *
1902668 TTATATTTTTAATAATGAAA-TAATATATTTTAATAATA
1 TTATATTTTAAACAATGAAATTAATATATTTTAATAATA
1902706 TAAAAATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
41 11 0.32
42 23 0.68
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (43 bp):
TTATATTTTAAACAATGAAATTAATATATTTTAATAATAATTT
Found at i:1902713 original size:21 final size:22
Alignment explanation
Indices: 1902669--1902713 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1902659 TAATAATTTT
*
1902669 TATATTTTTAATAATGAAATAA
1 TATATTTTTAATAATGAAAAAA
1902691 TATA-TTTTAATAAT-ATAAAAA
1 TATATTTTTAATAATGA-AAAAA
1902712 TA
1 TA
1902714 AAATTATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 1 0.05
21 16 0.76
22 4 0.19
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
TATATTTTTAATAATGAAAAAA
Found at i:1904044 original size:17 final size:16
Alignment explanation
Indices: 1904022--1904067 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 16
1904012 TTCCTAATTT
1904022 TTCTTCTTTTTCTTCC
1 TTCTTCTTTTTCTTCC
1904038 ATTCTTCTTTTTCTTCC
1 -TTCTTCTTTTTCTTCC
1904055 TTCTAT-TTTTTCT
1 TTCT-TCTTTTTCT
1904068 CAAATTTTCG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 11 0.39
17 17 0.61
ACGTcount: A:0.04, C:0.26, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTTCTTTTTCTTCC
Found at i:1905148 original size:32 final size:32
Alignment explanation
Indices: 1905107--1905167 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
1905097 AACCTAAGAT
* *
1905107 AGTACCTTGGGGCTTTAGAGCATACCCAATGG
1 AGTACCTTGGGGCCTAAGAGCATACCCAATGG
*
1905139 AGTACCTTGGGGCCTAAGAGCCTACCCAA
1 AGTACCTTGGGGCCTAAGAGCATACCCAA
1905168 GGGTCATCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.21
Consensus pattern (32 bp):
AGTACCTTGGGGCCTAAGAGCATACCCAATGG
Found at i:1910441 original size:14 final size:14
Alignment explanation
Indices: 1910415--1910456 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
1910405 CAAACACTAA
1910415 AATAATATATTATT
1 AATAATATATTATT
*
1910429 AAGTAAT-TATTATG
1 AA-TAATATATTATT
1910443 AATAATATATTATT
1 AATAATATATTATT
1910457 CCAACACAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 4 0.17
14 16 0.67
15 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (14 bp):
AATAATATATTATT
Found at i:1911243 original size:16 final size:16
Alignment explanation
Indices: 1911224--1911256 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1911214 TGAACTGATA
1911224 TGATATTTACATGACT
1 TGATATTTACATGACT
*
1911240 TGATATTTACCTGACT
1 TGATATTTACATGACT
1911256 T
1 T
1911257 ATAGGTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.45
Consensus pattern (16 bp):
TGATATTTACATGACT
Found at i:1911309 original size:18 final size:18
Alignment explanation
Indices: 1911286--1911324 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1911276 ATTTTGATAT
*
1911286 TTTGATGAAGTCGTGTGA
1 TTTGATGAAATCGTGTGA
*
1911304 TTTGATGAAATTGTGTGA
1 TTTGATGAAATCGTGTGA
1911322 TTT
1 TTT
1911325 TGAATTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.23, C:0.03, G:0.28, T:0.46
Consensus pattern (18 bp):
TTTGATGAAATCGTGTGA
Found at i:1911988 original size:263 final size:264
Alignment explanation
Indices: 1911405--1912027 Score: 833
Period size: 264 Copynumber: 2.4 Consensus size: 264
1911395 TCCAATACTC
* * * * *
1911405 CATCAACTTAAACTCAGATAATATTTTTGGCGCAACCC-TTATTATTATTCAAAATATTAAGATT
1 CATCAGCTTAAACTCTGATAACATTTTAGGCGCAACCCATT-TTATTATTAAAAATATTAAGATT
* * * * * *
1911469 CCAGATTGCAACATACTTTCTTAGTGAAACATGACATTCTTGGGTGCAACCTATTTTATTAATAA
65 CCACATTGCAACATATTTTCTTAGTGAACCATAACATTCTTGGGCGCAACATATTTTATTAATAA
* * * * *
1911534 ACATACTAACATTACATATCACAATCTATTTCTTAGTGAACAATGACATTATTAGGTGCGACCGT
130 ACATACTAACATTACAGATCACAATCTATTTCTTAATGAACAATCACATTATTAGGCGCGAACGT
* *
1911599 ATTTATTATACATATTCATAACATTTTCGTCTTTTAACTTATTTTCTTATTGTGGGAAAATACAA
195 ATTTATTATACATATTCATAACATTTTCGTCTTTTAACTTATTTTCTTATCGTGAGAAAATACAA
1911664 GGCTT
260 GGCTT
* * * *
1911669 CATCGGCTTAAACTCTGATTACATTTTAGGCACAACCCATTTTATTATTTAAAATATTAAGATTC
1 CATCAGCTTAAACTCTGATAACATTTTAGGCGCAACCCATTTTATTATTAAAAATATTAAGATTC
* * *
1911734 CACATTGCAAAATGTTTTCTTAATGAACCATAACATTCTTGGGCGCAACATATTTTATTAATAAA
66 CACATTGCAACATATTTTCTTAGTGAACCATAACATTCTTGGGCGCAACATATTTTATTAATAAA
* * * ** *
1911799 CATATTAACATTATAGATCACAATCTATTTTTTAATGAACCGTCACATTATTTGGCGC-AAC-TA
131 CATACTAACATTACAGATCACAATCTATTTCTTAATGAACAATCACATTATTAGGCGCGAACGTA
* * *
1911862 CTTTCTTATATATATTCATAACATTTTCCGT-TTTTAACTTATTTTCTTATCGTGAGTAAATACA
196 -TTTATTATACATATTCATAACATTTT-CGTCTTTTAACTTATTTTCTTATCGTGAGAAAATACA
1911926 AGGC-T
259 AGGCTT
*
1911931 CAATCAGCTTAAACTCTGATAACGTTTTAGGCGCAACCCATTTTATTATTAAAAATATTAAGATT
1 C-ATCAGCTTAAACTCTGATAACATTTTAGGCGCAACCCATTTTATTATTAAAAATATTAAGATT
* * *
1911996 CCATATTACAACATCTTTTCTTAGTGAACCAT
65 CCACATTGCAACATATTTTCTTAGTGAACCAT
1912028 GACGTTATTG
Statistics
Matches: 312, Mismatches: 43, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
262 4 0.01
263 145 0.46
264 161 0.52
265 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.39
Consensus pattern (264 bp):
CATCAGCTTAAACTCTGATAACATTTTAGGCGCAACCCATTTTATTATTAAAAATATTAAGATTC
CACATTGCAACATATTTTCTTAGTGAACCATAACATTCTTGGGCGCAACATATTTTATTAATAAA
CATACTAACATTACAGATCACAATCTATTTCTTAATGAACAATCACATTATTAGGCGCGAACGTA
TTTATTATACATATTCATAACATTTTCGTCTTTTAACTTATTTTCTTATCGTGAGAAAATACAAG
GCTT
Found at i:1913113 original size:29 final size:29
Alignment explanation
Indices: 1913080--1913157 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
1913070 AAAACTTTTG
* *
1913080 TTAATTCGGTTCGATTAATAATTTTTAAA
1 TTAATTTGGTTCGATTAATAATTTTCAAA
*
1913109 TTAATTTGGTTCGGTTAATAATTTTCAAA
1 TTAATTTGGTTCGATTAATAATTTTCAAA
* *
1913138 TAAATTTTGGTTTGATTAAT
1 TTAA-TTTGGTTCGATTAAT
1913158 CAAATTGAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 29 0.69
30 13 0.31
ACGTcount: A:0.32, C:0.05, G:0.13, T:0.50
Consensus pattern (29 bp):
TTAATTTGGTTCGATTAATAATTTTCAAA
Found at i:1913404 original size:29 final size:29
Alignment explanation
Indices: 1913360--1913429 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
1913350 AAAAAATCGG
*
1913360 TTAATTTGATTAGGTTAATAATTTTCAAA
1 TTAATTTGGTTAGGTTAATAATTTTCAAA
*
1913389 TTAATTTGGTTTGGTTAATAATTTTCAAA
1 TTAATTTGGTTAGGTTAATAATTTTCAAA
*
1913418 TAAATTTTGGTT
1 TTAA-TTTGGTT
1913430 CGATTAACCG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
29 30 0.81
30 7 0.19
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.51
Consensus pattern (29 bp):
TTAATTTGGTTAGGTTAATAATTTTCAAA
Found at i:1913418 original size:133 final size:137
Alignment explanation
Indices: 1913079--1913582 Score: 497
Period size: 144 Copynumber: 3.6 Consensus size: 137
1913069 AAAAACTTTT
* * * * *
1913079 GTTAATTCGGTTCGATTAATAATTTTTAAATTAATTTGGTTCGGTTAATAATTTTCAAATAAATT
1 GTTAATTCGATTAGGTTAATAATTTTCAAATTAATTCGGTTCGGTTAATAATTTTCAAATAAATT
* * * *** * * *
1913144 TTGGTTTGATTAATCAAATTGAATTAACCAAATTTTTTCTTCGATTAATTCGATTAATAATTTT-
66 TTGGTTCGATTAACCGAACCAAATTAACCAAA---ATT-TT-G--TCATTCGGTTAATAATTTTC
1913208 ---AAAAAAA-TCG
124 AAAAAAAAAATTCG
* * *
1913218 G-TAATTCGGTTCGGTTAATAATTTTCAAATTAATTCGGTTCAGTTAATAATTTCAATAATTTTC
1 GTTAATTCGATTAGGTTAATAATTTTCAAATTAATTCGGTTC-G-------GTT-AATAATTTTC
1913282 AAATAAATTTTGGTTCGATTAACCGAACCAAATTAACCAAAATTTTG-C-TTCGGTTAATAATTT
57 AAATAAATTTTGGTTCGATTAACCGAACCAAATTAACCAAAATTTTGTCATTCGGTTAATAATTT
1913345 T-AAAAAAAAAA-TCG
122 TCAAAAAAAAAATTCG
* * *
1913359 GTTAATTTGATTAGGTTAATAATTTTCAAATTAATTTGGTTTGGTTAATAATTTTCAAATAAATT
1 GTTAATTCGATTAGGTTAATAATTTTCAAATTAATTCGGTTCGGTTAATAATTTTCAAATAAATT
* *
1913424 TTGGTTCGATTAACCGAACCGAATTAACCAAATTTTTGCTTCAATTAATTCGGTTAATAATTTTC
66 TTGGTTCGATTAACCGAACCAAATTAACCAAAATTTTG--TC-----ATTCGGTTAATAATTTTC
1913489 AAAAAAAAAATTCG
124 AAAAAAAAAATTCG
* * * *
1913503 GTTAATTCGGTTCGGTTAATAATTTTTAAATTAATTCGGTTCGGTTAATAATTTCCAAATAAATT
1 GTTAATTCGATTAGGTTAATAATTTTCAAATTAATTCGGTTCGGTTAATAATTTTCAAATAAATT
1913568 TTGGTTCGATTAACC
66 TTGGTTCGATTAACC
1913583 AAACTGAATT
Statistics
Matches: 313, Mismatches: 28, Indels: 43
0.82 0.07 0.11
Matches are distributed among these distances:
133 55 0.18
134 2 0.01
136 1 0.00
138 52 0.17
139 2 0.01
141 12 0.04
142 52 0.17
143 12 0.04
144 78 0.25
146 2 0.01
147 45 0.14
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (137 bp):
GTTAATTCGATTAGGTTAATAATTTTCAAATTAATTCGGTTCGGTTAATAATTTTCAAATAAATT
TTGGTTCGATTAACCGAACCAAATTAACCAAAATTTTGTCATTCGGTTAATAATTTTCAAAAAAA
AAATTCG
Found at i:1913562 original size:29 final size:29
Alignment explanation
Indices: 1913504--1913567 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
1913494 AAAAATTCGG
**
1913504 TTAATTCGGTTCGGTTAATAATTTTTAAA
1 TTAATTCGGTTCGGTTAATAATTTCCAAA
1913533 TTAATTCGGTTCGGTTAATAATTTCCAAA
1 TTAATTCGGTTCGGTTAATAATTTCCAAA
*
1913562 TAAATT
1 TTAATT
1913568 TTGGTTCGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.45
Consensus pattern (29 bp):
TTAATTCGGTTCGGTTAATAATTTCCAAA
Found at i:1921222 original size:16 final size:16
Alignment explanation
Indices: 1921201--1921231 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1921191 GATGAGTAAG
*
1921201 TACCGATACTATCAAC
1 TACCGATACCATCAAC
1921217 TACCGATACCATCAA
1 TACCGATACCATCAA
1921232 GTTGTAGTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.32, G:0.06, T:0.23
Consensus pattern (16 bp):
TACCGATACCATCAAC
Found at i:1921727 original size:2 final size:2
Alignment explanation
Indices: 1921720--1921752 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1921710 TACTTGTAGA
1921720 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1921753 GTGCGATATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1922181 original size:21 final size:21
Alignment explanation
Indices: 1922157--1922216 Score: 75
Period size: 23 Copynumber: 2.8 Consensus size: 21
1922147 TCTTTGGAAT
*
1922157 ATATATGTGGTCCTTAAGGAG
1 ATATATGTGGTCCTTAAGGAC
**
1922178 ATATCTATGTGGTCCTTCGGGAC
1 ATA--TATGTGGTCCTTAAGGAC
1922201 ATATATGTGGTCCTTA
1 ATATATGTGGTCCTTA
1922217 GAGACATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 15 0.45
23 18 0.55
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.37
Consensus pattern (21 bp):
ATATATGTGGTCCTTAAGGAC
Found at i:1922186 original size:23 final size:22
Alignment explanation
Indices: 1922155--1922216 Score: 81
Period size: 21 Copynumber: 2.8 Consensus size: 22
1922145 GTTCTTTGGA
1922155 ATATATATGTGGTCCTTAAGGAG
1 ATATATATGTGGTCCTTAAGG-G
* *
1922178 ATATCTATGTGGTCCTT-CGGG
1 ATATATATGTGGTCCTTAAGGG
*
1922199 ACATATATGTGGTCCTTA
1 ATATATATGTGGTCCTTA
1922217 GAGACATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 16 0.47
22 2 0.06
23 16 0.47
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (22 bp):
ATATATATGTGGTCCTTAAGGG
Found at i:1922222 original size:21 final size:21
Alignment explanation
Indices: 1922157--1922223 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
1922147 TCTTTGGAAT
*
1922157 ATATATGTGGTCCTTAAGGAGAT
1 ATATATGTGGTCCTT-A-GAGAC
* * *
1922180 ATCTATGTGGTCCTTCGGGAC
1 ATATATGTGGTCCTTAGAGAC
1922201 ATATATGTGGTCCTTAGAGAC
1 ATATATGTGGTCCTTAGAGAC
1922222 AT
1 AT
1922224 TTTATATGGC
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
21 23 0.62
23 14 0.38
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.34
Consensus pattern (21 bp):
ATATATGTGGTCCTTAGAGAC
Done.