Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold432
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: 1706767
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.28
Warning! 187295 characters in sequence are not A, C, G, or T
File 7 of 8
Found at i:1082714 original size:13 final size:13
Alignment explanation
Indices: 1082667--1082696 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1082657 GTAAACCCAG
1082667 AATGTATCAATAC
1 AATGTATCAATAC
*
1082680 AATGTATCGATAC
1 AATGTATCAATAC
1082693 AATG
1 AATG
1082697 AACAATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (13 bp):
AATGTATCAATAC
Found at i:1082722 original size:24 final size:20
Alignment explanation
Indices: 1082576--1082714 Score: 92
Period size: 20 Copynumber: 6.8 Consensus size: 20
1082566 ATGTATCGAT
*
1082576 ACAATGTACCGATACAATGA
1 ACAATGTATCGATACAATGA
*
1082596 GCAATGTATCGATACAATGA
1 ACAATGTATCGATACAATGA
* * *
1082616 GCCATGTATCAATACAATGCA
1 ACAATGTATCGATACAATG-A
*
1082637 A-AATGTATCGATACATCTGGGTAA
1 ACAATGTATCGATACA-AT--G--A
* *
1082661 ACCCA-GAAT-G-TATCAAT--
1 A-CAATGTATCGATA-CAATGA
1082678 ACAATGTATCGATACAATGA
1 ACAATGTATCGATACAATGA
1082698 ACAATGTATCGATACAA
1 ACAATGTATCGATACAA
1082715 ATTGTGAAAA
Statistics
Matches: 92, Mismatches: 14, Indels: 26
0.70 0.11 0.20
Matches are distributed among these distances:
16 2 0.02
17 4 0.04
18 5 0.05
19 2 0.02
20 64 0.70
21 2 0.02
23 4 0.04
24 5 0.05
25 3 0.03
26 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (20 bp):
ACAATGTATCGATACAATGA
Found at i:1085609 original size:13 final size:13
Alignment explanation
Indices: 1085591--1085651 Score: 53
Period size: 13 Copynumber: 5.2 Consensus size: 13
1085581 ATACAAAGAT
1085591 CAATGTATCGATA
1 CAATGTATCGATA
1085604 CAATGTATCGAT-
1 CAATGTATCGATA
*
1085616 --A--TATTGA-A
1 CAATGTATCGATA
*
1085624 TAATGTATCGATA
1 CAATGTATCGATA
*
1085637 TAATGTATCGATA
1 CAATGTATCGATA
1085650 CA
1 CA
1085652 TTGAATAATG
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
8 5 0.13
10 2 0.05
12 5 0.13
13 27 0.69
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.34
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1085615 original size:33 final size:33
Alignment explanation
Indices: 1085573--1085671 Score: 146
Period size: 33 Copynumber: 3.0 Consensus size: 33
1085563 AAATTCCTAG
**
1085573 ATGTATCGATACAAAG-ATCAATGTATCGATACA
1 ATGTATCGATACATTGAAT-AATGTATCGATACA
* *
1085606 ATGTATCGATATATTGAATAATGTATCGATATA
1 ATGTATCGATACATTGAATAATGTATCGATACA
1085639 ATGTATCGATACATTGAATAATGTATCGATACA
1 ATGTATCGATACATTGAATAATGTATCGATACA
1085672 TTTCCTTGGC
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
33 57 0.97
34 2 0.03
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.33
Consensus pattern (33 bp):
ATGTATCGATACATTGAATAATGTATCGATACA
Found at i:1085670 original size:20 final size:20
Alignment explanation
Indices: 1085605--1085673 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
1085595 GTATCGATAC
*
1085605 AATGTATCGATATATTGAAT
1 AATGTATCGATACATTGAAT
1085625 AATGTATCG----A-T--AT
1 AATGTATCGATACATTGAAT
1085638 AATGTATCGATACATTGAAT
1 AATGTATCGATACATTGAAT
1085658 AATGTATCGATACATT
1 AATGTATCGATACATT
1085674 TCCTTGGCAG
Statistics
Matches: 42, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
13 11 0.26
15 1 0.02
16 1 0.02
17 1 0.02
18 1 0.02
20 27 0.64
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (20 bp):
AATGTATCGATACATTGAAT
Found at i:1086787 original size:28 final size:27
Alignment explanation
Indices: 1086753--1086834 Score: 85
Period size: 28 Copynumber: 3.0 Consensus size: 27
1086743 TTTGTCTTCA
*
1086753 TTGATTTCTTTTCCTTTGATATTTCTTG
1 TTGATTTCATTTCC-TTGATATTTCTTG
* *
1086781 CTT-ATTTCGTTTCCCTTAATATTTCTTG
1 -TTGATTTCATTT-CCTTGATATTTCTTG
* *
1086809 TTGATTTCACTTCCTTGATCTTTCTT
1 TTGATTTCATTTCCTTGATATTTCTT
1086835 ATCAAAGTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
27 14 0.31
28 27 0.60
29 4 0.09
ACGTcount: A:0.12, C:0.20, G:0.09, T:0.60
Consensus pattern (27 bp):
TTGATTTCATTTCCTTGATATTTCTTG
Found at i:1103352 original size:18 final size:18
Alignment explanation
Indices: 1103311--1103393 Score: 77
Period size: 16 Copynumber: 4.8 Consensus size: 18
1103301 CATTGGGGTT
*
1103311 GAAAATCTATGATT-ATA
1 GAAAATCTATGATTCTTA
1103328 G-AAATCTATGATTCTTA
1 GAAAATCTATGATTCTTA
*
1103345 GAAAATCTAAGATTCTTA
1 GAAAATCTATGATTCTTA
* *
1103363 -AAATATTCTGTGATTCCT-
1 GAAA-A-TCTATGATTCTTA
1103381 -AAAATCTATGATT
1 GAAAATCTATGATT
1103394 GATGTTGATC
Statistics
Matches: 56, Mismatches: 6, Indels: 9
0.79 0.08 0.13
Matches are distributed among these distances:
16 20 0.36
17 8 0.14
18 19 0.34
19 9 0.16
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.39
Consensus pattern (18 bp):
GAAAATCTATGATTCTTA
Found at i:1106131 original size:18 final size:18
Alignment explanation
Indices: 1106108--1106190 Score: 89
Period size: 18 Copynumber: 4.7 Consensus size: 18
1106098 ATGATTACAG
1106108 AAATCTATGATTCTTAGA
1 AAATCTATGATTCTTAGA
** *
1106126 AAATCTGCGATTCTTAAA
1 AAATCTATGATTCTTAGA
**
1106144 AAATCTGCGATTCTTAGA
1 AAATCTATGATTCTTAGA
*
1106162 AAATTCTATGATTCCT--A
1 AAA-TCTATGATTCTTAGA
1106179 AAATCTATGATT
1 AAATCTATGATT
1106191 GATGCTGATC
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
16 9 0.16
17 4 0.07
18 35 0.61
19 9 0.16
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.37
Consensus pattern (18 bp):
AAATCTATGATTCTTAGA
Found at i:1112557 original size:26 final size:29
Alignment explanation
Indices: 1112527--1112589 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
1112517 TTGGAAATAT
*
1112527 ATAATTAGA-CTCC-AA-TAATTAATCAC
1 ATAATTAGACCACCGAATTAATTAATCAC
*
1112553 ATAATTCATACCACCGAATTAATTAATCAC
1 ATAATT-AGACCACCGAATTAATTAATCAC
1112583 ATAATTA
1 ATAATTA
1112590 TTAATCTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 6 0.19
27 2 0.06
28 3 0.10
29 3 0.10
30 17 0.55
ACGTcount: A:0.46, C:0.19, G:0.03, T:0.32
Consensus pattern (29 bp):
ATAATTAGACCACCGAATTAATTAATCAC
Found at i:1113675 original size:15 final size:17
Alignment explanation
Indices: 1113646--1113678 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
1113636 TACTCTTATA
1113646 TGTAATATAATTAAATT
1 TGTAATATAATTAAATT
1113663 TGTAATA-AA-TAAATT
1 TGTAATATAATTAAATT
1113678 T
1 T
1113679 TGAGTTACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 2 0.12
17 7 0.44
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (17 bp):
TGTAATATAATTAAATT
Found at i:1119196 original size:9 final size:9
Alignment explanation
Indices: 1119179--1119237 Score: 52
Period size: 9 Copynumber: 6.9 Consensus size: 9
1119169 ATGATTGAAA
*
1119179 GAGAAATAG
1 GAGAGATAG
1119188 GAGAGATAG
1 GAGAGATAG
*
1119197 TAGAGATAG
1 GAGAGATAG
*
1119206 GAGGGAT--
1 GAGAGATAG
* *
1119213 GATAG-GAG
1 GAGAGATAG
1119221 GAGAGATAG
1 GAGAGATAG
1119230 GAGAGATA
1 GAGAGATA
1119238 ATAGAGAGAG
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
7 3 0.08
8 4 0.11
9 31 0.82
ACGTcount: A:0.44, C:0.00, G:0.42, T:0.14
Consensus pattern (9 bp):
GAGAGATAG
Found at i:1119218 original size:12 final size:12
Alignment explanation
Indices: 1119198--1119232 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
1119188 GAGAGATAGT
1119198 AGAGATAGGAGG
1 AGAGATAGGAGG
1119210 -GATGATAGGAGG
1 AGA-GATAGGAGG
1119222 AGAGATAGGAG
1 AGAGATAGGAG
1119233 AGATAATAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.10
12 17 0.81
13 2 0.10
ACGTcount: A:0.40, C:0.00, G:0.49, T:0.11
Consensus pattern (12 bp):
AGAGATAGGAGG
Found at i:1119241 original size:12 final size:12
Alignment explanation
Indices: 1119201--1119246 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
1119191 AGATAGTAGA
*
1119201 GATAGGAGGGAT
1 GATAGGAGAGAT
1119213 GATAGGAGGAGA-
1 GATAGGA-GAGAT
1119225 GATAGGAGAGAT
1 GATAGGAGAGAT
*
1119237 AATA-GAGAGA
1 GATAGGAGAGA
1119247 GGAGGGATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
11 10 0.33
12 17 0.57
13 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.43, T:0.13
Consensus pattern (12 bp):
GATAGGAGAGAT
Found at i:1119262 original size:42 final size:42
Alignment explanation
Indices: 1119156--1119265 Score: 157
Period size: 42 Copynumber: 2.6 Consensus size: 42
1119146 AAGAGAAAGA
* * * *
1119156 AGAGATAGGAGGGATGATTGAAAGAGAAATAGGAGAGATAGT
1 AGAGATAGGAGGGATGATAGGAGGAGAAATAGGAGAGATAAT
*
1119198 AGAGATAGGAGGGATGATAGGAGGAGAGATAGGAGAGATAAT
1 AGAGATAGGAGGGATGATAGGAGGAGAAATAGGAGAGATAAT
* *
1119240 AGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGGAGGGATGATAGGAGGAG
1119266 GAGAGAAGAA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 61 1.00
ACGTcount: A:0.43, C:0.01, G:0.44, T:0.13
Consensus pattern (42 bp):
AGAGATAGGAGGGATGATAGGAGGAGAAATAGGAGAGATAAT
Found at i:1119981 original size:13 final size:13
Alignment explanation
Indices: 1119963--1119989 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1119953 CACTAATCCT
1119963 TTACTTCTAGGCA
1 TTACTTCTAGGCA
1119976 TTACTTCTAGGCA
1 TTACTTCTAGGCA
1119989 T
1 T
1119990 AGGGAAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (13 bp):
TTACTTCTAGGCA
Found at i:1128136 original size:18 final size:18
Alignment explanation
Indices: 1128094--1128137 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1128084 TCCATCTTCT
1128094 TCTCTCCTCCTCCTATCA
1 TCTCTCCTCCTCCTATCA
* *
1128112 TCCCTCCT-CTCTCTATTA
1 TCTCTCCTCCTC-CTATCA
1128130 TCTCTCCT
1 TCTCTCCT
1128138 ATCCCTCCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.09, C:0.48, G:0.00, T:0.43
Consensus pattern (18 bp):
TCTCTCCTCCTCCTATCA
Found at i:1128140 original size:9 final size:9
Alignment explanation
Indices: 1128128--1128188 Score: 56
Period size: 9 Copynumber: 7.1 Consensus size: 9
1128118 CTCTCTCTAT
1128128 TATCTCTCC
1 TATCTCTCC
*
1128137 TATCCCTCC
1 TATCTCTCC
*
1128146 T-TCTAT-C
1 TATCTCTCC
* *
1128153 -ATCCCTTC
1 TATCTCTCC
*
1128161 TATCTCTAC
1 TATCTCTCC
1128170 TATCTCTCC
1 TATCTCTCC
1128179 TATCTCTCC
1 TATCTCTCC
1128188 T
1 T
1128189 CATATCATCC
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
7 4 0.10
8 4 0.10
9 33 0.80
ACGTcount: A:0.13, C:0.43, G:0.00, T:0.44
Consensus pattern (9 bp):
TATCTCTCC
Found at i:1128146 original size:42 final size:42
Alignment explanation
Indices: 1128099--1128218 Score: 159
Period size: 42 Copynumber: 2.9 Consensus size: 42
1128089 CTTCTTCTCT
* *
1128099 CCTCCTCCTATCATCCCTCCTCTCTCTATTATCTCTCCTATC
1 CCTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATC
* *
1128141 CCTCCTTCTATCATCCCTTCTATCTCTACTATCTCTCCTATC
1 CCTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATC
* * * * *
1128183 TCTCCTCATATCATCCCTCTTATCTCTTCTTTCTCT
1 CCTCCTCCTATCATCCCTCCTATCTCTACTATCTCT
1128219 TTGAGGGCTA
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 67 1.00
ACGTcount: A:0.12, C:0.43, G:0.00, T:0.44
Consensus pattern (42 bp):
CCTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATC
Found at i:1136185 original size:42 final size:42
Alignment explanation
Indices: 1136129--1136247 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
1136119 TTCTTCTCTC
* * *
1136129 CTCCTCCTGTCATCCCTCCTTTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1136171 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
* * *
1136213 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCT
1136248 TTGAGGGCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.08, C:0.45, G:0.03, T:0.44
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
Found at i:1136188 original size:12 final size:11
Alignment explanation
Indices: 1136162--1136237 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
1136152 TCTATTATCT
*
1136162 CTCCTGTCTCTC
1 CTCCTATCTC-C
1136174 CTCCTATCATCC
1 CTCCTATC-TCC
1136186 CTCCTATCT--
1 CTCCTATCTCC
*
1136195 CTACTATCT--
1 CTCCTATCTCC
*
1136204 CTCCTGTCTCTC
1 CTCCTATCTC-C
1136216 CTCCTATCATCC
1 CTCCTATC-TCC
*
1136228 CTCCTCTCTC
1 CTCCTATCTC
1136238 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:1136189 original size:24 final size:24
Alignment explanation
Indices: 1136153--1136238 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
1136143 CCTCCTTTCT
* *
1136153 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
1136177 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
1136198 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
1136219 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
1136239 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 5 0.10
24 21 0.43
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:1136213 original size:18 final size:18
Alignment explanation
Indices: 1136144--1136214 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
1136134 CCTGTCATCC
* *
1136144 CTCCTTTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
1136162 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
1136184 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
1136204 CTCCTGTCTCT
1 CTCCTGTCTCT
1136215 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.42, G:0.03, T:0.45
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:1139102 original size:17 final size:17
Alignment explanation
Indices: 1139080--1139112 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1139070 ATTTTTTTTC
1139080 AAGAATACAAAAAAAAA
1 AAGAATACAAAAAAAAA
1139097 AAGAATACAAAAAAAA
1 AAGAATACAAAAAAAA
1139113 GGAAAAACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.82, C:0.06, G:0.06, T:0.06
Consensus pattern (17 bp):
AAGAATACAAAAAAAAA
Found at i:1142274 original size:12 final size:11
Alignment explanation
Indices: 1142252--1142327 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
1142242 AGAGAAAGAA
*
1142252 GAGAGAGGAGG
1 GAGATAGGAGG
1142263 GATGATAGGAGG
1 GA-GATAGGAGG
*
1142275 AGAGACAGGA--
1 -GAGATAGGAGG
*
1142285 GAGATAGTA--
1 GAGATAGGAGG
1142294 GAGATAGGAGG
1 GAGATAGGAGG
1142305 GATGATAGGAGG
1 GA-GATAGGAGG
*
1142317 AGAGACAGGAG
1 -GAGATAGGAG
1142328 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:1142284 original size:24 final size:24
Alignment explanation
Indices: 1142251--1142336 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
1142241 AAGAGAAAGA
*
1142251 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
1142275 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
1142293 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
1142317 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
1142337 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:1142303 original size:42 final size:42
Alignment explanation
Indices: 1142242--1142360 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
1142232 TAGCCCTCAA
* *
1142242 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
1142284 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
1142326 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
1142361 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:1147363 original size:20 final size:20
Alignment explanation
Indices: 1147338--1147375 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1147328 GTTGTCATCA
1147338 AAAGGACACGGCTATCCACC
1 AAAGGACACGGCTATCCACC
*
1147358 AAAGGACACGGCTGTCCA
1 AAAGGACACGGCTATCCA
1147376 AAGTAGTAAA
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:0.34, C:0.32, G:0.24, T:0.11
Consensus pattern (20 bp):
AAAGGACACGGCTATCCACC
Found at i:1155991 original size:12 final size:11
Alignment explanation
Indices: 1155969--1156044 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
1155959 AGAGAAAGAA
*
1155969 GAGAGAGGAGG
1 GAGATAGGAGG
1155980 GATGATAGGAGG
1 GA-GATAGGAGG
*
1155992 AGAGACAGGA--
1 -GAGATAGGAGG
*
1156002 GAGATAGTA--
1 GAGATAGGAGG
1156011 GAGATAGGAGG
1 GAGATAGGAGG
1156022 GATGATAGGAGG
1 GA-GATAGGAGG
*
1156034 AGAGACAGGAG
1 -GAGATAGGAG
1156045 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:1156001 original size:24 final size:24
Alignment explanation
Indices: 1155968--1156053 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
1155958 AAGAGAAAGA
*
1155968 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
1155992 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
1156010 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
1156034 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
1156054 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:1156020 original size:42 final size:42
Alignment explanation
Indices: 1155959--1156077 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
1155949 TAGCCCTCAA
* *
1155959 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
1156001 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
1156043 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
1156078 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:1165445 original size:42 final size:42
Alignment explanation
Indices: 1165398--1165478 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 42
1165388 CTTCTTCTCT
* *
1165398 CCTCCTCCTATCAT-CCTTCCTCTCTCTATTATCTCTCCTATC
1 CCTCCTCCTATCATCCCTT-CTATCTCTACTATCTCTCCTATC
*
1165440 CCTCCTTCTATCATCCCTTCTATCTCTACTATCTCTCCT
1 CCTCCTCCTATCATCCCTTCTATCTCTACTATCTCTCCT
1165479 CCTATCATCC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
42 31 0.89
43 4 0.11
ACGTcount: A:0.12, C:0.44, G:0.00, T:0.43
Consensus pattern (42 bp):
CCTCCTCCTATCATCCCTTCTATCTCTACTATCTCTCCTATC
Found at i:1165457 original size:15 final size:15
Alignment explanation
Indices: 1165437--1165493 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
1165427 TATCTCTCCT
1165437 ATCCCTCCTTCTATC
1 ATCCCTCCTTCTATC
* *
1165452 ATCCCTTCTATCTCTAC
1 ATCCCTCCT-TCTAT-C
* *
1165469 TATCTCTCCTCCTATC
1 -ATCCCTCCTTCTATC
1165485 ATCCCTCCT
1 ATCCCTCCT
1165494 ATCTCTTCTT
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
15 16 0.50
16 5 0.16
17 4 0.12
18 7 0.22
ACGTcount: A:0.14, C:0.46, G:0.00, T:0.40
Consensus pattern (15 bp):
ATCCCTCCTTCTATC
Found at i:1165508 original size:33 final size:33
Alignment explanation
Indices: 1165427--1165508 Score: 110
Period size: 33 Copynumber: 2.5 Consensus size: 33
1165417 CTCTCTCTAT
* * * *
1165427 TATCTCTCCTATCCCTCCTTCTATCATCCCTTC
1 TATCTCTACTATCTCTCCTCCTATCATCCCTCC
1165460 TATCTCTACTATCTCTCCTCCTATCATCCCTCC
1 TATCTCTACTATCTCTCCTCCTATCATCCCTCC
* *
1165493 TATCTCTTCTTTCTCT
1 TATCTCTACTATCTCT
1165509 TTGAGGGCTA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.12, C:0.43, G:0.00, T:0.45
Consensus pattern (33 bp):
TATCTCTACTATCTCTCCTCCTATCATCCCTCC
Found at i:1176600 original size:42 final size:42
Alignment explanation
Indices: 1176545--1176663 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
1176535 TTCTTCTCTC
* *
1176545 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCCGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCCGTCT
* *
1176587 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCCGTCT
* *
1176629 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
1176664 TTGAGGGCTA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.08, C:0.47, G:0.03, T:0.42
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCCGTCT
Found at i:1176605 original size:24 final size:24
Alignment explanation
Indices: 1176569--1176647 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 24
1176559 CCTCCTCTCT
* *
1176569 CTATTATCTCTCCCGTCTCTCCTC
1 CTATCATCCCTCCCGTCTCTCCTC
* *
1176593 CTATCATCCCT-CC-TATCT-CTA
1 CTATCATCCCTCCCGTCTCTCCTC
*
1176614 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCCGTCTCTCCTC
1176635 CTATCATCCCTCC
1 CTATCATCCCTCC
1176648 TCTCTCTTCT
Statistics
Matches: 42, Mismatches: 7, Indels: 12
0.69 0.11 0.20
Matches are distributed among these distances:
18 2 0.05
19 1 0.02
20 5 0.12
21 14 0.33
22 5 0.12
23 2 0.05
24 13 0.31
ACGTcount: A:0.11, C:0.47, G:0.03, T:0.39
Consensus pattern (24 bp):
CTATCATCCCTCCCGTCTCTCCTC
Found at i:1176648 original size:24 final size:24
Alignment explanation
Indices: 1176569--1176654 Score: 76
Period size: 24 Copynumber: 3.8 Consensus size: 24
1176559 CCTCCTCTCT
* * *
1176569 CTATTATCTCTCCCGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
1176593 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
1176614 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
1176635 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
1176655 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 5 0.10
24 21 0.43
ACGTcount: A:0.10, C:0.47, G:0.02, T:0.41
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:1182104 original size:28 final size:28
Alignment explanation
Indices: 1182046--1182112 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
1182036 TTATTCTTCT
* *
1182046 TTGTTGATTTCTTTTCCTTTGAAATTCC
1 TTGTTGATTTCGTTTCCTTTCAAATTCC
* *
1182074 TTGCTT-ATTTCGTTTCCTTTCATATTTC
1 TTG-TTGATTTCGTTTCCTTTCAAATTCC
1182102 TTGTTGATTTC
1 TTGTTGATTTC
1182113 ACTACCTTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 2 0.06
28 29 0.88
29 2 0.06
ACGTcount: A:0.12, C:0.18, G:0.10, T:0.60
Consensus pattern (28 bp):
TTGTTGATTTCGTTTCCTTTCAAATTCC
Found at i:1196146 original size:20 final size:21
Alignment explanation
Indices: 1196104--1196154 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
1196094 TTCTACAATT
*
1196104 TGTATCGATACAACAAGTTAA
1 TGTATCGATACAACAAGTGAA
* *
1196125 TGTATCGAT-CCATAAGTGAA
1 TGTATCGATACAACAAGTGAA
*
1196145 TGTATTGATA
1 TGTATCGATA
1196155 TATGCTTGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (21 bp):
TGTATCGATACAACAAGTGAA
Found at i:1197728 original size:15 final size:15
Alignment explanation
Indices: 1197690--1197728 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1197680 AGAATACAAA
1197690 AAAAAAAAAAGAAAG
1 AAAAAAAAAAGAAAG
* * *
1197705 AATACAAAAAGAGAG
1 AAAAAAAAAAGAAAG
1197720 AAAAAAAAA
1 AAAAAAAAA
1197729 GCCAGCATTT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.82, C:0.03, G:0.13, T:0.03
Consensus pattern (15 bp):
AAAAAAAAAAGAAAG
Found at i:1198498 original size:12 final size:11
Alignment explanation
Indices: 1198476--1198551 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
1198466 AGAGAAAGAA
*
1198476 GAGAGAGGAGG
1 GAGATAGGAGG
1198487 GATGATAGGAGG
1 GA-GATAGGAGG
*
1198499 AGAGACAGGA--
1 -GAGATAGGAGG
*
1198509 GAGATAGTA--
1 GAGATAGGAGG
1198518 GAGATAGGAGG
1 GAGATAGGAGG
1198529 GATGATAGGAGG
1 GA-GATAGGAGG
*
1198541 AGAGACAGGAG
1 -GAGATAGGAG
1198552 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:1198508 original size:24 final size:24
Alignment explanation
Indices: 1198475--1198560 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
1198465 AAGAGAAAGA
*
1198475 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
1198499 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
1198517 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
1198541 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
1198561 AGAAAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:1198527 original size:42 final size:42
Alignment explanation
Indices: 1198466--1198584 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
1198456 TAGCCCTCAA
* * *
1198466 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAAAGGAGGGATGATAGGAGGAGAGACAGG
*
1198508 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAAAGGAGGGATGATAGGAGGAGAGACAGG
* *
1198550 AGAGATAATAGAGAAAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAAAGGAGGGATGATAGGAGGAG
1198585 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.44, C:0.03, G:0.45, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAAAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:1392533 original size:13 final size:13
Alignment explanation
Indices: 1392515--1392552 Score: 69
Period size: 12 Copynumber: 3.0 Consensus size: 13
1392505 ATAATCACCC
1392515 TGTATCGATACAA
1 TGTATCGATACAA
1392528 TGTATCGATAC-A
1 TGTATCGATACAA
1392540 TGTATCGATACAA
1 TGTATCGATACAA
1392553 AGAAAAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 12 0.50
13 12 0.50
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1394651 original size:15 final size:15
Alignment explanation
Indices: 1394631--1394661 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1394621 ATTTCGTTTG
*
1394631 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1394646 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1394661 G
1 G
1394662 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1396493 original size:21 final size:21
Alignment explanation
Indices: 1396464--1396508 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1396454 AAGTTTTCAT
*
1396464 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1396484 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1396506 TTT
1 TTT
1396509 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1398741 original size:13 final size:13
Alignment explanation
Indices: 1398723--1398748 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1398713 CAATTTTTTG
1398723 TGTATCGATACAT
1 TGTATCGATACAT
1398736 TGTATCGATACAT
1 TGTATCGATACAT
1398749 ACTTGCTATA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1404284 original size:51 final size:51
Alignment explanation
Indices: 1404228--1404344 Score: 180
Period size: 51 Copynumber: 2.3 Consensus size: 51
1404218 CACATGTATG
* * *
1404228 AATGTATTGATACATTCTATCTTTTTACCCAGACGTATCGATACATTTTTC
1 AATGTATCGATACATTCTATCTTTTTACCCAAACGTATCGATACATTTTGC
*
1404279 AATGTATCGATACATTCTATCTTTTTACCCAAATGTATCGATACATTTTGC
1 AATGTATCGATACATTCTATCTTTTTACCCAAACGTATCGATACATTTTGC
* *
1404330 AATGCATCAATACAT
1 AATGTATCGATACAT
1404345 GTATGAATGC
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (51 bp):
AATGTATCGATACATTCTATCTTTTTACCCAAACGTATCGATACATTTTGC
Found at i:1404287 original size:20 final size:20
Alignment explanation
Indices: 1404262--1404385 Score: 77
Period size: 20 Copynumber: 5.7 Consensus size: 20
1404252 TTACCCAGAC
1404262 GTATCGATACATTTTTCAAT
1 GTATCGATACATTTTTCAAT
1404282 GTATCGATACATTCTATCTTTTTACCCAAAT
1 GTATCGAT--A--C-A--TTTTT---CAA-T
*
1404313 GTATCGATACATTTTGCAAT
1 GTATCGATACATTTTTCAAT
* * * * *
1404333 GCATCAATACATGTATGAAT
1 GTATCGATACATTTTTCAAT
*
1404353 GCATCGATACATTTTTCAAT
1 GTATCGATACATTTTTCAAT
*
1404373 GTATCAATACATT
1 GTATCGATACATT
1404386 GTGTCTTTTT
Statistics
Matches: 80, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
20 50 0.62
21 3 0.04
22 1 0.01
24 5 0.06
25 1 0.01
26 1 0.01
27 6 0.08
29 1 0.01
30 3 0.04
31 9 0.11
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.40
Consensus pattern (20 bp):
GTATCGATACATTTTTCAAT
Found at i:1418306 original size:18 final size:17
Alignment explanation
Indices: 1418283--1418358 Score: 80
Period size: 18 Copynumber: 4.2 Consensus size: 17
1418273 CAAGTTAACA
1418283 AAAAAAAACCAAGAAAAC
1 AAAAAAAACCAA-AAAAC
*
1418301 AAAAAAAACCAAGAAAAA
1 AAAAAAAACCAA-AAAAC
*
1418319 AACAAGAAAACCCAAAAAC
1 AA-AA-AAAACCAAAAAAC
*
1418338 AAAAAAAAAACAAAAAAC
1 -AAAAAAAACCAAAAAAC
1418356 AAA
1 AAA
1418359 CAAATAAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
17 3 0.06
18 30 0.60
19 8 0.16
20 9 0.18
ACGTcount: A:0.80, C:0.16, G:0.04, T:0.00
Consensus pattern (17 bp):
AAAAAAAACCAAAAAAC
Found at i:1418317 original size:11 final size:11
Alignment explanation
Indices: 1418285--1418328 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
1418275 AGTTAACAAA
1418285 AAAAAACCAAG
1 AAAAAACCAAG
1418296 --AAAA-CAA-
1 AAAAAACCAAG
1418303 AAAAAACCAAG
1 AAAAAACCAAG
*
1418314 AAAAAAACAAG
1 AAAAAACCAAG
1418325 AAAA
1 AAAA
1418329 CCCAAAAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
8 3 0.11
9 8 0.29
10 3 0.11
11 14 0.50
ACGTcount: A:0.80, C:0.14, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAACCAAG
Found at i:1418343 original size:38 final size:38
Alignment explanation
Indices: 1418279--1418361 Score: 102
Period size: 38 Copynumber: 2.2 Consensus size: 38
1418269 GACTCAAGTT
*
1418279 AACAAA-AA-AAAACCAAGAAAACAAAAAAAACCAAGAA
1 AACAAACAAGAAAACCAAGAAAACAAAAAAAAACAA-AA
*
1418316 AA-AAACAAGAAAACCCA-AAAACAAAAAAAAAACAAAA
1 AACAAACAAGAAAACCAAGAAAAC-AAAAAAAAACAAAA
1418353 AACAAACAA
1 AACAAACAA
1418362 ATAAAAAGGG
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
36 3 0.08
37 13 0.32
38 24 0.60
ACGTcount: A:0.80, C:0.17, G:0.04, T:0.00
Consensus pattern (38 bp):
AACAAACAAGAAAACCAAGAAAACAAAAAAAAACAAAA
Found at i:1418346 original size:11 final size:11
Alignment explanation
Indices: 1418296--1418368 Score: 58
Period size: 11 Copynumber: 6.2 Consensus size: 11
1418286 AAAAACCAAG
1418296 AAAAC-AAAAA
1 AAAACAAAAAA
* *
1418306 AAACCAAGAAA
1 AAAACAAAAAA
1418317 AAAACAAGAAAACCCA
1 AAAAC-A-AAAA---A
1418333 AAAACAAAAAA
1 AAAACAAAAAA
1418344 AAAACAAAAAA
1 AAAACAAAAAA
*
1418355 CAAACAAATAAA
1 AAAACAAA-AAA
1418367 AA
1 AA
1418369 GGGTCCAGAT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
10 4 0.08
11 27 0.54
12 5 0.10
13 3 0.06
14 4 0.08
15 1 0.02
16 6 0.12
ACGTcount: A:0.81, C:0.15, G:0.03, T:0.01
Consensus pattern (11 bp):
AAAACAAAAAA
Found at i:1419620 original size:30 final size:30
Alignment explanation
Indices: 1419589--1419863 Score: 177
Period size: 29 Copynumber: 9.3 Consensus size: 30
1419579 CGTTCATCTC
*
1419589 TTCAAAGCCCACACAAGTCGATGGTAACTCTT
1 TTCAAAG-CCACACAAGTCGATGGCAACTC-T
* * * *
1419621 TTCAAAGCC-TATAAGTCAATGGCATCTC-
1 TTCAAAGCCACACAAGTCGATGGCAACTCT
* *
1419649 TTCAAAAGCC-CACAAGTTGATGGC-ACCCT
1 TTC-AAAGCCACACAAGTCGATGGCAACTCT
1419678 TTCAAAGCCACACAAGTC-AGTGGCAACTCTT
1 TTCAAAGCCACACAAGTCGA-TGGCAACTC-T
*
1419709 TTCAAAGCC-CACAAGTC-AGTGGCATCTC-
1 TTCAAAGCCACACAAGTCGA-TGGCAACTCT
* * *
1419737 TTCAAAAGAC-CACAAGTC-AGTGAC-ACCCT
1 TTC-AAAGCCACACAAGTCGA-TGGCAACTCT
* *
1419766 TTCAAAGCCCACACAAGTTGGTGGCAACTCTT
1 TTCAAAG-CCACACAAGTCGATGGCAACTC-T
*
1419798 TTCAAAGCC-CACAAGTC-AGTGGCATCTC-
1 TTCAAAGCCACACAAGTCGA-TGGCAACTCT
* *
1419826 TTCAAAAGCC-CACAAGTCAATGGC-ACCCT
1 TTC-AAAGCCACACAAGTCGATGGCAACTCT
*
1419855 TCCAAAGCC
1 TTCAAAGCC
1419864 CAGAAGTTAG
Statistics
Matches: 197, Mismatches: 29, Indels: 38
0.75 0.11 0.14
Matches are distributed among these distances:
28 32 0.16
29 72 0.37
30 61 0.31
31 17 0.09
32 15 0.08
ACGTcount: A:0.32, C:0.31, G:0.16, T:0.22
Consensus pattern (30 bp):
TTCAAAGCCACACAAGTCGATGGCAACTCT
Found at i:1419815 original size:89 final size:87
Alignment explanation
Indices: 1419589--1420081 Score: 529
Period size: 88 Copynumber: 5.6 Consensus size: 87
1419579 CGTTCATCTC
* * * *
1419589 TTCAAAGCCCACACAAGTC-GATGGTAACTCTTTTCAAAGCCTATAAGTCAATGGCATCTCTTCA
1 TTCAAAG-CC-CACAAGTCAG-TGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCATCTCTTCA
*
1419653 AAAGCCCACAAGT-TGATGGCACCCT
63 AAAGCCCACAAGTCAG-TGGCACCCT
1419678 TTCAAAGCCACACAAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCATCTCTTCAAA
1 TTCAAAGCC-CACAAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCATCTCTTCAAA
* *
1419743 AGACCACAAGTCAGTGACACCCT
65 AGCCCACAAGTCAGTGGCACCCT
**
1419766 TTCAAAGCCCACACAAGTTGGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCATCTCTTCAA
1 TTCAAAG-CC-CACAAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCATCTCTTCAA
*
1419831 AAGCCCACAAGTCAATGGCACCCT
64 AAGCCCACAAGTCAGTGGCACCCT
* * * * * * **
1419855 TCCAAAGCCCAGAAGTTAGTGGC-A-TCTCTTCAAAAGCCCAGAAGTCAGTGGCA-CCCTTTTAA
1 TTCAAAGCCCACAAGTCAGTGGCAACTCTTTTC-AAAGCCCACAAGTCAGTGGCATCTCTTCAAA
* *
1419917 AGCCCATAAGTCAGTGGCACCTT
65 AGCCCACAAGTCAGTGGCACCCT
* * * *
1419940 TTCAAGGCCCACAAGTCAGTGGCATA-TCCTTTCATAGCCCACACAAATCAGTGGCATC-CTTCC
1 TTCAAAGCCCACAAGTCAGTGGCA-ACTCTTTTCAAAG-CC-CACAAGTCAGTGGCATCTCTT-C
* *
1420003 AAAA-CCTATAAGTCAGTGGCACCCT
62 AAAAGCCCACAAGTCAGTGGCACCCT
* * ** *
1420028 TTCAAAGCCCACAAGTTAGTGG-TAC-CCCTTCAAAGCCCACAAGTCAGTAGCATC
1 TTCAAAGCCCACAAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCATC
1420082 CCCTTTCAAA
Statistics
Matches: 350, Mismatches: 43, Indels: 27
0.83 0.10 0.06
Matches are distributed among these distances:
84 15 0.04
85 53 0.15
86 33 0.09
87 20 0.06
88 134 0.38
89 95 0.27
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (87 bp):
TTCAAAGCCCACAAGTCAGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCATCTCTTCAAAA
GCCCACAAGTCAGTGGCACCCT
Found at i:1420036 original size:116 final size:113
Alignment explanation
Indices: 1419586--1420110 Score: 443
Period size: 116 Copynumber: 4.5 Consensus size: 113
1419576 GAACGTTCAT
* * * * * *
1419586 CTCTTCAAAGCCCACACAAGTC-GATGGTA-ACTCTTTTCAAAGCCTATAAGTCAATGGCATCTC
1 CTCTTCAAAG-CC-CACAAGTCAG-TGGCATAC-CCTTTCAAAGCCCACAAATCAGTGGCATC-C
*
1419649 TTCAAAAGCCCACAAGT-TGATGGCACCCTTTCAAAGCCACACAAGTCAGTGGCAAC
61 TTCAAAA-CCCACAAGTCAG-TGGCACCCTTTCAAAGCC-CACAAGTCAGTGGC-AC
* * * * * *
1419705 TCTTTTCAAAGCCCACAAGTCAGTGGCAT-CTC-TTCAAAAGACCACAAGTCAGTGACACCCTTT
1 -CTCTTCAAAGCCCACAAGTCAGTGGCATACCCTTTC-AAAGCCCACAAATCAGTGGCATCC-TT
* ** * *
1419768 CAAAGCCCACACAAGTTGGTGGCAACTCTTTTCAAAGCCCACAAGTCAGTGGCAT
63 CAAA-ACC-CACAAGTCAGTGGC-AC-CCTTTCAAAGCCCACAAGTCAGTGGCAC
* * * * *
1419823 CTCTTCAAAAGCCCACAAGTCAATGGC--ACCCTTCCAAAGCCCAGAAGTTAGTGGCATCTCTTC
1 CTCTTC-AAAGCCCACAAGTCAGTGGCATACCCTTTCAAAGCCCACAAATCAGTGGCATC-CTTC
* * *
1419886 AAAAGCCCAGAAGTCAGTGGCACCCTTTTAAAGCCCATAAGTCAGTGGCAC
64 AAAA-CCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC
* * * *
1419937 CTTTTCAAGGCCCACAAGTCAGTGGCATATCCTTTCATAGCCCACACAAATCAGTGGCATCCTTC
1 CTCTTCAAAGCCCACAAGTCAGTGGCATACCCTTTCAAAG-CC-CACAAATCAGTGGCATCCTT-
* * * *
1420002 CAAAACCTATAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGTAC
63 CAAAACCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC
* * * *
1420053 CCCTTCAAAGCCCACAAGTCAGTAGCATCCCCTTTCAAAGCTCACACAAATCGGTGGC
1 CTCTTCAAAGCCCACAAGTCAGTGGCATACCCTTTCAAAGC-C-CACAAATCAGTGGC
1420111 TTCAAAGCCC
Statistics
Matches: 331, Mismatches: 54, Indels: 44
0.77 0.13 0.10
Matches are distributed among these distances:
113 18 0.05
114 29 0.09
115 12 0.04
116 108 0.33
117 77 0.23
118 47 0.14
119 20 0.06
120 20 0.06
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.22
Consensus pattern (113 bp):
CTCTTCAAAGCCCACAAGTCAGTGGCATACCCTTTCAAAGCCCACAAATCAGTGGCATCCTTCAA
AACCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC
Found at i:1420084 original size:29 final size:28
Alignment explanation
Indices: 1419621--1420098 Score: 350
Period size: 28 Copynumber: 16.5 Consensus size: 28
1419611 GGTAACTCTT
* * * * *
1419621 TTCAAAGCCTATAAGTCAATGGCATCTC
1 TTCAAAGCCCACAAGTCAGTGGCACCCC
* *
1419649 TTCAAAAGCCCACAAGT-TGATGGCACCCT
1 TTC-AAAGCCCACAAGTCAG-TGGCACCCC
**
1419678 TTCAAAGCCACACAAGTCAGTGGCAACTCTT
1 TTCAAAGCC-CACAAGTCAGTGGC-AC-CCC
* *
1419709 TTCAAAGCCCACAAGTCAGTGGCATCTC
1 TTCAAAGCCCACAAGTCAGTGGCACCCC
* * *
1419737 TTCAAAAGACCACAAGTCAGTGACACCCT
1 TTC-AAAGCCCACAAGTCAGTGGCACCCC
** **
1419766 TTCAAAGCCCACACAAGTTGGTGGCAACTCTT
1 TTCAAAG-CC-CACAAGTCAGTGGC-AC-CCC
* *
1419798 TTCAAAGCCCACAAGTCAGTGGCATCTC
1 TTCAAAGCCCACAAGTCAGTGGCACCCC
*
1419826 TTCAAAAGCCCACAAGTCAATGGCA-CCC
1 TTC-AAAGCCCACAAGTCAGTGGCACCCC
* * * *
1419854 TTCCAAAGCCCAGAAGTTAGTGGCATCTC
1 TT-CAAAGCCCACAAGTCAGTGGCACCCC
* *
1419883 TTCAAAAGCCCAGAAGTCAGTGGCACCCT
1 TTC-AAAGCCCACAAGTCAGTGGCACCCC
* * **
1419912 TTTAAAGCCCATAAGTCAGTGGCACCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCC
* * *
1419940 TTCAAGGCCCACAAGTCAGTGGCATATCCT
1 TTCAAAGCCCACAAGTCAGTGGC--ACCCC
* * *
1419970 TTCATAGCCCACACAAATCAGTGGCA-TCC
1 TTCAAAG-CC-CACAAGTCAGTGGCACCCC
* * * *
1419999 TTCCAAAACCTATAAGTCAGTGGCACCCT
1 TT-CAAAGCCCACAAGTCAGTGGCACCCC
* *
1420028 TTCAAAGCCCACAAGTTAGTGGTACCCC
1 TTCAAAGCCCACAAGTCAGTGGCACCCC
*
1420056 TTCAAAGCCCACAAGTCAGTAGCATCCCC
1 TTCAAAGCCCACAAGTCAGTGGCA-CCCC
*
1420085 TTTCAAAGCTCACA
1 -TTCAAAGCCCACA
1420099 CAAATCGGTG
Statistics
Matches: 362, Mismatches: 65, Indels: 44
0.77 0.14 0.09
Matches are distributed among these distances:
28 142 0.39
29 117 0.32
30 64 0.18
31 17 0.05
32 22 0.06
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.22
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCC
Found at i:1420425 original size:48 final size:48
Alignment explanation
Indices: 1420212--1420415 Score: 234
Period size: 48 Copynumber: 4.3 Consensus size: 48
1420202 AAGTCCGATA
* * * *
1420212 TCGCTGGCATTGAATCAGCATATTG-GCACTTTT--ATTAGCTCAATG
1 TCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCCTTAGCTCAATG
* * * **
1420257 TTGTTGGCCTTGAATTAGCATGTTGTCCACTTTTCCCTTAGCTCAATG
1 TCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCCTTAGCTCAATG
* *
1420305 TCGCTGGCCTTGAATCAGTACATTGTCTACTTTTCCCTTAGCTCAATG
1 TCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCCTTAGCTCAATG
* * * *
1420353 TCGCTAGCCTTGAATCAGCACATTGTCCACTTTTCCCTCAGCTCGATT
1 TCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCCTTAGCTCAATG
**
1420401 TCATTGGCCTTGAAT
1 TCGCTGGCCTTGAAT
1420416 TGGGACATTG
Statistics
Matches: 133, Mismatches: 23, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
45 20 0.15
46 7 0.05
48 106 0.80
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.37
Consensus pattern (48 bp):
TCGCTGGCCTTGAATCAGCACATTGTCCACTTTTCCCTTAGCTCAATG
Found at i:1421182 original size:18 final size:20
Alignment explanation
Indices: 1421159--1421211 Score: 76
Period size: 18 Copynumber: 2.8 Consensus size: 20
1421149 TTTTACCCAG
1421159 ATGTATCGATACATTG-A-A
1 ATGTATCGATACATTGTAGA
1421177 ATGTATCGATACA-TGTATGA
1 ATGTATCGATACATTGTA-GA
1421197 ATGTATCGATACATT
1 ATGTATCGATACATT
1421212 CTGTCTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
17 2 0.06
18 14 0.45
20 14 0.45
21 1 0.03
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGTAGA
Found at i:1421201 original size:20 final size:19
Alignment explanation
Indices: 1421159--1421211 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
1421149 TTTTACCCAG
1421159 ATGTATCGATACA-TTGAA
1 ATGTATCGATACATTTGAA
1421177 ATGTATCGATACATGTATG-A
1 ATGTATCGATACAT-T-TGAA
1421197 ATGTATCGATACATT
1 ATGTATCGATACATT
1421212 CTGTCTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 13 0.41
19 1 0.03
20 16 0.50
21 2 0.06
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (19 bp):
ATGTATCGATACATTTGAA
Found at i:1421273 original size:20 final size:20
Alignment explanation
Indices: 1421250--1421287 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1421240 TACATGTATA
1421250 AATGTATCGATACATTCTTC
1 AATGTATCGATACATTCTTC
*
1421270 AATGTATCGATATATTCT
1 AATGTATCGATACATTCT
1421288 GTCTTTTTTT
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:0.32, C:0.16, G:0.11, T:0.42
Consensus pattern (20 bp):
AATGTATCGATACATTCTTC
Found at i:1425690 original size:163 final size:162
Alignment explanation
Indices: 1425310--1426094 Score: 1057
Period size: 161 Copynumber: 4.8 Consensus size: 162
1425300 CAAAAGTATT
* *
1425310 AATTCAATTTAATTTTATTTATTTT-TAAGAATACCATTTCGTACCCTAATGGAAGCCCGAAAGG
1 AATTCAATTTAATTTTATTTATTTTCGAA-AATACCATTTCGTACCCTAATGGAAGCCCGAAAAG
* *
1425374 ATACGAAAGGTTTTTGAAATCATTTATACCCCTACGGATATCCGCCCATAAGAATATAAAAGATT
65 ATACGAAAGGTTTTTGAAATCTTTTATACCCCTACGG--AT--GCCCATAGGAATATAAAAGATT
1425439 AGAAAAAATAAATATTAGAATTTATCCCAAGAATACC
126 AGAAAAAATAAATATTAGAATTTATCCCAAGAATACC
* *
1425476 AATTCAATTTTATTTTATTTATTTTCGAAAATACCATTTCGTACCCTAATGGAAGCCTGAAAAGA
1 AATTCAATTTAATTTTATTTATTTTCGAAAATACCATTTCGTACCCTAATGGAAGCCCGAAAAGA
1425541 TACGAAAGGTTTTTGAAATCTTTTATACCCCTACGGATGCCCATAGGAATATAAAAGATTAGAAA
66 TACGAAAGGTTTTTGAAATCTTTTATACCCCTACGGATGCCCATAGGAATATAAAAGATTAG-AA
* * *
1425606 AAAATAAGTATTAGAATTTATCCCAAGCATACA
130 AAAATAAATATTAGAATTTATCCCAAGAATACC
* * * **
1425639 AATTCACTTTAATTTTATTTATTTTTGAAAATACCATTTTGTACCCTAATGGAAGCTTG-AAAGA
1 AATTCAATTTAATTTTATTTATTTTCGAAAATACCATTTCGTACCCTAATGGAAGCCCGAAAAG-
* * *
1425703 ATACGAAAGGTTTTTAAAATCTTTTATACCCCTACGGATACCCATAGGAATATAAAAGATTACAA
65 ATACGAAAGGTTTTTGAAATCTTTTATACCCCTACGGATGCCCATAGGAATATAAAAGATTAGAA
*
1425768 AAATTAAATATTAGAATTTAT-CCAAGAATACC
130 AAAATAAATATTAGAATTTATCCCAAGAATACC
* * *
1425800 AAGTCAATTTAATTTTATTTATTTTCGAAAATACCATTTCATACCCTAATAGAAGCCCG-AAAGA
1 AATTCAATTTAATTTTATTTATTTTCGAAAATACCATTTCGTACCCTAATGGAAGCCCGAAAAG-
* * *
1425864 ATAC-AATAAGTTTTTGAAATCCTTTATACCTCTACGGATGCCCATAGGAATATAAAAGATTAGA
65 ATACGAA-AGGTTTTTGAAATCTTTTATACCCCTACGGATGCCCATAGGAATATAAAAGATTAGA
* * **
1425928 AAAAATAAATATTA-AATGTATCCTGAA-AATATT
129 AAAAATAAATATTAGAATTTATCC-CAAGAATACC
* * * * * * * *
1425961 AATTCATTTTGATTTTATTTACTTTCAAAAATAACATTTCATACCCTAATAGAAGCCCGAAAGGA
1 AATTCAATTTAATTTTATTTATTTTCGAAAATACCATTTCGTACCCTAATGGAAGCCCGAAAAGA
** * *
1426026 TACGAAACATTTTTGAAAT-TTTTATACCCCTATGGAAGCCCATAGGAATATAAAAGATTA-AAA
66 TACGAAAGGTTTTTGAAATCTTTTATACCCCTACGGATGCCCATAGGAATATAAAAGATTAGAAA
1426089 AAATAA
131 AAATAA
1426095 TAAACATGAA
Statistics
Matches: 558, Mismatches: 53, Indels: 23
0.88 0.08 0.04
Matches are distributed among these distances:
159 9 0.02
160 45 0.08
161 206 0.37
162 55 0.10
163 146 0.26
164 2 0.00
166 93 0.17
167 2 0.00
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (162 bp):
AATTCAATTTAATTTTATTTATTTTCGAAAATACCATTTCGTACCCTAATGGAAGCCCGAAAAGA
TACGAAAGGTTTTTGAAATCTTTTATACCCCTACGGATGCCCATAGGAATATAAAAGATTAGAAA
AAATAAATATTAGAATTTATCCCAAGAATACC
Found at i:1425911 original size:324 final size:323
Alignment explanation
Indices: 1425310--1426092 Score: 1096
Period size: 324 Copynumber: 2.4 Consensus size: 323
1425300 CAAAAGTATT
1425310 AATTCAATTTAATTTTATTTATTTTTAAGAATACCATTTCGTACCCTAATGGAAGCCCGAAAGGA
1 AATTCAATTTAATTTTATTTATTTTTAA-AATACCATTTCGTACCCTAATGGAAGCCCGAAAGGA
* *
1425375 TACGAAAGGTTTTTGAAATCATTTATACCCCTACGGATATCCGCCCATAAGAATATAAAAGATTA
65 TACGAAAGGTTTTTGAAATCTTTTATACCCCTACGGATA--C-CCCATAGGAATATAAAAGATTA
* *
1425440 GAAAAAA-TAAATATTAGAATTTATCCCAAGAATACCAATTCAATTTTATTTTATTTATTTTCGA
127 -AAAAAATTAAATATTAGAATTTATCCCAAGAATACCAAGTCAATTTAATTTTATTTATTTTCGA
* * * * *
1425504 AAATACCATTTCGTACCCTAATGGAAGCCTGAAAAGATACGAAAGGTTTTTGAAATCTTTTATAC
191 AAATACCATTTCATACCCTAATAGAAGCCCGAAAAGATACGAAAAGTTTTTGAAATCCTTTATAC
* *
1425569 CCCTACGGATGCCCATAGGAATATAAAAGATTAGAAAAAAATAAGTATTAGAATTTATCC-CAAG
256 CCCTACGGATGCCCATAGGAATATAAAAGATTAG-AAAAAATAAATATTA-AATGTATCCTCAA-
*
1425633 CATACA
318 AATACA
* * ** *
1425639 AATTCACTTTAATTTTATTTATTTTTGAAAATACCATTTTGTACCCTAATGGAAGCTTGAAAGAA
1 AATTCAATTTAATTTTATTTATTTTT-AAAATACCATTTCGTACCCTAATGGAAGCCCGAAAGGA
* *
1425704 TACGAAAGGTTTTTAAAATCTTTTATACCCCTACGGATA-CCCATAGGAATATAAAAGATTACAA
65 TACGAAAGGTTTTTGAAATCTTTTATACCCCTACGGATACCCCATAGGAATATAAAAGATTAAAA
1425768 AAATTAAATATTAGAATTTAT-CCAAGAATACCAAGTCAATTTAATTTTATTTATTTTCGAAAAT
130 AAATTAAATATTAGAATTTATCCCAAGAATACCAAGTCAATTTAATTTTATTTATTTTCGAAAAT
*
1425832 ACCATTTCATACCCTAATAGAAGCCCG-AAAGAATAC-AATAAGTTTTTGAAATCCTTTATACCT
195 ACCATTTCATACCCTAATAGAAGCCCGAAAAG-ATACGAA-AAGTTTTTGAAATCCTTTATACCC
* *
1425895 CTACGGATGCCCATAGGAATATAAAAGATTAGAAAAAATAAATATTAAATGTATCCTGAAAATAT
258 CTACGGATGCCCATAGGAATATAAAAGATTAGAAAAAATAAATATTAAATGTATCCTCAAAATAC
*
1425960 T
323 A
* * ** * * *
1425961 AATTCATTTTGATTTTATTTACTTTCAAAAATAACATTTCATACCCTAATAGAAGCCCGAAAGGA
1 AATTCAATTTAATTTTATTTA-TTTTTAAAATACCATTTCGTACCCTAATGGAAGCCCGAAAGGA
** * *
1426026 TACGAAACATTTTTGAAAT-TTTTATACCCCTATGGA-AGCCCATAGGAATATAAAAGATTAAAA
65 TACGAAAGGTTTTTGAAATCTTTTATACCCCTACGGATACCCCATAGGAATATAAAAGATTAAAA
1426089 AAAT
130 AAAT
1426093 AATAAACATG
Statistics
Matches: 408, Mismatches: 39, Indels: 22
0.87 0.08 0.05
Matches are distributed among these distances:
320 1 0.00
321 44 0.11
322 77 0.19
323 25 0.06
324 127 0.31
325 38 0.09
329 94 0.23
330 2 0.00
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (323 bp):
AATTCAATTTAATTTTATTTATTTTTAAAATACCATTTCGTACCCTAATGGAAGCCCGAAAGGAT
ACGAAAGGTTTTTGAAATCTTTTATACCCCTACGGATACCCCATAGGAATATAAAAGATTAAAAA
AATTAAATATTAGAATTTATCCCAAGAATACCAAGTCAATTTAATTTTATTTATTTTCGAAAATA
CCATTTCATACCCTAATAGAAGCCCGAAAAGATACGAAAAGTTTTTGAAATCCTTTATACCCCTA
CGGATGCCCATAGGAATATAAAAGATTAGAAAAAATAAATATTAAATGTATCCTCAAAATACA
Found at i:1427603 original size:17 final size:18
Alignment explanation
Indices: 1427583--1427623 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1427573 AAAATTTACG
1427583 GAAATGAATGAATT-TT-T
1 GAAAT-AATGAATTATTGT
1427600 GAAA-AATGAATTATTGT
1 GAAATAATGAATTATTGT
1427617 GAAATAA
1 GAAATAA
1427624 ATAATAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 8 0.38
16 2 0.10
17 9 0.43
18 2 0.10
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (18 bp):
GAAATAATGAATTATTGT
Found at i:1427622 original size:165 final size:160
Alignment explanation
Indices: 1427300--1427862 Score: 600
Period size: 164 Copynumber: 3.4 Consensus size: 160
1427290 GTTCAATGAA
* * ** * * *
1427300 AATATTAGATGAATTATAAAAATTTTAAACCGAGAAAAATTCTCCCCAAAAAATTTACGGAGAAG
1 AATATTTGATGAATTTTAAAAA-TAAAAACCAAGAAAAA-TC-CCTCAAAAAATTTACGGAGTAG
* * * * * *
1427365 AAAA-TTCG-GTTTCTAAAAAAAAGAGATTTTTAA-AGAAAAATTCAAAACTCTT-GGAAATGAA
63 AAAACTCCGTATTTC-AAAAAAAGGA-AATTTCAAGAAAAAAATTCAAAA-T-TTAGGAAATGAA
* *
1427426 TTAATTTTTTAAAACTAATTTAATATGAAATAAATAAT
124 TGAATTTTTGAAAACTAA-TTAATATGAAATAAATAAT
* * *
1427464 AATATTTTATGAATTTTAAAAATCAAAAACCAAGAAAAATCCCTCGAAAAATTTACGGAATAGAA
1 AATATTTGATGAATTTTAAAAAT-AAAAACCAAGAAAAATCCCTCAAAAAATTTACGGAGTAGAA
*
1427529 AATTCCGTATTT-AAGAAAAAGGGAAATTTCAAGAAAAAAAATTCAAAATTTACGGAAATGAATG
65 AACTCCGTATTTCAA-AAAAA-GGAAATTTCAAG-AAAAAAATTCAAAATTTA-GGAAATGAATG
* * *
1427593 AATTTTTGAAAAATGAATTATTGTGAAATAAATAAT
126 AATTTTTGAAAACT-AATTAATATGAAATAAATAAT
* *
1427629 AATATTTGAT-AAATTTAGAAAATTAAAAACCAAGAAAAATCCTCTCAAAAAATTTACGGTGTAG
1 AATATTTGATGAATTTTA-AAAA-TAAAAACCAAGAAAAATCC-CTCAAAAAATTTACGGAGTAG
* * * *
1427693 AGAACTCCGTATTTCAAAGAAAGGAAATTTCAAGGAAAAAATTCGAAATTTATGGAAATGAATGA
63 AAAACTCCGTATTTCAAAAAAAGGAAATTTCAAGAAAAAAATTCAAAATTTA-GGAAATGAATGA
**
1427758 ATTTTTGAAAACTAAATTAATATGAAGCAAATAAT
127 ATTTTTGAAAACT-AATTAATATGAAATAAATAAT
* *
1427793 AGTATTTGATGAATTTTAAAAATAAAAAACAAGAAAAAT-CCTCCAAAACAATTTACGGAGTAGA
1 AATATTTGATGAATTTTAAAAATAAAAACCAAGAAAAATCCCT-CAAAA-AATTTACGGAGTAGA
1427857 AAACTC
64 AAACTC
1427863 TGTAATTTGA
Statistics
Matches: 339, Mismatches: 43, Indels: 35
0.81 0.10 0.08
Matches are distributed among these distances:
161 2 0.01
162 30 0.09
163 54 0.16
164 113 0.33
165 101 0.30
166 37 0.11
167 2 0.01
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.29
Consensus pattern (160 bp):
AATATTTGATGAATTTTAAAAATAAAAACCAAGAAAAATCCCTCAAAAAATTTACGGAGTAGAAA
ACTCCGTATTTCAAAAAAAGGAAATTTCAAGAAAAAAATTCAAAATTTAGGAAATGAATGAATTT
TTGAAAACTAATTAATATGAAATAAATAAT
Found at i:1430834 original size:62 final size:62
Alignment explanation
Indices: 1430737--1430882 Score: 283
Period size: 62 Copynumber: 2.4 Consensus size: 62
1430727 ACTTAGCCAA
*
1430737 GAACTTCTGAGTTAACATAGGCCAGGAATTGAGATACGTCCCTTCATATCACTTGCAGTGAT
1 GAACTTTTGAGTTAACATAGGCCAGGAATTGAGATACGTCCCTTCATATCACTTGCAGTGAT
1430799 GAACTTTTGAGTTAACATAGGCCAGGAATTGAGATACGTCCCTTCATATCACTTGCAGTGAT
1 GAACTTTTGAGTTAACATAGGCCAGGAATTGAGATACGTCCCTTCATATCACTTGCAGTGAT
1430861 GAACTTTTGAGTTAACATAGGC
1 GAACTTTTGAGTTAACATAGGC
1430883 TAAGAACAAT
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
62 83 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.30
Consensus pattern (62 bp):
GAACTTTTGAGTTAACATAGGCCAGGAATTGAGATACGTCCCTTCATATCACTTGCAGTGAT
Found at i:1434051 original size:11 final size:11
Alignment explanation
Indices: 1434035--1434074 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
1434025 CAGTAAATAC
1434035 GAACAGTACCT
1 GAACAGTACCT
***
1434046 GAACAGTGTGT
1 GAACAGTACCT
1434057 GAACAGTACCT
1 GAACAGTACCT
1434068 GAACAGT
1 GAACAGT
1434075 GATAATGAAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (11 bp):
GAACAGTACCT
Found at i:1439294 original size:19 final size:19
Alignment explanation
Indices: 1439270--1439343 Score: 112
Period size: 19 Copynumber: 3.8 Consensus size: 19
1439260 GTATCGATAA
1439270 ATTGTATCGATACATGCTC
1 ATTGTATCGATACATGCTC
1439289 ATTGTATCGATACATGCTC
1 ATTGTATCGATACATGCTC
**
1439308 ATTGTATCGATACAAACTC
1 ATTGTATCGATACATGCTC
*
1439327 AATTGTATTGATACATG
1 -ATTGTATCGATACATG
1439344 AAACTGGCAG
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 36 0.73
20 13 0.27
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (19 bp):
ATTGTATCGATACATGCTC
Found at i:1439406 original size:13 final size:13
Alignment explanation
Indices: 1439388--1439417 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1439378 GATACATTGG
1439388 ACATTGTATCAAT
1 ACATTGTATCAAT
*
1439401 ACATTGTATCGAT
1 ACATTGTATCAAT
1439414 ACAT
1 ACAT
1439418 GAAGAATTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (13 bp):
ACATTGTATCAAT
Found at i:1439414 original size:33 final size:32
Alignment explanation
Indices: 1439372--1439438 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 32
1439362 TTAAGTGAAA
1439372 TGTATCGATACATTG-GACATTGTATCAATACAT
1 TGTATCGATACA-TGAGA-ATTGTATCAATACAT
*
1439405 TGTATCGATACATGAAGAATTGTATCGATACAT
1 TGTATCGATACATG-AGAATTGTATCAATACAT
1439438 T
1 T
1439439 ATGCCCAACG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
32 2 0.06
33 27 0.87
34 2 0.06
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATGAGAATTGTATCAATACAT
Found at i:1441009 original size:3 final size:3
Alignment explanation
Indices: 1440996--1441029 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
1440986 ATCAAAGATA
* *
1440996 ATG AAG ATG ATG ATG ATG GTG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1441030 AGAAGTTGAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.29
Consensus pattern (3 bp):
ATG
Found at i:1452246 original size:42 final size:42
Alignment explanation
Indices: 1452191--1452300 Score: 184
Period size: 42 Copynumber: 2.6 Consensus size: 42
1452181 TTCTTCTCTC
* *
1452191 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCCCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCCCCTGTCT
* *
1452233 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCCCCTGTCT
1452275 CTCCTCCTATCATCCCTCCTCTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCT
1452301 TCTTTCTCTT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.09, C:0.48, G:0.03, T:0.40
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCCCCTGTCT
Found at i:1456392 original size:9 final size:9
Alignment explanation
Indices: 1456380--1456440 Score: 65
Period size: 9 Copynumber: 7.1 Consensus size: 9
1456370 TTCTCTCTAT
1456380 TATCTCTCC
1 TATCTCTCC
1456389 TATCTCTCC
1 TATCTCTCC
* *
1456398 T-CCTAT-C
1 TATCTCTCC
*
1456405 -ATCCCTCC
1 TATCTCTCC
*
1456413 TATCTCTAC
1 TATCTCTCC
1456422 TATCTCTCC
1 TATCTCTCC
1456431 TATCTCTCC
1 TATCTCTCC
1456440 T
1 T
1456441 CCTATCATCC
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
7 3 0.07
8 4 0.10
9 34 0.83
ACGTcount: A:0.13, C:0.44, G:0.00, T:0.43
Consensus pattern (9 bp):
TATCTCTCC
Found at i:1456400 original size:12 final size:12
Alignment explanation
Indices: 1456385--1456461 Score: 71
Period size: 12 Copynumber: 6.9 Consensus size: 12
1456375 TCTATTATCT
1456385 CTCCTATCTCTC
1 CTCCTATCTCTC
1456397 CTCCTATCATC-C
1 CTCCTATC-TCTC
1456409 CTCCTA--TCT-
1 CTCCTATCTCTC
*
1456418 CTACTA--TCT-
1 CTCCTATCTCTC
1456427 CTCCTATCTCTC
1 CTCCTATCTCTC
1456439 CTCCTATCATC-C
1 CTCCTATC-TCTC
1456451 CTCCTATCTCT
1 CTCCTATCTCT
1456462 TCTTTCTCTT
Statistics
Matches: 56, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
9 15 0.27
11 5 0.09
12 32 0.57
13 4 0.07
ACGTcount: A:0.13, C:0.47, G:0.00, T:0.40
Consensus pattern (12 bp):
CTCCTATCTCTC
Found at i:1456419 original size:42 final size:42
Alignment explanation
Indices: 1456373--1456470 Score: 169
Period size: 42 Copynumber: 2.3 Consensus size: 42
1456363 CACCTTCTTC
*
1456373 TCTCTATTATCTCTCCTATCTCTCCTCCTATCATCCCTCCTA
1 TCTCTACTATCTCTCCTATCTCTCCTCCTATCATCCCTCCTA
1456415 TCTCTACTATCTCTCCTATCTCTCCTCCTATCATCCCTCCTA
1 TCTCTACTATCTCTCCTATCTCTCCTCCTATCATCCCTCCTA
* *
1456457 TCTCTTCTTTCTCT
1 TCTCTACTATCTCT
1456471 TTGAGGGCTA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.12, C:0.43, G:0.00, T:0.45
Consensus pattern (42 bp):
TCTCTACTATCTCTCCTATCTCTCCTCCTATCATCCCTCCTA
Found at i:1459157 original size:20 final size:21
Alignment explanation
Indices: 1459115--1459161 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
1459105 CAAATCTTTT
1459115 TCAAAACTAATCTTTTTCACA
1 TCAAAACTAATCTTTTTCACA
*
1459136 TCAAAACT-ATCTATTTT-TCA
1 TCAAAACTAATCT-TTTTCACA
1459156 TCAAAA
1 TCAAAA
1459162 TCATCAACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.40, C:0.21, G:0.00, T:0.38
Consensus pattern (21 bp):
TCAAAACTAATCTTTTTCACA
Found at i:1461581 original size:20 final size:20
Alignment explanation
Indices: 1461556--1461608 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
1461546 CTAAGTGAAA
*
1461556 TGTATCGATACATG-GGACAT
1 TGTATCGATACATGAAGA-AT
1461576 TGTATCGATACATGAAGAAT
1 TGTATCGATACATGAAGAAT
1461596 TGTATCGATACAT
1 TGTATCGATACAT
1461609 TATGCCCAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 29 0.94
21 2 0.06
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (20 bp):
TGTATCGATACATGAAGAAT
Found at i:1464535 original size:12 final size:12
Alignment explanation
Indices: 1464518--1464543 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1464508 AAAATACTTT
1464518 TATGATGAACAG
1 TATGATGAACAG
1464530 TATGATGAACAG
1 TATGATGAACAG
1464542 TA
1 TA
1464544 CCTGAACAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.27
Consensus pattern (12 bp):
TATGATGAACAG
Found at i:1475613 original size:34 final size:31
Alignment explanation
Indices: 1475522--1475745 Score: 114
Period size: 31 Copynumber: 7.0 Consensus size: 31
1475512 TGTGTGGACA
* *
1475522 AAGGATGCCACTAGCTTGTGTGGACTTTGTC
1 AAGGATGCCACCAGCTTGTGTGGACTTTGAC
* * *
1475553 AAGGATGCCACCA-ATTCATGTAGACTTTGAC
1 AAGGATGCCACCAGCTT-GTGTGGACTTTGAC
*
1475584 TAGGATTATGCCACCAGCTTGTGTGGACTTTGGA-
1 AAGG---ATGCCACCAGCTTGTGTGGACTTT-GAC
* * *
1475618 AAGTTTTGGTTGCCGCCAACTTGTGTGGACTTTGA-
1 AA-----GGATGCCACCAGCTTGTGTGGACTTTGAC
* * * * * *
1475653 ATGGGGTGCCACCAACTCGTGTGAACTTTAAC
1 A-AGGATGCCACCAGCTTGTGTGGACTTTGAC
** *
1475685 TGGGATGCCACCAACTTGTGTGGACTTTGA-
1 AAGGATGCCACCAGCTTGTGTGGACTTTGAC
* * * *
1475715 ATGGGGTGCCACCAACTCGTGTGGACTTTGA
1 A-AGGATGCCACCAGCTTGTGTGGACTTTGA
1475746 AAAAGGTTTG
Statistics
Matches: 152, Mismatches: 27, Indels: 28
0.73 0.13 0.14
Matches are distributed among these distances:
30 2 0.01
31 101 0.66
34 19 0.12
35 7 0.05
36 21 0.14
39 2 0.01
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.30
Consensus pattern (31 bp):
AAGGATGCCACCAGCTTGTGTGGACTTTGAC
Found at i:1475668 original size:31 final size:32
Alignment explanation
Indices: 1475592--1475746 Score: 172
Period size: 31 Copynumber: 4.8 Consensus size: 32
1475582 ACTAGGATTA
* * *
1475592 TGCCACCAGCTTGTGTGGACTTTGGAAAGTTTTGGT
1 TGCCACCAACTTGTGTGGACTTT-G-AA--TTGGGG
*
1475628 TGCCGCCAACTTGTGTGGACTTTGAA-TGGGG
1 TGCCACCAACTTGTGTGGACTTTGAATTGGGG
* * * *
1475659 TGCCACCAACTCGTGTGAACTTT-AACTGGGA
1 TGCCACCAACTTGTGTGGACTTTGAATTGGGG
1475690 TGCCACCAACTTGTGTGGACTTTGAA-TGGGG
1 TGCCACCAACTTGTGTGGACTTTGAATTGGGG
*
1475721 TGCCACCAACTCGTGTGGACTTTGAA
1 TGCCACCAACTTGTGTGGACTTTGAA
1475747 AAAGGTTTGA
Statistics
Matches: 105, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
30 2 0.02
31 77 0.73
32 2 0.02
34 2 0.02
35 1 0.01
36 21 0.20
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (32 bp):
TGCCACCAACTTGTGTGGACTTTGAATTGGGG
Found at i:1475827 original size:55 final size:55
Alignment explanation
Indices: 1475752--1476031 Score: 452
Period size: 55 Copynumber: 5.1 Consensus size: 55
1475742 TTGAAAAAGG
** * * **
1475752 TTTGACATGGGTGTCGATGTGCTAATTCAAGGCCAATAACATTGGACTTAAAGAT
1 TTTGACAAAGGTGTCAATGTGCTAATTCAACGCCAGCAACATTGGACTTAAAGAT
1475807 TTTGACAAAGGTGTCAATGTGCTAATTCAACGCCAGCAACATTGGACTTAAAGAT
1 TTTGACAAAGGTGTCAATGTGCTAATTCAACGCCAGCAACATTGGACTTAAAGAT
*
1475862 TTTTACAAAGGTGTCAATGTGCTAATTCAACGCCAGCAACATTGGACTTAAAGAT
1 TTTGACAAAGGTGTCAATGTGCTAATTCAACGCCAGCAACATTGGACTTAAAGAT
*
1475917 TTTGACAAAGGTGTCAATGTGCTAATTCAACGCCAGCAACATTAGACTTAAAGAT
1 TTTGACAAAGGTGTCAATGTGCTAATTCAACGCCAGCAACATTGGACTTAAAGAT
* * * *
1475972 TTTGACAAAGGTGTCAATGTGCTGATTCAAGGCCAGCAACACTGGACTTAAAAAT
1 TTTGACAAAGGTGTCAATGTGCTAATTCAACGCCAGCAACATTGGACTTAAAGAT
1476027 TTTGA
1 TTTGA
1476032 TAAATTTTGA
Statistics
Matches: 211, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 211 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (55 bp):
TTTGACAAAGGTGTCAATGTGCTAATTCAACGCCAGCAACATTGGACTTAAAGAT
Found at i:1476054 original size:13 final size:13
Alignment explanation
Indices: 1476036--1476069 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1476026 TTTTGATAAA
1476036 TTTTGACAAAAGT
1 TTTTGACAAAAGT
*
1476049 TTTTGACACAAGT
1 TTTTGACAAAAGT
*
1476062 TCTTGACA
1 TTTTGACA
1476070 GAGATTTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTTTGACAAAAGT
Found at i:1477036 original size:122 final size:122
Alignment explanation
Indices: 1476818--1477064 Score: 422
Period size: 122 Copynumber: 2.0 Consensus size: 122
1476808 TGAAAGGTTC
*
1476818 ATGACATTTGCCAATCGAGGCACGAGCAGAACTTCCTATACTTTTCCTGCCTTTTGATATAATAT
1 ATGACATTTGCCAATCGAGGCACGAGCAGAACTCCCTATACTTTTCCTGCCTTTTGATATAATAT
* * *
1476883 CAAGATATCCTGATGCAGATATTACTTGGTTATCAAATATTATCAACTAAATGACAA
66 CAAGATATCATGATGCAGATAATACTCGGTTATCAAATATTATCAACTAAATGACAA
* * *
1476940 ATGACCTTTGCCAATCGAGGCACGAGTAGAACTCCCTATACTTTTCTTGCCTTTTGATATAATAT
1 ATGACATTTGCCAATCGAGGCACGAGCAGAACTCCCTATACTTTTCCTGCCTTTTGATATAATAT
*
1477005 CAAGATATCATGATGTAGATAATACTCGGTTATCAAATATTATCAACTAAATGACAA
66 CAAGATATCATGATGCAGATAATACTCGGTTATCAAATATTATCAACTAAATGACAA
1477062 ATG
1 ATG
1477065 CAAATATATT
Statistics
Matches: 117, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
122 117 1.00
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (122 bp):
ATGACATTTGCCAATCGAGGCACGAGCAGAACTCCCTATACTTTTCCTGCCTTTTGATATAATAT
CAAGATATCATGATGCAGATAATACTCGGTTATCAAATATTATCAACTAAATGACAA
Found at i:1482666 original size:9 final size:9
Alignment explanation
Indices: 1482641--1482714 Score: 64
Period size: 9 Copynumber: 8.6 Consensus size: 9
1482631 CCTGTCATCC
1482641 CTCCTATCT
1 CTCCTATCT
**
1482650 CTATTATCT
1 CTCCTATCT
1482659 CTCCTATCT
1 CTCCTATCT
*
1482668 CTCCT-CCT
1 CTCCTATCT
* *
1482676 AT-C-ATCC
1 CTCCTATCT
*
1482683 CTCATATCT
1 CTCCTATCT
*
1482692 CTACTATCT
1 CTCCTATCT
1482701 CTCCTATCT
1 CTCCTATCT
1482710 CTCCT
1 CTCCT
1482715 CCTATCATCC
Statistics
Matches: 48, Mismatches: 14, Indels: 6
0.71 0.21 0.09
Matches are distributed among these distances:
7 3 0.06
8 3 0.06
9 42 0.88
ACGTcount: A:0.15, C:0.42, G:0.00, T:0.43
Consensus pattern (9 bp):
CTCCTATCT
Found at i:1482674 original size:12 final size:12
Alignment explanation
Indices: 1482659--1482735 Score: 62
Period size: 12 Copynumber: 6.9 Consensus size: 12
1482649 TCTATTATCT
1482659 CTCCTATCTCTC
1 CTCCTATCTCTC
1482671 CTCCTATCATC-C
1 CTCCTATC-TCTC
*
1482683 CT-C-ATATCT-
1 CTCCTATCTCTC
*
1482692 CTACTA--TCT-
1 CTCCTATCTCTC
1482701 CTCCTATCTCTC
1 CTCCTATCTCTC
1482713 CTCCTATCATC-C
1 CTCCTATC-TCTC
1482725 CTCCTATCTCT
1 CTCCTATCTCT
1482736 TCTTTTTCTT
Statistics
Matches: 54, Mismatches: 2, Indels: 18
0.73 0.03 0.24
Matches are distributed among these distances:
9 12 0.22
10 3 0.06
11 7 0.13
12 28 0.52
13 4 0.07
ACGTcount: A:0.14, C:0.45, G:0.00, T:0.40
Consensus pattern (12 bp):
CTCCTATCTCTC
Found at i:1482682 original size:42 final size:42
Alignment explanation
Indices: 1482626--1482735 Score: 193
Period size: 42 Copynumber: 2.6 Consensus size: 42
1482616 TTTTTCTCTC
* *
1482626 CTCCTCCTGTCATCCCTCCTATCTCTATTATCTCTCCTATCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATCT
*
1482668 CTCCTCCTATCATCCCTCATATCTCTACTATCTCTCCTATCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATCT
1482710 CTCCTCCTATCATCCCTCCTATCTCT
1 CTCCTCCTATCATCCCTCCTATCTCT
1482736 TCTTTTTCTT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.14, C:0.45, G:0.01, T:0.41
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATCT
Found at i:1483725 original size:89 final size:89
Alignment explanation
Indices: 1483574--1483753 Score: 351
Period size: 89 Copynumber: 2.0 Consensus size: 89
1483564 CAGCAACAGT
*
1483574 ATGATGAACAGTAAATACGAACCTGATAGTGATAATGAATTTAATCCAACTCCAAACCAAAGCTC
1 ATGATGAACAGTAAACACGAACCTGATAGTGATAATGAATTTAATCCAACTCCAAACCAAAGCTC
1483639 TGATACCAATTGATGACAACCATG
66 TGATACCAATTGATGACAACCATG
1483663 ATGATGAACAGTAAACACGAACCTGATAGTGATAATGAATTTAATCCAACTCCAAACCAAAGCTC
1 ATGATGAACAGTAAACACGAACCTGATAGTGATAATGAATTTAATCCAACTCCAAACCAAAGCTC
1483728 TGATACCAATTGATGACAACCATG
66 TGATACCAATTGATGACAACCATG
1483752 AT
1 AT
1483754 CCAAGGTTGC
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 90 1.00
ACGTcount: A:0.42, C:0.21, G:0.14, T:0.23
Consensus pattern (89 bp):
ATGATGAACAGTAAACACGAACCTGATAGTGATAATGAATTTAATCCAACTCCAAACCAAAGCTC
TGATACCAATTGATGACAACCATG
Found at i:1492368 original size:140 final size:140
Alignment explanation
Indices: 1492111--1492455 Score: 505
Period size: 140 Copynumber: 2.5 Consensus size: 140
1492101 TTTTAAACTT
* * * *
1492111 TACCCCTACGACAAACCAGAGGAATAATAG-AATCTTAAAAAAATTAAGATAATAATTTTTATTT
1 TACCCCTACGAAAAACCATAGGAATATTAGAAATCTT-GAAAAATTAAGATAATAATTTTTATTT
* * **
1492175 AATTTTTAATTTCTAAAATTTCATTTCTTACCTTAATGGAGAACCAAAAAGATACGAAAAGTTTT
65 AATTTTTAATTTCTAAAAATTCATTTCGTACCTTAATACAGAACCAAAAAGATACGAAAAGTTTT
1492240 GAAGACTTCTA
130 GAAGACTTCTA
* *
1492251 TACCTCTACGAAAAACCATAGGAATATTAGAAATCTTGAAAAATTAAAATAATAATTTTTATTTA
1 TACCCCTACGAAAAACCATAGGAATATTAGAAATCTTGAAAAATTAAGATAATAATTTTTATTTA
*
1492316 ATTTTTAACTTTC-AAAAATTCATTTCGTATCTTAATACAGAACCAAAAAGATACGAAAAGTTTT
66 ATTTTTAA-TTTCTAAAAATTCATTTCGTACCTTAATACAGAACCAAAAAGATACGAAAAGTTTT
*
1492380 GAAGATTTCTA
130 GAAGACTTCTA
** * * *
1492391 TACCCCTGTGGAAAACCATAAGAATATTATAAATCTTGAAAAATTAAGATAATAATTTTTATTTA
1 TACCCCTACGAAAAACCATAGGAATATTAGAAATCTTGAAAAATTAAGATAATAATTTTTATTTA
1492456 GTGGTAAAAT
Statistics
Matches: 184, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
140 174 0.95
141 10 0.05
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.34
Consensus pattern (140 bp):
TACCCCTACGAAAAACCATAGGAATATTAGAAATCTTGAAAAATTAAGATAATAATTTTTATTTA
ATTTTTAATTTCTAAAAATTCATTTCGTACCTTAATACAGAACCAAAAAGATACGAAAAGTTTTG
AAGACTTCTA
Found at i:1494324 original size:168 final size:165
Alignment explanation
Indices: 1494079--1494466 Score: 548
Period size: 168 Copynumber: 2.3 Consensus size: 165
1494069 GGAAATAGGG
* * * *
1494079 GAATTTCAAGGGAAAAATGAAAAACTCATGAAAATAAATAAATTTTTCAATACTGATTCACTATG
1 GAATTTCAAGGAAAAAATGAAAAACTCATAAAAATAAATAAATTTTTCAAAACTAATTCACTATG
*
1494144 ATTTAAATGGTGATATTTAATGAATATTAAAAATTTTAAACTGAG-AAAACCCCTCGAAAATATT
66 ATTTAAATGGTGATATTTAATGAATATTAAAAATTTTAAACTGAGAAAAACCCCTCGAAAACATT
*
1494208 TATAGAACAAAAAACTCGGTTTTTAAAAAATAAGTAA
131 TATAGAACAAAAAACTCAGTTTTTAAAAAATAA--AA
* *
1494245 -AATTTTAAGGAAAGAAATGAAAAACTCATAAAAATAAATAAAGTTTTTTCAAAACTAATTTACT
1 GAATTTCAAGGAAA-AAATGAAAAACTCATAAAAATAAATAAA--TTTTTCAAAACTAATTCACT
*
1494309 ATGATTTAAATGGTGATATTTAATGAATATTAAAAATTTTAAACTGAGAAAAATCCCTCGAAAAC
63 ATGATTTAAATGGTGATATTTAATGAATATTAAAAATTTTAAACTGAGAAAAACCCCTCGAAAAC
* * **
1494374 ATTTATGGAATAAAAAACTCAGTTTTTCGAAAATAAAA
128 ATTTATAGAACAAAAAACTCAGTTTTTAAAAAATAAAA
* * *
1494412 GAATTTCAAGAAAAAAAATGAAAAACTCATAAAAATATATGAAA-ATTTCAAAACT
1 GAATTTCAAG-GAAAAAATGAAAAACTCATAAAAATAAAT-AAATTTTTCAAAACT
1494467 GACTAAATGG
Statistics
Matches: 198, Mismatches: 17, Indels: 14
0.86 0.07 0.06
Matches are distributed among these distances:
165 11 0.06
166 37 0.19
167 2 0.01
168 97 0.49
169 51 0.26
ACGTcount: A:0.51, C:0.09, G:0.10, T:0.30
Consensus pattern (165 bp):
GAATTTCAAGGAAAAAATGAAAAACTCATAAAAATAAATAAATTTTTCAAAACTAATTCACTATG
ATTTAAATGGTGATATTTAATGAATATTAAAAATTTTAAACTGAGAAAAACCCCTCGAAAACATT
TATAGAACAAAAAACTCAGTTTTTAAAAAATAAAA
Found at i:1500088 original size:68 final size:68
Alignment explanation
Indices: 1499979--1500130 Score: 259
Period size: 68 Copynumber: 2.2 Consensus size: 68
1499969 GCCCTAAAAT
* * *
1499979 CTGTAGAGTCCTAACTAAATAAGGACTATCCTGTCCAATAAGGAAAAGTCTATCCTAAACATAAT
1 CTGTAGAGTCCTAACTAAACAAGGACTATCCTATCCAATAAGGAAAAGTCTATCCTAAACACAAT
1500044 AAC
66 AAC
* *
1500047 CTGTAGAGTACTAACTAAACAAGGACTATCCTATCCAATAAGGAAAAGTCTATCCTAAAGACAAT
1 CTGTAGAGTCCTAACTAAACAAGGACTATCCTATCCAATAAGGAAAAGTCTATCCTAAACACAAT
1500112 AAC
66 AAC
1500115 CTGTAGAGTCCTAACT
1 CTGTAGAGTCCTAACT
1500131 TAATCCAATA
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 78 1.00
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.24
Consensus pattern (68 bp):
CTGTAGAGTCCTAACTAAACAAGGACTATCCTATCCAATAAGGAAAAGTCTATCCTAAACACAAT
AAC
Found at i:1505819 original size:58 final size:58
Alignment explanation
Indices: 1505729--1505840 Score: 188
Period size: 58 Copynumber: 1.9 Consensus size: 58
1505719 TCTTATTCAT
*
1505729 AATATATGCAAATTGGGCTCCACTCTTCTTGGACATGTGAATTAGGCTCCAAGCCATG
1 AATATATGCAAATTGGGCTCCACTCTTCTTGGACATATGAATTAGGCTCCAAGCCATG
* * *
1505787 AATATATGCAAATTGGGCTTCATTCTTCTTGGACATATGAATTGGGCTCCAAGC
1 AATATATGCAAATTGGGCTCCACTCTTCTTGGACATATGAATTAGGCTCCAAGC
1505841 TTTATTCTTC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 50 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (58 bp):
AATATATGCAAATTGGGCTCCACTCTTCTTGGACATATGAATTAGGCTCCAAGCCATG
Found at i:1506458 original size:86 final size:86
Alignment explanation
Indices: 1506313--1506473 Score: 286
Period size: 86 Copynumber: 1.9 Consensus size: 86
1506303 CAACTAACAC
*
1506313 TTGCTTTGTCACTTTAACTTCTCCACAATCATTCAACCACTGTAGGTTATACAGTCTTGGATGCT
1 TTGCTTTGTCACTTTAACTTCTCCACAATCATTCAACCACTGTAGCTTATACAGTCTTGGATGCT
1506378 TTAATGTAGGCAGATTTAGCT
66 TTAATGTAGGCAGATTTAGCT
* **
1506399 TTGCTTTGTCACTTTAACTTCTCCACAATCATTCAACCATTGTAGCTTATATGGTCTTGGATGCT
1 TTGCTTTGTCACTTTAACTTCTCCACAATCATTCAACCACTGTAGCTTATACAGTCTTGGATGCT
1506464 TTAATGTAGG
66 TTAATGTAGG
1506474 ACAATTGATG
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 71 1.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (86 bp):
TTGCTTTGTCACTTTAACTTCTCCACAATCATTCAACCACTGTAGCTTATACAGTCTTGGATGCT
TTAATGTAGGCAGATTTAGCT
Found at i:1508166 original size:24 final size:24
Alignment explanation
Indices: 1508133--1508183 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1508123 TCAAAGAGAA
* * *
1508133 AGAAGAAGAGATAGGAGGGATGAT
1 AGAAGAAGAGATAAGAGAGATAAT
*
1508157 AGAAGGAGAGATAAGAGAGATAAT
1 AGAAGAAGAGATAAGAGAGATAAT
1508181 AGA
1 AGA
1508184 GAGAGGAGGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.51, C:0.00, G:0.37, T:0.12
Consensus pattern (24 bp):
AGAAGAAGAGATAAGAGAGATAAT
Found at i:1508206 original size:42 final size:42
Alignment explanation
Indices: 1508139--1508219 Score: 103
Period size: 42 Copynumber: 1.9 Consensus size: 42
1508129 AGAAAGAAGA
* * *
1508139 AGAGATAGGAGGGATGATAGAAGGA-GAGATAAGAGAGATAAT
1 AGAGAGAGGAGGGATGACAGAAGGAGGAGAGAAGA-AGATAAT
1508181 AGAGAGAGGAGGGATGACATG-AGGAGGAGAGAAGAAGAT
1 AGAGAGAGGAGGGATGACA-GAAGGAGGAGAGAAGAAGAT
1508220 GGAAGAGTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
42 25 0.74
43 9 0.26
ACGTcount: A:0.46, C:0.01, G:0.42, T:0.11
Consensus pattern (42 bp):
AGAGAGAGGAGGGATGACAGAAGGAGGAGAGAAGAAGATAAT
Found at i:1510429 original size:58 final size:58
Alignment explanation
Indices: 1510364--1510480 Score: 207
Period size: 58 Copynumber: 2.0 Consensus size: 58
1510354 GAAGAATAAA
*
1510364 GCTTGGAGCCCAATTCATATGTCCAAGAAGAGTGAAGCCCAATTTGCATATATTCATG
1 GCTTGGAGCCCAATTCACATGTCCAAGAAGAGTGAAGCCCAATTTGCATATATTCATG
* *
1510422 GCTTGGAGCCCAATTCACATGTCCAAGAAGAGTGGAGCCCAATTTGCATATATTTATG
1 GCTTGGAGCCCAATTCACATGTCCAAGAAGAGTGAAGCCCAATTTGCATATATTCATG
1510480 G
1 G
1510481 GCCTATTGTT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (58 bp):
GCTTGGAGCCCAATTCACATGTCCAAGAAGAGTGAAGCCCAATTTGCATATATTCATG
Found at i:1510457 original size:29 final size:29
Alignment explanation
Indices: 1510367--1510465 Score: 103
Period size: 29 Copynumber: 3.4 Consensus size: 29
1510357 GAATAAAGCT
1510367 TGGAGCCCAATTCATATGTCCAAGAAGAG
1 TGGAGCCCAATTCATATGTCCAAGAAGAG
* * * * **
1510396 TGAAGCCCAATTTGCATATATTCATG--GCT
1 TGGAGCCCAA-TT-CATATGTCCAAGAAGAG
*
1510425 TGGAGCCCAATTCACATGTCCAAGAAGAG
1 TGGAGCCCAATTCATATGTCCAAGAAGAG
1510454 TGGAGCCCAATT
1 TGGAGCCCAATT
1510466 TGCATATATT
Statistics
Matches: 53, Mismatches: 13, Indels: 8
0.72 0.18 0.11
Matches are distributed among these distances:
27 8 0.15
28 2 0.04
29 32 0.60
30 2 0.04
31 9 0.17
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.24
Consensus pattern (29 bp):
TGGAGCCCAATTCATATGTCCAAGAAGAG
Found at i:1516186 original size:42 final size:42
Alignment explanation
Indices: 1516125--1516244 Score: 186
Period size: 42 Copynumber: 2.8 Consensus size: 42
1516115 TGGCCCTCAA
* * *
1516125 AGAGAAAGAAGAGAGAGGAGGGATGACAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
1516167 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
1516209 AGAGATAATAGAGAGAGGAGGGATGATAGGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATA-GGAGGAG
1516245 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
42 64 0.90
43 7 0.10
ACGTcount: A:0.42, C:0.03, G:0.47, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:1516227 original size:18 final size:18
Alignment explanation
Indices: 1516200--1516250 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
1516190 TGATAGGAGG
*
1516200 AGAGACAGGAGAGATAAT
1 AGAGAGAGGAGAGATAAT
* *
1516218 AGAGAGAGGAGGGATGAT
1 AGAGAGAGGAGAGATAAT
*
1516236 AGGGAGGAGGAGAGA
1 AGAGA-GAGGAGAGA
1516251 AGAAGATGGA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 19 0.70
19 8 0.30
ACGTcount: A:0.43, C:0.02, G:0.47, T:0.08
Consensus pattern (18 bp):
AGAGAGAGGAGAGATAAT
Found at i:1534950 original size:45 final size:44
Alignment explanation
Indices: 1534901--1535036 Score: 110
Period size: 45 Copynumber: 3.1 Consensus size: 44
1534891 AGGACTTGGG
1534901 TTATTTTGTAATAATGGGCCTGCTGGTTGTGACTTGCTTTGGGCT
1 TTATTTTGTAATAATGGG-CTGCTGGTTGTGACTTGCTTTGGGCT
* * *
1534946 TTA--TTG--AT-ATGGGCTCCAATGGAT-TGAATTAGGAC-TTGGG--
1 TTATTTTGTAATAATGGGCTGC--TGGTTGTGACTT--G-CTTTGGGCT
*
1534986 TTATTTTGTAATAAAGGGACTGCTGGTTGTGACTTGCTTTGGGCT
1 TTATTTTGTAATAATGGG-CTGCTGGTTGTGACTTGCTTTGGGCT
1535031 TTATTT
1 TTATTT
1535037 AGCATAAAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 30
0.65 0.07 0.28
Matches are distributed among these distances:
39 3 0.04
40 13 0.19
41 6 0.09
42 10 0.14
43 10 0.14
44 6 0.09
45 18 0.26
46 3 0.04
ACGTcount: A:0.18, C:0.11, G:0.28, T:0.43
Consensus pattern (44 bp):
TTATTTTGTAATAATGGGCTGCTGGTTGTGACTTGCTTTGGGCT
Found at i:1535009 original size:85 final size:85
Alignment explanation
Indices: 1534866--1535035 Score: 304
Period size: 85 Copynumber: 2.0 Consensus size: 85
1534856 ATATTTGGAA
* *
1534866 GATATGGGCTCCAACGGATTCAATTAGGACTTGGGTTATTTTGTAATAATGGGCCTGCTGGTTGT
1 GATATGGGCTCCAACGGATTCAATTAGGACTTGGGTTATTTTGTAATAAAGGGACTGCTGGTTGT
1534931 GACTTGCTTTGGGCTTTATT
66 GACTTGCTTTGGGCTTTATT
* *
1534951 GATATGGGCTCCAATGGATTGAATTAGGACTTGGGTTATTTTGTAATAAAGGGACTGCTGGTTGT
1 GATATGGGCTCCAACGGATTCAATTAGGACTTGGGTTATTTTGTAATAAAGGGACTGCTGGTTGT
1535016 GACTTGCTTTGGGCTTTATT
66 GACTTGCTTTGGGCTTTATT
1535036 TAGCATAAAA
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 81 1.00
ACGTcount: A:0.20, C:0.12, G:0.29, T:0.39
Consensus pattern (85 bp):
GATATGGGCTCCAACGGATTCAATTAGGACTTGGGTTATTTTGTAATAAAGGGACTGCTGGTTGT
GACTTGCTTTGGGCTTTATT
Found at i:1536370 original size:12 final size:11
Alignment explanation
Indices: 1536351--1536426 Score: 70
Period size: 12 Copynumber: 6.9 Consensus size: 11
1536341 AGAGAAAGAA
1536351 GAGATAGGAGG
1 GAGATAGGAGG
1536362 GATGATAGGAGG
1 GA-GATAGGAGG
1536374 AGAGATAGGA--
1 -GAGATAGGAGG
*
1536384 GAGATAGTA--
1 GAGATAGGAGG
1536393 GAGATAGGAGG
1 GAGATAGGAGG
*
1536404 AATGATAGGAGG
1 GA-GATAGGAGG
1536416 AGAGATAGGAG
1 -GAGATAGGAG
1536427 AGATAATAGA
Statistics
Matches: 55, Mismatches: 4, Indels: 11
0.79 0.06 0.16
Matches are distributed among these distances:
9 16 0.29
11 3 0.05
12 33 0.60
13 3 0.05
ACGTcount: A:0.41, C:0.00, G:0.46, T:0.13
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:1536385 original size:9 final size:9
Alignment explanation
Indices: 1536371--1536431 Score: 65
Period size: 9 Copynumber: 7.1 Consensus size: 9
1536361 GGATGATAGG
1536371 AGGAGAGAT
1 AGGAGAGAT
1536380 AGGAGAGAT
1 AGGAGAGAT
*
1536389 AGTAGAGAT
1 AGGAGAGAT
1536398 AGGAG-GA-
1 AGGAGAGAT
* * *
1536405 ATGATAG-G
1 AGGAGAGAT
1536413 AGGAGAGAT
1 AGGAGAGAT
1536422 AGGAGAGAT
1 AGGAGAGAT
1536431 A
1 A
1536432 ATAGAGAGAG
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
7 3 0.07
8 8 0.19
9 31 0.74
ACGTcount: A:0.44, C:0.00, G:0.43, T:0.13
Consensus pattern (9 bp):
AGGAGAGAT
Found at i:1536397 original size:18 final size:18
Alignment explanation
Indices: 1536374--1536444 Score: 61
Period size: 18 Copynumber: 3.6 Consensus size: 18
1536364 TGATAGGAGG
1536374 AGAGATAGGAGAGATAGT
1 AGAGATAGGAGAGATAGT
*
1536392 AGAGATAGGAGGAATGATAGGAGG
1 AGAGATAGGA-G-A-GAT---AGT
*
1536416 AGAGATAGGAGAGATAAT
1 AGAGATAGGAGAGATAGT
*
1536434 AGAGAGAGGAG
1 AGAGATAGGAG
1536445 GGATGACAGG
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
18 21 0.49
19 1 0.02
20 1 0.02
21 6 0.14
22 1 0.02
23 1 0.02
24 12 0.28
ACGTcount: A:0.45, C:0.00, G:0.42, T:0.13
Consensus pattern (18 bp):
AGAGATAGGAGAGATAGT
Found at i:1536400 original size:42 final size:42
Alignment explanation
Indices: 1536341--1536459 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
1536331 TAGCCTTCAA
* *
1536341 AGAGAAAGAAGAGATAGGAGGGATGATAGGAGGAGAGATAGG
1 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGATAGG
*
1536383 AGAGATAGTAGAGATAGGAGGAATGATAGGAGGAGAGATAGG
1 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGATAGG
* * *
1536425 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAG
1536460 GAGAGAAGAA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.44, C:0.01, G:0.45, T:0.11
Consensus pattern (42 bp):
AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGATAGG
Found at i:1543461 original size:333 final size:333
Alignment explanation
Indices: 1542855--1543841 Score: 1965
Period size: 333 Copynumber: 3.0 Consensus size: 333
1542845 CCCATGAATA
1542855 CATCTTGCAAATTGGGCTCCAATCATCTTAAACATGTGAATTGGGCTTGTAGACACCTTGGTTTG
1 CATCTTGCAAATTGGGCTCCAATCATCTTAAACATGTGAATTGGGCTTGTAGACACCTTGGTTTG
1542920 CCCAGGCTTCCATTCAAGGTGTCAAAGGATGTGTAGTTCAAGGTAGTTTGGGGAACATGCGATAA
66 CCCAGGCTTCCATTCAAGGTGTCAAAGGATGTGTAGTTCAAGGTAGTTTGGGGAACATGCGATAA
1542985 TGCATAGACCAATTCTTCAGTGTTCGAGGTAAGGAAAGGTGTTCAGGAACAAAAGGCATGAAAAA
131 TGCATAGACCAATTCTTCAGTGTTCGAGGTAAGGAAAGGTGTTCAGGAACAAAAGGCATGAAAAA
1543050 TTCATAATTTTGCCTAAATATCGATAGTTTTTATGTATCGGTACAATGCTCCAATGACCCATAAA
196 TTCATAATTTTGCCTAAATATCGATAGTTTTTATGTATCGGTACAATGCTCCAATGACCCATAAA
1543115 TTCAAAATGTCACCATTTGTATCAGTACAATGTGTAAATGTATTAGTATATGAGTTTATGTGTAA
261 TTCAAAATGTCACCATTTGTATCAGTACAATGTGTAAATGTATTAGTATATGAGTTTATGTGTAA
1543180 AATGTCAC
326 AATGTCAC
1543188 CATCTTGCAAATTGGGCTCCAATCATCTTAAACATGTGAATTGGGCTTGTAGACACCTTGGTTTG
1 CATCTTGCAAATTGGGCTCCAATCATCTTAAACATGTGAATTGGGCTTGTAGACACCTTGGTTTG
1543253 CCCAGGCTTCCATTCAAGGTGTCAAAGGATGTGTAGTTCAAGGTAGTTTGGGGAACATGCGATAA
66 CCCAGGCTTCCATTCAAGGTGTCAAAGGATGTGTAGTTCAAGGTAGTTTGGGGAACATGCGATAA
1543318 TGCATAGACCAATTCTTCAGTGTTCGAGGTAAGGAAAGGTGTTCAGGAACAAAAGGCATGAAAAA
131 TGCATAGACCAATTCTTCAGTGTTCGAGGTAAGGAAAGGTGTTCAGGAACAAAAGGCATGAAAAA
1543383 TTCATAATTTTGCCTAAATATCGATAGTTTTTATGTATCGGTACAATGCTCCAATGACCCATAAA
196 TTCATAATTTTGCCTAAATATCGATAGTTTTTATGTATCGGTACAATGCTCCAATGACCCATAAA
1543448 TTCAAAATGTCACCATTTGTATCAGTACAATGTGTAAATGTATTAGTATATGAGTTTATGTGTAA
261 TTCAAAATGTCACCATTTGTATCAGTACAATGTGTAAATGTATTAGTATATGAGTTTATGTGTAA
1543513 AATGTCAC
326 AATGTCAC
1543521 CATCTTGCAAATTGGGCTCCAATCATCTTAAACATGTGAATTGGGCTTGTAGACACCTTGGTTTG
1 CATCTTGCAAATTGGGCTCCAATCATCTTAAACATGTGAATTGGGCTTGTAGACACCTTGGTTTG
1543586 CCCAGGCTTCCATTCAAGGTGTCAAAGGATGTGTAGTTCAAGGTAGTTTGGGGAACATGCGATAA
66 CCCAGGCTTCCATTCAAGGTGTCAAAGGATGTGTAGTTCAAGGTAGTTTGGGGAACATGCGATAA
1543651 TGCATAGACCAATTCTTCAGTGTTCGAGGTAAGGAAAGGTGTTCAGGAACAAAAGGCATGAAAAA
131 TGCATAGACCAATTCTTCAGTGTTCGAGGTAAGGAAAGGTGTTCAGGAACAAAAGGCATGAAAAA
1543716 TTCATAATTTTGCCTAAATATCGATAGTTTTTATGTATCGGTACAATGCTCCAATGACCCATAAA
196 TTCATAATTTTGCCTAAATATCGATAGTTTTTATGTATCGGTACAATGCTCCAATGACCCATAAA
*
1543781 TTCAAAATGTCACCATTTGTATCAGTACAATGTGTAAATGTATTAGTATATGATTTTATGT
261 TTCAAAATGTCACCATTTGTATCAGTACAATGTGTAAATGTATTAGTATATGAGTTTATGT
1543842 ATCGATACTA
Statistics
Matches: 653, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
333 653 1.00
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (333 bp):
CATCTTGCAAATTGGGCTCCAATCATCTTAAACATGTGAATTGGGCTTGTAGACACCTTGGTTTG
CCCAGGCTTCCATTCAAGGTGTCAAAGGATGTGTAGTTCAAGGTAGTTTGGGGAACATGCGATAA
TGCATAGACCAATTCTTCAGTGTTCGAGGTAAGGAAAGGTGTTCAGGAACAAAAGGCATGAAAAA
TTCATAATTTTGCCTAAATATCGATAGTTTTTATGTATCGGTACAATGCTCCAATGACCCATAAA
TTCAAAATGTCACCATTTGTATCAGTACAATGTGTAAATGTATTAGTATATGAGTTTATGTGTAA
AATGTCAC
Found at i:1545629 original size:12 final size:11
Alignment explanation
Indices: 1545607--1545682 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
1545597 AGAGAAAGAA
*
1545607 GAGAGAGGAGG
1 GAGATAGGAGG
1545618 GATGATAGGAGG
1 GA-GATAGGAGG
*
1545630 AGAGACAGGA--
1 -GAGATAGGAGG
*
1545640 GAGATAGTA--
1 GAGATAGGAGG
1545649 GAGATAGGAGG
1 GAGATAGGAGG
1545660 GATGATAGGAGG
1 GA-GATAGGAGG
*
1545672 AGAGACAGGAG
1 -GAGATAGGAG
1545683 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:1545639 original size:24 final size:24
Alignment explanation
Indices: 1545606--1545691 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
1545596 AAGAGAAAGA
*
1545606 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
1545630 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
1545648 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
1545672 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
1545692 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:1545658 original size:42 final size:42
Alignment explanation
Indices: 1545597--1545715 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
1545587 TAGCCCTCAA
* *
1545597 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
1545639 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* **
1545681 AGAGATAATAGAGAGAGGAGGGATGGCAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
1545716 GAGAGAAGAA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.42, C:0.03, G:0.47, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:1554883 original size:157 final size:156
Alignment explanation
Indices: 1554573--1555767 Score: 901
Period size: 157 Copynumber: 7.6 Consensus size: 156
1554563 TCTCCATCAT
* * * *
1554573 TTTCATTCGACCATTTTCCTTAGAATCAAAGTTCGTCTCTCAAATAAGACAAACATGGATTGC-C
1 TTTCTTTCCACCATTTTCCTTAGAATCAAAGTTCATC-CTCAAATGAGACAAACATGGATT-CTC
* * * * * *
1554637 ATTAGAATCTCCATTCA-TTTCATGATTGGGCTCCAAAAACATGTTCTGCTCATTGGATACATGA
64 ATTAGAATCTCCATT-ATTTTCATGATTGGCCTACAAAATCACGTTTTTCTCATTGGATACATGA
* * *
1554701 TATTCATTCTCTGGTTTTGCAAGAAAAGC
128 TATTGATGCTTTGGTTTTGCAAGAAAAGC
* ** * * * *
1554730 TTGCTTTCCATTATTTTCCTTAAAATCAAAGTTCATCCTCAAATGAGGCAAATAAGGATTCTCAT
1 TTTCTTTCCACCATTTTCCTTAGAATCAAAGTTCATCCTCAAATGAGACAAACATGGATTCTCAT
* *
1554795 TA-AATTCTCCATTATTTTCATGGTTGGCCAACAAAATCACGTTTTTCTCATTGGGATACATGAT
66 TAGAA-TCTCCATTATTTTCATGATTGGCCTACAAAATCACGTTTTTCTCATT-GGATACATGAT
* *
1554859 ATTGATGCTTT-GTCTTTGCGAGAAAAAC
129 ATTGATGCTTTGGT-TTTGCAAGAAAAGC
**
1554887 TTTTCATTTGGCCACTCA---T-CTTAGAATCAAAGTTTGTCCTCAAATGAGACAAACATGGATT
1 -TTTC-TTT--CCAC-CATTTTCCTTAGAATCAAAGTTCATCCTCAAATGAGACAAACATGGATT
* * * * * * *
1554948 CTCTTTAAAATCTCCATTATTTTCATGATTGGTCTACAAAAACAC-ATTCTCTTCATTGGAAACA
61 CTCATTAGAATCTCCATTATTTTCATGATTGGCCTACAAAATCACGTTTTTC-TCATTGGATACA
* * *
1555012 TGATATTGATGCTTTGGTTTTGCGAGTAAAGA
125 TGATATTGATGCTTTGGTTTTGCAAGAAAAGC
** * * * * * * * *
1555044 AGT-TTTCAACCATTTTCCTTAGATTTAAAGTTCATCCCTCAGATGACATAAGCATGGATTCTTA
1 TTTCTTTCCACCATTTTCCTTAGAATCAAAGTTCAT-CCTCAAATGAGACAAACATGGATTCTCA
* * * *
1555108 TTAGAATCTCCGTTCTTTTCATGGTTGGCCAAC-AAATCACGTTTTTCTCATTGGGATACATGAT
65 TTAGAATCTCCATTATTTTCATGATTGGCCTACAAAATCACGTTTTTCTCATT-GGATACATGAT
* * * *
1555172 ATTGATGCCTTGTTTTTGCAATAAAAAC
129 ATTGATGCTTTGGTTTTGCAAGAAAAGC
* * * ** *
1555200 TTT-TCATCTGACCACTTAT-CTTAGAATCAAAGTTTGTCCTCAAATGAGATAAACATGGATTCT
1 TTTCT-TTC-CACCA-TTTTCCTTAGAATCAAAGTTCATCCTCAAATGAGACAAACATGGATTCT
* * * ** * * *
1555263 CTTTAAAATCTCCATTCTTTTCATGATTGGTTTACAAACA-CAC-ATTCTCTTCATTGGAAACAT
63 CATTAGAATCTCCATTATTTTCATGATTGGCCTACAAA-ATCACGTTTTTC-TCATTGGATACAT
* *
1555326 GATATTGATGCTTTGGTTTTGCAAGTAAAGA
126 GATATTGATGCTTTGGTTTTGCAAGAAAAGC
** * * * *
1555357 AAT-TTTCAACCATTTTCCTTAGATTCAAAGTTCATCCCTCAAATGACATAAACATGGATTCTCA
1 TTTCTTTCCACCATTTTCCTTAGAATCAAAGTTCAT-CCTCAAATGAGACAAACATGGATTCTCA
* * *
1555421 TTAGAATCTCCATTCTTTTCATGATTGGGCTACAAAATTTTACACATTTTTCCTCATTGGGATAC
65 TTAGAATCTCCATTATTTTCATGATTGGCCTACAAAA---T-CACGTTTTT-CTCATT-GGATAC
* ** *
1555486 ATGATATT-AGTGCTTTGGTCTCACAAGAAAAGTT
124 ATGATATTGA-TGCTTTGGTTTTGCAAGAAAAG-C
* * * * *
1555520 TTTCTTTCCACCATTTTCTTTAAAATCAAAGTTCATCACTAAAATGAGAGAAACATGGATTCTTA
1 TTTCTTTCCACCATTTTCCTTAGAATCAAAGTTCATC-CTCAAATGAGACAAACATGGATTCTCA
* ** * * * * * *
1555585 TTAGAATCTCTATT-TGTTTTGTGATTGGGC-ACCATAAA-CATGGTCTACTCATTGGTATATAT
65 TTAGAATCTCCATTAT-TTTCATGATTGGCCTA-CA-AAATCACGTTTTTCTCATTGG-ATACAT
* * *
1555647 CATATTGATTCTTTGGTTTTTTG-GAG-AAA-C
126 GATATTGATGCTTTGG--TTTTGCAAGAAAAGC
* * * * *
1555677 TCTTCTTTCCACCTTTTTCCTTAGGATCATA-TTCATGCCTCAAATGAGACAAACATAGATTCTT
1 T-TTCTTTCCACCATTTTCCTTAGAATCAAAGTTCAT-CCTCAAATGAGACAAACATGGATTCTC
* * *
1555741 GTTAGAGTCTTCA-TACTTTTCATGATT
64 ATTAGAATCTCCATTA-TTTTCATGATT
1555768 AGCCCCATAA
Statistics
Matches: 823, Mismatches: 164, Indels: 102
0.76 0.15 0.09
Matches are distributed among these distances:
151 2 0.00
152 3 0.00
154 7 0.01
155 49 0.06
156 212 0.26
157 233 0.28
158 139 0.17
159 36 0.04
160 10 0.01
161 14 0.02
162 33 0.04
163 4 0.00
164 78 0.09
165 3 0.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (156 bp):
TTTCTTTCCACCATTTTCCTTAGAATCAAAGTTCATCCTCAAATGAGACAAACATGGATTCTCAT
TAGAATCTCCATTATTTTCATGATTGGCCTACAAAATCACGTTTTTCTCATTGGATACATGATAT
TGATGCTTTGGTTTTGCAAGAAAAGC
Found at i:1555130 original size:156 final size:155
Alignment explanation
Indices: 1554582--1555594 Score: 843
Period size: 156 Copynumber: 6.4 Consensus size: 155
1554572 TTTTCATTCG
* * * *
1554582 ACCATTTTCCTTAGAATCAAAGTTCGTCTCTCAAATAAGACAAACATGGATTGC-CATTAGAATC
1 ACCATTTTCCTTAGAATCAAAGTTCATC-CTCAAATGACATAAACATGGATT-CTCATTAGAATC
* * * * * *
1554646 TCCATTCATTTCATGATTGGGCTCCAAAAACATGTTCTGC-TCATTGGATACATGATATTCATTC
64 TCCATTCTTTTCATGATTGGCCTACAAAAACACGTTCT-CTTCATTGGATACATGATATTGATGC
* * *
1554710 TCTGGTTTTGCAAG-AAA-AGCTTGCTTTCC
128 TTTGGTTTTGCAAGTAAAGAAC-T--TTTCA
** * *** * *
1554739 ATTATTTTCCTTAAAATCAAAGTTCATCCTCAAATGAGGCAAATAAGGATTCTCATTA-AATTCT
1 ACCATTTTCCTTAGAATCAAAGTTCATCCTCAAATGACATAAACATGGATTCTCATTAGAA-TCT
* * * * *
1554803 CCATTATTTTCATGGTTGGCCAACAAAATCACGTT-TTTCTCATTGGGATACATGATATTGATGC
65 CCATTCTTTTCATGATTGGCCTACAAAAACACGTTCTCT-TCATT-GGATACATGATATTGATGC
*
1554867 TTT-GTCTTTGCGAG-AAA-AACTTTTCA
128 TTTGGT-TTTGCAAGTAAAGAACTTTTCA
* ** ** * * * *
1554893 TTTGGCCACTCAT-CTTAGAATCAAAGTTTGTCCTCAAATGAGACAAACATGGATTCTCTTTAAA
1 ----ACCA-TTTTCCTTAGAATCAAAGTTCATCCTCAAATGACATAAACATGGATTCTCATTAGA
* * * *
1554957 ATCTCCATTATTTTCATGATTGGTCTACAAAAACACATTCTCTTCATTGGAAACATGATATTGAT
61 ATCTCCATTCTTTTCATGATTGGCCTACAAAAACACGTTCTCTTCATTGGATACATGATATTGAT
* *
1555022 GCTTTGGTTTTGCGAGTAAAGAAGTTTTCA
126 GCTTTGGTTTTGCAAGTAAAGAACTTTTCA
* * * * *
1555052 ACCATTTTCCTTAGATTTAAAGTTCATCCCTCAGATGACATAAGCATGGATTCTTATTAGAATCT
1 ACCATTTTCCTTAGAATCAAAGTTCAT-CCTCAAATGACATAAACATGGATTCTCATTAGAATCT
* * * * *
1555117 CCGTTCTTTTCATGGTTGGCCAAC-AAATCACGTT-TTTCTCATTGGGATACATGATATTGATGC
65 CCATTCTTTTCATGATTGGCCTACAAAAACACGTTCTCT-TCATT-GGATACATGATATTGATGC
* *
1555180 CTTGTTTTTGCAA-TAAA-AACTTTTCA
128 TTTGGTTTTGCAAGTAAAGAACTTTTCA
* ** * * *
1555206 TCTGACCACTTAT-CTTAGAATCAAAGTTTGTCCTCAAATGAGATAAACATGGATTCTCTTTAAA
1 ----ACCA-TTTTCCTTAGAATCAAAGTTCATCCTCAAATGACATAAACATGGATTCTCATTAGA
** * * *
1555270 ATCTCCATTCTTTTCATGATTGGTTTACAAACACACATTCTCTTCATTGGAAACATGATATTGAT
61 ATCTCCATTCTTTTCATGATTGGCCTACAAAAACACGTTCTCTTCATTGGATACATGATATTGAT
*
1555335 GCTTTGGTTTTGCAAGTAAAGAAATTTTCA
126 GCTTTGGTTTTGCAAGTAAAGAACTTTTCA
*
1555365 ACCATTTTCCTTAGATTCAAAGTTCATCCCTCAAATGACATAAACATGGATTCTCATTAGAATCT
1 ACCATTTTCCTTAGAATCAAAGTTCAT-CCTCAAATGACATAAACATGGATTCTCATTAGAATCT
* * * *
1555430 CCATTCTTTTCATGATTGGGCTACAAAATTTTACACATTTTTCCTCATTGGGATACATGATATT-
65 CCATTCTTTTCATGATTGGCCTACAAAA----ACAC-GTTCTCTTCATT-GGATACATGATATTG
* ** * *** *
1555494 AGTGCTTTGGTCTCACAAGAAAAGTTTTTCTTTCC
124 A-TGCTTTGGTTTTGCAAGTAAAG-AACT-TTTCA
* * * * * *
1555529 ACCATTTTCTTTAAAATCAAAGTTCATCACTAAAATGAGAGAAACATGGATTCTTATTAGAATCT
1 ACCATTTTCCTTAGAATCAAAGTTCATC-CTCAAATGACATAAACATGGATTCTCATTAGAATCT
1555594 C
65 C
1555595 TATTTGTTTT
Statistics
Matches: 692, Mismatches: 123, Indels: 75
0.78 0.14 0.08
Matches are distributed among these distances:
154 19 0.03
155 57 0.08
156 198 0.29
157 163 0.24
158 120 0.17
159 27 0.04
160 4 0.01
161 10 0.01
162 31 0.04
163 2 0.00
164 61 0.09
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (155 bp):
ACCATTTTCCTTAGAATCAAAGTTCATCCTCAAATGACATAAACATGGATTCTCATTAGAATCTC
CATTCTTTTCATGATTGGCCTACAAAAACACGTTCTCTTCATTGGATACATGATATTGATGCTTT
GGTTTTGCAAGTAAAGAACTTTTCA
Found at i:1555245 original size:313 final size:313
Alignment explanation
Indices: 1554591--1555493 Score: 1217
Period size: 313 Copynumber: 2.9 Consensus size: 313
1554581 GACCATTTTC
* * * *
1554591 CTTAGAATCAAAGTTCGTCTCTCAAATAAGACAAACATGGATTGC-CATTAGAATCTCCATTCA-
1 CTTAGAATCAAAGTTTGTC-CTCAAATGAGACAAACATGGATT-CTCTTTAAAATCTCCATT-AT
* * ** * * * *
1554654 TTTCATGATTGGGCTCCAAAAACATGTTCTGC-TCATTGGATACATGATATTCATTCTCTGGTTT
63 TTTCATGATTGGTCTACAAAAACACATTCT-CTTCATTGGAAACATGATATTGATGCTTTGGTTT
* ** * * ** * *
1554718 TGCAAGAAAAGCTTGCTTTCCATTATTTTCCTTAAAATCAAAGTTCAT-CCTCAAATGAGGCA-A
127 TGCAAGTAAAG-AAGTTTTCAACCATTTTCCTTAGATTCAAAGTTCATCCCTCAAATGA--CATA
* * *
1554781 ATAAGGATTCTCATTA-AATTCTCCATTATTTTCATGGTTGGCCAACAAAATCACGTTTTTCTCA
189 ACATGGATTCTCATTAGAA-TCTCCATTCTTTTCATGGTTGGCCAACAAAATCACGTTTTTCTCA
* * * *
1554845 TTGGGATACATGATATTGATGCTTTGTCTTTGCGAGAAAAACTTTTCATTTGGCCACTCAT
253 TTGGGATACATGATATTGATGCCTTGTCTTTGCAAGAAAAACTTTTCATCTGACCACTCAT
1554906 CTTAGAATCAAAGTTTGTCCTCAAATGAGACAAACATGGATTCTCTTTAAAATCTCCATTATTTT
1 CTTAGAATCAAAGTTTGTCCTCAAATGAGACAAACATGGATTCTCTTTAAAATCTCCATTATTTT
*
1554971 CATGATTGGTCTACAAAAACACATTCTCTTCATTGGAAACATGATATTGATGCTTTGGTTTTGCG
66 CATGATTGGTCTACAAAAACACATTCTCTTCATTGGAAACATGATATTGATGCTTTGGTTTTGCA
* *
1555036 AGTAAAGAAGTTTTCAACCATTTTCCTTAGATTTAAAGTTCATCCCTCAGATGACATAAGCATGG
131 AGTAAAGAAGTTTTCAACCATTTTCCTTAGATTCAAAGTTCATCCCTCAAATGACATAA-CATGG
* *
1555101 ATTCTTATTAGAATCTCCGTTCTTTTCATGGTTGGCCAAC-AAATCACGTTTTTCTCATTGGGAT
195 ATTCTCATTAGAATCTCCATTCTTTTCATGGTTGGCCAACAAAATCACGTTTTTCTCATTGGGAT
* * *
1555165 ACATGATATTGATGCCTTGTTTTTGCAATAAAAACTTTTCATCTGACCACTTAT
260 ACATGATATTGATGCCTTGTCTTTGCAAGAAAAACTTTTCATCTGACCACTCAT
* *
1555219 CTTAGAATCAAAGTTTGTCCTCAAATGAGATAAACATGGATTCTCTTTAAAATCTCCATTCTTTT
1 CTTAGAATCAAAGTTTGTCCTCAAATGAGACAAACATGGATTCTCTTTAAAATCTCCATTATTTT
* *
1555284 CATGATTGGTTTACAAACACACATTCTCTTCATTGGAAACATGATATTGATGCTTTGGTTTTGCA
66 CATGATTGGTCTACAAAAACACATTCTCTTCATTGGAAACATGATATTGATGCTTTGGTTTTGCA
*
1555349 AGTAAAGAAATTTTCAACCATTTTCCTTAGATTCAAAGTTCATCCCTCAAATGACATAAACATGG
131 AGTAAAGAAGTTTTCAACCATTTTCCTTAGATTCAAAGTTCATCCCTCAAATGACAT-AACATGG
* * * *
1555414 ATTCTCATTAGAATCTCCATTCTTTTCATGATTGGGCTACAAAATTTTACACATTTTTCCTCATT
195 ATTCTCATTAGAATCTCCATTCTTTTCATGGTTGGCCAACAAAA---T-CACGTTTTT-CTCATT
1555479 GGGATACATGATATT
255 GGGATACATGATATT
1555494 AGTGCTTTGG
Statistics
Matches: 524, Mismatches: 50, Indels: 24
0.88 0.08 0.04
Matches are distributed among these distances:
312 2 0.00
313 322 0.61
314 150 0.29
315 20 0.04
317 1 0.00
318 8 0.02
319 21 0.04
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (313 bp):
CTTAGAATCAAAGTTTGTCCTCAAATGAGACAAACATGGATTCTCTTTAAAATCTCCATTATTTT
CATGATTGGTCTACAAAAACACATTCTCTTCATTGGAAACATGATATTGATGCTTTGGTTTTGCA
AGTAAAGAAGTTTTCAACCATTTTCCTTAGATTCAAAGTTCATCCCTCAAATGACATAACATGGA
TTCTCATTAGAATCTCCATTCTTTTCATGGTTGGCCAACAAAATCACGTTTTTCTCATTGGGATA
CATGATATTGATGCCTTGTCTTTGCAAGAAAAACTTTTCATCTGACCACTCAT
Found at i:1558807 original size:18 final size:18
Alignment explanation
Indices: 1558784--1558820 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1558774 TCATACTAAA
1558784 ATGGAAAGGGTTAAGAGT
1 ATGGAAAGGGTTAAGAGT
*
1558802 ATGGAAAGGGTTTAGAGT
1 ATGGAAAGGGTTAAGAGT
1558820 A
1 A
1558821 GACCCTGAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.24
Consensus pattern (18 bp):
ATGGAAAGGGTTAAGAGT
Found at i:1559218 original size:58 final size:58
Alignment explanation
Indices: 1559123--1559232 Score: 175
Period size: 58 Copynumber: 1.9 Consensus size: 58
1559113 AGAATAAAGG
* ** *
1559123 TTGGAGTCCAATTCGTATGTCCAAGAAGAGTGAAGCCCAATTTGCATGTATTCATCGC
1 TTGGAGCCCAATTCACATGTCCAAGAAGAGTGAAGCCCAATTTGCATATATTCATCGC
*
1559181 TTGGAGCCCAATTCACATGTCCAAGAAGAGTGGAGCCCAATTTGCATATATT
1 TTGGAGCCCAATTCACATGTCCAAGAAGAGTGAAGCCCAATTTGCATATATT
1559233 TATGGGCCTA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
58 47 1.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (58 bp):
TTGGAGCCCAATTCACATGTCCAAGAAGAGTGAAGCCCAATTTGCATATATTCATCGC
Found at i:1559947 original size:41 final size:41
Alignment explanation
Indices: 1559861--1560072 Score: 347
Period size: 40 Copynumber: 5.2 Consensus size: 41
1559851 TATCATCCAT
1559861 AAAAAAAAGTGTTCTAGTAGTATAACCCTTTTCCATCTTC-
1 AAAAAAAAGTGTTCTAGTAGTATAACCCTTTTCCATCTTCA
1559901 AAAAAAAAGTGTTCTAGTAGTATAACCCTTTTCCATCTTC-
1 AAAAAAAAGTGTTCTAGTAGTATAACCCTTTTCCATCTTCA
* * *
1559941 ACAAAAAAGAGTTCTGGTAGTATAACCCTTTTCCATCTTCAA
1 AAAAAAAAGTGTTCTAGTAGTATAACCCTTTTCCATCTTC-A
*
1559983 AAAAAAAAGCGTTCTAGTAGTATAACCCTTTTCCATCTTCA
1 AAAAAAAAGTGTTCTAGTAGTATAACCCTTTTCCATCTTCA
* *
1560024 AAAAAAAAGTGTTCTAGTATTGTAACCCTTTTCCATCTTCA
1 AAAAAAAAGTGTTCTAGTAGTATAACCCTTTTCCATCTTCA
1560065 AAAAAAAA
1 AAAAAAAA
1560073 AAGAGAAAAA
Statistics
Matches: 161, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
40 77 0.48
41 47 0.29
42 37 0.23
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.33
Consensus pattern (41 bp):
AAAAAAAAGTGTTCTAGTAGTATAACCCTTTTCCATCTTCA
Found at i:1560184 original size:28 final size:27
Alignment explanation
Indices: 1560143--1560221 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 27
1560133 TTCTTTATTC
* *
1560143 TTCTTTATTGATTTCTTTTCCTTTGAAAT
1 TTCTTT-TT-ATTTCATTTCCTTTCAAAT
*
1560172 TTCTTTCTTATTTCATTTCCTTTCATAT
1 TTCTTT-TTATTTCATTTCCTTTCAAAT
*
1560200 TTCTTGTTTATTTCACTTCCTT
1 TTCTT-TTTATTTCATTTCCTT
1560222 AATCTTTTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
28 35 0.80
29 9 0.20
ACGTcount: A:0.14, C:0.19, G:0.04, T:0.63
Consensus pattern (27 bp):
TTCTTTTTATTTCATTTCCTTTCAAAT
Found at i:1567579 original size:30 final size:30
Alignment explanation
Indices: 1567545--1567657 Score: 190
Period size: 30 Copynumber: 3.8 Consensus size: 30
1567535 TTCTCTCCTC
* * *
1567545 CTCCTGTCATCCCTCCTCTCTCTATTATCT
1 CTCCTATCATCCCTCCTATCTCTACTATCT
1567575 CTCCTATCATCCCTCCTATCTCTACTATCT
1 CTCCTATCATCCCTCCTATCTCTACTATCT
*
1567605 CTCCTATCATTCCTCCTATCTCTACTATCT
1 CTCCTATCATCCCTCCTATCTCTACTATCT
1567635 CTCCTATCATCCCTCCTATCTCT
1 CTCCTATCATCCCTCCTATCTCT
1567658 TCATTCTTTT
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 78 1.00
ACGTcount: A:0.14, C:0.43, G:0.01, T:0.42
Consensus pattern (30 bp):
CTCCTATCATCCCTCCTATCTCTACTATCT
Found at i:1567582 original size:9 final size:9
Alignment explanation
Indices: 1567570--1567657 Score: 77
Period size: 9 Copynumber: 8.8 Consensus size: 9
1567560 CTCTCTCTAT
1567570 TATCTCTCC
1 TATCTCTCC
1567579 TATCATCCCTCC
1 TATC-T--CTCC
*
1567591 TATCTCTAC
1 TATCTCTCC
1567600 TATCTCTCC
1 TATCTCTCC
1567609 TATCATTCCTCC
1 TATC--T-CTCC
*
1567621 TATCTCTAC
1 TATCTCTCC
1567630 TATCTCTCC
1 TATCTCTCC
1567639 TATCATCCCTCC
1 TATC-T--CTCC
1567651 TATCTCT
1 TATCTCT
1567658 TCATTCTTTT
Statistics
Matches: 66, Mismatches: 4, Indels: 18
0.75 0.05 0.20
Matches are distributed among these distances:
9 36 0.55
10 3 0.05
11 3 0.05
12 24 0.36
ACGTcount: A:0.16, C:0.42, G:0.00, T:0.42
Consensus pattern (9 bp):
TATCTCTCC
Found at i:1567595 original size:21 final size:18
Alignment explanation
Indices: 1567570--1567657 Score: 77
Period size: 21 Copynumber: 4.4 Consensus size: 18
1567560 CTCTCTCTAT
1567570 TATCTCTCCTATCATCCCTCC
1 TATCTCTCCTATC-T--CTCC
*
1567591 TATCTCTACTATCTCTCC
1 TATCTCTCCTATCTCTCC
*
1567609 TATCATTCCTCCTATCTCTAC
1 TATC--T-CTCCTATCTCTCC
1567630 TATCTCTCCTATCATCCCTCC
1 TATCTCTCCTATC-T--CTCC
1567651 TATCTCT
1 TATCTCT
1567658 TCATTCTTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
18 16 0.28
19 2 0.04
20 2 0.04
21 37 0.65
ACGTcount: A:0.16, C:0.42, G:0.00, T:0.42
Consensus pattern (18 bp):
TATCTCTCCTATCTCTCC
Found at i:1580735 original size:42 final size:42
Alignment explanation
Indices: 1580680--1580798 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
1580670 TTCTTCTCTC
* * *
1580680 CTCCTCCTGTCATCTCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
1580722 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
1580764 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
1580799 TTGAGGGCTA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.08, C:0.45, G:0.03, T:0.44
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:1580739 original size:12 final size:11
Alignment explanation
Indices: 1580713--1580788 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
1580703 TCTATTATCT
*
1580713 CTCCTGTCTCTC
1 CTCCTATCTC-C
1580725 CTCCTATCATCC
1 CTCCTATC-TCC
1580737 CTCCTATCT--
1 CTCCTATCTCC
*
1580746 CTACTATCT--
1 CTCCTATCTCC
*
1580755 CTCCTGTCTCTC
1 CTCCTATCTC-C
1580767 CTCCTATCATCC
1 CTCCTATC-TCC
*
1580779 CTCCTCTCTC
1 CTCCTATCTC
1580789 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:1580740 original size:24 final size:24
Alignment explanation
Indices: 1580704--1580789 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
1580694 TCTCCTCTCT
* *
1580704 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
1580728 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
1580749 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
1580770 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
1580790 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 5 0.10
24 21 0.43
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Done.